Build branch v0.3 with version v0.3.0 (d86bd5c)
Build pipeline: viash-hub.biobox.v0.3-cl68g
Source commit: d86bd5cf62
Source message: Merge remote-tracking branch 'origin/main' into v0.3
This commit is contained in:
18
.gitignore
vendored
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18
.gitignore
vendored
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@@ -0,0 +1,18 @@
|
||||
*.DS_Store
|
||||
*__pycache__
|
||||
|
||||
# IDE ignores
|
||||
.idea/
|
||||
.vscode/
|
||||
|
||||
# R specific ignores
|
||||
.Rhistory
|
||||
.Rproj.user
|
||||
*.Rproj
|
||||
|
||||
# viash specific ignores
|
||||
target/
|
||||
|
||||
# nextflow specific ignores
|
||||
.nextflow*
|
||||
work
|
||||
250
CHANGELOG.md
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250
CHANGELOG.md
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@@ -0,0 +1,250 @@
|
||||
# biobox 0.3.0
|
||||
|
||||
## NEW FUNCTIONALITY
|
||||
|
||||
* `agat`:
|
||||
- `agat/agat_convert_genscan2gff`: convert a genscan file into a GFF file (PR #100).
|
||||
- `agat/agat_sp_add_introns`: add intron features to gtf/gff file without intron features (PR #104).
|
||||
- `agat/agat_sp_filter_feature_from_kill_list`: remove features in a GFF file based on a kill list (PR #105).
|
||||
- `agat/agat_sp_merge_annotations`: merge different gff annotation files in one (PR #106).
|
||||
- `agat/agat_sp_statistics`: provides exhaustive statistics of a gft/gff file (PR #107).
|
||||
- `agat/agat_sq_stat_basic`: provide basic statistics of a gtf/gff file (PR #110).
|
||||
|
||||
* `bd_rhapsody/bd_rhapsody_sequence_analysis`: BD Rhapsody Sequence Analysis CWL pipeline (PR #96).
|
||||
|
||||
* `bedtools`:
|
||||
- `bedtools/bedtools_bamtobed`: Converts BAM alignments to BED6 or BEDPE format (PR #109).
|
||||
|
||||
* `rsem/rsem_calculate_expression`: Calculate expression levels (PR #93).
|
||||
|
||||
* `cellranger`:
|
||||
- `cellranger/cellranger_mkref`: Build a Cell Ranger-compatible reference folder from user-supplied genome FASTA and gene GTF files (PR #164).
|
||||
|
||||
* `rseqc`:
|
||||
- `rseqc/rseqc_inner_distance`: Calculate inner distance between read pairs (PR #159).
|
||||
- `rseqc/rseqc_inferexperiment`: Infer strandedness from sequencing reads (PR #158).
|
||||
- `rseqc/bam_stat`: Generate statistics from a bam file (PR #155).
|
||||
|
||||
* `nanoplot`: Plotting tool for long read sequencing data and alignments (PR #95).
|
||||
|
||||
* `sgedemux`: demultiplexing sequencing data generated on Singular Genomics' sequencing instruments (PR #166).
|
||||
|
||||
* `bases2fasta`: demultiplexing sequencing data generated by Element Biosciences instruments (PR #167).
|
||||
|
||||
## BUG FIXES
|
||||
|
||||
* `falco`: Fix a typo in the `--reverse_complement` argument (PR #157).
|
||||
|
||||
* `cutadapt`: Fix the the non-functional `action` parameter (PR #161).
|
||||
|
||||
* `bbmap_bbsplit`: Change argument type of `build` to `file` and add output argument `index` (PR #162).
|
||||
|
||||
* `kallisto/kallisto_index`: Fix command script to use `--threads` option (PR #162).
|
||||
|
||||
* `kallisto/kallisto_quant`: Change type of argument `output_dir` to `file` and add output argument `log` (PR #162).
|
||||
|
||||
* `rsem/rsem_calculate_expression`: Fix output handling (PR #162).
|
||||
|
||||
* `sortmerna`: Change type pf argument `aligned` to `file`; update docker image; accept more than two reference files (PR #162).
|
||||
|
||||
* `umi_tools/umi_tools_extract`: Remove `umi_discard_reads` option and change `log2stderr` to input argument (PR #162).
|
||||
|
||||
## MINOR CHANGES
|
||||
|
||||
* `agat_convert_bed2gff`: change type of argument `inflate_off` from `boolean_false` to `boolean_true` (PR #160).
|
||||
|
||||
* `cutadapt`: change type of argument `no_indels` and `no_match_adapter_wildcards` from `boolean_false` to `boolean_true` (PR #160).
|
||||
|
||||
* Upgrade to Viash 0.9.0.
|
||||
|
||||
* `bbmap_bbsplit`: Move to namespace `bbmap` (PR #162).
|
||||
|
||||
# biobox 0.2.0
|
||||
|
||||
## BREAKING CHANGES
|
||||
|
||||
* `star/star_align_reads`: Change all arguments from `--camelCase` to `--snake_case` (PR #62).
|
||||
|
||||
* `star/star_genome_generate`: Change all arguments from `--camelCase` to `--snake_case` (PR #62).
|
||||
|
||||
## NEW FUNCTIONALITY
|
||||
|
||||
* `star/star_align_reads`: Add star solo related arguments (PR #62).
|
||||
|
||||
* `bd_rhapsody/bd_rhapsody_make_reference`: Create a reference for the BD Rhapsody pipeline (PR #75).
|
||||
|
||||
* `umitools/umitools_dedup`: Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read (PR #54).
|
||||
|
||||
* `seqtk`:
|
||||
- `seqtk/seqtk_sample`: Subsamples sequences from FASTA/Q files (PR #68).
|
||||
- `seqtk/seqtk_subseq`: Extract the sequences (complete or subsequence) from the FASTA/FASTQ files
|
||||
based on a provided sequence IDs or region coordinates file (PR #85).
|
||||
|
||||
* `agat`:
|
||||
- `agat_convert_sp_gff2gtf`: convert any GTF/GFF file into a proper GTF file (PR #76).
|
||||
- `agat_convert_bed2gff`: convert bed file to gff format (PR #97).
|
||||
- `agat_convert_embl2gff`: convert an EMBL file into GFF format (PR #99).
|
||||
- `agat/agat_convert_sp_gff2gtf`: convert any GTF/GFF file into a proper GTF file (PR #76).
|
||||
- `agat/agat_convert_bed2gff`: convert bed file to gff format (PR #97).
|
||||
- `agat/agat_convert_mfannot2gff`: convert MFannot "masterfile" annotation to gff format (PR #112).
|
||||
- `agat/agat_convert_embl2gff`: convert an EMBL file into GFF format (PR #99).
|
||||
- `agat/agat_convert_sp_gff2tsv`: convert gtf/gff file into tabulated file (PR #102).
|
||||
- `agat/agat_convert_sp_gxf2gxf`: fixes and/or standardizes any GTF/GFF file into full sorted GTF/GFF file (PR #103).
|
||||
|
||||
* `bedtools`:
|
||||
- `bedtools/bedtools_intersect`: Allows one to screen for overlaps between two sets of genomic features (PR #94).
|
||||
- `bedtools/bedtools_sort`: Sorts a feature file (bed/gff/vcf) by chromosome and other criteria (PR #98).
|
||||
- `bedtools/bedtools_genomecov`: Compute the coverage of a feature file (bed/gff/vcf/bam) among a genome (PR #128).
|
||||
- `bedtools/bedtools_groupby`: Summarizes a dataset column based upon common column groupings. Akin to the SQL "group by" command (PR #123).
|
||||
- `bedtools/bedtools_merge`: Merges overlapping BED/GFF/VCF entries into a single interval (PR #118).
|
||||
- `bedtools/bedtools_bamtofastq`: Convert BAM alignments to FASTQ files (PR #101).
|
||||
- `bedtools/bedtools_bedtobam`: Converts genomic feature records (bed/gff/vcf) to BAM format (PR #111).
|
||||
- `bedtools/bedtools_bed12tobed6`: Converts BED12 files to BED6 files (PR #140).
|
||||
- `bedtools/bedtools_links`: Creates an HTML file with links to an instance of the UCSC Genome Browser for all features / intervals in a (bed/gff/vcf) file (PR #137).
|
||||
|
||||
* `qualimap/qualimap_rnaseq`: RNA-seq QC analysis using qualimap (PR #74).
|
||||
|
||||
* `rsem/rsem_prepare_reference`: Prepare transcript references for RSEM (PR #89).
|
||||
|
||||
* `bcftools`:
|
||||
- `bcftools/bcftools_concat`: Concatenate or combine VCF/BCF files (PR #145).
|
||||
- `bcftools/bcftools_norm`: Left-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; recover multiallelics from multiple rows (PR #144).
|
||||
- `bcftools/bcftools_annotate`: Add or remove annotations from a VCF/BCF file (PR #143).
|
||||
- `bcftools/bcftools_stats`: Parses VCF or BCF and produces a txt stats file which can be plotted using plot-vcfstats (PR #142).
|
||||
- `bcftools/bcftools_sort`: Sorts BCF/VCF files by position and other criteria (PR #141).
|
||||
|
||||
* `fastqc`: High throughput sequence quality control analysis tool (PR #92).
|
||||
|
||||
* `sortmerna`: Local sequence alignment tool for mapping, clustering, and filtering rRNA from
|
||||
metatranscriptomic data (PR #146).
|
||||
|
||||
* `fq_subsample`: Sample a subset of records from single or paired FASTQ files (PR #147).
|
||||
|
||||
* `kallisto`:
|
||||
- `kallisto_index`: Create a kallisto index (PR #149).
|
||||
- `kallisto_quant`: Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads (PR #152).
|
||||
|
||||
* `trimgalore`: Quality and adapter trimming for fastq files (PR #117).
|
||||
|
||||
|
||||
## MINOR CHANGES
|
||||
|
||||
* `busco` components: update BUSCO to `5.7.1` (PR #72).
|
||||
|
||||
* Update CI to reusable workflow in `viash-io/viash-actions` (PR #86).
|
||||
|
||||
* Update several components in order to avoid duplicate code when using `unset` on boolean arguments (PR #133).
|
||||
|
||||
* Bump viash to `0.9.0-RC7` (PR #134)
|
||||
|
||||
## DOCUMENTATION
|
||||
|
||||
* Extend the contributing guidelines (PR #82):
|
||||
|
||||
- Update format to Viash 0.9.
|
||||
|
||||
- Descriptions should be formatted in markdown.
|
||||
|
||||
- Add defaults to descriptions, not as a default of the argument.
|
||||
|
||||
- Explain parameter expansion.
|
||||
|
||||
- Mention that the contents of the output of components in tests should be checked.
|
||||
|
||||
* Add authorship to existing components (PR #88).
|
||||
|
||||
## BUG FIXES
|
||||
|
||||
* `pear`: fix component not exiting with the correct exitcode when PEAR fails (PR #70).
|
||||
|
||||
* `cutadapt`: fix `--par_quality_cutoff_r2` argument (PR #69).
|
||||
|
||||
* `cutadapt`: demultiplexing is now disabled by default. It can be re-enabled by using `demultiplex_mode` (PR #69).
|
||||
|
||||
* `multiqc`: update multiple separator to `;` (PR #81).
|
||||
|
||||
|
||||
# biobox 0.1.0
|
||||
|
||||
## NEW FEATURES
|
||||
|
||||
* `arriba`: Detect gene fusions from RNA-seq data (PR #1).
|
||||
|
||||
* `fastp`: An ultra-fast all-in-one FASTQ preprocessor (PR #3).
|
||||
|
||||
* `busco`:
|
||||
- `busco/busco_run`: Assess genome assembly and annotation completeness with single copy orthologs (PR #6).
|
||||
- `busco/busco_list_datasets`: Lists available busco datasets (PR #18).
|
||||
- `busco/busco_download_datasets`: Download busco datasets (PR #19).
|
||||
|
||||
* `cutadapt`: Remove adapter sequences from high-throughput sequencing reads (PR #7).
|
||||
|
||||
* `featurecounts`: Assign sequence reads to genomic features (PR #11).
|
||||
|
||||
* `bgzip`: Add bgzip functionality to compress and decompress files (PR #13).
|
||||
|
||||
* `pear`: Paired-end read merger (PR #10).
|
||||
|
||||
* `lofreq/call`: Call variants from a BAM file (PR #17).
|
||||
|
||||
* `lofreq/indelqual`: Insert indel qualities into BAM file (PR #17).
|
||||
|
||||
* `multiqc`: Aggregate results from bioinformatics analyses across many samples into a single report (PR #42).
|
||||
|
||||
* `star`:
|
||||
- `star/star_align_reads`: Align reads to a reference genome (PR #22).
|
||||
- `star/star_genome_generate`: Generate a genome index for STAR alignment (PR #58).
|
||||
|
||||
* `gffread`: Validate, filter, convert and perform other operations on GFF files (PR #29).
|
||||
|
||||
* `salmon`:
|
||||
- `salmon/salmon_index`: Create a salmon index for the transcriptome to use Salmon in the mapping-based mode (PR #24).
|
||||
- `salmon/salmon_quant`: Transcript quantification from RNA-seq data (PR #24).
|
||||
|
||||
* `samtools`:
|
||||
- `samtools/samtools_flagstat`: Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type (PR #31).
|
||||
- `samtools/samtools_idxstats`: Reports alignment summary statistics for a SAM/BAM/CRAM file (PR #32).
|
||||
- `samtools/samtools_index`: Index SAM/BAM/CRAM files (PR #35).
|
||||
- `samtools/samtools_sort`: Sort SAM/BAM/CRAM files (PR #36).
|
||||
- `samtools/samtools_stats`: Reports alignment summary statistics for a BAM file (PR #39).
|
||||
- `samtools/samtools_faidx`: Indexes FASTA files to enable random access to fasta and fastq files (PR #41).
|
||||
- `samtools/samtools_collate`: Shuffles and groups reads in SAM/BAM/CRAM files together by their names (PR #42).
|
||||
- `samtools/samtools_view`: Views and converts SAM/BAM/CRAM files (PR #48).
|
||||
- `samtools/samtools_fastq`: Converts a SAM/BAM/CRAM file to FASTQ (PR #52).
|
||||
- `samtools/samtools_fastq`: Converts a SAM/BAM/CRAM file to FASTA (PR #53).
|
||||
|
||||
* `umi_tools`:
|
||||
- `umi_tools/umi_tools_extract`: Flexible removal of UMI sequences from fastq reads (PR #71).
|
||||
- `umi_tools/umi_tools_prepareforrsem`: Fix paired-end reads in name sorted BAM file to prepare for RSEM (PR #148).
|
||||
|
||||
* `falco`: A C++ drop-in replacement of FastQC to assess the quality of sequence read data (PR #43).
|
||||
|
||||
* `bedtools`:
|
||||
- `bedtools_getfasta`: extract sequences from a FASTA file for each of the
|
||||
intervals defined in a BED/GFF/VCF file (PR #59).
|
||||
|
||||
* `bbmap`:
|
||||
- `bbmap_bbsplit`: Split sequencing reads by mapping them to multiple references simultaneously (PR #138).
|
||||
|
||||
|
||||
## MINOR CHANGES
|
||||
|
||||
* Uniformize component metadata (PR #23).
|
||||
|
||||
* Update to Viash 0.8.5 (PR #25).
|
||||
|
||||
* Update to Viash 0.9.0-RC3 (PR #51).
|
||||
|
||||
* Update to Viash 0.9.0-RC6 (PR #63).
|
||||
|
||||
* Switch to viash-hub/toolbox actions (PR #64).
|
||||
|
||||
## DOCUMENTATION
|
||||
|
||||
* Update README (PR #64).
|
||||
|
||||
## BUG FIXES
|
||||
|
||||
* Add escaping character before leading hashtag in the description field of the config file (PR #50).
|
||||
|
||||
* Format URL in biobase/bcl_convert description (PR #55).
|
||||
445
CONTRIBUTING.md
Normal file
445
CONTRIBUTING.md
Normal file
@@ -0,0 +1,445 @@
|
||||
|
||||
# Contributing guidelines
|
||||
|
||||
We encourage contributions from the community. To contribute:
|
||||
|
||||
1. **Fork the Repository**: Start by forking this repository to your account.
|
||||
2. **Develop Your Component**: Create your Viash component, ensuring it aligns with our best practices (detailed below).
|
||||
3. **Submit a Pull Request**: After testing your component, submit a pull request for review.
|
||||
|
||||
## Procedure of adding a component
|
||||
|
||||
### Step 1: Find a component to contribute
|
||||
|
||||
* Find a tool to contribute to this repo.
|
||||
|
||||
* Check whether it is already in the [Project board](https://github.com/orgs/viash-hub/projects/1).
|
||||
|
||||
* Check whether there is a corresponding [Snakemake wrapper](https://github.com/snakemake/snakemake-wrappers/blob/master/bio) or [nf-core module](https://github.com/nf-core/modules/tree/master/modules/nf-core) which we can use as inspiration.
|
||||
|
||||
* Create an issue to show that you are working on this component.
|
||||
|
||||
|
||||
### Step 2: Add config template
|
||||
|
||||
Change all occurrences of `xxx` to the name of the component.
|
||||
|
||||
Create a file at `src/xxx/config.vsh.yaml` with contents:
|
||||
|
||||
```yaml
|
||||
name: xxx
|
||||
description: xxx
|
||||
keywords: [tag1, tag2]
|
||||
links:
|
||||
homepage: yyy
|
||||
documentation: yyy
|
||||
issue_tracker: yyy
|
||||
repository: yyy
|
||||
references:
|
||||
doi: 12345/12345678.yz
|
||||
license: MIT/Apache-2.0/GPL-3.0/...
|
||||
argument_groups:
|
||||
- name: Inputs
|
||||
arguments: <...>
|
||||
- name: Outputs
|
||||
arguments: <...>
|
||||
- name: Arguments
|
||||
arguments: <...>
|
||||
resources:
|
||||
- type: bash_script
|
||||
path: script.sh
|
||||
test_resources:
|
||||
- type: bash_script
|
||||
path: test.sh
|
||||
- type: file
|
||||
path: test_data
|
||||
engines:
|
||||
- <...>
|
||||
runners:
|
||||
- type: executable
|
||||
- type: nextflow
|
||||
```
|
||||
|
||||
### Step 3: Fill in the metadata
|
||||
|
||||
Fill in the relevant metadata fields in the config. Here is an example of the metadata of an existing component.
|
||||
|
||||
```yaml
|
||||
name: arriba
|
||||
description: Detect gene fusions from RNA-Seq data
|
||||
keywords: [Gene fusion, RNA-Seq]
|
||||
links:
|
||||
homepage: https://arriba.readthedocs.io/en/latest/
|
||||
documentation: https://arriba.readthedocs.io/en/latest/
|
||||
repository: https://github.com/suhrig/arriba
|
||||
issue_tracker: https://github.com/suhrig/arriba/issues
|
||||
references:
|
||||
doi: 10.1101/gr.257246.119
|
||||
bibtex: |
|
||||
@article{
|
||||
... a bibtex entry in case the doi is not available ...
|
||||
}
|
||||
license: MIT
|
||||
```
|
||||
|
||||
### Step 4: Find a suitable container
|
||||
|
||||
Google `biocontainer <name of component>` and find the container that is most suitable. Typically the link will be `https://quay.io/repository/biocontainers/xxx?tab=tags`.
|
||||
|
||||
If no such container is found, you can create a custom container in the next step.
|
||||
|
||||
|
||||
### Step 5: Create help file
|
||||
|
||||
To help develop the component, we store the `--help` output of the tool in a file at `src/xxx/help.txt`.
|
||||
|
||||
````bash
|
||||
cat <<EOF > src/xxx/help.txt
|
||||
```sh
|
||||
xxx --help
|
||||
```
|
||||
EOF
|
||||
|
||||
docker run quay.io/biocontainers/xxx:tag xxx --help >> src/xxx/help.txt
|
||||
````
|
||||
|
||||
Notes:
|
||||
|
||||
* This help file has no functional purpose, but it is useful for the developer to see the help output of the tool.
|
||||
|
||||
* Some tools might not have a `--help` argument but instead have a `-h` argument. For example, for `arriba`, the help message is obtained by running `arriba -h`:
|
||||
|
||||
```bash
|
||||
docker run quay.io/biocontainers/arriba:2.4.0--h0033a41_2 arriba -h
|
||||
```
|
||||
|
||||
|
||||
### Step 6: Create or fetch test data
|
||||
|
||||
To help develop the component, it's interesting to have some test data available. In most cases, we can use the test data from the Snakemake wrappers.
|
||||
|
||||
To make sure we can reproduce the test data in the future, we store the command to fetch the test data in a file at `src/xxx/test_data/script.sh`.
|
||||
|
||||
```bash
|
||||
cat <<EOF > src/xxx/test_data/script.sh
|
||||
|
||||
# clone repo
|
||||
if [ ! -d /tmp/snakemake-wrappers ]; then
|
||||
git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers /tmp/snakemake-wrappers
|
||||
fi
|
||||
|
||||
# copy test data
|
||||
cp -r /tmp/snakemake-wrappers/bio/xxx/test/* src/xxx/test_data
|
||||
EOF
|
||||
```
|
||||
|
||||
The test data should be suitable for testing this component. Ensure that the test data is small enough: ideally <1KB, preferably <10KB, if need be <100KB.
|
||||
|
||||
### Step 7: Add arguments for the input files
|
||||
|
||||
By looking at the help file, we add the input arguments to the config file. Here is an example of the input arguments of an existing component.
|
||||
|
||||
For instance, in the [arriba help file](src/arriba/help.txt), we see the following:
|
||||
|
||||
Usage: arriba [-c Chimeric.out.sam] -x Aligned.out.bam \
|
||||
-g annotation.gtf -a assembly.fa [-b blacklists.tsv] [-k known_fusions.tsv] \
|
||||
[-t tags.tsv] [-p protein_domains.gff3] [-d structural_variants_from_WGS.tsv] \
|
||||
-o fusions.tsv [-O fusions.discarded.tsv] \
|
||||
[OPTIONS]
|
||||
|
||||
-x FILE File in SAM/BAM/CRAM format with main alignments as generated by STAR
|
||||
(Aligned.out.sam). Arriba extracts candidate reads from this file.
|
||||
|
||||
Based on this information, we can add the following input arguments to the config file.
|
||||
|
||||
```yaml
|
||||
argument_groups:
|
||||
- name: Inputs
|
||||
arguments:
|
||||
- name: --bam
|
||||
alternatives: -x
|
||||
type: file
|
||||
description: |
|
||||
File in SAM/BAM/CRAM format with main alignments as generated by STAR
|
||||
(`Aligned.out.sam`). Arriba extracts candidate reads from this file.
|
||||
required: true
|
||||
example: Aligned.out.bam
|
||||
```
|
||||
|
||||
Check the [documentation](https://viash.io/reference/config/functionality/arguments) for more information on the format of input arguments.
|
||||
|
||||
Several notes:
|
||||
|
||||
* Argument names should be formatted in `--snake_case`. This means arguments like `--foo-bar` should be formatted as `--foo_bar`, and short arguments like `-f` should receive a longer name like `--foo`.
|
||||
|
||||
* Input arguments can have `multiple: true` to allow the user to specify multiple files.
|
||||
|
||||
* The description should be formatted in markdown.
|
||||
|
||||
### Step 8: Add arguments for the output files
|
||||
|
||||
By looking at the help file, we now also add output arguments to the config file.
|
||||
|
||||
For example, in the [arriba help file](src/arriba/help.txt), we see the following:
|
||||
|
||||
|
||||
Usage: arriba [-c Chimeric.out.sam] -x Aligned.out.bam \
|
||||
-g annotation.gtf -a assembly.fa [-b blacklists.tsv] [-k known_fusions.tsv] \
|
||||
[-t tags.tsv] [-p protein_domains.gff3] [-d structural_variants_from_WGS.tsv] \
|
||||
-o fusions.tsv [-O fusions.discarded.tsv] \
|
||||
[OPTIONS]
|
||||
|
||||
-o FILE Output file with fusions that have passed all filters.
|
||||
|
||||
-O FILE Output file with fusions that were discarded due to filtering.
|
||||
|
||||
Based on this information, we can add the following output arguments to the config file.
|
||||
|
||||
```yaml
|
||||
argument_groups:
|
||||
- name: Outputs
|
||||
arguments:
|
||||
- name: --fusions
|
||||
alternatives: -o
|
||||
type: file
|
||||
direction: output
|
||||
description: |
|
||||
Output file with fusions that have passed all filters.
|
||||
required: true
|
||||
example: fusions.tsv
|
||||
- name: --fusions_discarded
|
||||
alternatives: -O
|
||||
type: file
|
||||
direction: output
|
||||
description: |
|
||||
Output file with fusions that were discarded due to filtering.
|
||||
required: false
|
||||
example: fusions.discarded.tsv
|
||||
```
|
||||
|
||||
Note:
|
||||
|
||||
* Preferably, these outputs should not be directories but files. For example, if a tool outputs a directory `foo/` containing files `foo/bar.txt` and `foo/baz.txt`, there should be two output arguments `--bar` and `--baz` (as opposed to one output argument which outputs the whole `foo/` directory).
|
||||
|
||||
### Step 9: Add arguments for the other arguments
|
||||
|
||||
Finally, add all other arguments to the config file. There are a few exceptions:
|
||||
|
||||
* Arguments related to specifying CPU and memory requirements are handled separately and should not be added to the config file.
|
||||
|
||||
* Arguments related to printing the information such as printing the version (`-v`, `--version`) or printing the help (`-h`, `--help`) should not be added to the config file.
|
||||
|
||||
* If the help lists defaults, do not add them as defaults but to the description. Example: `description: <Explanation of parameter>. Default: 10.`
|
||||
|
||||
Note:
|
||||
|
||||
* Prefer using `boolean_true` over `boolean_false`. This avoids confusion when specifying values for this argument in a Nextflow workflow.
|
||||
For example, consider the CLI option `--no-indels` for `cutadapt`. If the config for `cutadapt` would specify an argument `no_indels` of type `boolean_false`,
|
||||
the script of the component must pass a `--no-indels` argument to `cutadapt` when `par_no_indels` is set to `false`. This becomes problematic setting a value for this argument using `fromState` in a nextflow workflow: with `fromState: ["no_indels": true]`, the value that gets passed to the script is `true` and the `--no-indels` flag would *not* be added to the options for `cutadapt`. This is inconsitent to what one might expect when interpreting `["no_indels": true]`.
|
||||
When using `boolean_true`, the reasoning becomes simpler because its value no longer represents the effect of the argument, but wether or not the flag is set.
|
||||
|
||||
### Step 10: Add a Docker engine
|
||||
|
||||
To ensure reproducibility of components, we require that all components are run in a Docker container.
|
||||
|
||||
```yaml
|
||||
engines:
|
||||
- type: docker
|
||||
image: quay.io/biocontainers/xxx:0.1.0--py_0
|
||||
```
|
||||
|
||||
The container should have your tool installed, as well as `ps`.
|
||||
|
||||
If you didn't find a suitable container in the previous step, you can create a custom container. For example:
|
||||
|
||||
```yaml
|
||||
engines:
|
||||
- type: docker
|
||||
image: python:3.10
|
||||
setup:
|
||||
- type: python
|
||||
packages: numpy
|
||||
```
|
||||
|
||||
For more information on how to do this, see the [documentation](https://viash.io/guide/component/add-dependencies.html#steps-for-creating-a-custom-docker-platform).
|
||||
|
||||
Here is a list of base containers we can recommend:
|
||||
|
||||
* Bash: [`bash`](https://hub.docker.com/_/bash), [`ubuntu`](https://hub.docker.com/_/ubuntu)
|
||||
* C#: [`ghcr.io/data-intuitive/dotnet-script`](https://github.com/data-intuitive/ghcr-dotnet-script/pkgs/container/dotnet-script)
|
||||
* JavaScript: [`node`](https://hub.docker.com/_/node)
|
||||
* Python: [`python`](https://hub.docker.com/_/python), [`nvcr.io/nvidia/pytorch`](https://catalog.ngc.nvidia.com/orgs/nvidia/containers/pytorch)
|
||||
* R: [`eddelbuettel/r2u`](https://hub.docker.com/r/eddelbuettel/r2u), [`rocker/tidyverse`](https://hub.docker.com/r/rocker/tidyverse)
|
||||
* Scala: [`sbtscala/scala-sbt`](https://hub.docker.com/r/sbtscala/scala-sbt)
|
||||
|
||||
### Step 11: Write a runner script
|
||||
|
||||
Next, we need to write a runner script that runs the tool with the input arguments. Create a Bash script named `src/xxx/script.sh` which runs the tool with the input arguments.
|
||||
|
||||
```bash
|
||||
#!/bin/bash
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
# unset flags
|
||||
[[ "$par_option" == "false" ]] && unset par_option
|
||||
|
||||
xxx \
|
||||
--input "$par_input" \
|
||||
--output "$par_output" \
|
||||
${par_option:+--option}
|
||||
```
|
||||
|
||||
When building a Viash component, Viash will automatically replace the `## VIASH START` and `## VIASH END` lines (and anything in between) with environment variables based on the arguments specified in the config.
|
||||
|
||||
As an example, this is what the Bash script for the `arriba` component looks like:
|
||||
|
||||
```bash
|
||||
#!/bin/bash
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
# unset flags
|
||||
[[ "$par_skip_duplicate_marking" == "false" ]] && unset par_skip_duplicate_marking
|
||||
[[ "$par_extra_information" == "false" ]] && unset par_extra_information
|
||||
[[ "$par_fill_gaps" == "false" ]] && unset par_fill_gaps
|
||||
|
||||
arriba \
|
||||
-x "$par_bam" \
|
||||
-a "$par_genome" \
|
||||
-g "$par_gene_annotation" \
|
||||
-o "$par_fusions" \
|
||||
${par_known_fusions:+-k "${par_known_fusions}"} \
|
||||
${par_blacklist:+-b "${par_blacklist}"} \
|
||||
# ...
|
||||
${par_extra_information:+-X} \
|
||||
${par_fill_gaps:+-I}
|
||||
```
|
||||
|
||||
Notes:
|
||||
|
||||
* If your arguments can contain special variables (e.g. `$`), you can use quoting (need to find a documentation page for this) to make sure you can use the string as input. Example: `-x ${par_bam@Q}`.
|
||||
|
||||
* Optional arguments can be passed to the command conditionally using Bash [parameter expansion](https://www.gnu.org/software/bash/manual/html_node/Shell-Parameter-Expansion.html). For example: `${par_known_fusions:+-k ${par_known_fusions@Q}}`
|
||||
|
||||
* If your tool allows for multiple inputs using a separator other than `;` (which is the default Viash multiple separator), you can substitute these values with a command like: `par_disable_filters=$(echo $par_disable_filters | tr ';' ',')`.
|
||||
|
||||
* If you have a lot of boolean variables that you would like to unset when the value is `false`, you can avoid duplicate code by using the following syntax:
|
||||
|
||||
```bash
|
||||
unset_if_false=(
|
||||
par_argument_1
|
||||
par_argument_2
|
||||
par_argument_3
|
||||
par_argument_4
|
||||
)
|
||||
|
||||
for par in ${unset_if_false[@]}; do
|
||||
test_val="${!par}"
|
||||
[[ "$test_val" == "false" ]] && unset $par
|
||||
done
|
||||
```
|
||||
|
||||
this code is equivalent to
|
||||
|
||||
```bash
|
||||
[[ "$par_argument_1" == "false" ]] && unset par_argument_1
|
||||
[[ "$par_argument_2" == "false" ]] && unset par_argument_2
|
||||
[[ "$par_argument_3" == "false" ]] && unset par_argument_3
|
||||
[[ "$par_argument_4" == "false" ]] && unset par_argument_4
|
||||
```
|
||||
|
||||
|
||||
### Step 12: Create test script
|
||||
|
||||
If the unit test requires test resources, these should be provided in the `test_resources` section of the component.
|
||||
|
||||
```yaml
|
||||
test_resources:
|
||||
- type: bash_script
|
||||
path: test.sh
|
||||
- type: file
|
||||
path: test_data
|
||||
```
|
||||
|
||||
Create a test script at `src/xxx/test.sh` that runs the component with the test data. This script should run the component (available with `$meta_executable`) with the test data and check if the output is as expected. The script should exit with a non-zero exit code if the output is not as expected. For example:
|
||||
|
||||
```bash
|
||||
#!/bin/bash
|
||||
|
||||
set -e
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
#############################################
|
||||
# helper functions
|
||||
assert_file_exists() {
|
||||
[ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; }
|
||||
}
|
||||
assert_file_doesnt_exist() {
|
||||
[ ! -f "$1" ] || { echo "File '$1' exists but shouldn't" && exit 1; }
|
||||
}
|
||||
assert_file_empty() {
|
||||
[ ! -s "$1" ] || { echo "File '$1' is not empty but should be" && exit 1; }
|
||||
}
|
||||
assert_file_not_empty() {
|
||||
[ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; }
|
||||
}
|
||||
assert_file_contains() {
|
||||
grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
|
||||
}
|
||||
assert_file_not_contains() {
|
||||
grep -q "$2" "$1" && { echo "File '$1' contains '$2' but shouldn't" && exit 1; }
|
||||
}
|
||||
assert_file_contains_regex() {
|
||||
grep -q -E "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
|
||||
}
|
||||
assert_file_not_contains_regex() {
|
||||
grep -q -E "$2" "$1" && { echo "File '$1' contains '$2' but shouldn't" && exit 1; }
|
||||
}
|
||||
#############################################
|
||||
|
||||
echo "> Run $meta_name with test data"
|
||||
"$meta_executable" \
|
||||
--input "$meta_resources_dir/test_data/reads_R1.fastq" \
|
||||
--output "output.txt" \
|
||||
--option
|
||||
|
||||
echo ">> Check if output exists"
|
||||
assert_file_exists "output.txt"
|
||||
|
||||
echo ">> Check if output is empty"
|
||||
assert_file_not_empty "output.txt"
|
||||
|
||||
echo ">> Check if output is correct"
|
||||
assert_file_contains "output.txt" "some expected output"
|
||||
|
||||
echo "> All tests succeeded!"
|
||||
```
|
||||
|
||||
Notes:
|
||||
|
||||
* Do always check the contents of the output file. If the output is not deterministic, you can use regular expressions to check the output.
|
||||
|
||||
* If possible, generate your own test data instead of copying it from an external resource.
|
||||
|
||||
### Step 13: Create a `/var/software_versions.txt` file
|
||||
|
||||
For the sake of transparency and reproducibility, we require that the versions of the software used in the component are documented.
|
||||
|
||||
For now, this is managed by creating a file `/var/software_versions.txt` in the `setup` section of the Docker engine.
|
||||
|
||||
```yaml
|
||||
engines:
|
||||
- type: docker
|
||||
image: quay.io/biocontainers/xxx:0.1.0--py_0
|
||||
setup:
|
||||
- type: docker
|
||||
# note: /var/software_versions.txt should contain:
|
||||
# arriba: "2.4.0"
|
||||
run: |
|
||||
echo "xxx: \"0.1.0\"" > /var/software_versions.txt
|
||||
```
|
||||
21
LICENSE
Normal file
21
LICENSE
Normal file
@@ -0,0 +1,21 @@
|
||||
MIT License
|
||||
|
||||
Copyright (c) 2024 Data Intuitive
|
||||
|
||||
Permission is hereby granted, free of charge, to any person obtaining a copy
|
||||
of this software and associated documentation files (the "Software"), to deal
|
||||
in the Software without restriction, including without limitation the rights
|
||||
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
copies of the Software, and to permit persons to whom the Software is
|
||||
furnished to do so, subject to the following conditions:
|
||||
|
||||
The above copyright notice and this permission notice shall be included in all
|
||||
copies or substantial portions of the Software.
|
||||
|
||||
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
||||
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
||||
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
||||
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
||||
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
||||
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
|
||||
SOFTWARE.
|
||||
72
README.md
Normal file
72
README.md
Normal file
@@ -0,0 +1,72 @@
|
||||
|
||||
|
||||
# 🌱📦 biobox
|
||||
|
||||
[](https://web.viash-hub.com/packages/biobox)
|
||||
[](https://github.com/viash-hub/biobox)
|
||||
[](https://github.com/viash-hub/biobox/blob/main/LICENSE)
|
||||
[](https://github.com/viash-hub/biobox/issues)
|
||||
[](https://viash.io)
|
||||
|
||||
A collection of bioinformatics tools for working with sequence data.
|
||||
|
||||
## Objectives
|
||||
|
||||
- **Reusability**: Facilitating the use of components across various
|
||||
projects and contexts.
|
||||
- **Reproducibility**: Ensuring that components are reproducible and can
|
||||
be easily shared.
|
||||
- **Best Practices**: Adhering to established standards in software
|
||||
development and bioinformatics.
|
||||
|
||||
## Contributing
|
||||
|
||||
We encourage contributions from the community. To contribute:
|
||||
|
||||
1. **Fork the Repository**: Start by forking this repository to your
|
||||
account.
|
||||
2. **Develop Your Component**: Create your Viash component, ensuring it
|
||||
aligns with our best practices (detailed below).
|
||||
3. **Submit a Pull Request**: After testing your component, submit a
|
||||
pull request for review.
|
||||
|
||||
## Contribution Guidelines
|
||||
|
||||
The contribution guidelines describes which steps you should follow to
|
||||
contribute a component to this repository.
|
||||
|
||||
1. Find a component to contribute
|
||||
2. Add config template
|
||||
3. Fill in the metadata
|
||||
4. Find a suitable container
|
||||
5. Create help file
|
||||
6. Create or fetch test data
|
||||
7. Add arguments for the input files
|
||||
8. Add arguments for the output files
|
||||
9. Add arguments for the other arguments
|
||||
10. Add a Docker engine
|
||||
11. Write a runner script
|
||||
12. Create test script
|
||||
13. Create a `/var/software_versions.txt` file
|
||||
|
||||
See the
|
||||
[CONTRIBUTING](https://github.com/viash-hub/biobox/blob/main/CONTRIBUTING.md)
|
||||
file for more details.
|
||||
|
||||
## Support and Community
|
||||
|
||||
For support, questions, or to join our community:
|
||||
|
||||
- **Issues**: Submit questions or issues via the [GitHub issue
|
||||
tracker](https://github.com/viash-hub/biobox/issues).
|
||||
- **Discussions**: Join our discussions via [GitHub
|
||||
Discussions](https://github.com/viash-hub/biobox/discussions).
|
||||
|
||||
## License
|
||||
|
||||
This repository is licensed under an MIT license. See the
|
||||
[LICENSE](https://github.com/viash-hub/biobox/blob/main/LICENSE) file
|
||||
for details.
|
||||
62
README.qmd
Normal file
62
README.qmd
Normal file
@@ -0,0 +1,62 @@
|
||||
---
|
||||
format: gfm
|
||||
---
|
||||
```{r setup, include=FALSE}
|
||||
project <- yaml::read_yaml("_viash.yaml")
|
||||
license <- paste0(project$links$repository, "/blob/main/LICENSE")
|
||||
contributing <- paste0(project$links$repository, "/blob/main/CONTRIBUTING.md")
|
||||
```
|
||||
# 🌱📦 `r project$name`
|
||||
|
||||
[](https://web.viash-hub.com/packages/`r project$name`)
|
||||
[](`r project$links$repository`)
|
||||
[](`r license`)
|
||||
[](`r project$links$issue_tracker`)
|
||||
[![Viash version](https://img.shields.io/badge/Viash-v`r gsub("-", "--", project$viash_version)`-blue)](https://viash.io)
|
||||
|
||||
`r project$description`
|
||||
|
||||
## Objectives
|
||||
|
||||
- **Reusability**: Facilitating the use of components across various projects and contexts.
|
||||
- **Reproducibility**: Ensuring that components are reproducible and can be easily shared.
|
||||
- **Best Practices**: Adhering to established standards in software development and bioinformatics.
|
||||
|
||||
## Contributing
|
||||
|
||||
We encourage contributions from the community. To contribute:
|
||||
|
||||
1. **Fork the Repository**: Start by forking this repository to your account.
|
||||
2. **Develop Your Component**: Create your Viash component, ensuring it aligns with our best practices (detailed below).
|
||||
3. **Submit a Pull Request**: After testing your component, submit a pull request for review.
|
||||
|
||||
## Contribution Guidelines
|
||||
|
||||
The contribution guidelines describes which steps you should follow to contribute a component to this repository.
|
||||
|
||||
```{r echo=FALSE}
|
||||
lines <- readr::read_lines("CONTRIBUTING.md")
|
||||
|
||||
index_start <- grep("^### Step [0-9]*:", lines)
|
||||
|
||||
index_end <- c(index_start[-1] - 1, length(lines))
|
||||
|
||||
name <- gsub("^### Step [0-9]*: *", "", lines[index_start])
|
||||
|
||||
knitr::asis_output(
|
||||
paste(paste0(" 1. ", name, "\n"), collapse = "")
|
||||
)
|
||||
```
|
||||
|
||||
See the [CONTRIBUTING](`r contributing`) file for more details.
|
||||
|
||||
|
||||
## Support and Community
|
||||
|
||||
For support, questions, or to join our community:
|
||||
|
||||
- **Issues**: Submit questions or issues via the [GitHub issue tracker](`r project$links$issue_tracker`).
|
||||
- **Discussions**: Join our discussions via [GitHub Discussions](`r project$links$repository`/discussions).
|
||||
|
||||
## License
|
||||
This repository is licensed under an MIT license. See the [LICENSE](`r license`) file for details.
|
||||
14
_viash.yaml
Normal file
14
_viash.yaml
Normal file
@@ -0,0 +1,14 @@
|
||||
name: biobox
|
||||
version: v0.3.0
|
||||
description: |
|
||||
A collection of bioinformatics tools for working with sequence data.
|
||||
license: MIT
|
||||
keywords: [bioinformatics, modules, sequencing]
|
||||
links:
|
||||
issue_tracker: https://github.com/viash-hub/biobox/issues
|
||||
repository: https://github.com/viash-hub/biobox
|
||||
|
||||
viash_version: 0.9.0
|
||||
|
||||
config_mods: |
|
||||
.requirements.commands := ['ps']
|
||||
3
main.nf
Normal file
3
main.nf
Normal file
@@ -0,0 +1,3 @@
|
||||
workflow {
|
||||
print("This is a dummy placeholder for pipeline execution. Please use the corresponding nf files for running pipelines.")
|
||||
}
|
||||
6
nextflow.config
Normal file
6
nextflow.config
Normal file
@@ -0,0 +1,6 @@
|
||||
manifest {
|
||||
name = "biobox"
|
||||
version = "v0.3.0"
|
||||
defaultBranch = "main"
|
||||
nextflowVersion = "!>=20.12.1-edge"
|
||||
}
|
||||
14
src/_authors/angela_o_pisco.yaml
Normal file
14
src/_authors/angela_o_pisco.yaml
Normal file
@@ -0,0 +1,14 @@
|
||||
name: Angela Oliveira Pisco
|
||||
info:
|
||||
role: Contributor
|
||||
links:
|
||||
github: aopisco
|
||||
orcid: "0000-0003-0142-2355"
|
||||
linkedin: aopisco
|
||||
organizations:
|
||||
- name: Insitro
|
||||
href: https://insitro.com
|
||||
role: Director of Computational Biology
|
||||
- name: Open Problems
|
||||
href: https://openproblems.bio
|
||||
role: Core Member
|
||||
10
src/_authors/dorien_roosen.yaml
Normal file
10
src/_authors/dorien_roosen.yaml
Normal file
@@ -0,0 +1,10 @@
|
||||
name: Dorien Roosen
|
||||
info:
|
||||
links:
|
||||
email: dorien@data-intuitive.com
|
||||
github: dorien-er
|
||||
linkedin: dorien-roosen
|
||||
organizations:
|
||||
- name: Data Intuitive
|
||||
href: https://www.data-intuitive.com
|
||||
role: Data Scientist
|
||||
11
src/_authors/dries_schaumont.yaml
Normal file
11
src/_authors/dries_schaumont.yaml
Normal file
@@ -0,0 +1,11 @@
|
||||
name: Dries Schaumont
|
||||
info:
|
||||
links:
|
||||
email: dries@data-intuitive.com
|
||||
github: DriesSchaumont
|
||||
orcid: "0000-0002-4389-0440"
|
||||
linkedin: dries-schaumont
|
||||
organizations:
|
||||
- name: Data Intuitive
|
||||
href: https://www.data-intuitive.com
|
||||
role: Data Scientist
|
||||
10
src/_authors/emma_rousseau.yaml
Normal file
10
src/_authors/emma_rousseau.yaml
Normal file
@@ -0,0 +1,10 @@
|
||||
name: Emma Rousseau
|
||||
info:
|
||||
links:
|
||||
email: emma@data-intuitive.com
|
||||
github: emmarousseau
|
||||
linkedin: emmarousseau1
|
||||
organizations:
|
||||
- name: Data Intuitive
|
||||
href: https://www.data-intuitive.com
|
||||
role: Bioinformatician
|
||||
10
src/_authors/jakub_majercik.yaml
Normal file
10
src/_authors/jakub_majercik.yaml
Normal file
@@ -0,0 +1,10 @@
|
||||
name: Jakub Majercik
|
||||
info:
|
||||
links:
|
||||
email: jakub@data-intuitive.com
|
||||
github: jakubmajercik
|
||||
linkedin: jakubmajercik
|
||||
organizations:
|
||||
- name: Data Intuitive
|
||||
href: https://www.data-intuitive.com
|
||||
role: Bioinformatics Engineer
|
||||
14
src/_authors/kai_waldrant.yaml
Normal file
14
src/_authors/kai_waldrant.yaml
Normal file
@@ -0,0 +1,14 @@
|
||||
name: Kai Waldrant
|
||||
info:
|
||||
links:
|
||||
email: kai@data-intuitive.com
|
||||
github: KaiWaldrant
|
||||
orcid: "0009-0003-8555-1361"
|
||||
linkedin: kaiwaldrant
|
||||
organizations:
|
||||
- name: Data Intuitive
|
||||
href: https://www.data-intuitive.com
|
||||
role: Bioinformatician
|
||||
- name: Open Problems
|
||||
href: https://openproblems.bio
|
||||
role: Contributor
|
||||
10
src/_authors/leila_paquay.yaml
Normal file
10
src/_authors/leila_paquay.yaml
Normal file
@@ -0,0 +1,10 @@
|
||||
name: Leïla Paquay
|
||||
info:
|
||||
links:
|
||||
email: leila@data-intuitive.com
|
||||
github: Leila011
|
||||
linkedin: leilapaquay
|
||||
organizations:
|
||||
- name: Data Intuitive
|
||||
href: https://www.data-intuitive.com
|
||||
role: Software Developer
|
||||
14
src/_authors/robrecht_cannoodt.yaml
Normal file
14
src/_authors/robrecht_cannoodt.yaml
Normal file
@@ -0,0 +1,14 @@
|
||||
name: Robrecht Cannoodt
|
||||
info:
|
||||
links:
|
||||
email: robrecht@data-intuitive.com
|
||||
github: rcannood
|
||||
orcid: "0000-0003-3641-729X"
|
||||
linkedin: robrechtcannoodt
|
||||
organizations:
|
||||
- name: Data Intuitive
|
||||
href: https://www.data-intuitive.com
|
||||
role: Data Science Engineer
|
||||
- name: Open Problems
|
||||
href: https://openproblems.bio
|
||||
role: Core Member
|
||||
10
src/_authors/sai_nirmayi_yasa.yaml
Normal file
10
src/_authors/sai_nirmayi_yasa.yaml
Normal file
@@ -0,0 +1,10 @@
|
||||
name: Sai Nirmayi Yasa
|
||||
info:
|
||||
links:
|
||||
email: nirmayi@data-intuitive.com
|
||||
github: sainirmayi
|
||||
linkedin: sai-nirmayi-yasa
|
||||
organizations:
|
||||
- name: Data Intuitive
|
||||
href: https://www.data-intuitive.com
|
||||
role: Junior Bioinformatics Researcher
|
||||
10
src/_authors/theodoro_gasperin.yaml
Normal file
10
src/_authors/theodoro_gasperin.yaml
Normal file
@@ -0,0 +1,10 @@
|
||||
name: Theodoro Gasperin Terra Camargo
|
||||
info:
|
||||
links:
|
||||
email: theodorogtc@gmail.com
|
||||
github: tgaspe
|
||||
linkedin: theodoro-gasperin-terra-camargo
|
||||
organizations:
|
||||
- name: Data Intuitive
|
||||
href: https://www.data-intuitive.com
|
||||
role: Bioinformatician
|
||||
9
src/_authors/toni_verbeiren.yaml
Normal file
9
src/_authors/toni_verbeiren.yaml
Normal file
@@ -0,0 +1,9 @@
|
||||
name: Toni Verbeiren
|
||||
info:
|
||||
links:
|
||||
github: tverbeiren
|
||||
linkedin: verbeiren
|
||||
organizations:
|
||||
- name: Data Intuitive
|
||||
href: https://www.data-intuitive.com
|
||||
role: Data Scientist and CEO
|
||||
5
src/_authors/weiwei_schultz.yaml
Normal file
5
src/_authors/weiwei_schultz.yaml
Normal file
@@ -0,0 +1,5 @@
|
||||
name: Weiwei Schultz
|
||||
info:
|
||||
organizations:
|
||||
- name: Janssen R&D US
|
||||
role: Associate Director Data Sciences
|
||||
86
src/agat/agat_convert_bed2gff/config.vsh.yaml
Normal file
86
src/agat/agat_convert_bed2gff/config.vsh.yaml
Normal file
@@ -0,0 +1,86 @@
|
||||
name: agat_convert_bed2gff
|
||||
namespace: agat
|
||||
description: |
|
||||
The script takes a bed file as input, and will translate it in gff format. The BED format is described here The script converts 0-based, half-open [start-1, end) bed file to 1-based, closed [start, end] General Feature Format v3 (GFF3).
|
||||
keywords: [gene annotations, GFF conversion]
|
||||
links:
|
||||
homepage: https://github.com/NBISweden/AGAT
|
||||
documentation: https://agat.readthedocs.io/en/latest/tools/agat_convert_bed2gff.html
|
||||
issue_tracker: https://github.com/NBISweden/AGAT/issues
|
||||
repository: https://github.com/NBISweden/AGAT
|
||||
references:
|
||||
doi: 10.5281/zenodo.3552717
|
||||
license: GPL-3.0
|
||||
authors:
|
||||
- __merge__: /src/_authors/leila_paquay.yaml
|
||||
roles: [ author, maintainer ]
|
||||
argument_groups:
|
||||
- name: Inputs
|
||||
arguments:
|
||||
- name: --bed
|
||||
description: Input bed file that will be converted.
|
||||
type: file
|
||||
required: true
|
||||
direction: input
|
||||
example: input.bed
|
||||
- name: Outputs
|
||||
arguments:
|
||||
- name: --output
|
||||
alternatives: [-o, --out, --outfile, --gff]
|
||||
description: Output GFF file. If no output file is specified, the output will be written to STDOUT.
|
||||
type: file
|
||||
direction: output
|
||||
required: true
|
||||
example: output.gff
|
||||
- name: Arguments
|
||||
arguments:
|
||||
- name: --source
|
||||
description: |
|
||||
The source informs about the tool used to produce the data and is stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc. [default: data]
|
||||
type: string
|
||||
required: false
|
||||
example: Stringtie
|
||||
- name: --primary_tag
|
||||
description: |
|
||||
The primary_tag corresponds to the data type and is stored in 3rd field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]
|
||||
type: string
|
||||
required: false
|
||||
example: gene
|
||||
- name: --inflate_off
|
||||
description: |
|
||||
By default we inflate the block fields (blockCount, blockSizes, blockStarts) to create subfeatures of the main feature (primary_tag). The type of subfeature created is based on the inflate_type parameter. If you do not want this inflating behaviour you can deactivate it by using the --inflate_off option.
|
||||
type: boolean_true
|
||||
- name: --inflate_type
|
||||
description: |
|
||||
Feature type (3rd column in gff) created when inflate parameter activated [default: exon].
|
||||
type: string
|
||||
required: false
|
||||
example: exon
|
||||
- name: --verbose
|
||||
description: add verbosity
|
||||
type: boolean_true
|
||||
- name: --config
|
||||
alternatives: [-c]
|
||||
description: |
|
||||
Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
|
||||
type: file
|
||||
required: false
|
||||
example: custom_agat_config.yaml
|
||||
resources:
|
||||
- type: bash_script
|
||||
path: script.sh
|
||||
test_resources:
|
||||
- type: bash_script
|
||||
path: test.sh
|
||||
- type: file
|
||||
path: test_data
|
||||
engines:
|
||||
- type: docker
|
||||
image: quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0
|
||||
setup:
|
||||
- type: docker
|
||||
run: |
|
||||
agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.txt
|
||||
runners:
|
||||
- type: executable
|
||||
- type: nextflow
|
||||
89
src/agat/agat_convert_bed2gff/help.txt
Normal file
89
src/agat/agat_convert_bed2gff/help.txt
Normal file
@@ -0,0 +1,89 @@
|
||||
```sh
|
||||
agat_convert_bed2gff.pl --help
|
||||
```
|
||||
------------------------------------------------------------------------------
|
||||
| Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0 |
|
||||
| https://github.com/NBISweden/AGAT |
|
||||
| National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se |
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
Name:
|
||||
agat_convert_bed2gff.pl
|
||||
|
||||
Description:
|
||||
The script takes a bed file as input, and will translate it in gff
|
||||
format. The BED format is described here:
|
||||
https://genome.ucsc.edu/FAQ/FAQformat.html#format1 The script converts
|
||||
0-based, half-open [start-1, end) bed file to 1-based, closed [start,
|
||||
end] General Feature Format v3 (GFF3).
|
||||
|
||||
Usage:
|
||||
agat_convert_bed2gff.pl --bed infile.bed [ -o outfile ]
|
||||
agat_convert_bed2gff.pl -h
|
||||
|
||||
Options:
|
||||
--bed Input bed file that will be converted.
|
||||
|
||||
--source
|
||||
The source informs about the tool used to produce the data and
|
||||
is stored in 2nd field of a gff file. Example:
|
||||
Stringtie,Maker,Augustus,etc. [default: data]
|
||||
|
||||
--primary_tag
|
||||
The primary_tag corresponds to the data type and is stored in
|
||||
3rd field of a gff file. Example: gene,mRNA,CDS,etc. [default:
|
||||
gene]
|
||||
|
||||
--inflate_off
|
||||
By default we inflate the block fields (blockCount, blockSizes,
|
||||
blockStarts) to create subfeatures of the main feature
|
||||
(primary_tag). The type of subfeature created is based on the
|
||||
inflate_type parameter. If you do not want this inflating
|
||||
behaviour you can deactivate it by using the --inflate_off
|
||||
option.
|
||||
|
||||
--inflate_type
|
||||
Feature type (3rd column in gff) created when inflate parameter
|
||||
activated [default: exon].
|
||||
|
||||
--verbose
|
||||
add verbosity
|
||||
|
||||
-o , --output , --out , --outfile or --gff
|
||||
Output GFF file. If no output file is specified, the output will
|
||||
be written to STDOUT.
|
||||
|
||||
-c or --config
|
||||
String - Input agat config file. By default AGAT takes as input
|
||||
agat_config.yaml file from the working directory if any,
|
||||
otherwise it takes the orignal agat_config.yaml shipped with
|
||||
AGAT. To get the agat_config.yaml locally type: "agat config
|
||||
--expose". The --config option gives you the possibility to use
|
||||
your own AGAT config file (located elsewhere or named
|
||||
differently).
|
||||
|
||||
-h or --help
|
||||
Display this helpful text.
|
||||
|
||||
Feedback:
|
||||
Did you find a bug?:
|
||||
Do not hesitate to report bugs to help us keep track of the bugs and
|
||||
their resolution. Please use the GitHub issue tracking system available
|
||||
at this address:
|
||||
|
||||
https://github.com/NBISweden/AGAT/issues
|
||||
|
||||
Ensure that the bug was not already reported by searching under Issues.
|
||||
If you're unable to find an (open) issue addressing the problem, open a new one.
|
||||
Try as much as possible to include in the issue when relevant:
|
||||
- a clear description,
|
||||
- as much relevant information as possible,
|
||||
- the command used,
|
||||
- a data sample,
|
||||
- an explanation of the expected behaviour that is not occurring.
|
||||
|
||||
Do you want to contribute?:
|
||||
You are very welcome, visit this address for the Contributing
|
||||
guidelines:
|
||||
https://github.com/NBISweden/AGAT/blob/master/CONTRIBUTING.md
|
||||
19
src/agat/agat_convert_bed2gff/script.sh
Normal file
19
src/agat/agat_convert_bed2gff/script.sh
Normal file
@@ -0,0 +1,19 @@
|
||||
#!/bin/bash
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
# unset flags
|
||||
[[ "$par_inflate_off" == "false" ]] && unset par_inflate_off
|
||||
[[ "$par_verbose" == "false" ]] && unset par_verbose
|
||||
|
||||
# run agat_convert_sp_bed2gff.pl
|
||||
agat_convert_bed2gff.pl \
|
||||
--bed "$par_bed" \
|
||||
-o "$par_output" \
|
||||
${par_source:+--source "${par_source}"} \
|
||||
${par_primary_tag:+--primary_tag "${par_primary_tag}"} \
|
||||
${par_inflate_off:+--inflate_off} \
|
||||
${par_inflate_type:+--inflate_type "${par_inflate_type}"} \
|
||||
${par_verbose:+--verbose}
|
||||
${par_config:+--config "${par_config}"} \
|
||||
27
src/agat/agat_convert_bed2gff/test.sh
Normal file
27
src/agat/agat_convert_bed2gff/test.sh
Normal file
@@ -0,0 +1,27 @@
|
||||
#!/bin/bash
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
test_dir="${meta_resources_dir}/test_data"
|
||||
out_dir="${meta_resources_dir}/out_data"
|
||||
|
||||
echo "> Run $meta_name with test data"
|
||||
"$meta_executable" \
|
||||
--bed "$test_dir/test.bed" \
|
||||
--output "$out_dir/output.gff"
|
||||
|
||||
echo ">> Checking output"
|
||||
[ ! -f "$out_dir/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
|
||||
|
||||
echo ">> Check if output is empty"
|
||||
[ ! -s "$out_dir/output.gff" ] && echo "Output file output.gff is empty" && exit 1
|
||||
|
||||
echo ">> Check if output matches expected output"
|
||||
diff "$out_dir/output.gff" "$test_dir/agat_convert_bed2gff_1.gff"
|
||||
if [ $? -ne 0 ]; then
|
||||
echo "Output file output.gff does not match expected output"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
echo "> Test successful"
|
||||
@@ -0,0 +1,12 @@
|
||||
##gff-version 3
|
||||
scaffold625 data gene 337818 343277 . + . ID=1;Name=CLUHART00000008717;blockCount=4;blockSizes=154%2C109%2C111%2C1314;blockStarts=0%2C2915%2C3700%2C4146;itemRgb=255%2C0%2C0;thickEnd=343033;thickStart=337914
|
||||
scaffold625 data exon 337818 337971 . + . ID=exon1;Parent=1
|
||||
scaffold625 data exon 340733 340841 . + . ID=exon2;Parent=1
|
||||
scaffold625 data exon 341518 341628 . + . ID=exon3;Parent=1
|
||||
scaffold625 data exon 341964 343277 . + . ID=exon4;Parent=1
|
||||
scaffold625 data CDS 337915 337971 . + 0 ID=CDS1;Parent=1
|
||||
scaffold625 data CDS 340733 340841 . + 0 ID=CDS2;Parent=1
|
||||
scaffold625 data CDS 341518 341628 . + 2 ID=CDS3;Parent=1
|
||||
scaffold625 data CDS 341964 343033 . + 2 ID=CDS4;Parent=1
|
||||
scaffold625 data five_prime_UTR 337818 337914 . + . ID=five_prime_UTR1;Parent=1
|
||||
scaffold625 data three_prime_UTR 343034 343277 . + . ID=three_prime_UTR1;Parent=1
|
||||
10
src/agat/agat_convert_bed2gff/test_data/script.sh
Executable file
10
src/agat/agat_convert_bed2gff/test_data/script.sh
Executable file
@@ -0,0 +1,10 @@
|
||||
#!/bin/bash
|
||||
|
||||
# clone repo
|
||||
if [ ! -d /tmp/agat_source ]; then
|
||||
git clone --depth 1 --single-branch --branch master https://github.com/NBISweden/AGAT /tmp/agat_source
|
||||
fi
|
||||
|
||||
# copy test data
|
||||
cp -r /tmp/agat_source/t/scripts_output/in/test.bed src/agat/agat_convert_bed2gff/test_data/test.bed
|
||||
cp -r /tmp/agat_source/t/scripts_output/out/agat_convert_bed2gff_1.gff src/agat/agat_convert_bed2gff/test_data/agat_convert_bed2gff_1.gff
|
||||
1
src/agat/agat_convert_bed2gff/test_data/test.bed
Normal file
1
src/agat/agat_convert_bed2gff/test_data/test.bed
Normal file
@@ -0,0 +1 @@
|
||||
scaffold625 337817 343277 CLUHART00000008717 0 + 337914 343033 255,0,0 4 154,109,111,1314 0,2915,3700,4146
|
||||
84
src/agat/agat_convert_embl2gff/config.vsh.yaml
Normal file
84
src/agat/agat_convert_embl2gff/config.vsh.yaml
Normal file
@@ -0,0 +1,84 @@
|
||||
name: agat_convert_embl2gff
|
||||
namespace: agat
|
||||
description: |
|
||||
The script takes an EMBL file as input, and will translate it in gff format.
|
||||
keywords: [gene annotations, GFF conversion]
|
||||
links:
|
||||
homepage: https://github.com/NBISweden/AGAT
|
||||
documentation: https://agat.readthedocs.io/en/latest/tools/agat_convert_embl2gff.html
|
||||
issue_tracker: https://github.com/NBISweden/AGAT/issues
|
||||
repository: https://github.com/NBISweden/AGAT
|
||||
references:
|
||||
doi: 10.5281/zenodo.3552717
|
||||
license: GPL-3.0
|
||||
authors:
|
||||
- __merge__: /src/_authors/leila_paquay.yaml
|
||||
roles: [ author, maintainer ]
|
||||
|
||||
argument_groups:
|
||||
- name: Inputs
|
||||
arguments:
|
||||
- name: --embl
|
||||
description: Input EMBL file that will be read.
|
||||
type: file
|
||||
required: true
|
||||
direction: input
|
||||
example: input.embl
|
||||
- name: Outputs
|
||||
arguments:
|
||||
- name: --output
|
||||
alternatives: [-o, --out, --outfile, --gff]
|
||||
description: Output GFF file. If no output file is specified, the output will be written to STDOUT.
|
||||
type: file
|
||||
direction: output
|
||||
required: false
|
||||
example: output.gff
|
||||
- name: Arguments
|
||||
arguments:
|
||||
- name: --emblmygff3
|
||||
description: |
|
||||
Means that the EMBL flat file comes from the EMBLmyGFF3 software. This is an EMBL format dedicated for submission and contains particularity to deal with. This parameter is needed to get a proper sequence id in the GFF3 from an embl made with EMBLmyGFF3.
|
||||
type: boolean_true
|
||||
- name: --primary_tag
|
||||
alternatives: [--pt, -t]
|
||||
description: |
|
||||
List of "primary tag". Useful to discard or keep specific features. Multiple tags must be comma-separated.
|
||||
type: string
|
||||
multiple: true
|
||||
required: false
|
||||
example: [tag1, tag2]
|
||||
- name: --discard
|
||||
alternatives: [-d]
|
||||
description: |
|
||||
Means that primary tags provided by the option "primary_tag" will be discarded.
|
||||
type: boolean_true
|
||||
- name: --keep
|
||||
alternatives: [-k]
|
||||
description: |
|
||||
Means that only primary tags provided by the option "primary_tag" will be kept.
|
||||
type: boolean_true
|
||||
- name: --config
|
||||
alternatives: [-c]
|
||||
description: |
|
||||
Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
|
||||
type: file
|
||||
required: false
|
||||
example: custom_agat_config.yaml
|
||||
resources:
|
||||
- type: bash_script
|
||||
path: script.sh
|
||||
test_resources:
|
||||
- type: bash_script
|
||||
path: test.sh
|
||||
- type: file
|
||||
path: test_data
|
||||
engines:
|
||||
- type: docker
|
||||
image: quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0
|
||||
setup:
|
||||
- type: docker
|
||||
run: |
|
||||
agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.txt
|
||||
runners:
|
||||
- type: executable
|
||||
- type: nextflow
|
||||
78
src/agat/agat_convert_embl2gff/help.txt
Normal file
78
src/agat/agat_convert_embl2gff/help.txt
Normal file
@@ -0,0 +1,78 @@
|
||||
```sh
|
||||
agat_convert_embl2gff.pl --help
|
||||
```
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
| Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0 |
|
||||
| https://github.com/NBISweden/AGAT |
|
||||
| National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se |
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
Name:
|
||||
agat_converter_embl2gff.pl
|
||||
|
||||
Description:
|
||||
The script takes an EMBL file as input, and will translate it in gff
|
||||
format.
|
||||
|
||||
Usage:
|
||||
agat_converter_embl2gff.pl --embl infile.embl [ -o outfile ]
|
||||
|
||||
Options:
|
||||
--embl Input EMBL file that will be read
|
||||
|
||||
--emblmygff3
|
||||
Bolean - Means that the EMBL flat file comes from the EMBLmyGFF3
|
||||
software. This is an EMBL format dedicated for submission and
|
||||
contains particularity to deal with. This parameter is needed to
|
||||
get a proper sequence id in the GFF3 from an embl made with
|
||||
EMBLmyGFF3.
|
||||
|
||||
--primary_tag, --pt, -t
|
||||
List of "primary tag". Useful to discard or keep specific
|
||||
features. Multiple tags must be coma-separated.
|
||||
|
||||
-d Bolean - Means that primary tags provided by the option
|
||||
"primary_tag" will be discarded.
|
||||
|
||||
-k Bolean - Means that only primary tags provided by the option
|
||||
"primary_tag" will be kept.
|
||||
|
||||
-o, --output, --out, --outfile or --gff
|
||||
Output GFF file. If no output file is specified, the output will
|
||||
be written to STDOUT.
|
||||
|
||||
-c or --config
|
||||
String - Input agat config file. By default AGAT takes as input
|
||||
agat_config.yaml file from the working directory if any,
|
||||
otherwise it takes the orignal agat_config.yaml shipped with
|
||||
AGAT. To get the agat_config.yaml locally type: "agat config
|
||||
--expose". The --config option gives you the possibility to use
|
||||
your own AGAT config file (located elsewhere or named
|
||||
differently).
|
||||
|
||||
-h or --help
|
||||
Display this helpful text.
|
||||
|
||||
Feedback:
|
||||
Did you find a bug?:
|
||||
Do not hesitate to report bugs to help us keep track of the bugs and
|
||||
their resolution. Please use the GitHub issue tracking system available
|
||||
at this address:
|
||||
|
||||
https://github.com/NBISweden/AGAT/issues
|
||||
|
||||
Ensure that the bug was not already reported by searching under Issues.
|
||||
If you're unable to find an (open) issue addressing the problem, open a new one.
|
||||
Try as much as possible to include in the issue when relevant:
|
||||
- a clear description,
|
||||
- as much relevant information as possible,
|
||||
- the command used,
|
||||
- a data sample,
|
||||
- an explanation of the expected behaviour that is not occurring.
|
||||
|
||||
Do you want to contribute?:
|
||||
You are very welcome, visit this address for the Contributing
|
||||
guidelines:
|
||||
https://github.com/NBISweden/AGAT/blob/master/CONTRIBUTING.md
|
||||
23
src/agat/agat_convert_embl2gff/script.sh
Normal file
23
src/agat/agat_convert_embl2gff/script.sh
Normal file
@@ -0,0 +1,23 @@
|
||||
#!/bin/bash
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
|
||||
# unset flags
|
||||
[[ "$par_emblmygff3" == "false" ]] && unset par_emblmygff3
|
||||
[[ "$par_discard" == "false" ]] && unset par_discard
|
||||
[[ "$par_keep" == "false" ]] && unset par_keep
|
||||
|
||||
# replace ';' with ','
|
||||
par_primary_tag=$(echo $par_primary_tag | tr ';' ',')
|
||||
|
||||
# run agat_convert_embl2gff
|
||||
agat_convert_embl2gff.pl \
|
||||
--embl "$par_embl" \
|
||||
-o "$par_output" \
|
||||
${par_emblmygff3:+--emblmygff3} \
|
||||
${par_primary_tag:+--primary_tag "${par_primary_tag}"} \
|
||||
${par_discard:+-d} \
|
||||
${par_keep:+-k} \
|
||||
${par_config:+--config "${par_config}"}
|
||||
28
src/agat/agat_convert_embl2gff/test.sh
Normal file
28
src/agat/agat_convert_embl2gff/test.sh
Normal file
@@ -0,0 +1,28 @@
|
||||
#!/bin/bash
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
test_dir="${meta_resources_dir}/test_data"
|
||||
out_dir="${meta_resources_dir}/out_data"
|
||||
|
||||
echo "> Run $meta_name with test data and --emblmygff3"
|
||||
"$meta_executable" \
|
||||
--embl "$test_dir/agat_convert_embl2gff_1.embl" \
|
||||
--output "$out_dir/output.gff" \
|
||||
--emblmygff3
|
||||
|
||||
echo ">> Checking output"
|
||||
[ ! -f "$out_dir/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
|
||||
|
||||
echo ">> Check if output is empty"
|
||||
[ ! -s "$out_dir/output.gff" ] && echo "Output file output.gff is empty" && exit 1
|
||||
|
||||
echo ">> Check if output matches expected output"
|
||||
diff "$out_dir/output.gff" "$test_dir/agat_convert_embl2gff_1.gff"
|
||||
if [ $? -ne 0 ]; then
|
||||
echo "Output file output.gff does not match expected output"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
echo "> Test successful"
|
||||
@@ -0,0 +1,51 @@
|
||||
ID patatrac; SV 1; circular; genomic DNA; XXX; PRO; 317941 BP.
|
||||
XX
|
||||
AC XXX;
|
||||
XX
|
||||
AC * _ERS324955|SC|contig000001
|
||||
XX
|
||||
PR Project:PRJEBNNNN;
|
||||
XX
|
||||
DE XXX
|
||||
XX
|
||||
RN [1]
|
||||
RP 1-2149
|
||||
RA XXX;
|
||||
RT ;
|
||||
RL Submitted {(DD-MMM-YYYY)} to the INSDC.
|
||||
XX
|
||||
FH Key Location/Qualifiers
|
||||
FH
|
||||
FT source 1..588788
|
||||
FT /organism={"scientific organism name"}
|
||||
FT /mol_type={"in vivo molecule type of sequence"}
|
||||
XX
|
||||
SQ Sequence 588788 BP; 101836 A; 193561 C; 192752 G; 100639 T; 0 other;
|
||||
tgcgtactcg aagagacgcg cccagattat ataagggcgt cgtctcgagg ccgacggcgc 60
|
||||
gccggcgagt acgcgtgatc cacaacccga agcgaccgtc gggagaccga gggtcgtcga 120
|
||||
gggtggatac gttcctgcct tcgtgccggg aaacggccga agggaacgtg gcgacctgcg 180
|
||||
//
|
||||
ID fdssf; SV 1; circular; genomic DNA; XXX; PRO; 317941 BP.
|
||||
XX
|
||||
AC XXX;
|
||||
XX
|
||||
AC * _ERS344554
|
||||
XX
|
||||
PR Project:PRJEBNNNN;
|
||||
XX
|
||||
DE XXX
|
||||
XX
|
||||
RN [1]
|
||||
RP 1-2149
|
||||
RA XXX;
|
||||
RT ;
|
||||
RL Submitted {(DD-MMM-YYYY)} to the INSDC.
|
||||
XX
|
||||
FH Key Location/Qualifiers
|
||||
FH
|
||||
FT source 1..588788
|
||||
FT /organism={"scientific organism name"}
|
||||
FT /mol_type={"in vivo molecule type of sequence"}
|
||||
XX
|
||||
SQ Sequence 588788 BP; 101836 A; 193561 C; 192752 G; 100639 T; 0 other;
|
||||
TTTTTTTTTT aagagacgcg cccagattat ataagggcgt cgtctcgagg ccgacggcgc 60
|
||||
@@ -0,0 +1,10 @@
|
||||
##gff-version 3
|
||||
ERS324955|SC|contig000001 EMBL/GenBank/SwissProt source 1 588788 . + 1 mol_type={"in vivo molecule type of sequence"};organism={"scientific organism name"}
|
||||
ERS344554 EMBL/GenBank/SwissProt source 1 588788 . + 1 mol_type={"in vivo molecule type of sequence"};organism={"scientific organism name"}
|
||||
##FASTA
|
||||
>ERS324955|SC|contig000001 XXX
|
||||
TGCGTACTCGAAGAGACGCGCCCAGATTATATAAGGGCGTCGTCTCGAGGCCGACGGCGCGCCGGCGAGTACGCGTGATC
|
||||
CACAACCCGAAGCGACCGTCGGGAGACCGAGGGTCGTCGAGGGTGGATACGTTCCTGCCTTCGTGCCGGGAAACGGCCGA
|
||||
AGGGAACGTGGCGACCTGCG
|
||||
>ERS344554 XXX
|
||||
TTTTTTTTTTAAGAGACGCGCCCAGATTATATAAGGGCGTCGTCTCGAGGCCGACGGCGC
|
||||
10
src/agat/agat_convert_embl2gff/test_data/script.sh
Executable file
10
src/agat/agat_convert_embl2gff/test_data/script.sh
Executable file
@@ -0,0 +1,10 @@
|
||||
#!/bin/bash
|
||||
|
||||
# clone repo
|
||||
if [ ! -d /tmp/agat_source ]; then
|
||||
git clone --depth 1 --single-branch --branch master https://github.com/NBISweden/AGAT /tmp/agat_source
|
||||
fi
|
||||
|
||||
# copy test data
|
||||
cp -r /tmp/agat_source/t/scripts_output/in/agat_convert_embl2gff_1.embl src/agat/agat_convert_embl2gff/test_data/agat_convert_embl2gff_1.embl
|
||||
cp -r /tmp/agat_source/t/scripts_output/out/agat_convert_embl2gff_1.gff src/agat/agat_convert_embl2gff/test_data/agat_convert_embl2gff_1.gff
|
||||
95
src/agat/agat_convert_genscan2gff/config.vsh.yaml
Normal file
95
src/agat/agat_convert_genscan2gff/config.vsh.yaml
Normal file
@@ -0,0 +1,95 @@
|
||||
name: agat_convert_genscan2gff
|
||||
namespace: agat
|
||||
description: |
|
||||
The script takes a GENSCAN file as input, and will translate it in gff
|
||||
format. The GENSCAN format is described [here](http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/genscan.html).
|
||||
|
||||
**Known problem**
|
||||
|
||||
You must have submited only DNA sequence, without any header!! Indeed the tool expects only DNA
|
||||
sequences and does not crash/warn if an header is submited along the
|
||||
sequence. e.g If you have an header ">seq" s-e-q are seen as the 3 first
|
||||
nucleotides of the sequence. Then all prediction location are shifted
|
||||
accordingly. (checked only on the [online version](http://argonaute.mit.edu/GENSCAN.html).
|
||||
I don't know if there is the same problem elsewhere.)
|
||||
keywords: [gene annotations, GFF conversion, GENSCAN]
|
||||
links:
|
||||
homepage: https://github.com/NBISweden/AGAT
|
||||
documentation: https://agat.readthedocs.io/en/latest/tools/agat_convert_genscan2gff.html
|
||||
issue_tracker: https://github.com/NBISweden/AGAT/issues
|
||||
repository: https://github.com/NBISweden/AGAT
|
||||
references:
|
||||
doi: 10.5281/zenodo.3552717
|
||||
license: GPL-3.0
|
||||
requirements:
|
||||
- commands: [agat]
|
||||
authors:
|
||||
- __merge__: /src/_authors/leila_paquay.yaml
|
||||
roles: [ author, maintainer ]
|
||||
|
||||
argument_groups:
|
||||
- name: Inputs
|
||||
arguments:
|
||||
- name: --genscan
|
||||
alternatives: [-g]
|
||||
description: Input genscan bed file that will be converted.
|
||||
type: file
|
||||
required: true
|
||||
direction: input
|
||||
- name: Outputs
|
||||
arguments:
|
||||
- name: --output
|
||||
alternatives: [-o, --out, --outfile, --gff]
|
||||
description: Output GFF file. If no output file is specified, the output will be written to STDOUT.
|
||||
type: file
|
||||
direction: output
|
||||
required: true
|
||||
example: output.gff
|
||||
- name: Arguments
|
||||
arguments:
|
||||
- name: --source
|
||||
description: |
|
||||
The source informs about the tool used to produce the data and is stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc. [default: data]
|
||||
type: string
|
||||
required: false
|
||||
example: Stringtie
|
||||
- name: --primary_tag
|
||||
description: |
|
||||
The primary_tag corresponds to the data type and is stored in 3rd field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]
|
||||
type: string
|
||||
required: false
|
||||
example: gene
|
||||
- name: --inflate_type
|
||||
description: |
|
||||
Feature type (3rd column in gff) created when inflate parameter activated [default: exon].
|
||||
type: string
|
||||
required: false
|
||||
example: exon
|
||||
- name: --verbose
|
||||
description: add verbosity
|
||||
type: boolean_true
|
||||
- name: --config
|
||||
alternatives: [-c]
|
||||
description: |
|
||||
AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. The `--config` option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
|
||||
type: file
|
||||
required: false
|
||||
example: custom_agat_config.yaml
|
||||
resources:
|
||||
- type: bash_script
|
||||
path: script.sh
|
||||
test_resources:
|
||||
- type: bash_script
|
||||
path: test.sh
|
||||
- type: file
|
||||
path: test_data
|
||||
engines:
|
||||
- type: docker
|
||||
image: quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0
|
||||
setup:
|
||||
- type: docker
|
||||
run: |
|
||||
agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.txt
|
||||
runners:
|
||||
- type: executable
|
||||
- type: nextflow
|
||||
94
src/agat/agat_convert_genscan2gff/help.txt
Normal file
94
src/agat/agat_convert_genscan2gff/help.txt
Normal file
@@ -0,0 +1,94 @@
|
||||
```sh
|
||||
agat_convert_genscan2gff.pl --help
|
||||
```
|
||||
------------------------------------------------------------------------------
|
||||
| Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0 |
|
||||
| https://github.com/NBISweden/AGAT |
|
||||
| National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se |
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
Name:
|
||||
agat_convert_genscan2gff.pl
|
||||
|
||||
Description:
|
||||
The script takes a genscan file as input, and will translate it in gff
|
||||
format. The genscan format is described here:
|
||||
http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/gens
|
||||
can.html /!\ vvv Known problem vvv /!\ You must have submited only DNA
|
||||
sequence, wihtout any header!! Indeed the tool expects only DNA
|
||||
sequences and does not crash/warn if an header is submited along the
|
||||
sequence. e.g If you have an header ">seq" s-e-q are seen as the 3 first
|
||||
nucleotides of the sequence. Then all prediction location are shifted
|
||||
accordingly. (checked only on the online version
|
||||
http://argonaute.mit.edu/GENSCAN.html. I don't know if there is the same
|
||||
pronlem elsewhere.) /!\ ^^^ Known problem ^^^^ /!\
|
||||
|
||||
Usage:
|
||||
agat_convert_genscan2gff.pl --genscan infile.bed [ -o outfile ]
|
||||
agat_convert_genscan2gff.pl -h
|
||||
|
||||
Options:
|
||||
--genscan or -g
|
||||
Input genscan bed file that will be convert.
|
||||
|
||||
--source
|
||||
The source informs about the tool used to produce the data and
|
||||
is stored in 2nd field of a gff file. Example:
|
||||
Stringtie,Maker,Augustus,etc. [default: data]
|
||||
|
||||
--primary_tag
|
||||
The primary_tag corresponf to the data type and is stored in 3rd
|
||||
field of a gff file. Example: gene,mRNA,CDS,etc. [default: gene]
|
||||
|
||||
--inflate_off
|
||||
By default we inflate the block fields (blockCount, blockSizes,
|
||||
blockStarts) to create subfeatures of the main feature
|
||||
(primary_tag). Type of subfeature created based on the
|
||||
inflate_type parameter. If you don't want this inflating
|
||||
behaviour you can deactivate it by using the option
|
||||
--inflate_off.
|
||||
|
||||
--inflate_type
|
||||
Feature type (3rd column in gff) created when inflate parameter
|
||||
activated [default: exon].
|
||||
|
||||
--verbose
|
||||
add verbosity
|
||||
|
||||
-o , --output , --out , --outfile or --gff
|
||||
Output GFF file. If no output file is specified, the output will
|
||||
be written to STDOUT.
|
||||
|
||||
-c or --config
|
||||
String - Input agat config file. By default AGAT takes as input
|
||||
agat_config.yaml file from the working directory if any,
|
||||
otherwise it takes the orignal agat_config.yaml shipped with
|
||||
AGAT. To get the agat_config.yaml locally type: "agat config
|
||||
--expose". The --config option gives you the possibility to use
|
||||
your own AGAT config file (located elsewhere or named
|
||||
differently).
|
||||
|
||||
-h or --help
|
||||
Display this helpful text.
|
||||
|
||||
Feedback:
|
||||
Did you find a bug?:
|
||||
Do not hesitate to report bugs to help us keep track of the bugs and
|
||||
their resolution. Please use the GitHub issue tracking system available
|
||||
at this address:
|
||||
|
||||
https://github.com/NBISweden/AGAT/issues
|
||||
|
||||
Ensure that the bug was not already reported by searching under Issues.
|
||||
If you're unable to find an (open) issue addressing the problem, open a new one.
|
||||
Try as much as possible to include in the issue when relevant:
|
||||
- a clear description,
|
||||
- as much relevant information as possible,
|
||||
- the command used,
|
||||
- a data sample,
|
||||
- an explanation of the expected behaviour that is not occurring.
|
||||
|
||||
Do you want to contribute?:
|
||||
You are very welcome, visit this address for the Contributing
|
||||
guidelines:
|
||||
https://github.com/NBISweden/AGAT/blob/master/CONTRIBUTING.md
|
||||
21
src/agat/agat_convert_genscan2gff/script.sh
Normal file
21
src/agat/agat_convert_genscan2gff/script.sh
Normal file
@@ -0,0 +1,21 @@
|
||||
#!/bin/bash
|
||||
|
||||
set -eo pipefail
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
# unset flags
|
||||
[[ "$par_inflate_off" == "true" ]] && unset par_inflate_off
|
||||
[[ "$par_verbose" == "false" ]] && unset par_verbose
|
||||
|
||||
# run agat_convert_genscan2gff
|
||||
agat_convert_genscan2gff.pl \
|
||||
--genscan "$par_genscan" \
|
||||
--output "$par_output" \
|
||||
${par_source:+--source "${par_source}"} \
|
||||
${par_primary_tag:+--primary_tag "${par_primary_tag}"} \
|
||||
${par_inflate_off:+--inflate_off} \
|
||||
${par_inflate_type:+--inflate_type "${par_inflate_type}"} \
|
||||
${par_verbose:+--verbose} \
|
||||
${par_config:+--config "${par_config}"}
|
||||
35
src/agat/agat_convert_genscan2gff/test.sh
Normal file
35
src/agat/agat_convert_genscan2gff/test.sh
Normal file
@@ -0,0 +1,35 @@
|
||||
#!/bin/bash
|
||||
|
||||
set -eo pipefail
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
test_dir="${meta_resources_dir}/test_data"
|
||||
|
||||
# create temporary directory and clean up on exit
|
||||
TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_name-XXXXXX")
|
||||
function clean_up {
|
||||
[[ -d "$TMPDIR" ]] && rm -rf "$TMPDIR"
|
||||
}
|
||||
trap clean_up EXIT
|
||||
|
||||
echo "> Run $meta_name with test data"
|
||||
"$meta_executable" \
|
||||
--genscan "$test_dir/test.genscan" \
|
||||
--output "$TMPDIR/output.gff"
|
||||
|
||||
echo ">> Checking output"
|
||||
[ ! -f "$TMPDIR/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
|
||||
|
||||
echo ">> Check if output is empty"
|
||||
[ ! -s "$TMPDIR/output.gff" ] && echo "Output file output.gff is empty" && exit 1
|
||||
|
||||
echo ">> Check if output matches expected output"
|
||||
diff "$TMPDIR/output.gff" "$test_dir/agat_convert_genscan2gff_1.gff"
|
||||
if [ $? -ne 0 ]; then
|
||||
echo "Output file output.gff does not match expected output"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
echo "> Test successful"
|
||||
@@ -0,0 +1,25 @@
|
||||
##gff-version 3
|
||||
unknown genscan gene 2223 4605 75.25 + . ID=gene_1
|
||||
unknown genscan mRNA 2223 4605 75.25 + . ID=mrna_1;Parent=gene_1
|
||||
unknown genscan exon 2223 3020 75.25 + . ID=exon_1;Parent=mrna_1
|
||||
unknown genscan exon 4249 4605 13.03 + . ID=exon_2;Parent=mrna_1
|
||||
unknown genscan CDS 2223 3020 75.25 + 0 ID=cds_1;Parent=mrna_1
|
||||
unknown genscan CDS 4249 4605 13.03 + 0 ID=cds_2;Parent=mrna_1
|
||||
unknown genscan gene 6829 8789 20.06 - . ID=gene_2
|
||||
unknown genscan mRNA 6829 8789 20.06 - . ID=mrna_2;Parent=gene_2
|
||||
unknown genscan exon 6829 7297 20.06 - . ID=exon_3;Parent=mrna_2
|
||||
unknown genscan exon 7730 7888 12.78 - . ID=exon_4;Parent=mrna_2
|
||||
unknown genscan exon 8029 8185 7.45 - . ID=exon_5;Parent=mrna_2
|
||||
unknown genscan exon 8278 8546 17.45 - . ID=exon_6;Parent=mrna_2
|
||||
unknown genscan exon 8647 8789 18.65 - . ID=exon_7;Parent=mrna_2
|
||||
unknown genscan CDS 6829 7297 20.06 - 1 ID=cds_3;Parent=mrna_2
|
||||
unknown genscan CDS 7730 7888 12.78 - 1 ID=cds_4;Parent=mrna_2
|
||||
unknown genscan CDS 8029 8185 7.45 - 2 ID=cds_5;Parent=mrna_2
|
||||
unknown genscan CDS 8278 8546 17.45 - 1 ID=cds_6;Parent=mrna_2
|
||||
unknown genscan CDS 8647 8789 18.65 - 0 ID=cds_7;Parent=mrna_2
|
||||
unknown genscan gene 10209 11924 16.18 + . ID=gene_3
|
||||
unknown genscan mRNA 10209 11924 16.18 + . ID=mrna_3;Parent=gene_3
|
||||
unknown genscan exon 10209 11313 16.18 + . ID=exon_8;Parent=mrna_3
|
||||
unknown genscan exon 11850 11924 3.27 + . ID=exon_9;Parent=mrna_3
|
||||
unknown genscan CDS 10209 11313 16.18 + 0 ID=cds_8;Parent=mrna_3
|
||||
unknown genscan CDS 11850 11924 3.27 + 2 ID=cds_9;Parent=mrna_3
|
||||
11
src/agat/agat_convert_genscan2gff/test_data/script.sh
Executable file
11
src/agat/agat_convert_genscan2gff/test_data/script.sh
Executable file
@@ -0,0 +1,11 @@
|
||||
#!/bin/bash
|
||||
|
||||
# clone repo
|
||||
if [ ! -d /tmp/agat_source ]; then
|
||||
git clone --depth 1 --single-branch --branch master https://github.com/NBISweden/AGAT /tmp/agat_source
|
||||
fi
|
||||
|
||||
# copy test data
|
||||
cp -r /tmp/agat_source/t/scripts_output/in/test.genscan src/agat/agat_convert_genscan2gff/test_data/test.genscan
|
||||
cp -r /tmp/agat_source/t/scripts_output/out/agat_convert_genscan2gff_1.gff src/agat/agat_convert_genscan2gff/test_data/agat_convert_genscan2gff_1.gff
|
||||
|
||||
127
src/agat/agat_convert_genscan2gff/test_data/test.genscan
Normal file
127
src/agat/agat_convert_genscan2gff/test_data/test.genscan
Normal file
@@ -0,0 +1,127 @@
|
||||
GENSCAN 1.0 Date run: 7-Mar-120 Time: 14:46:49
|
||||
|
||||
|
||||
|
||||
Sequence /tmp/03_07_20-14:46:49.fasta : 12217 bp : 42.83% C+G : Isochore 1 ( 0 - 43 C+G%)
|
||||
|
||||
|
||||
|
||||
Parameter matrix: HumanIso.smat
|
||||
|
||||
|
||||
|
||||
Predicted genes/exons:
|
||||
|
||||
|
||||
|
||||
Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr..
|
||||
|
||||
----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------
|
||||
|
||||
|
||||
|
||||
1.01 Init + 2223 3020 798 2 0 55 2 924 0.940 75.25
|
||||
|
||||
1.02 Term + 4249 4605 357 0 0 26 38 307 0.976 13.03
|
||||
|
||||
1.03 PlyA + 4711 4716 6 -0.45
|
||||
|
||||
|
||||
|
||||
2.06 PlyA - 4852 4847 6 -0.45
|
||||
|
||||
2.05 Term - 7297 6829 469 0 1 13 42 387 0.281 20.06
|
||||
|
||||
2.04 Intr - 7888 7730 159 0 0 85 93 144 0.998 12.78
|
||||
|
||||
2.03 Intr - 8185 8029 157 2 1 65 60 144 0.787 7.45
|
||||
|
||||
2.02 Intr - 8546 8278 269 1 2 36 65 287 0.946 17.45
|
||||
|
||||
2.01 Init - 8789 8647 143 2 2 94 96 176 0.550 18.65
|
||||
|
||||
2.00 Prom - 9720 9681 40 -6.55
|
||||
|
||||
|
||||
|
||||
3.00 Prom + 10160 10199 40 -11.84
|
||||
|
||||
3.01 Init + 10209 11313 1105 2 1 66 57 269 0.512 16.18
|
||||
|
||||
3.02 Intr + 11850 11924 75 1 0 80 86 57 0.507 3.27
|
||||
|
||||
|
||||
|
||||
Suboptimal exons with probability > 1.000
|
||||
|
||||
|
||||
|
||||
Exnum Type S .Begin ...End .Len Fr Ph B/Ac Do/T CodRg P.... Tscr..
|
||||
|
||||
----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------
|
||||
|
||||
|
||||
|
||||
NO EXONS FOUND AT GIVEN PROBABILITY CUTOFF
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Predicted peptide sequence(s):
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
>/tmp/03_03_20-07:33:11.fasta|GENSCAN_predicted_peptide_1|384_aa
|
||||
|
||||
MSSKNKVSKQDIDSIVESLMKKQKSYFEPRLAQIQQVGMENVQKLSAIHAELALLTASIS
|
||||
|
||||
TVKSDVDKLKCKVENNFSAIDGHDQAFGELELKMADMEDRSRRCNIRVIGLKERLEGFNA
|
||||
|
||||
IQYLTHSLPKWFPALADVPVEVMSAHRIYSDAKRGDNRTLIFNVLRYTTRQAILRAAKKD
|
||||
|
||||
PLSVDDRKVRFSPDYSNFTVKRCQAFHQAKDAARNKCLDFFLLYPATLKIKEGAQYRSFT
|
||||
|
||||
SPKEAEDYVNSAASNHAATPASPRQHGTILTIYRRIHSLYDGERARKIQLLEQAASVALT
|
||||
|
||||
GDNWTSVRNDNYLGVTAHFIDNVWKLRCFALEVKKKKKHSRHTAEDCAEEFIDVSNRWEI
|
||||
|
||||
NGKLTTLGTDSALIMLAAARLLPF
|
||||
|
||||
|
||||
|
||||
>/tmp/03_03_20-07:33:11.fasta|GENSCAN_predicted_peptide_2|398_aa
|
||||
|
||||
MASTMPSSSSTEDEENTPECLNKDHYHFHHYTMEYIQDKPTNVARVGGFTDKKSIAKVER
|
||||
|
||||
CLARERQEATEDHEAIPSTSGATSLTKKLRSRSGLPIAGSGLVLPALCIICQKKEKFINR
|
||||
|
||||
AGKRQRDPLSKAETLTVGQLQKAAELKDDQSILLHIKDKDCVALEVQYHKGCYNQYTRFM
|
||||
|
||||
TRPEKPEKEQNEPTFDVGYKILCERIIRQRLLVNQEVLRMGQLRMAFIELVKANEGLDAS
|
||||
|
||||
NYSIKNLERSRRADAGSQRIQIFDPDQRTPTQWKKFLSEGTKKEALAEFLYVAWKNADLT
|
||||
|
||||
IVGKNLCLYIAHTNQCHCVTVKEGVQSVRVVEDLLLFLHAQHAAREHKAVIIKSSDTDVA
|
||||
|
||||
VIAVSVQTDLPCSLYVFTGTGNRTRIIDITKVSSANKI
|
||||
|
||||
|
||||
|
||||
>/tmp/03_03_20-07:33:11.fasta|GENSCAN_predicted_peptide_3|394_aa
|
||||
|
||||
MQRGRAAGINGIPPEFYVAFWEQLSPFFLHMINFSIEKGGFLRDVNTALISLLMKKDKNP
|
||||
|
||||
TDCSSYRPLSLLNSDVKIFAKLLPLRLEPHMPELVSSDQTGFIKSRTAADNIRRLLHIIA
|
||||
|
||||
AAPGCETPMSVLSLDAMKAFDRLEWSFLWSVLEAMGFISTFIGMVKVLYSNPSARVLTGQ
|
||||
|
||||
TFSSLFPVSRSSRQGCPLSPALFVLSLEPLAQAVRLSNLVLPICICDTQHKLSLFADDVI
|
||||
|
||||
VFLEHPTQSLPHFLSICEEFRKLSGFKMNWSKSALMHLNDNARKSVTPVNIPLVGQLKYL
|
||||
|
||||
GIEVFPSLNQIVKHNYSLAFTNVLKDMDRWISLPMSIQARISIIKMNGLPRIHFVSSMVP
|
||||
|
||||
LPPPSDYWIKISAQGVRCPLAKPFTHSPYSKTKX
|
||||
66
src/agat/agat_convert_mfannot2gff/config.vsh.yaml
Normal file
66
src/agat/agat_convert_mfannot2gff/config.vsh.yaml
Normal file
@@ -0,0 +1,66 @@
|
||||
name: agat_convert_mfannot2gff
|
||||
namespace: agat
|
||||
description: |
|
||||
Conversion utility for MFannot "masterfile" annotation produced by the
|
||||
[MFannot pipeline](http://megasun.bch.umontreal.ca/RNAweasel/). Reports
|
||||
GFF3 format.
|
||||
keywords: [gene annotations, GFF , Mfannot]
|
||||
links:
|
||||
homepage: https://github.com/NBISweden/AGAT
|
||||
documentation: https://agat.readthedocs.io/en/latest/tools/agat_convert_mfannot2gff.html
|
||||
issue_tracker: https://github.com/NBISweden/AGAT/issues
|
||||
repository: https://github.com/NBISweden/AGAT
|
||||
references:
|
||||
doi: 10.5281/zenodo.3552717
|
||||
license: GPL-3.
|
||||
requirements:
|
||||
- command: [agat]
|
||||
authors:
|
||||
- __merge__: /src/_authors/leila_paquay.yaml
|
||||
roles: [ author, maintainer ]
|
||||
argument_groups:
|
||||
- name: Inputs
|
||||
arguments:
|
||||
- name: --mfannot
|
||||
alternatives: [-m, -i]
|
||||
description: The mfannot input file.
|
||||
type: file
|
||||
required: true
|
||||
direction: input
|
||||
example: input.mfannot
|
||||
- name: Outputs
|
||||
arguments:
|
||||
- name: --gff
|
||||
alternatives: [-g, -o]
|
||||
description: The GFF output file.
|
||||
type: file
|
||||
direction: output
|
||||
required: true
|
||||
example: output.gff
|
||||
- name: Arguments
|
||||
arguments:
|
||||
- name: --config
|
||||
alternatives: [-c]
|
||||
description: |
|
||||
AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. The `--config` option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
|
||||
type: file
|
||||
required: false
|
||||
example: custom_agat_config.yaml
|
||||
resources:
|
||||
- type: bash_script
|
||||
path: script.sh
|
||||
test_resources:
|
||||
- type: bash_script
|
||||
path: test.sh
|
||||
- type: file
|
||||
path: test_data
|
||||
engines:
|
||||
- type: docker
|
||||
image: quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0
|
||||
setup:
|
||||
- type: docker
|
||||
run: |
|
||||
agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.txt
|
||||
runners:
|
||||
- type: executable
|
||||
- type: nextflow
|
||||
67
src/agat/agat_convert_mfannot2gff/help.txt
Normal file
67
src/agat/agat_convert_mfannot2gff/help.txt
Normal file
@@ -0,0 +1,67 @@
|
||||
```sh
|
||||
agat_convert_mfannot2gff.pl --help
|
||||
```
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
| Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0 |
|
||||
| https://github.com/NBISweden/AGAT |
|
||||
| National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se |
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
Name:
|
||||
agat_convert_mfannot2gff.pl
|
||||
|
||||
Description:
|
||||
Conversion utility for MFannot "masterfile" annotation produced by the
|
||||
MFannot pipeline (http://megasun.bch.umontreal.ca/RNAweasel/). Reports
|
||||
GFF3 format.
|
||||
|
||||
Usage:
|
||||
agat_convert_mfannot2gff.pl -m <mfannot> -o <gff>
|
||||
agat_convert_mfannot2gff.pl --help
|
||||
|
||||
Copyright and License:
|
||||
Copyright (C) 2015, Brandon Seah (kbseah@mpi-bremen.de) ... GPL-3 ...
|
||||
modified by jacques dainat 2017-11
|
||||
|
||||
Options:
|
||||
-m or -i or --mfannot
|
||||
The mfannot input file
|
||||
|
||||
-g or -o or --gff
|
||||
the gff output file
|
||||
|
||||
-c or --config
|
||||
String - Input agat config file. By default AGAT takes as input
|
||||
agat_config.yaml file from the working directory if any,
|
||||
otherwise it takes the orignal agat_config.yaml shipped with
|
||||
AGAT. To get the agat_config.yaml locally type: "agat config
|
||||
--expose". The --config option gives you the possibility to use
|
||||
your own AGAT config file (located elsewhere or named
|
||||
differently).
|
||||
|
||||
-h or --help
|
||||
Display this helpful text.
|
||||
|
||||
Feedback:
|
||||
Did you find a bug?:
|
||||
Do not hesitate to report bugs to help us keep track of the bugs and
|
||||
their resolution. Please use the GitHub issue tracking system available
|
||||
at this address:
|
||||
|
||||
https://github.com/NBISweden/AGAT/issues
|
||||
|
||||
Ensure that the bug was not already reported by searching under Issues.
|
||||
If you're unable to find an (open) issue addressing the problem, open a new one.
|
||||
Try as much as possible to include in the issue when relevant:
|
||||
- a clear description,
|
||||
- as much relevant information as possible,
|
||||
- the command used,
|
||||
- a data sample,
|
||||
- an explanation of the expected behaviour that is not occurring.
|
||||
|
||||
Do you want to contribute?:
|
||||
You are very welcome, visit this address for the Contributing
|
||||
guidelines:
|
||||
https://github.com/NBISweden/AGAT/blob/master/CONTRIBUTING.md
|
||||
11
src/agat/agat_convert_mfannot2gff/script.sh
Normal file
11
src/agat/agat_convert_mfannot2gff/script.sh
Normal file
@@ -0,0 +1,11 @@
|
||||
#!/bin/bash
|
||||
|
||||
set -eo pipefail
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
agat_convert_mfannot2gff.pl \
|
||||
--mfannot "$par_mfannot" \
|
||||
--gff "$par_gff" \
|
||||
${par_config:+--config "${par_config}"}
|
||||
35
src/agat/agat_convert_mfannot2gff/test.sh
Normal file
35
src/agat/agat_convert_mfannot2gff/test.sh
Normal file
@@ -0,0 +1,35 @@
|
||||
#!/bin/bash
|
||||
|
||||
set -eo pipefail
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
test_dir="${meta_resources_dir}/test_data"
|
||||
|
||||
# create temporary directory and clean up on exit
|
||||
TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXX")
|
||||
function clean_up {
|
||||
[[ -d "$TMPDIR" ]] && rm -rf "$TMPDIR"
|
||||
}
|
||||
trap clean_up EXIT
|
||||
|
||||
echo "> Run $meta_name with test data"
|
||||
"$meta_executable" \
|
||||
--mfannot "$test_dir/test.mfannot" \
|
||||
--gff "$TMPDIR/output.gff"
|
||||
|
||||
echo ">> Checking output"
|
||||
[ ! -f "$TMPDIR/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
|
||||
|
||||
echo ">> Check if output is empty"
|
||||
[ ! -s "$TMPDIR/output.gff" ] && echo "Output file output.gff is empty" && exit 1
|
||||
|
||||
echo ">> Check if output matches expected output"
|
||||
diff "$TMPDIR/output.gff" "$test_dir/agat_convert_mfannot2gff_1.gff"
|
||||
if [ $? -ne 0 ]; then
|
||||
echo "Output file output.gff does not match expected output"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
echo "> Test successful"
|
||||
@@ -0,0 +1,240 @@
|
||||
##gff-version 3
|
||||
tig00000088 mfannot mRNA 375 3557 . - . ID=mRNA_1;Name=atp1;gene=atp1;transl_table=4
|
||||
tig00000088 mfannot exon 375 3557 . - . ID=exon_1;Parent=atp1;Name=atp1;gene=atp1;transl_table=4
|
||||
tig00000088 mfannot mRNA 2947 3618 . + . ID=mRNA_2;Name=orf223;gene=orf223;transl_table=4
|
||||
tig00000088 mfannot exon 2947 3618 . + . ID=exon_2;Parent=orf223;Name=orf223;gene=orf223;transl_table=4
|
||||
tig00000088 mfannot mRNA 3948 8683 . - . ID=mRNA_3;Name=cox3;gene=cox3;transl_table=4
|
||||
tig00000088 mfannot exon 3948 8683 . - . ID=exon_3;Parent=cox3;Name=cox3;gene=cox3;transl_table=4
|
||||
tig00000088 mfannot group_II_intron 8789 9291 . + . ID=group_II_intron_1;Name=group%3DII;gene=group%3DII;transl_table=4
|
||||
tig00000088 mfannot mRNA 9292 9432 . - . ID=mRNA_4;Name=nad9;gene=nad9;transl_table=4
|
||||
tig00000088 mfannot exon 9292 9432 . - . ID=exon_4;Parent=nad9;Name=nad9;gene=nad9;transl_table=4
|
||||
tig00000088 mfannot group_II_intron 9491 9970 . + . ID=group_II_intron_2;Name=group%3DII(derived);gene=group%3DII(derived);transl_table=4
|
||||
tig00000088 mfannot mRNA 9971 10423 . - . ID=mRNA_5;Name=nad9;gene=nad9;transl_table=4
|
||||
tig00000088 mfannot exon 9971 10423 . - . ID=exon_5;Parent=nad9;Name=nad9;gene=nad9;transl_table=4
|
||||
tig00000088 mfannot mRNA 10429 10545 . - . ID=mRNA_6;Name=cox2;gene=cox2;transl_table=4
|
||||
tig00000088 mfannot exon 10429 10545 . - . ID=exon_6;Parent=cox2;Name=cox2;gene=cox2;transl_table=4
|
||||
tig00000088 mfannot group_II_intron 10613 11201 . + . ID=group_II_intron_3;Name=group%3DII;gene=group%3DII;transl_table=4
|
||||
tig00000088 mfannot mRNA 11202 11519 . - . ID=mRNA_7;Name=cox2;gene=cox2;transl_table=4
|
||||
tig00000088 mfannot exon 11202 11519 . - . ID=exon_7;Parent=cox2;Name=cox2;gene=cox2;transl_table=4
|
||||
tig00000088 mfannot group_II_intron 11584 12755 . + . ID=group_II_intron_4;Name=group%3DII(derived);gene=group%3DII(derived);transl_table=4
|
||||
tig00000088 mfannot mRNA 12756 13190 . - . ID=mRNA_8;Name=cox2;gene=cox2;transl_table=4
|
||||
tig00000088 mfannot exon 12756 13190 . - . ID=exon_8;Parent=cox2;Name=cox2;gene=cox2;transl_table=4
|
||||
tig00000088 mfannot mRNA 13595 15460 . - . ID=mRNA_9;Name=orf621;gene=orf621;transl_table=4
|
||||
tig00000088 mfannot exon 13595 15460 . - . ID=exon_9;Parent=orf621;Name=orf621;gene=orf621;transl_table=4
|
||||
tig00000088 mfannot mRNA 15841 33346 . - . ID=mRNA_10;Name=cox1;gene=cox1;transl_table=4
|
||||
tig00000088 mfannot exon 15841 33346 . - . ID=exon_10;Parent=cox1;Name=cox1;gene=cox1;transl_table=4
|
||||
tig00000088 mfannot group_II_intron 33462 34862 . + . ID=group_II_intron_5;Name=group%3DII;gene=group%3DII;transl_table=4
|
||||
tig00000088 mfannot group_II_intron 35352 35430 . + . ID=group_II_intron_6;Name=group%3DII(derived);gene=group%3DII(derived);transl_table=4
|
||||
tig00000088 mfannot mRNA 35431 37011 . - . ID=mRNA_11;Name=orf526;gene=orf526;transl_table=4
|
||||
tig00000088 mfannot exon 35431 37011 . - . ID=exon_11;Parent=orf526;Name=orf526;gene=orf526;transl_table=4
|
||||
tig00000088 mfannot mRNA 37784 38089 . - . ID=mRNA_12;Name=nad4L;gene=nad4L;transl_table=4
|
||||
tig00000088 mfannot exon 37784 38089 . - . ID=exon_12;Parent=nad4L;Name=nad4L;gene=nad4L;transl_table=4
|
||||
tig00000088 mfannot group_II_intron 38283 38632 . + . ID=group_II_intron_7;Name=group%3DII(derived);gene=group%3DII(derived);transl_table=4
|
||||
tig00000088 mfannot mRNA 38633 40147 . - . ID=mRNA_13;Name=orf504;gene=orf504;transl_table=4
|
||||
tig00000088 mfannot exon 38633 40147 . - . ID=exon_13;Parent=orf504;Name=orf504;gene=orf504;transl_table=4
|
||||
tig00000088 mfannot mRNA 43290 43955 . - . ID=mRNA_14;Name=nad1;gene=nad1;transl_table=4
|
||||
tig00000088 mfannot exon 43290 43955 . - . ID=exon_14;Parent=nad1;Name=nad1;gene=nad1;transl_table=4
|
||||
tig00000088 mfannot group_II_intron 44168 44599 . + . ID=group_II_intron_8;Name=group%3DII;gene=group%3DII;transl_table=4
|
||||
tig00000088 mfannot mRNA 44600 53026 . - . ID=mRNA_15;Name=cob;gene=cob;transl_table=4
|
||||
tig00000088 mfannot exon 44600 53026 . - . ID=exon_15;Parent=cob;Name=cob;gene=cob;transl_table=4
|
||||
tig00000088 mfannot mRNA 54956 55507 . - . ID=mRNA_16;Name=rpl5;gene=rpl5;transl_table=4
|
||||
tig00000088 mfannot exon 54956 55507 . - . ID=exon_16;Parent=rpl5;Name=rpl5;gene=rpl5;transl_table=4
|
||||
tig00000088 mfannot mRNA 55526 55897 . - . ID=mRNA_17;Name=rpl14;gene=rpl14;transl_table=4
|
||||
tig00000088 mfannot exon 55526 55897 . - . ID=exon_17;Parent=rpl14;Name=rpl14;gene=rpl14;transl_table=4
|
||||
tig00000088 mfannot mRNA 56168 56542 . - . ID=mRNA_18;Name=atp8;gene=atp8;transl_table=4
|
||||
tig00000088 mfannot exon 56168 56542 . - . ID=exon_18;Parent=atp8;Name=atp8;gene=atp8;transl_table=4
|
||||
tig00000088 mfannot mRNA 57298 58023 . - . ID=mRNA_19;Name=orf241;gene=orf241;transl_table=4
|
||||
tig00000088 mfannot exon 57298 58023 . - . ID=exon_19;Parent=orf241;Name=orf241;gene=orf241;transl_table=4
|
||||
tig00000088 mfannot mRNA 58024 58434 . - . ID=mRNA_20;Name=rpl16;gene=rpl16;transl_table=4
|
||||
tig00000088 mfannot exon 58024 58434 . - . ID=exon_20;Parent=rpl16;Name=rpl16;gene=rpl16;transl_table=4
|
||||
tig00000088 mfannot mRNA 58447 59346 . - . ID=mRNA_21;Name=rps3;gene=rps3;transl_table=4
|
||||
tig00000088 mfannot exon 58447 59346 . - . ID=exon_21;Parent=rps3;Name=rps3;gene=rps3;transl_table=4
|
||||
tig00000088 mfannot mRNA 58447 59430 . - . ID=mRNA_22;Name=orf327;gene=orf327;transl_table=4
|
||||
tig00000088 mfannot exon 58447 59430 . - . ID=exon_22;Parent=orf327;Name=orf327;gene=orf327;transl_table=4
|
||||
tig00000088 mfannot mRNA 59324 59578 . - . ID=mRNA_23;Name=rps19;gene=rps19;transl_table=4
|
||||
tig00000088 mfannot exon 59324 59578 . - . ID=exon_23;Parent=rps19;Name=rps19;gene=rps19;transl_table=4
|
||||
tig00000088 mfannot mRNA 62407 64761 . - . ID=mRNA_24;Name=orf784;gene=orf784;transl_table=4
|
||||
tig00000088 mfannot exon 62407 64761 . - . ID=exon_24;Parent=orf784;Name=orf784;gene=orf784;transl_table=4
|
||||
tig00000088 mfannot mRNA 62484 64694 . - . ID=mRNA_25;Name=orf736;gene=orf736;transl_table=4
|
||||
tig00000088 mfannot exon 62484 64694 . - . ID=exon_25;Parent=orf736;Name=orf736;gene=orf736;transl_table=4
|
||||
tig00000088 mfannot mRNA 62497 64800 . + . ID=mRNA_26;Name=orf767;gene=orf767;transl_table=4
|
||||
tig00000088 mfannot exon 62497 64800 . + . ID=exon_26;Parent=orf767;Name=orf767;gene=orf767;transl_table=4
|
||||
tig00000088 mfannot mRNA 62505 64790 . + . ID=mRNA_27;Name=orf761;gene=orf761;transl_table=4
|
||||
tig00000088 mfannot exon 62505 64790 . + . ID=exon_27;Parent=orf761;Name=orf761;gene=orf761;transl_table=4
|
||||
tig00000088 mfannot mRNA 62579 64786 . + . ID=mRNA_28;Name=orf735;gene=orf735;transl_table=4
|
||||
tig00000088 mfannot exon 62579 64786 . + . ID=exon_28;Parent=orf735;Name=orf735;gene=orf735;transl_table=4
|
||||
tig00000088 mfannot mRNA 67403 71938 . - . ID=mRNA_29;Name=orf1511;gene=orf1511;transl_table=4
|
||||
tig00000088 mfannot exon 67403 71938 . - . ID=exon_29;Parent=orf1511;Name=orf1511;gene=orf1511;transl_table=4
|
||||
tig00000088 mfannot mRNA 67413 71873 . - . ID=mRNA_30;Name=orf1486;gene=orf1486;transl_table=4
|
||||
tig00000088 mfannot exon 67413 71873 . - . ID=exon_30;Parent=orf1486;Name=orf1486;gene=orf1486;transl_table=4
|
||||
tig00000088 mfannot mRNA 67417 71835 . - . ID=mRNA_31;Name=orf1472;gene=orf1472;transl_table=4
|
||||
tig00000088 mfannot exon 67417 71835 . - . ID=exon_31;Parent=orf1472;Name=orf1472;gene=orf1472;transl_table=4
|
||||
tig00000088 mfannot mRNA 68331 70100 . + . ID=mRNA_32;Name=orf589;gene=orf589;transl_table=4
|
||||
tig00000088 mfannot exon 68331 70100 . + . ID=exon_32;Parent=orf589;Name=orf589;gene=orf589;transl_table=4
|
||||
tig00000088 mfannot mRNA 68495 70594 . + . ID=mRNA_33;Name=orf699;gene=orf699;transl_table=4
|
||||
tig00000088 mfannot exon 68495 70594 . + . ID=exon_33;Parent=orf699;Name=orf699;gene=orf699;transl_table=4
|
||||
tig00000088 mfannot mRNA 69979 71091 . + . ID=mRNA_34;Name=orf370;gene=orf370;transl_table=4
|
||||
tig00000088 mfannot exon 69979 71091 . + . ID=exon_34;Parent=orf370;Name=orf370;gene=orf370;transl_table=4
|
||||
tig00000088 mfannot tRNA 72094 72164 . + . ID=tRNA_1;Name=trnW(uca)_1;gene=trnW(uca)_1;transl_table=4
|
||||
tig00000088 mfannot exon 72094 72164 . + . ID=exon_35;Parent=tRNA_1;Name=trnW(uca)_1;gene=trnW(uca)_1;transl_table=4
|
||||
tig00000088 mfannot mRNA 72179 72577 . + . ID=mRNA_35;Name=rps13_1;gene=rps13_1;transl_table=4
|
||||
tig00000088 mfannot exon 72179 72577 . + . ID=exon_36;Parent=rps13_1;Name=rps13_1;gene=rps13_1;transl_table=4
|
||||
tig00000088 mfannot mRNA 72669 91559 . + . ID=mRNA_36;Name=rps11;gene=rps11;transl_table=4
|
||||
tig00000088 mfannot exon 72669 91559 . + . ID=exon_37;Parent=rps11;Name=rps11;gene=rps11;transl_table=4
|
||||
tig00000088 mfannot mRNA 72981 73280 . + . ID=mRNA_37;Name=rps14_1;gene=rps14_1;transl_table=4
|
||||
tig00000088 mfannot exon 72981 73280 . + . ID=exon_38;Parent=rps14_1;Name=rps14_1;gene=rps14_1;transl_table=4
|
||||
tig00000088 mfannot mRNA 73309 74238 . + . ID=mRNA_38;Name=rps8_1;gene=rps8_1;transl_table=4
|
||||
tig00000088 mfannot exon 73309 74238 . + . ID=exon_39;Parent=rps8_1;Name=rps8_1;gene=rps8_1;transl_table=4
|
||||
tig00000088 mfannot mRNA 73708 74238 . + . ID=mRNA_39;Name=rpl6_1;gene=rpl6_1;transl_table=4
|
||||
tig00000088 mfannot exon 73708 74238 . + . ID=exon_40;Parent=rpl6_1;Name=rpl6_1;gene=rpl6_1;transl_table=4
|
||||
tig00000088 mfannot mRNA 74288 74656 . + . ID=mRNA_40;Name=rps12_1;gene=rps12_1;transl_table=4
|
||||
tig00000088 mfannot exon 74288 74656 . + . ID=exon_41;Parent=rps12_1;Name=rps12_1;gene=rps12_1;transl_table=4
|
||||
tig00000088 mfannot mRNA 74597 74917 . - . ID=mRNA_41;Name=orf106;gene=orf106;transl_table=4
|
||||
tig00000088 mfannot exon 74597 74917 . - . ID=exon_42;Parent=orf106;Name=orf106;gene=orf106;transl_table=4
|
||||
tig00000088 mfannot tRNA 75137 75208 . + . ID=tRNA_2;Name=trnP(ugg)_1;gene=trnP(ugg)_1;transl_table=4
|
||||
tig00000088 mfannot exon 75137 75208 . + . ID=exon_43;Parent=tRNA_2;Name=trnP(ugg)_1;gene=trnP(ugg)_1;transl_table=4
|
||||
tig00000088 mfannot mRNA 76605 77011 . - . ID=mRNA_42;Name=rpl16;gene=rpl16;transl_table=4
|
||||
tig00000088 mfannot exon 76605 77011 . - . ID=exon_44;Parent=rpl16;Name=rpl16;gene=rpl16;transl_table=4
|
||||
tig00000088 mfannot mRNA 81073 83373 . + . ID=mRNA_43;Name=orf766;gene=orf766;transl_table=4
|
||||
tig00000088 mfannot exon 81073 83373 . + . ID=exon_45;Parent=orf766;Name=orf766;gene=orf766;transl_table=4
|
||||
tig00000088 mfannot mRNA 81081 83363 . + . ID=mRNA_44;Name=orf760;gene=orf760;transl_table=4
|
||||
tig00000088 mfannot exon 81081 83363 . + . ID=exon_46;Parent=orf760;Name=orf760;gene=orf760;transl_table=4
|
||||
tig00000088 mfannot mRNA 81155 83359 . + . ID=mRNA_45;Name=orf734;gene=orf734;transl_table=4
|
||||
tig00000088 mfannot exon 81155 83359 . + . ID=exon_47;Parent=orf734;Name=orf734;gene=orf734;transl_table=4
|
||||
tig00000088 mfannot mRNA 81661 82935 . - . ID=mRNA_46;Name=orf424;gene=orf424;transl_table=4
|
||||
tig00000088 mfannot exon 81661 82935 . - . ID=exon_48;Parent=orf424;Name=orf424;gene=orf424;transl_table=4
|
||||
tig00000088 mfannot mRNA 82320 83267 . - . ID=mRNA_47;Name=orf315;gene=orf315;transl_table=4
|
||||
tig00000088 mfannot exon 82320 83267 . - . ID=exon_49;Parent=orf315;Name=orf315;gene=orf315;transl_table=4
|
||||
tig00000088 mfannot mRNA 85976 90457 . - . ID=mRNA_48;Name=orf1493;gene=orf1493;transl_table=4
|
||||
tig00000088 mfannot exon 85976 90457 . - . ID=exon_50;Parent=orf1493;Name=orf1493;gene=orf1493;transl_table=4
|
||||
tig00000088 mfannot mRNA 85986 90419 . - . ID=mRNA_49;Name=orf1477;gene=orf1477;transl_table=4
|
||||
tig00000088 mfannot exon 85986 90419 . - . ID=exon_51;Parent=orf1477;Name=orf1477;gene=orf1477;transl_table=4
|
||||
tig00000088 mfannot mRNA 85990 90522 . - . ID=mRNA_50;Name=orf1510;gene=orf1510;transl_table=4
|
||||
tig00000088 mfannot exon 85990 90522 . - . ID=exon_52;Parent=orf1510;Name=orf1510;gene=orf1510;transl_table=4
|
||||
tig00000088 mfannot mRNA 86082 89342 . + . ID=mRNA_51;Name=orf1086;gene=orf1086;transl_table=4
|
||||
tig00000088 mfannot exon 86082 89342 . + . ID=exon_53;Parent=orf1086;Name=orf1086;gene=orf1086;transl_table=4
|
||||
tig00000088 mfannot mRNA 86161 89838 . + . ID=mRNA_52;Name=orf1225;gene=orf1225;transl_table=4
|
||||
tig00000088 mfannot exon 86161 89838 . + . ID=exon_54;Parent=orf1225;Name=orf1225;gene=orf1225;transl_table=4
|
||||
tig00000088 mfannot mRNA 89216 90571 . + . ID=mRNA_53;Name=orf451;gene=orf451;transl_table=4
|
||||
tig00000088 mfannot exon 89216 90571 . + . ID=exon_55;Parent=orf451;Name=orf451;gene=orf451;transl_table=4
|
||||
tig00000088 mfannot tRNA 90678 90748 . + . ID=tRNA_3;Name=trnW(uca)_2;gene=trnW(uca)_2;transl_table=4
|
||||
tig00000088 mfannot exon 90678 90748 . + . ID=exon_56;Parent=tRNA_3;Name=trnW(uca)_2;gene=trnW(uca)_2;transl_table=4
|
||||
tig00000088 mfannot mRNA 90763 91161 . + . ID=mRNA_54;Name=rps13_2;gene=rps13_2;transl_table=4
|
||||
tig00000088 mfannot exon 90763 91161 . + . ID=exon_57;Parent=rps13_2;Name=rps13_2;gene=rps13_2;transl_table=4
|
||||
tig00000088 mfannot mRNA 91566 91865 . + . ID=mRNA_55;Name=rps14_2;gene=rps14_2;transl_table=4
|
||||
tig00000088 mfannot exon 91566 91865 . + . ID=exon_58;Parent=rps14_2;Name=rps14_2;gene=rps14_2;transl_table=4
|
||||
tig00000088 mfannot mRNA 91894 92277 . + . ID=mRNA_56;Name=rps8_2;gene=rps8_2;transl_table=4
|
||||
tig00000088 mfannot exon 91894 92277 . + . ID=exon_59;Parent=rps8_2;Name=rps8_2;gene=rps8_2;transl_table=4
|
||||
tig00000088 mfannot mRNA 92295 92825 . + . ID=mRNA_57;Name=rpl6_2;gene=rpl6_2;transl_table=4
|
||||
tig00000088 mfannot exon 92295 92825 . + . ID=exon_60;Parent=rpl6_2;Name=rpl6_2;gene=rpl6_2;transl_table=4
|
||||
tig00000088 mfannot mRNA 92875 93243 . + . ID=mRNA_58;Name=rps12_2;gene=rps12_2;transl_table=4
|
||||
tig00000088 mfannot exon 92875 93243 . + . ID=exon_61;Parent=rps12_2;Name=rps12_2;gene=rps12_2;transl_table=4
|
||||
tig00000088 mfannot mRNA 93224 93682 . + . ID=mRNA_59;Name=rps7;gene=rps7;transl_table=4
|
||||
tig00000088 mfannot exon 93224 93682 . + . ID=exon_62;Parent=rps7;Name=rps7;gene=rps7;transl_table=4
|
||||
tig00000088 mfannot tRNA 93720 93791 . + . ID=tRNA_4;Name=trnP(ugg)_2;gene=trnP(ugg)_2;transl_table=4
|
||||
tig00000088 mfannot exon 93720 93791 . + . ID=exon_63;Parent=tRNA_4;Name=trnP(ugg)_2;gene=trnP(ugg)_2;transl_table=4
|
||||
tig00000088 mfannot mRNA 93823 94440 . + . ID=mRNA_60;Name=rps4;gene=rps4;transl_table=4
|
||||
tig00000088 mfannot exon 93823 94440 . + . ID=exon_64;Parent=rps4;Name=rps4;gene=rps4;transl_table=4
|
||||
tig00000088 mfannot mRNA 95255 96652 . + . ID=mRNA_61;Name=orf465;gene=orf465;transl_table=4
|
||||
tig00000088 mfannot exon 95255 96652 . + . ID=exon_65;Parent=orf465;Name=orf465;gene=orf465;transl_table=4
|
||||
tig00000088 mfannot group_II_intron 96715 97278 . + . ID=group_II_intron_9;Name=group%3DII;gene=group%3DII;transl_table=4
|
||||
tig00000088 mfannot group_II_intron 97835 97857 . + . ID=group_II_intron_10;Name=group%3DII;gene=group%3DII;transl_table=4
|
||||
tig00000088 mfannot mRNA 97858 100740 . + . ID=mRNA_62;Name=nad5;gene=nad5;transl_table=4
|
||||
tig00000088 mfannot exon 97858 100740 . + . ID=exon_66;Parent=nad5;Name=nad5;gene=nad5;transl_table=4
|
||||
tig00000088 mfannot mRNA 100756 100971 . + . ID=mRNA_63;Name=nad6;gene=nad6;transl_table=4
|
||||
tig00000088 mfannot exon 100756 100971 . + . ID=exon_67;Parent=nad6;Name=nad6;gene=nad6;transl_table=4
|
||||
tig00000088 mfannot mRNA 101416 103482 . + . ID=mRNA_64;Name=orf688;gene=orf688;transl_table=4
|
||||
tig00000088 mfannot exon 101416 103482 . + . ID=exon_68;Parent=orf688;Name=orf688;gene=orf688;transl_table=4
|
||||
tig00000088 mfannot group_II_intron 103569 103575 . + . ID=group_II_intron_11;Name=group%3DII;gene=group%3DII;transl_table=4
|
||||
tig00000088 mfannot mRNA 103576 103974 . + . ID=mRNA_65;Name=orf132;gene=orf132;transl_table=4
|
||||
tig00000088 mfannot exon 103576 103974 . + . ID=exon_69;Parent=orf132;Name=orf132;gene=orf132;transl_table=4
|
||||
tig00000088 mfannot tRNA 104056 104128 . + . ID=tRNA_5;Name=trnR(ucu);gene=trnR(ucu);transl_table=4
|
||||
tig00000088 mfannot exon 104056 104128 . + . ID=exon_70;Parent=tRNA_5;Name=trnR(ucu);gene=trnR(ucu);transl_table=4
|
||||
tig00000088 mfannot mRNA 104153 104224 . - . ID=mRNA_66;Name=nad3;gene=nad3;transl_table=4
|
||||
tig00000088 mfannot exon 104153 104224 . - . ID=exon_71;Parent=nad3;Name=nad3;gene=nad3;transl_table=4
|
||||
tig00000088 mfannot group_II_intron 104436 105029 . + . ID=group_II_intron_12;Name=group%3DII(derived);gene=group%3DII(derived);transl_table=4
|
||||
tig00000088 mfannot mRNA 105030 107969 . - . ID=mRNA_67;Name=atp6;gene=atp6;transl_table=4
|
||||
tig00000088 mfannot exon 105030 107969 . - . ID=exon_72;Parent=atp6;Name=atp6;gene=atp6;transl_table=4
|
||||
tig00000088 mfannot mRNA 108059 108412 . - . ID=mRNA_68;Name=rps10;gene=rps10;transl_table=4
|
||||
tig00000088 mfannot exon 108059 108412 . - . ID=exon_73;Parent=rps10;Name=rps10;gene=rps10;transl_table=4
|
||||
tig00000088 mfannot mRNA 108421 109893 . - . ID=mRNA_69;Name=nad2;gene=nad2;transl_table=4
|
||||
tig00000088 mfannot exon 108421 109893 . - . ID=exon_74;Parent=nad2;Name=nad2;gene=nad2;transl_table=4
|
||||
tig00000088 mfannot mRNA 110001 118556 . + . ID=mRNA_70;Name=nad7;gene=nad7;transl_table=4
|
||||
tig00000088 mfannot exon 110001 118556 . + . ID=exon_75;Parent=nad7;Name=nad7;gene=nad7;transl_table=4
|
||||
tig00000088 mfannot group_II_intron 119144 119308 . + . ID=group_II_intron_13;Name=group%3DII;gene=group%3DII;transl_table=4
|
||||
tig00000088 mfannot mRNA 119309 121269 . + . ID=mRNA_71;Name=nad4;gene=nad4;transl_table=4
|
||||
tig00000088 mfannot exon 119309 121269 . + . ID=exon_76;Parent=nad4;Name=nad4;gene=nad4;transl_table=4
|
||||
tig00000088 mfannot mRNA 121551 121778 . + . ID=mRNA_72;Name=atp9;gene=atp9;transl_table=4
|
||||
tig00000088 mfannot exon 121551 121778 . + . ID=exon_77;Parent=atp9;Name=atp9;gene=atp9;transl_table=4
|
||||
tig00000088 mfannot tRNA 121887 121959 . + . ID=tRNA_6;Name=trnD(guc);gene=trnD(guc);transl_table=4
|
||||
tig00000088 mfannot exon 121887 121959 . + . ID=exon_78;Parent=tRNA_6;Name=trnD(guc);gene=trnD(guc);transl_table=4
|
||||
tig00000088 mfannot tRNA 121962 122033 . + . ID=tRNA_7;Name=trnC(gca);gene=trnC(gca);transl_table=4
|
||||
tig00000088 mfannot exon 121962 122033 . + . ID=exon_79;Parent=tRNA_7;Name=trnC(gca);gene=trnC(gca);transl_table=4
|
||||
tig00000088 mfannot tRNA 122051 122123 . + . ID=tRNA_8;Name=trnH(gug);gene=trnH(gug);transl_table=4
|
||||
tig00000088 mfannot exon 122051 122123 . + . ID=exon_80;Parent=tRNA_8;Name=trnH(gug);gene=trnH(gug);transl_table=4
|
||||
tig00000088 mfannot tRNA 122142 122214 . + . ID=tRNA_9;Name=trnV(uac);gene=trnV(uac);transl_table=4
|
||||
tig00000088 mfannot exon 122142 122214 . + . ID=exon_81;Parent=tRNA_9;Name=trnV(uac);gene=trnV(uac);transl_table=4
|
||||
tig00000088 mfannot mRNA 122234 122446 . + . ID=mRNA_73;Name=rnpB;gene=rnpB;transl_table=4
|
||||
tig00000088 mfannot exon 122234 122446 . + . ID=exon_82;Parent=rnpB;Name=rnpB;gene=rnpB;transl_table=4
|
||||
tig00000088 mfannot rRNA 122544 123762 . + . ID=rRNA_1;Name=rns;gene=rns;transl_table=4
|
||||
tig00000088 mfannot exon 122544 123762 . + . ID=exon_83;Parent=rRNA_1;Name=rns;gene=rns;transl_table=4
|
||||
tig00000088 mfannot group_II_intron 123576 123762 . + . ID=group_II_intron_14;Name=group%3DII;gene=group%3DII;transl_table=4
|
||||
tig00000088 mfannot rRNA 123763 124009 . + . ID=rRNA_2;Name=rns;gene=rns;transl_table=4
|
||||
tig00000088 mfannot exon 123763 124009 . + . ID=exon_84;Parent=rRNA_2;Name=rns;gene=rns;transl_table=4
|
||||
tig00000088 mfannot rRNA 124010 124127 . + . ID=rRNA_3;Name=rns;gene=rns;transl_table=4
|
||||
tig00000088 mfannot exon 124010 124127 . + . ID=exon_85;Parent=rRNA_3;Name=rns;gene=rns;transl_table=4
|
||||
tig00000088 mfannot rRNA 124128 124832 . + . ID=rRNA_4;Name=rns;gene=rns;transl_table=4
|
||||
tig00000088 mfannot exon 124128 124832 . + . ID=exon_86;Parent=rRNA_4;Name=rns;gene=rns;transl_table=4
|
||||
tig00000088 mfannot mRNA 124833 125279 . + . ID=mRNA_74;Name=orf148;gene=orf148;transl_table=4
|
||||
tig00000088 mfannot exon 124833 125279 . + . ID=exon_87;Parent=orf148;Name=orf148;gene=orf148;transl_table=4
|
||||
tig00000088 mfannot group_II_intron 124847 124962 . + . ID=group_II_intron_15;Name=group%3DII;gene=group%3DII;transl_table=4
|
||||
tig00000088 mfannot rRNA 124963 125117 . + . ID=rRNA_5;Name=rns;gene=rns;transl_table=4
|
||||
tig00000088 mfannot exon 124963 125117 . + . ID=exon_88;Parent=rRNA_5;Name=rns;gene=rns;transl_table=4
|
||||
tig00000088 mfannot rRNA 125118 125231 . + . ID=rRNA_6;Name=rns;gene=rns;transl_table=4
|
||||
tig00000088 mfannot exon 125118 125231 . + . ID=exon_89;Parent=rRNA_6;Name=rns;gene=rns;transl_table=4
|
||||
tig00000088 mfannot rRNA 125232 125279 . + . ID=rRNA_7;Name=rns;gene=rns;transl_table=4
|
||||
tig00000088 mfannot exon 125232 125279 . + . ID=exon_90;Parent=rRNA_7;Name=rns;gene=rns;transl_table=4
|
||||
tig00000088 mfannot rRNA 125493 125529 . + . ID=rRNA_8;Name=rns;gene=rns;transl_table=4
|
||||
tig00000088 mfannot exon 125493 125529 . + . ID=exon_91;Parent=rRNA_8;Name=rns;gene=rns;transl_table=4
|
||||
tig00000088 mfannot mRNA 125530 125635 . + . ID=mRNA_75;Name=rrn5;gene=rrn5;transl_table=4
|
||||
tig00000088 mfannot exon 125530 125635 . + . ID=exon_92;Parent=rrn5;Name=rrn5;gene=rrn5;transl_table=4
|
||||
tig00000088 mfannot tRNA 125644 125715 . + . ID=tRNA_10;Name=trnF(gaa);gene=trnF(gaa);transl_table=4
|
||||
tig00000088 mfannot exon 125644 125715 . + . ID=exon_93;Parent=tRNA_10;Name=trnF(gaa);gene=trnF(gaa);transl_table=4
|
||||
tig00000088 mfannot tRNA 125734 125806 . + . ID=tRNA_11;Name=trnK(uuu);gene=trnK(uuu);transl_table=4
|
||||
tig00000088 mfannot exon 125734 125806 . + . ID=exon_94;Parent=tRNA_11;Name=trnK(uuu);gene=trnK(uuu);transl_table=4
|
||||
tig00000088 mfannot tRNA 126093 126165 . + . ID=tRNA_12;Name=trnT(ugu);gene=trnT(ugu);transl_table=4
|
||||
tig00000088 mfannot exon 126093 126165 . + . ID=exon_95;Parent=tRNA_12;Name=trnT(ugu);gene=trnT(ugu);transl_table=4
|
||||
tig00000088 mfannot tRNA 126180 126251 . + . ID=tRNA_13;Name=trnM(cau)_1;gene=trnM(cau)_1;transl_table=4
|
||||
tig00000088 mfannot exon 126180 126251 . + . ID=exon_96;Parent=tRNA_13;Name=trnM(cau)_1;gene=trnM(cau)_1;transl_table=4
|
||||
tig00000088 mfannot tRNA 126284 126356 . + . ID=tRNA_14;Name=trnM(cau)_2;gene=trnM(cau)_2;transl_table=4
|
||||
tig00000088 mfannot exon 126284 126356 . + . ID=exon_97;Parent=tRNA_14;Name=trnM(cau)_2;gene=trnM(cau)_2;transl_table=4
|
||||
tig00000088 mfannot tRNA 126364 126435 . + . ID=tRNA_15;Name=trnA(ugc);gene=trnA(ugc);transl_table=4
|
||||
tig00000088 mfannot exon 126364 126435 . + . ID=exon_98;Parent=tRNA_15;Name=trnA(ugc);gene=trnA(ugc);transl_table=4
|
||||
tig00000088 mfannot tRNA 126453 126525 . + . ID=tRNA_16;Name=trnR(ucg);gene=trnR(ucg);transl_table=4
|
||||
tig00000088 mfannot exon 126453 126525 . + . ID=exon_99;Parent=tRNA_16;Name=trnR(ucg);gene=trnR(ucg);transl_table=4
|
||||
tig00000088 mfannot tRNA 126528 126600 . + . ID=tRNA_17;Name=trnI(gau);gene=trnI(gau);transl_table=4
|
||||
tig00000088 mfannot exon 126528 126600 . + . ID=exon_100;Parent=tRNA_17;Name=trnI(gau);gene=trnI(gau);transl_table=4
|
||||
tig00000088 mfannot tRNA 126629 126710 . + . ID=tRNA_18;Name=trnL(uag);gene=trnL(uag);transl_table=4
|
||||
tig00000088 mfannot exon 126629 126710 . + . ID=exon_101;Parent=tRNA_18;Name=trnL(uag);gene=trnL(uag);transl_table=4
|
||||
tig00000088 mfannot tRNA 126724 126796 . + . ID=tRNA_19;Name=trnN(guu);gene=trnN(guu);transl_table=4
|
||||
tig00000088 mfannot exon 126724 126796 . + . ID=exon_102;Parent=tRNA_19;Name=trnN(guu);gene=trnN(guu);transl_table=4
|
||||
tig00000088 mfannot tRNA 126797 126881 . + . ID=tRNA_20;Name=trnY(gua);gene=trnY(gua);transl_table=4
|
||||
tig00000088 mfannot exon 126797 126881 . + . ID=exon_103;Parent=tRNA_20;Name=trnY(gua);gene=trnY(gua);transl_table=4
|
||||
tig00000088 mfannot tRNA 126907 126978 . + . ID=tRNA_21;Name=trnE(uuc);gene=trnE(uuc);transl_table=4
|
||||
tig00000088 mfannot exon 126907 126978 . + . ID=exon_104;Parent=tRNA_21;Name=trnE(uuc);gene=trnE(uuc);transl_table=4
|
||||
tig00000088 mfannot tRNA 127002 127072 . + . ID=tRNA_22;Name=trnQ(uug);gene=trnQ(uug);transl_table=4
|
||||
tig00000088 mfannot exon 127002 127072 . + . ID=exon_105;Parent=tRNA_22;Name=trnQ(uug);gene=trnQ(uug);transl_table=4
|
||||
tig00000088 mfannot tRNA 127097 127167 . + . ID=tRNA_23;Name=trnG(ucc);gene=trnG(ucc);transl_table=4
|
||||
tig00000088 mfannot exon 127097 127167 . + . ID=exon_106;Parent=tRNA_23;Name=trnG(ucc);gene=trnG(ucc);transl_table=4
|
||||
tig00000088 mfannot rRNA 127170 132900 . + . ID=rRNA_9;Name=rnl;gene=rnl;transl_table=4
|
||||
tig00000088 mfannot exon 127170 132900 . + . ID=exon_107;Parent=rRNA_9;Name=rnl;gene=rnl;transl_table=4
|
||||
tig00000088 mfannot group_II_intron 128101 130559 . + . ID=group_II_intron_16;Name=group%3DII;gene=group%3DII;transl_table=4
|
||||
tig00000088 mfannot group_II_intron 132446 132900 . + . ID=group_II_intron_17;Name=group%3DII(derived);gene=group%3DII(derived);transl_table=4
|
||||
tig00000088 mfannot rRNA 132901 132923 . + . ID=rRNA_10;Name=rnl;gene=rnl;transl_table=4
|
||||
tig00000088 mfannot exon 132901 132923 . + . ID=exon_108;Parent=rRNA_10;Name=rnl;gene=rnl;transl_table=4
|
||||
tig00000088 mfannot tRNA 132924 133010 . + . ID=tRNA_24;Name=trnS(gcu);gene=trnS(gcu);transl_table=4
|
||||
tig00000088 mfannot exon 132924 133010 . + . ID=exon_109;Parent=tRNA_24;Name=trnS(gcu);gene=trnS(gcu);transl_table=4
|
||||
tig00000088 mfannot tRNA 133023 133103 . + . ID=tRNA_25;Name=trnL(uaa);gene=trnL(uaa);transl_table=4
|
||||
tig00000088 mfannot exon 133023 133103 . + . ID=exon_110;Parent=tRNA_25;Name=trnL(uaa);gene=trnL(uaa);transl_table=4
|
||||
tig00000088 mfannot tRNA 133131 133218 . + . ID=tRNA_26;Name=trnS(uga);gene=trnS(uga);transl_table=4
|
||||
tig00000088 mfannot exon 133131 133218 . + . ID=exon_111;Parent=tRNA_26;Name=trnS(uga);gene=trnS(uga);transl_table=4
|
||||
10
src/agat/agat_convert_mfannot2gff/test_data/script.sh
Executable file
10
src/agat/agat_convert_mfannot2gff/test_data/script.sh
Executable file
@@ -0,0 +1,10 @@
|
||||
#!/bin/bash
|
||||
|
||||
# clone repo
|
||||
if [ ! -d /tmp/agat_source ]; then
|
||||
git clone --depth 1 --single-branch --branch master https://github.com/NBISweden/AGAT /tmp/agat_source
|
||||
fi
|
||||
|
||||
# copy test data
|
||||
cp -r /tmp/agat_source/t/scripts_output/in/test.mfannot src/agat/agat_convert_mfannot2gff/test_data/
|
||||
cp -r /tmp/agat_source/t/scripts_output/out/agat_convert_mfannot2gff_1.gff src/agat/agat_convert_mfannot2gff/test_data/
|
||||
2914
src/agat/agat_convert_mfannot2gff/test_data/test.mfannot
Normal file
2914
src/agat/agat_convert_mfannot2gff/test_data/test.mfannot
Normal file
File diff suppressed because it is too large
Load Diff
94
src/agat/agat_convert_sp_gff2gtf/config.vsh.yaml
Normal file
94
src/agat/agat_convert_sp_gff2gtf/config.vsh.yaml
Normal file
@@ -0,0 +1,94 @@
|
||||
name: agat_convert_sp_gff2gtf
|
||||
namespace: agat
|
||||
description: |
|
||||
The script aims to convert any GTF/GFF file into a proper GTF file. Full
|
||||
information about the format can be found here:
|
||||
https://agat.readthedocs.io/en/latest/gxf.html You can choose among 7
|
||||
different GTF types (1, 2, 2.1, 2.2, 2.5, 3 or relax). Depending the
|
||||
version selected the script will filter out the features that are not
|
||||
accepted. For GTF2.5 and 3, every level1 feature (e.g nc_gene
|
||||
pseudogene) will be converted into gene feature and every level2 feature
|
||||
(e.g mRNA ncRNA) will be converted into transcript feature. Using the
|
||||
"relax" option you will produce a GTF-like output keeping all original
|
||||
feature types (3rd column). No modification will occur e.g. mRNA to
|
||||
transcript.
|
||||
|
||||
To be fully GTF compliant all feature have a gene_id and a transcript_id
|
||||
attribute. The gene_id is unique identifier for the genomic source of
|
||||
the transcript, which is used to group transcripts into genes. The
|
||||
transcript_id is a unique identifier for the predicted transcript, which
|
||||
is used to group features into transcripts.
|
||||
keywords: [gene annotations, GTF conversion]
|
||||
links:
|
||||
homepage: https://github.com/NBISweden/AGAT
|
||||
documentation: https://agat.readthedocs.io/
|
||||
issue_tracker: https://github.com/NBISweden/AGAT/issues
|
||||
repository: https://github.com/NBISweden/AGAT
|
||||
references:
|
||||
doi: 10.5281/zenodo.3552717
|
||||
license: GPL-3.0
|
||||
authors:
|
||||
- __merge__: /src/_authors/leila_paquay.yaml
|
||||
roles: [ author, maintainer ]
|
||||
|
||||
argument_groups:
|
||||
- name: Inputs
|
||||
arguments:
|
||||
- name: --gff
|
||||
alternatives: [-i]
|
||||
description: Input GFF/GTF file that will be read
|
||||
type: file
|
||||
required: true
|
||||
direction: input
|
||||
example: input.gff
|
||||
- name: Outputs
|
||||
arguments:
|
||||
- name: --output
|
||||
alternatives: [-o, --out, --outfile, --gtf]
|
||||
description: Output GTF file. If no output file is specified, the output will be written to STDOUT.
|
||||
type: file
|
||||
direction: output
|
||||
required: true
|
||||
example: output.gtf
|
||||
- name: Arguments
|
||||
arguments:
|
||||
- name: --gtf_version
|
||||
description: |
|
||||
Version of the GTF output (1,2,2.1,2.2,2.5,3 or relax). Default value from AGAT config file (relax for the default config). The script option has the higher priority.
|
||||
|
||||
* relax: all feature types are accepted.
|
||||
* GTF3 (9 feature types accepted): gene, transcript, exon, CDS, Selenocysteine, start_codon, stop_codon, three_prime_utr and five_prime_utr.
|
||||
* GTF2.5 (8 feature types accepted): gene, transcript, exon, CDS, UTR, start_codon, stop_codon, Selenocysteine.
|
||||
* GTF2.2 (9 feature types accepted): CDS, start_codon, stop_codon, 5UTR, 3UTR, inter, inter_CNS, intron_CNS and exon.
|
||||
* GTF2.1 (6 feature types accepted): CDS, start_codon, stop_codon, exon, 5UTR, 3UTR.
|
||||
* GTF2 (4 feature types accepted): CDS, start_codon, stop_codon, exon.
|
||||
* GTF1 (5 feature types accepted): CDS, start_codon, stop_codon, exon, intron.
|
||||
type: string
|
||||
choices: [relax, "1", "2", "2.1", "2.2", "2.5", "3"]
|
||||
required: false
|
||||
example: "3"
|
||||
- name: --config
|
||||
alternatives: [-c]
|
||||
description: |
|
||||
Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
|
||||
type: file
|
||||
required: false
|
||||
example: custom_agat_config.yaml
|
||||
resources:
|
||||
- type: bash_script
|
||||
path: script.sh
|
||||
test_resources:
|
||||
- type: bash_script
|
||||
path: test.sh
|
||||
- type: file
|
||||
path: test_data
|
||||
engines:
|
||||
- type: docker
|
||||
image: quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0
|
||||
setup:
|
||||
- type: docker
|
||||
run: |
|
||||
agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.txt
|
||||
runners:
|
||||
- type: executable
|
||||
- type: nextflow
|
||||
102
src/agat/agat_convert_sp_gff2gtf/help.txt
Normal file
102
src/agat/agat_convert_sp_gff2gtf/help.txt
Normal file
@@ -0,0 +1,102 @@
|
||||
```sh
|
||||
agat_convert_sp_gff2gtf.pl --help
|
||||
```
|
||||
------------------------------------------------------------------------------
|
||||
| Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0 |
|
||||
| https://github.com/NBISweden/AGAT |
|
||||
| National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se |
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
Name:
|
||||
agat_convert_sp_gff2gtf.pl
|
||||
|
||||
Description:
|
||||
The script aims to convert any GTF/GFF file into a proper GTF file. Full
|
||||
information about the format can be found here:
|
||||
https://agat.readthedocs.io/en/latest/gxf.html You can choose among 7
|
||||
different GTF types (1, 2, 2.1, 2.2, 2.5, 3 or relax). Depending the
|
||||
version selected the script will filter out the features that are not
|
||||
accepted. For GTF2.5 and 3, every level1 feature (e.g nc_gene
|
||||
pseudogene) will be converted into gene feature and every level2 feature
|
||||
(e.g mRNA ncRNA) will be converted into transcript feature. Using the
|
||||
"relax" option you will produce a GTF-like output keeping all original
|
||||
feature types (3rd column). No modification will occur e.g. mRNA to
|
||||
transcript.
|
||||
|
||||
To be fully GTF compliant all feature have a gene_id and a transcript_id
|
||||
attribute. The gene_id is unique identifier for the genomic source of
|
||||
the transcript, which is used to group transcripts into genes. The
|
||||
transcript_id is a unique identifier for the predicted transcript, which
|
||||
is used to group features into transcripts.
|
||||
|
||||
Usage:
|
||||
agat_convert_sp_gff2gtf.pl --gff infile.gff [ -o outfile ]
|
||||
agat_convert_sp_gff2gtf -h
|
||||
|
||||
Options:
|
||||
--gff, --gtf or -i
|
||||
Input GFF/GTF file that will be read
|
||||
|
||||
--gtf_version version of the GTF output (1,2,2.1,2.2,2.5,3 or relax).
|
||||
Default value from AGAT config file (relax for the default config). The
|
||||
script option has the higher priority.
|
||||
relax: all feature types are accepted.
|
||||
|
||||
GTF3 (9 feature types accepted): gene, transcript, exon, CDS,
|
||||
Selenocysteine, start_codon, stop_codon, three_prime_utr and
|
||||
five_prime_utr
|
||||
|
||||
GTF2.5 (8 feature types accepted): gene, transcript, exon, CDS,
|
||||
UTR, start_codon, stop_codon, Selenocysteine
|
||||
|
||||
GTF2.2 (9 feature types accepted): CDS, start_codon, stop_codon,
|
||||
5UTR, 3UTR, inter, inter_CNS, intron_CNS and exon
|
||||
|
||||
GTF2.1 (6 feature types accepted): CDS, start_codon, stop_codon,
|
||||
exon, 5UTR, 3UTR
|
||||
|
||||
GTF2 (4 feature types accepted): CDS, start_codon, stop_codon,
|
||||
exon
|
||||
|
||||
GTF1 (5 feature types accepted): CDS, start_codon, stop_codon,
|
||||
exon, intron
|
||||
|
||||
-o , --output , --out , --outfile or --gtf
|
||||
Output GTF file. If no output file is specified, the output will
|
||||
be written to STDOUT.
|
||||
|
||||
-c or --config
|
||||
String - Input agat config file. By default AGAT takes as input
|
||||
agat_config.yaml file from the working directory if any,
|
||||
otherwise it takes the orignal agat_config.yaml shipped with
|
||||
AGAT. To get the agat_config.yaml locally type: "agat config
|
||||
--expose". The --config option gives you the possibility to use
|
||||
your own AGAT config file (located elsewhere or named
|
||||
differently).
|
||||
|
||||
-h or --help
|
||||
Display this helpful text.
|
||||
|
||||
Feedback:
|
||||
Did you find a bug?:
|
||||
Do not hesitate to report bugs to help us keep track of the bugs and
|
||||
their resolution. Please use the GitHub issue tracking system available
|
||||
at this address:
|
||||
|
||||
https://github.com/NBISweden/AGAT/issues
|
||||
|
||||
Ensure that the bug was not already reported by searching under Issues.
|
||||
If you're unable to find an (open) issue addressing the problem, open a new one.
|
||||
Try as much as possible to include in the issue when relevant:
|
||||
- a clear description,
|
||||
- as much relevant information as possible,
|
||||
- the command used,
|
||||
- a data sample,
|
||||
- an explanation of the expected behaviour that is not occurring.
|
||||
|
||||
Do you want to contribute?:
|
||||
You are very welcome, visit this address for the Contributing
|
||||
guidelines:
|
||||
https://github.com/NBISweden/AGAT/blob/master/CONTRIBUTING.md
|
||||
|
||||
10
src/agat/agat_convert_sp_gff2gtf/script.sh
Normal file
10
src/agat/agat_convert_sp_gff2gtf/script.sh
Normal file
@@ -0,0 +1,10 @@
|
||||
#!/bin/bash
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
agat_convert_sp_gff2gtf.pl \
|
||||
-i "$par_gff" \
|
||||
-o "$par_output" \
|
||||
${par_gtf_version:+--gtf_version "${par_gtf_version}"} \
|
||||
${par_config:+--config "${par_config}"}
|
||||
37
src/agat/agat_convert_sp_gff2gtf/test.sh
Normal file
37
src/agat/agat_convert_sp_gff2gtf/test.sh
Normal file
@@ -0,0 +1,37 @@
|
||||
#!/bin/bash
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
test_dir="${meta_resources_dir}/test_data"
|
||||
|
||||
echo "> Run $meta_name with test data"
|
||||
"$meta_executable" \
|
||||
--gff "$test_dir/0_test.gff" \
|
||||
--output "output.gtf"
|
||||
|
||||
echo ">> Checking output"
|
||||
[ ! -f "output.gtf" ] && echo "Output file output.gtf does not exist" && exit 1
|
||||
|
||||
echo ">> Check if output is empty"
|
||||
[ ! -s "output.gtf" ] && echo "Output file output.gtf is empty" && exit 1
|
||||
|
||||
echo ">> Check if the conversion resulted in the right GTF format"
|
||||
idGFF=$(head -n 2 "$test_dir/0_test.gff" | grep -o 'ID=[^;]*' | cut -d '=' -f 2-)
|
||||
expectedGTF="gene_id \"$idGFF\"; ID \"$idGFF\";"
|
||||
extractedGTF=$(head -n 3 "output.gtf" | grep -o 'gene_id "[^"]*"; ID "[^"]*";')
|
||||
[ "$extractedGTF" != "$expectedGTF" ] && echo "Output file output.gtf does not have the right format" && exit 1
|
||||
|
||||
rm output.gtf
|
||||
|
||||
echo "> Run $meta_name with test data and GTF version 2.5"
|
||||
"$meta_executable" \
|
||||
--gff "$test_dir/0_test.gff" \
|
||||
--output "output.gtf" \
|
||||
--gtf_version "2.5"
|
||||
|
||||
echo ">> Check if the output file header display the right GTF version"
|
||||
grep -q "##gtf-version 2.5" "output.gtf"
|
||||
[ $? -ne 0 ] && echo "Output file output.gtf header does not display the right GTF version" && exit 1
|
||||
|
||||
echo "> Test successful"
|
||||
36
src/agat/agat_convert_sp_gff2gtf/test_data/0_test.gff
Normal file
36
src/agat/agat_convert_sp_gff2gtf/test_data/0_test.gff
Normal file
@@ -0,0 +1,36 @@
|
||||
##gff-version 3
|
||||
scaffold625 maker gene 337818 343277 . + . ID=CLUHARG00000005458;Name=TUBB3_2
|
||||
scaffold625 maker mRNA 337818 343277 . + . ID=CLUHART00000008717;Parent=CLUHARG00000005458
|
||||
scaffold625 maker exon 337818 337971 . + . ID=CLUHART00000008717:exon:1404;Parent=CLUHART00000008717
|
||||
scaffold625 maker exon 340733 340841 . + . ID=CLUHART00000008717:exon:1405;Parent=CLUHART00000008717
|
||||
scaffold625 maker exon 341518 341628 . + . ID=CLUHART00000008717:exon:1406;Parent=CLUHART00000008717
|
||||
scaffold625 maker exon 341964 343277 . + . ID=CLUHART00000008717:exon:1407;Parent=CLUHART00000008717
|
||||
scaffold625 maker CDS 337915 337971 . + 0 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
|
||||
scaffold625 maker CDS 340733 340841 . + 0 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
|
||||
scaffold625 maker CDS 341518 341628 . + 2 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
|
||||
scaffold625 maker CDS 341964 343033 . + 2 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
|
||||
scaffold625 maker five_prime_UTR 337818 337914 . + . ID=CLUHART00000008717:five_prime_utr;Parent=CLUHART00000008717
|
||||
scaffold625 maker three_prime_UTR 343034 343277 . + . ID=CLUHART00000008717:three_prime_utr;Parent=CLUHART00000008717
|
||||
scaffold789 maker gene 558184 564780 . + . ID=CLUHARG00000003852;Name=PF11_0240
|
||||
scaffold789 maker mRNA 558184 564780 . + . ID=CLUHART00000006146;Parent=CLUHARG00000003852
|
||||
scaffold789 maker exon 558184 560123 . + . ID=CLUHART00000006146:exon:995;Parent=CLUHART00000006146
|
||||
scaffold789 maker exon 561401 561519 . + . ID=CLUHART00000006146:exon:996;Parent=CLUHART00000006146
|
||||
scaffold789 maker exon 564171 564235 . + . ID=CLUHART00000006146:exon:997;Parent=CLUHART00000006146
|
||||
scaffold789 maker exon 564372 564780 . + . ID=CLUHART00000006146:exon:998;Parent=CLUHART00000006146
|
||||
scaffold789 maker CDS 558191 560123 . + 0 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
|
||||
scaffold789 maker CDS 561401 561519 . + 2 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
|
||||
scaffold789 maker CDS 564171 564235 . + 0 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
|
||||
scaffold789 maker CDS 564372 564588 . + 1 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
|
||||
scaffold789 maker five_prime_UTR 558184 558190 . + . ID=CLUHART00000006146:five_prime_utr;Parent=CLUHART00000006146
|
||||
scaffold789 maker three_prime_UTR 564589 564780 . + . ID=CLUHART00000006146:three_prime_utr;Parent=CLUHART00000006146
|
||||
scaffold789 maker mRNA 558184 564780 . + . ID=CLUHART00000006147;Parent=CLUHARG00000003852
|
||||
scaffold789 maker exon 558184 560123 . + . ID=CLUHART00000006147:exon:997;Parent=CLUHART00000006147
|
||||
scaffold789 maker exon 561401 561519 . + . ID=CLUHART00000006147:exon:998;Parent=CLUHART00000006147
|
||||
scaffold789 maker exon 562057 562121 . + . ID=CLUHART00000006147:exon:999;Parent=CLUHART00000006147
|
||||
scaffold789 maker exon 564372 564780 . + . ID=CLUHART00000006147:exon:1000;Parent=CLUHART00000006147
|
||||
scaffold789 maker CDS 558191 560123 . + 0 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
|
||||
scaffold789 maker CDS 561401 561519 . + 2 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
|
||||
scaffold789 maker CDS 562057 562121 . + 0 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
|
||||
scaffold789 maker CDS 564372 564588 . + 1 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
|
||||
scaffold789 maker five_prime_UTR 558184 558190 . + . ID=CLUHART00000006147:five_prime_utr;Parent=CLUHART00000006147
|
||||
scaffold789 maker three_prime_UTR 564589 564780 . + . ID=CLUHART00000006147:three_prime_utr;Parent=CLUHART00000006147
|
||||
9
src/agat/agat_convert_sp_gff2gtf/test_data/script.sh
Executable file
9
src/agat/agat_convert_sp_gff2gtf/test_data/script.sh
Executable file
@@ -0,0 +1,9 @@
|
||||
#!/bin/bash
|
||||
|
||||
# clone repo
|
||||
if [ ! -d /tmp/agat_source ]; then
|
||||
git clone --depth 1 --single-branch --branch master https://github.com/NBISweden/AGAT /tmp/agat_source
|
||||
fi
|
||||
|
||||
# copy test data
|
||||
cp -r /tmp/agat_source/t/gff_syntax/in/0_test.gff src/agat/agat_convert_sp_gff2gtf/test_data
|
||||
70
src/agat/agat_convert_sp_gff2tsv/config.vsh.yaml
Normal file
70
src/agat/agat_convert_sp_gff2tsv/config.vsh.yaml
Normal file
@@ -0,0 +1,70 @@
|
||||
name: agat_convert_sp_gff2tsv
|
||||
namespace: agat
|
||||
description: |
|
||||
The script aims to convert gtf/gff file into tabulated file. Attribute's
|
||||
tags from the 9th column become column titles.
|
||||
keywords: [gene annotations, GFF conversion]
|
||||
links:
|
||||
homepage: https://github.com/NBISweden/AGAT
|
||||
documentation: https://agat.readthedocs.io/en/latest/tools/agat_convert_sp_gff2tsv.html
|
||||
issue_tracker: https://github.com/NBISweden/AGAT/issues
|
||||
repository: https://github.com/NBISweden/AGAT
|
||||
references:
|
||||
doi: 10.5281/zenodo.3552717
|
||||
license: GPL-3.0
|
||||
authors:
|
||||
- __merge__: /src/_authors/leila_paquay.yaml
|
||||
roles: [ author, maintainer ]
|
||||
|
||||
argument_groups:
|
||||
- name: Inputs
|
||||
arguments:
|
||||
- name: --gff
|
||||
alternatives: [-f]
|
||||
description: Input GTF/GFF file.
|
||||
type: file
|
||||
required: true
|
||||
direction: input
|
||||
example: input.gff
|
||||
- name: Outputs
|
||||
arguments:
|
||||
- name: --output
|
||||
alternatives: [-o, --out, --outfile]
|
||||
description: Output GFF file. If no output file is specified, the output will be written to STDOUT.
|
||||
type: file
|
||||
direction: output
|
||||
required: true
|
||||
example: output.gff
|
||||
- name: Arguments
|
||||
arguments:
|
||||
- name: --config
|
||||
alternatives: [-c]
|
||||
description: |
|
||||
String - Input agat config file. By default AGAT takes as input
|
||||
agat_config.yaml file from the working directory if any,
|
||||
otherwise it takes the orignal agat_config.yaml shipped with
|
||||
AGAT. To get the agat_config.yaml locally type: "agat config
|
||||
--expose". The --config option gives you the possibility to use
|
||||
your own AGAT config file (located elsewhere or named
|
||||
differently).
|
||||
type: file
|
||||
required: false
|
||||
example: custom_agat_config.yaml
|
||||
resources:
|
||||
- type: bash_script
|
||||
path: script.sh
|
||||
test_resources:
|
||||
- type: bash_script
|
||||
path: test.sh
|
||||
- type: file
|
||||
path: test_data
|
||||
engines:
|
||||
- type: docker
|
||||
image: quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0
|
||||
setup:
|
||||
- type: docker
|
||||
run: |
|
||||
agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.txt
|
||||
runners:
|
||||
- type: executable
|
||||
- type: nextflow
|
||||
63
src/agat/agat_convert_sp_gff2tsv/help.txt
Normal file
63
src/agat/agat_convert_sp_gff2tsv/help.txt
Normal file
@@ -0,0 +1,63 @@
|
||||
```sh
|
||||
agat_convert_sp_gff2tsv.pl --help
|
||||
```
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
| Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0 |
|
||||
| https://github.com/NBISweden/AGAT |
|
||||
| National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se |
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
Name:
|
||||
agat_convert_sp_gff2tsv.pl
|
||||
|
||||
Description:
|
||||
The script aims to convert gtf/gff file into tabulated file. Attribute's
|
||||
tags from the 9th column become column titles.
|
||||
|
||||
Usage:
|
||||
agat_convert_sp_gff2tsv.pl -gff file.gff [ -o outfile ]
|
||||
agat_convert_sp_gff2tsv.pl --help
|
||||
|
||||
Options:
|
||||
--gff or -f
|
||||
Input GTF/GFF file.
|
||||
|
||||
-o , --output , --out or --outfile
|
||||
Output GFF file. If no output file is specified, the output will
|
||||
be written to STDOUT.
|
||||
|
||||
-c or --config
|
||||
String - Input agat config file. By default AGAT takes as input
|
||||
agat_config.yaml file from the working directory if any,
|
||||
otherwise it takes the orignal agat_config.yaml shipped with
|
||||
AGAT. To get the agat_config.yaml locally type: "agat config
|
||||
--expose". The --config option gives you the possibility to use
|
||||
your own AGAT config file (located elsewhere or named
|
||||
differently).
|
||||
|
||||
-h or --help
|
||||
Display this helpful text.
|
||||
|
||||
Feedback:
|
||||
Did you find a bug?:
|
||||
Do not hesitate to report bugs to help us keep track of the bugs and
|
||||
their resolution. Please use the GitHub issue tracking system available
|
||||
at this address:
|
||||
|
||||
https://github.com/NBISweden/AGAT/issues
|
||||
|
||||
Ensure that the bug was not already reported by searching under Issues.
|
||||
If you're unable to find an (open) issue addressing the problem, open a new one.
|
||||
Try as much as possible to include in the issue when relevant:
|
||||
- a clear description,
|
||||
- as much relevant information as possible,
|
||||
- the command used,
|
||||
- a data sample,
|
||||
- an explanation of the expected behaviour that is not occurring.
|
||||
|
||||
Do you want to contribute?:
|
||||
You are very welcome, visit this address for the Contributing
|
||||
guidelines:
|
||||
https://github.com/NBISweden/AGAT/blob/master/CONTRIBUTING.md
|
||||
9
src/agat/agat_convert_sp_gff2tsv/script.sh
Normal file
9
src/agat/agat_convert_sp_gff2tsv/script.sh
Normal file
@@ -0,0 +1,9 @@
|
||||
#!/bin/bash
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
agat_convert_sp_gff2tsv.pl \
|
||||
-f "$par_gff" \
|
||||
-o "$par_output" \
|
||||
${par_config:+--config "${par_config}"}
|
||||
27
src/agat/agat_convert_sp_gff2tsv/test.sh
Normal file
27
src/agat/agat_convert_sp_gff2tsv/test.sh
Normal file
@@ -0,0 +1,27 @@
|
||||
#!/bin/bash
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
test_dir="${meta_resources_dir}/test_data"
|
||||
out_dir="${meta_resources_dir}/out_data"
|
||||
|
||||
echo "> Run $meta_name with test data"
|
||||
"$meta_executable" \
|
||||
--gff "$test_dir/1.gff" \
|
||||
--output "$out_dir/output.gff"
|
||||
|
||||
echo ">> Checking output"
|
||||
[ ! -f "$out_dir/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
|
||||
|
||||
echo ">> Check if output is empty"
|
||||
[ ! -s "$out_dir/output.gff" ] && echo "Output file output.gff is empty" && exit 1
|
||||
|
||||
echo ">> Check if output matches expected output"
|
||||
diff "$out_dir/output.gff" "$test_dir/agat_convert_sp_gff2tsv_1.tsv"
|
||||
if [ $? -ne 0 ]; then
|
||||
echo "Output file output.gff does not match expected output"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
echo "> Test successful"
|
||||
942
src/agat/agat_convert_sp_gff2tsv/test_data/1.gff
Normal file
942
src/agat/agat_convert_sp_gff2tsv/test_data/1.gff
Normal file
@@ -0,0 +1,942 @@
|
||||
##gff-version 3
|
||||
##sequence-region 1 1 43270923
|
||||
#!genome-build RAP-DB IRGSP-1.0
|
||||
#!genome-version IRGSP-1.0
|
||||
#!genome-date 2015-10
|
||||
#!genome-build-accession GCA_001433935.1
|
||||
1 RAP-DB chromosome 1 43270923 . . . ID=chromosome:1;Alias=Chr1,AP014957.1,NC_029256.1
|
||||
###
|
||||
1 irgsp repeat_region 2000 2100 . + . ID=fakeRepeat1
|
||||
###
|
||||
1 irgsp gene 2983 10815 . + . ID=gene:Os01g0100100;biotype=protein_coding;description=RabGAP/TBC domain containing protein. (Os01t0100100-01);gene_id=Os01g0100100;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 2983 10815 . + . ID=transcript:Os01t0100100-01;Parent=gene:Os01g0100100;biotype=protein_coding;transcript_id=Os01t0100100-01
|
||||
1 irgsp exon 2983 3268 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 2983 3268 . + . Parent=transcript:Os01t0100100-01
|
||||
1 irgsp five_prime_UTR 3354 3448 . + . Parent=transcript:Os01t0100100-01
|
||||
1 irgsp exon 3354 3616 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0100100-01.exon2;rank=2
|
||||
1 irgsp CDS 3449 3616 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 4357 4455 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100100-01.exon3;rank=3
|
||||
1 irgsp CDS 4357 4455 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 5457 5560 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100100-01.exon4;rank=4
|
||||
1 irgsp CDS 5457 5560 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 7136 7944 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon5;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0100100-01.exon5;rank=5
|
||||
1 irgsp CDS 7136 7944 . + 1 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 8028 8150 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon6;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0100100-01.exon6;rank=6
|
||||
1 irgsp CDS 8028 8150 . + 2 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 8232 8320 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100100-01.exon7;rank=7
|
||||
1 irgsp CDS 8232 8320 . + 2 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 8408 8608 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon8;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100100-01.exon8;rank=8
|
||||
1 irgsp CDS 8408 8608 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 9210 9615 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon9;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0100100-01.exon9;rank=9
|
||||
1 irgsp CDS 9210 9615 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 10102 10187 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon10;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100100-01.exon10;rank=10
|
||||
1 irgsp CDS 10102 10187 . + 2 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp CDS 10274 10297 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 10274 10430 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon11;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0100100-01.exon11;rank=11
|
||||
1 irgsp three_prime_UTR 10298 10430 . + . Parent=transcript:Os01t0100100-01
|
||||
1 irgsp exon 10504 10815 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon12;rank=12
|
||||
1 irgsp three_prime_UTR 10504 10815 . + . Parent=transcript:Os01t0100100-01
|
||||
###
|
||||
1 irgsp gene 11218 12435 . + . ID=gene:Os01g0100200;biotype=protein_coding;description=Conserved hypothetical protein. (Os01t0100200-01);gene_id=Os01g0100200;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 11218 12435 . + . ID=transcript:Os01t0100200-01;Parent=gene:Os01g0100200;biotype=protein_coding;transcript_id=Os01t0100200-01
|
||||
1 irgsp five_prime_UTR 11218 11797 . + . Parent=transcript:Os01t0100200-01
|
||||
1 irgsp exon 11218 12060 . + . Parent=transcript:Os01t0100200-01;Name=Os01t0100200-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100200-01.exon1;rank=1
|
||||
1 irgsp CDS 11798 12060 . + 0 ID=CDS:Os01t0100200-01;Parent=transcript:Os01t0100200-01;protein_id=Os01t0100200-01
|
||||
1 irgsp CDS 12152 12317 . + 1 ID=CDS:Os01t0100200-01;Parent=transcript:Os01t0100200-01;protein_id=Os01t0100200-01
|
||||
1 irgsp exon 12152 12435 . + . Parent=transcript:Os01t0100200-01;Name=Os01t0100200-01.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100200-01.exon2;rank=2
|
||||
1 irgsp three_prime_UTR 12318 12435 . + . Parent=transcript:Os01t0100200-01
|
||||
###
|
||||
1 irgsp gene 11372 12284 . - . ID=gene:Os01g0100300;biotype=protein_coding;description=Cytochrome P450 domain containing protein. (Os01t0100300-00);gene_id=Os01g0100300;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 11372 12284 . - . ID=transcript:Os01t0100300-00;Parent=gene:Os01g0100300;biotype=protein_coding;transcript_id=Os01t0100300-00
|
||||
1 irgsp exon 11372 12042 . - . Parent=transcript:Os01t0100300-00;Name=Os01t0100300-00.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100300-00.exon2;rank=2
|
||||
1 irgsp CDS 11372 12042 . - 2 ID=CDS:Os01t0100300-00;Parent=transcript:Os01t0100300-00;protein_id=Os01t0100300-00
|
||||
1 irgsp exon 12146 12284 . - . Parent=transcript:Os01t0100300-00;Name=Os01t0100300-00.exon1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0100300-00.exon1;rank=1
|
||||
1 irgsp CDS 12146 12284 . - 0 ID=CDS:Os01t0100300-00;Parent=transcript:Os01t0100300-00;protein_id=Os01t0100300-00
|
||||
###
|
||||
1 irgsp gene 12721 15685 . + . ID=gene:Os01g0100400;biotype=protein_coding;description=Similar to Pectinesterase-like protein. (Os01t0100400-01);gene_id=Os01g0100400;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 12721 15685 . + . ID=transcript:Os01t0100400-01;Parent=gene:Os01g0100400;biotype=protein_coding;transcript_id=Os01t0100400-01
|
||||
1 irgsp five_prime_UTR 12721 12773 . + . Parent=transcript:Os01t0100400-01
|
||||
1 irgsp exon 12721 13813 . + . Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100400-01.exon1;rank=1
|
||||
1 irgsp CDS 12774 13813 . + 0 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp exon 13906 14271 . + . Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100400-01.exon2;rank=2
|
||||
1 irgsp CDS 13906 14271 . + 1 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp exon 14359 14437 . + . Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0100400-01.exon3;rank=3
|
||||
1 irgsp CDS 14359 14437 . + 1 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp exon 14969 15171 . + . Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100400-01.exon4;rank=4
|
||||
1 irgsp CDS 14969 15171 . + 0 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp CDS 15266 15359 . + 1 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp exon 15266 15685 . + . Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon5;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100400-01.exon5;rank=5
|
||||
1 irgsp three_prime_UTR 15360 15685 . + . Parent=transcript:Os01t0100400-01
|
||||
###
|
||||
1 irgsp gene 12808 13978 . - . ID=gene:Os01g0100466;biotype=protein_coding;description=Hypothetical protein. (Os01t0100466-00);gene_id=Os01g0100466;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 12808 13978 . - . ID=transcript:Os01t0100466-00;Parent=gene:Os01g0100466;biotype=protein_coding;transcript_id=Os01t0100466-00
|
||||
1 irgsp three_prime_UTR 12808 12868 . - . Parent=transcript:Os01t0100466-00
|
||||
1 irgsp exon 12808 13782 . - . Parent=transcript:Os01t0100466-00;Name=Os01t0100466-00.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100466-00.exon2;rank=2
|
||||
1 irgsp CDS 12869 13102 . - 0 ID=CDS:Os01t0100466-00;Parent=transcript:Os01t0100466-00;protein_id=Os01t0100466-00
|
||||
1 irgsp five_prime_UTR 13103 13782 . - . Parent=transcript:Os01t0100466-00
|
||||
1 irgsp exon 13880 13978 . - . Parent=transcript:Os01t0100466-00;Name=Os01t0100466-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100466-00.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 13880 13978 . - . Parent=transcript:Os01t0100466-00
|
||||
###
|
||||
1 irgsp gene 16399 20144 . + . ID=gene:Os01g0100500;biotype=protein_coding;description=Immunoglobulin-like domain containing protein. (Os01t0100500-01);gene_id=Os01g0100500;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 16399 20144 . + . ID=transcript:Os01t0100500-01;Parent=gene:Os01g0100500;biotype=protein_coding;transcript_id=Os01t0100500-01
|
||||
1 irgsp five_prime_UTR 16399 16598 . + . Parent=transcript:Os01t0100500-01
|
||||
1 irgsp exon 16399 16976 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0100500-01.exon1;rank=1
|
||||
1 irgsp CDS 16599 16976 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp exon 17383 17474 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100500-01.exon2;rank=2
|
||||
1 irgsp CDS 17383 17474 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp exon 17558 18258 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0100500-01.exon3;rank=3
|
||||
1 irgsp CDS 17558 18258 . + 1 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp exon 18501 18571 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100500-01.exon4;rank=4
|
||||
1 irgsp CDS 18501 18571 . + 2 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp exon 18968 19057 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100500-01.exon5;rank=5
|
||||
1 irgsp CDS 18968 19057 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp exon 19142 19321 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100500-01.exon6;rank=6
|
||||
1 irgsp CDS 19142 19321 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp CDS 19531 19593 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp exon 19531 19629 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon7;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0100500-01.exon7;rank=7
|
||||
1 irgsp three_prime_UTR 19594 19629 . + . Parent=transcript:Os01t0100500-01
|
||||
1 irgsp exon 19734 20144 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon8;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100500-01.exon8;rank=8
|
||||
1 irgsp three_prime_UTR 19734 20144 . + . Parent=transcript:Os01t0100500-01
|
||||
###
|
||||
1 irgsp gene 22841 26892 . + . ID=gene:Os01g0100600;biotype=protein_coding;description=Single-stranded nucleic acid binding R3H domain containing protein. (Os01t0100600-01);gene_id=Os01g0100600;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 22841 26892 . + . ID=transcript:Os01t0100600-01;Parent=gene:Os01g0100600;biotype=protein_coding;transcript_id=Os01t0100600-01
|
||||
1 irgsp five_prime_UTR 22841 23231 . + . Parent=transcript:Os01t0100600-01
|
||||
1 irgsp exon 22841 23281 . + . Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100600-01.exon1;rank=1
|
||||
1 irgsp CDS 23232 23281 . + 0 ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
|
||||
1 irgsp exon 23572 23847 . + . Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100600-01.exon2;rank=2
|
||||
1 irgsp CDS 23572 23847 . + 1 ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
|
||||
1 irgsp exon 23962 24033 . + . Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon3;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100600-01.exon3;rank=3
|
||||
1 irgsp CDS 23962 24033 . + 1 ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
|
||||
1 irgsp exon 24492 24577 . + . Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon4;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0100600-01.exon4;rank=4
|
||||
1 irgsp CDS 24492 24577 . + 1 ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
|
||||
1 irgsp exon 25445 25519 . + . Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon5;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0100600-01.exon5;rank=5
|
||||
1 irgsp CDS 25445 25519 . + 2 ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
|
||||
1 irgsp CDS 25883 26391 . + 2 ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
|
||||
1 irgsp exon 25883 26892 . + . Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon6;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0100600-01.exon6;rank=6
|
||||
1 irgsp three_prime_UTR 26392 26892 . + . Parent=transcript:Os01t0100600-01
|
||||
###
|
||||
1 irgsp gene 25861 26424 . - . ID=gene:Os01g0100650;biotype=protein_coding;description=Hypothetical gene. (Os01t0100650-00);gene_id=Os01g0100650;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 25861 26424 . - . ID=transcript:Os01t0100650-00;Parent=gene:Os01g0100650;biotype=protein_coding;transcript_id=Os01t0100650-00
|
||||
1 irgsp three_prime_UTR 25861 26039 . - . Parent=transcript:Os01t0100650-00
|
||||
1 irgsp exon 25861 26424 . - . Parent=transcript:Os01t0100650-00;Name=Os01t0100650-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100650-00.exon1;rank=1
|
||||
1 irgsp CDS 26040 26423 . - 0 ID=CDS:Os01t0100650-00;Parent=transcript:Os01t0100650-00;protein_id=Os01t0100650-00
|
||||
1 irgsp five_prime_UTR 26424 26424 . - . Parent=transcript:Os01t0100650-00
|
||||
###
|
||||
1 irgsp gene 27143 28644 . + . ID=gene:Os01g0100700;biotype=protein_coding;description=Similar to 40S ribosomal protein S5-1. (Os01t0100700-01);gene_id=Os01g0100700;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 27143 28644 . + . ID=transcript:Os01t0100700-01;Parent=gene:Os01g0100700;biotype=protein_coding;transcript_id=Os01t0100700-01
|
||||
1 irgsp five_prime_UTR 27143 27220 . + . Parent=transcript:Os01t0100700-01
|
||||
1 irgsp exon 27143 27292 . + . Parent=transcript:Os01t0100700-01;Name=Os01t0100700-01.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0100700-01.exon1;rank=1
|
||||
1 irgsp CDS 27221 27292 . + 0 ID=CDS:Os01t0100700-01;Parent=transcript:Os01t0100700-01;protein_id=Os01t0100700-01
|
||||
1 irgsp exon 27370 27641 . + . Parent=transcript:Os01t0100700-01;Name=Os01t0100700-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100700-01.exon2;rank=2
|
||||
1 irgsp CDS 27370 27641 . + 0 ID=CDS:Os01t0100700-01;Parent=transcript:Os01t0100700-01;protein_id=Os01t0100700-01
|
||||
1 irgsp exon 28090 28293 . + . Parent=transcript:Os01t0100700-01;Name=Os01t0100700-01.exon3;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100700-01.exon3;rank=3
|
||||
1 irgsp CDS 28090 28293 . + 1 ID=CDS:Os01t0100700-01;Parent=transcript:Os01t0100700-01;protein_id=Os01t0100700-01
|
||||
1 irgsp CDS 28365 28419 . + 1 ID=CDS:Os01t0100700-01;Parent=transcript:Os01t0100700-01;protein_id=Os01t0100700-01
|
||||
1 irgsp exon 28365 28644 . + . Parent=transcript:Os01t0100700-01;Name=Os01t0100700-01.exon4;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100700-01.exon4;rank=4
|
||||
1 irgsp three_prime_UTR 28420 28644 . + . Parent=transcript:Os01t0100700-01
|
||||
###
|
||||
1 irgsp gene 29818 34453 . + . ID=gene:Os01g0100800;biotype=protein_coding;description=Protein of unknown function DUF1664 family protein. (Os01t0100800-01);gene_id=Os01g0100800;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 29818 34453 . + . ID=transcript:Os01t0100800-01;Parent=gene:Os01g0100800;biotype=protein_coding;transcript_id=Os01t0100800-01
|
||||
1 irgsp five_prime_UTR 29818 29939 . + . Parent=transcript:Os01t0100800-01
|
||||
1 irgsp exon 29818 29976 . + . Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon1;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0100800-01.exon1;rank=1
|
||||
1 irgsp CDS 29940 29976 . + 0 ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
|
||||
1 irgsp exon 30146 30228 . + . Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100800-01.exon2;rank=2
|
||||
1 irgsp CDS 30146 30228 . + 2 ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
|
||||
1 irgsp exon 30735 30806 . + . Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100800-01.exon3;rank=3
|
||||
1 irgsp CDS 30735 30806 . + 0 ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
|
||||
1 irgsp exon 30885 30963 . + . Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon4;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0100800-01.exon4;rank=4
|
||||
1 irgsp CDS 30885 30963 . + 0 ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
|
||||
1 irgsp exon 31258 31325 . + . Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100800-01.exon5;rank=5
|
||||
1 irgsp CDS 31258 31325 . + 2 ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
|
||||
1 irgsp exon 31505 31606 . + . Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100800-01.exon6;rank=6
|
||||
1 irgsp CDS 31505 31606 . + 0 ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
|
||||
1 irgsp exon 32377 32466 . + . Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100800-01.exon7;rank=7
|
||||
1 irgsp CDS 32377 32466 . + 0 ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
|
||||
1 irgsp exon 32542 32616 . + . Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon8;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100800-01.exon8;rank=8
|
||||
1 irgsp CDS 32542 32616 . + 0 ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
|
||||
1 irgsp exon 32712 32744 . + . Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon9;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100800-01.exon9;rank=9
|
||||
1 irgsp CDS 32712 32744 . + 0 ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
|
||||
1 irgsp exon 32828 32905 . + . Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon10;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100800-01.exon10;rank=10
|
||||
1 irgsp CDS 32828 32905 . + 0 ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
|
||||
1 irgsp exon 33274 33330 . + . Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon11;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100800-01.exon11;rank=11
|
||||
1 irgsp CDS 33274 33330 . + 0 ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
|
||||
1 irgsp exon 33400 33471 . + . Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon12;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100800-01.exon12;rank=12
|
||||
1 irgsp CDS 33400 33471 . + 0 ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
|
||||
1 irgsp exon 33543 33617 . + . Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon13;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100800-01.exon13;rank=13
|
||||
1 irgsp CDS 33543 33617 . + 0 ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
|
||||
1 irgsp CDS 33975 34124 . + 0 ID=CDS:Os01t0100800-01;Parent=transcript:Os01t0100800-01;protein_id=Os01t0100800-01
|
||||
1 irgsp exon 33975 34453 . + . Parent=transcript:Os01t0100800-01;Name=Os01t0100800-01.exon14;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0100800-01.exon14;rank=14
|
||||
1 irgsp three_prime_UTR 34125 34453 . + . Parent=transcript:Os01t0100800-01
|
||||
###
|
||||
1 irgsp gene 35623 41136 . + . ID=gene:Os01g0100900;Name=SPHINGOSINE-1-PHOSPHATE LYASE 1%2C Sphingosine-1-Phoshpate Lyase 1;biotype=protein_coding;description=Sphingosine-1-phosphate lyase%2C Disease resistance response (Os01t0100900-01);gene_id=Os01g0100900;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 35623 41136 . + . ID=transcript:Os01t0100900-01;Parent=gene:Os01g0100900;biotype=protein_coding;transcript_id=Os01t0100900-01
|
||||
1 irgsp five_prime_UTR 35623 35742 . + . Parent=transcript:Os01t0100900-01
|
||||
1 irgsp exon 35623 35939 . + . Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100900-01.exon1;rank=1
|
||||
1 irgsp CDS 35743 35939 . + 0 ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
|
||||
1 irgsp exon 36027 36072 . + . Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0100900-01.exon2;rank=2
|
||||
1 irgsp CDS 36027 36072 . + 1 ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
|
||||
1 irgsp exon 36517 36668 . + . Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon3;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100900-01.exon3;rank=3
|
||||
1 irgsp CDS 36517 36668 . + 0 ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
|
||||
1 irgsp exon 36818 36877 . + . Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon4;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100900-01.exon4;rank=4
|
||||
1 irgsp CDS 36818 36877 . + 1 ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
|
||||
1 irgsp exon 37594 37818 . + . Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon5;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100900-01.exon5;rank=5
|
||||
1 irgsp CDS 37594 37818 . + 1 ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
|
||||
1 irgsp exon 37892 38033 . + . Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0100900-01.exon6;rank=6
|
||||
1 irgsp CDS 37892 38033 . + 1 ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
|
||||
1 irgsp exon 38276 38326 . + . Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100900-01.exon7;rank=7
|
||||
1 irgsp CDS 38276 38326 . + 0 ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
|
||||
1 irgsp exon 38434 38525 . + . Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon8;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100900-01.exon8;rank=8
|
||||
1 irgsp CDS 38434 38525 . + 0 ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
|
||||
1 irgsp exon 39319 39445 . + . Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon9;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0100900-01.exon9;rank=9
|
||||
1 irgsp CDS 39319 39445 . + 1 ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
|
||||
1 irgsp exon 39553 39568 . + . Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon10;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0100900-01.exon10;rank=10
|
||||
1 irgsp CDS 39553 39568 . + 0 ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
|
||||
1 irgsp exon 39939 40046 . + . Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon11;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0100900-01.exon11;rank=11
|
||||
1 irgsp CDS 39939 40046 . + 2 ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
|
||||
1 irgsp exon 40135 40189 . + . Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon12;constitutive=1;ensembl_end_phase=2;ensembl_phase=1;exon_id=Os01t0100900-01.exon12;rank=12
|
||||
1 irgsp CDS 40135 40189 . + 2 ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
|
||||
1 irgsp exon 40456 40602 . + . Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon13;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100900-01.exon13;rank=13
|
||||
1 irgsp CDS 40456 40602 . + 1 ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
|
||||
1 irgsp exon 40703 40781 . + . Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon14;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0100900-01.exon14;rank=14
|
||||
1 irgsp CDS 40703 40781 . + 1 ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
|
||||
1 irgsp CDS 40885 41007 . + 0 ID=CDS:Os01t0100900-01;Parent=transcript:Os01t0100900-01;protein_id=Os01t0100900-01
|
||||
1 irgsp exon 40885 41136 . + . Parent=transcript:Os01t0100900-01;Name=Os01t0100900-01.exon15;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0100900-01.exon15;rank=15
|
||||
1 irgsp three_prime_UTR 41008 41136 . + . Parent=transcript:Os01t0100900-01
|
||||
###
|
||||
1 irgsp gene 58658 61090 . + . ID=gene:Os01g0101150;biotype=protein_coding;description=Hypothetical conserved gene. (Os01t0101150-00);gene_id=Os01g0101150;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 58658 61090 . + . ID=transcript:Os01t0101150-00;Parent=gene:Os01g0101150;biotype=protein_coding;transcript_id=Os01t0101150-00
|
||||
1 irgsp exon 58658 61090 . + . Parent=transcript:Os01t0101150-00;Name=Os01t0101150-00.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0101150-00.exon1;rank=1
|
||||
1 irgsp CDS 58658 61090 . + 0 ID=CDS:Os01t0101150-00;Parent=transcript:Os01t0101150-00;protein_id=Os01t0101150-00
|
||||
###
|
||||
1 irgsp gene 62060 65537 . + . ID=gene:Os01g0101200;biotype=protein_coding;description=2%2C3-diketo-5-methylthio-1-phosphopentane phosphatase domain containing protein. (Os01t0101200-01)%3B2%2C3-diketo-5-methylthio-1-phosphopentane phosphatase domain containing protein. (Os01t0101200-02);gene_id=Os01g0101200;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 62060 63576 . + . ID=transcript:Os01t0101200-01;Parent=gene:Os01g0101200;biotype=protein_coding;transcript_id=Os01t0101200-01
|
||||
1 irgsp five_prime_UTR 62060 62103 . + . Parent=transcript:Os01t0101200-01
|
||||
1 irgsp exon 62060 62295 . + . Parent=transcript:Os01t0101200-01;Name=Os01t0101200-01.exon1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0101200-01.exon1;rank=1
|
||||
1 irgsp CDS 62104 62295 . + 0 ID=CDS:Os01t0101200-01;Parent=transcript:Os01t0101200-01;protein_id=Os01t0101200-01
|
||||
1 irgsp exon 62385 62905 . + . Parent=transcript:Os01t0101200-01;Name=Os01t0101200-02.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0101200-02.exon2;rank=2
|
||||
1 irgsp CDS 62385 62905 . + 0 ID=CDS:Os01t0101200-01;Parent=transcript:Os01t0101200-01;protein_id=Os01t0101200-01
|
||||
1 irgsp exon 62996 63114 . + . Parent=transcript:Os01t0101200-01;Name=Os01t0101200-02.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0101200-02.exon3;rank=3
|
||||
1 irgsp CDS 62996 63114 . + 1 ID=CDS:Os01t0101200-01;Parent=transcript:Os01t0101200-01;protein_id=Os01t0101200-01
|
||||
1 irgsp CDS 63248 63345 . + 2 ID=CDS:Os01t0101200-01;Parent=transcript:Os01t0101200-01;protein_id=Os01t0101200-01
|
||||
1 irgsp exon 63248 63576 . + . Parent=transcript:Os01t0101200-01;Name=Os01t0101200-01.exon4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0101200-01.exon4;rank=4
|
||||
1 irgsp three_prime_UTR 63346 63576 . + . Parent=transcript:Os01t0101200-01
|
||||
1 irgsp mRNA 62112 65537 . + . ID=transcript:Os01t0101200-02;Parent=gene:Os01g0101200;biotype=protein_coding;transcript_id=Os01t0101200-02
|
||||
1 irgsp five_prime_UTR 62112 62112 . + . Parent=transcript:Os01t0101200-02
|
||||
1 irgsp exon 62112 62295 . + . Parent=transcript:Os01t0101200-02;Name=Os01t0101200-02.exon1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0101200-02.exon1;rank=1
|
||||
1 irgsp CDS 62113 62295 . + 0 ID=CDS:Os01t0101200-02;Parent=transcript:Os01t0101200-02;protein_id=Os01t0101200-02
|
||||
1 irgsp exon 62385 62905 . + . Parent=transcript:Os01t0101200-02;Name=Os01t0101200-02.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0101200-02.exon2;rank=2
|
||||
1 irgsp CDS 62385 62905 . + 0 ID=CDS:Os01t0101200-02;Parent=transcript:Os01t0101200-02;protein_id=Os01t0101200-02
|
||||
1 irgsp exon 62996 63114 . + . Parent=transcript:Os01t0101200-02;Name=Os01t0101200-02.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0101200-02.exon3;rank=3
|
||||
1 irgsp CDS 62996 63114 . + 1 ID=CDS:Os01t0101200-02;Parent=transcript:Os01t0101200-02;protein_id=Os01t0101200-02
|
||||
1 irgsp CDS 63248 63345 . + 2 ID=CDS:Os01t0101200-02;Parent=transcript:Os01t0101200-02;protein_id=Os01t0101200-02
|
||||
1 irgsp exon 63248 65537 . + . Parent=transcript:Os01t0101200-02;Name=Os01t0101200-02.exon4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0101200-02.exon4;rank=4
|
||||
1 irgsp three_prime_UTR 63346 65537 . + . Parent=transcript:Os01t0101200-02
|
||||
###
|
||||
1 irgsp gene 63350 66302 . - . ID=gene:Os01g0101300;biotype=protein_coding;description=Similar to MRNA%2C partial cds%2C clone: RAFL22-26-L17. (Fragment). (Os01t0101300-01);gene_id=Os01g0101300;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 63350 66302 . - . ID=transcript:Os01t0101300-01;Parent=gene:Os01g0101300;biotype=protein_coding;transcript_id=Os01t0101300-01
|
||||
1 irgsp three_prime_UTR 63350 63669 . - . Parent=transcript:Os01t0101300-01
|
||||
1 irgsp exon 63350 63783 . - . Parent=transcript:Os01t0101300-01;Name=Os01t0101300-01.exon7;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0101300-01.exon7;rank=7
|
||||
1 irgsp CDS 63670 63783 . - 0 ID=CDS:Os01t0101300-01;Parent=transcript:Os01t0101300-01;protein_id=Os01t0101300-01
|
||||
1 irgsp exon 63877 64020 . - . Parent=transcript:Os01t0101300-01;Name=Os01t0101300-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0101300-01.exon6;rank=6
|
||||
1 irgsp CDS 63877 64020 . - 0 ID=CDS:Os01t0101300-01;Parent=transcript:Os01t0101300-01;protein_id=Os01t0101300-01
|
||||
1 irgsp exon 64339 64431 . - . Parent=transcript:Os01t0101300-01;Name=Os01t0101300-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0101300-01.exon5;rank=5
|
||||
1 irgsp CDS 64339 64431 . - 0 ID=CDS:Os01t0101300-01;Parent=transcript:Os01t0101300-01;protein_id=Os01t0101300-01
|
||||
1 irgsp exon 64665 64779 . - . Parent=transcript:Os01t0101300-01;Name=Os01t0101300-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0101300-01.exon4;rank=4
|
||||
1 irgsp CDS 64665 64779 . - 1 ID=CDS:Os01t0101300-01;Parent=transcript:Os01t0101300-01;protein_id=Os01t0101300-01
|
||||
1 irgsp exon 64902 65152 . - . Parent=transcript:Os01t0101300-01;Name=Os01t0101300-01.exon3;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0101300-01.exon3;rank=3
|
||||
1 irgsp CDS 64902 65152 . - 0 ID=CDS:Os01t0101300-01;Parent=transcript:Os01t0101300-01;protein_id=Os01t0101300-01
|
||||
1 irgsp exon 65248 65431 . - . Parent=transcript:Os01t0101300-01;Name=Os01t0101300-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0101300-01.exon2;rank=2
|
||||
1 irgsp CDS 65248 65431 . - 1 ID=CDS:Os01t0101300-01;Parent=transcript:Os01t0101300-01;protein_id=Os01t0101300-01
|
||||
1 irgsp CDS 65628 65950 . - 0 ID=CDS:Os01t0101300-01;Parent=transcript:Os01t0101300-01;protein_id=Os01t0101300-01
|
||||
1 irgsp exon 65628 66302 . - . Parent=transcript:Os01t0101300-01;Name=Os01t0101300-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0101300-01.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 65951 66302 . - . Parent=transcript:Os01t0101300-01
|
||||
###
|
||||
1 irgsp gene 72816 78349 . + . ID=gene:Os01g0101600;biotype=protein_coding;description=Immunoglobulin-like fold domain containing protein. (Os01t0101600-01)%3BImmunoglobulin-like fold domain containing protein. (Os01t0101600-02)%3BHypothetical conserved gene. (Os01t0101600-03);gene_id=Os01g0101600;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 72816 78349 . + . ID=transcript:Os01t0101600-01;Parent=gene:Os01g0101600;biotype=protein_coding;transcript_id=Os01t0101600-01
|
||||
1 irgsp five_prime_UTR 72816 72902 . + . Parent=transcript:Os01t0101600-01
|
||||
1 irgsp exon 72816 73935 . + . Parent=transcript:Os01t0101600-01;Name=Os01t0101600-01.exon1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0101600-01.exon1;rank=1
|
||||
1 irgsp CDS 72903 73935 . + 0 ID=CDS:Os01t0101600-01;Parent=transcript:Os01t0101600-01;protein_id=Os01t0101600-01
|
||||
1 irgsp exon 74468 74981 . + . Parent=transcript:Os01t0101600-01;Name=Os01t0101600-02.exon2;constitutive=0;ensembl_end_phase=2;ensembl_phase=1;exon_id=Os01t0101600-02.exon2;rank=2
|
||||
1 irgsp CDS 74468 74981 . + 2 ID=CDS:Os01t0101600-01;Parent=transcript:Os01t0101600-01;protein_id=Os01t0101600-01
|
||||
1 irgsp CDS 75619 77008 . + 1 ID=CDS:Os01t0101600-01;Parent=transcript:Os01t0101600-01;protein_id=Os01t0101600-01
|
||||
1 irgsp exon 75619 77205 . + . Parent=transcript:Os01t0101600-01;Name=Os01t0101600-01.exon3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0101600-01.exon3;rank=3
|
||||
1 irgsp three_prime_UTR 77009 77205 . + . Parent=transcript:Os01t0101600-01
|
||||
1 irgsp exon 77333 78349 . + . Parent=transcript:Os01t0101600-01;Name=Os01t0101600-01.exon4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0101600-01.exon4;rank=4
|
||||
1 irgsp three_prime_UTR 77333 78349 . + . Parent=transcript:Os01t0101600-01
|
||||
1 irgsp mRNA 72823 77699 . + . ID=transcript:Os01t0101600-02;Parent=gene:Os01g0101600;biotype=protein_coding;transcript_id=Os01t0101600-02
|
||||
1 irgsp five_prime_UTR 72823 72902 . + . Parent=transcript:Os01t0101600-02
|
||||
1 irgsp exon 72823 73935 . + . Parent=transcript:Os01t0101600-02;Name=Os01t0101600-02.exon1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0101600-02.exon1;rank=1
|
||||
1 irgsp CDS 72903 73935 . + 0 ID=CDS:Os01t0101600-02;Parent=transcript:Os01t0101600-02;protein_id=Os01t0101600-02
|
||||
1 irgsp exon 74468 74981 . + . Parent=transcript:Os01t0101600-02;Name=Os01t0101600-02.exon2;constitutive=0;ensembl_end_phase=2;ensembl_phase=1;exon_id=Os01t0101600-02.exon2;rank=2
|
||||
1 irgsp CDS 74468 74981 . + 2 ID=CDS:Os01t0101600-02;Parent=transcript:Os01t0101600-02;protein_id=Os01t0101600-02
|
||||
1 irgsp CDS 75619 77008 . + 1 ID=CDS:Os01t0101600-02;Parent=transcript:Os01t0101600-02;protein_id=Os01t0101600-02
|
||||
1 irgsp exon 75619 77699 . + . Parent=transcript:Os01t0101600-02;Name=Os01t0101600-02.exon3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0101600-02.exon3;rank=3
|
||||
1 irgsp three_prime_UTR 77009 77699 . + . Parent=transcript:Os01t0101600-02
|
||||
1 irgsp mRNA 75942 77699 . + . ID=transcript:Os01t0101600-03;Parent=gene:Os01g0101600;biotype=protein_coding;transcript_id=Os01t0101600-03
|
||||
1 irgsp five_prime_UTR 75942 75943 . + . Parent=transcript:Os01t0101600-03
|
||||
1 irgsp exon 75942 77699 . + . Parent=transcript:Os01t0101600-03;Name=Os01t0101600-03.exon1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0101600-03.exon1;rank=1
|
||||
1 irgsp CDS 75944 77008 . + 0 ID=CDS:Os01t0101600-03;Parent=transcript:Os01t0101600-03;protein_id=Os01t0101600-03
|
||||
1 irgsp three_prime_UTR 77009 77699 . + . Parent=transcript:Os01t0101600-03
|
||||
###
|
||||
1 irgsp gene 82426 84095 . + . ID=gene:Os01g0101700;Name=DnaJ domain protein C1%2C rice DJC26 homolog;biotype=protein_coding;description=Similar to chaperone protein dnaJ 20. (Os01t0101700-00);gene_id=Os01g0101700;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 82426 84095 . + . ID=transcript:Os01t0101700-00;Parent=gene:Os01g0101700;biotype=protein_coding;transcript_id=Os01t0101700-00
|
||||
1 irgsp five_prime_UTR 82426 82506 . + . Parent=transcript:Os01t0101700-00
|
||||
1 irgsp exon 82426 82932 . + . Parent=transcript:Os01t0101700-00;Name=Os01t0101700-00.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0101700-00.exon1;rank=1
|
||||
1 irgsp CDS 82507 82932 . + 0 ID=CDS:Os01t0101700-00;Parent=transcript:Os01t0101700-00;protein_id=Os01t0101700-00
|
||||
1 irgsp CDS 83724 83864 . + 0 ID=CDS:Os01t0101700-00;Parent=transcript:Os01t0101700-00;protein_id=Os01t0101700-00
|
||||
1 irgsp exon 83724 84095 . + . Parent=transcript:Os01t0101700-00;Name=Os01t0101700-00.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0101700-00.exon2;rank=2
|
||||
1 irgsp three_prime_UTR 83865 84095 . + . Parent=transcript:Os01t0101700-00
|
||||
###
|
||||
1 irgsp gene 85337 88844 . + . ID=gene:Os01g0101800;biotype=protein_coding;description=Conserved hypothetical protein. (Os01t0101800-01);gene_id=Os01g0101800;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 85337 88844 . + . ID=transcript:Os01t0101800-01;Parent=gene:Os01g0101800;biotype=protein_coding;transcript_id=Os01t0101800-01
|
||||
1 irgsp five_prime_UTR 85337 85378 . + . Parent=transcript:Os01t0101800-01
|
||||
1 irgsp exon 85337 85600 . + . Parent=transcript:Os01t0101800-01;Name=Os01t0101800-01.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0101800-01.exon1;rank=1
|
||||
1 irgsp CDS 85379 85600 . + 0 ID=CDS:Os01t0101800-01;Parent=transcript:Os01t0101800-01;protein_id=Os01t0101800-01
|
||||
1 irgsp exon 85737 85830 . + . Parent=transcript:Os01t0101800-01;Name=Os01t0101800-01.exon2;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0101800-01.exon2;rank=2
|
||||
1 irgsp CDS 85737 85830 . + 0 ID=CDS:Os01t0101800-01;Parent=transcript:Os01t0101800-01;protein_id=Os01t0101800-01
|
||||
1 irgsp exon 85935 86086 . + . Parent=transcript:Os01t0101800-01;Name=Os01t0101800-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0101800-01.exon3;rank=3
|
||||
1 irgsp CDS 85935 86086 . + 2 ID=CDS:Os01t0101800-01;Parent=transcript:Os01t0101800-01;protein_id=Os01t0101800-01
|
||||
1 irgsp exon 86212 86299 . + . Parent=transcript:Os01t0101800-01;Name=Os01t0101800-01.exon4;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0101800-01.exon4;rank=4
|
||||
1 irgsp CDS 86212 86299 . + 0 ID=CDS:Os01t0101800-01;Parent=transcript:Os01t0101800-01;protein_id=Os01t0101800-01
|
||||
1 irgsp exon 86399 87681 . + . Parent=transcript:Os01t0101800-01;Name=Os01t0101800-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0101800-01.exon5;rank=5
|
||||
1 irgsp CDS 86399 87681 . + 2 ID=CDS:Os01t0101800-01;Parent=transcript:Os01t0101800-01;protein_id=Os01t0101800-01
|
||||
1 irgsp exon 88291 88398 . + . Parent=transcript:Os01t0101800-01;Name=Os01t0101800-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0101800-01.exon6;rank=6
|
||||
1 irgsp CDS 88291 88398 . + 0 ID=CDS:Os01t0101800-01;Parent=transcript:Os01t0101800-01;protein_id=Os01t0101800-01
|
||||
1 irgsp CDS 88500 88583 . + 0 ID=CDS:Os01t0101800-01;Parent=transcript:Os01t0101800-01;protein_id=Os01t0101800-01
|
||||
1 irgsp exon 88500 88844 . + . Parent=transcript:Os01t0101800-01;Name=Os01t0101800-01.exon7;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0101800-01.exon7;rank=7
|
||||
1 irgsp three_prime_UTR 88584 88844 . + . Parent=transcript:Os01t0101800-01
|
||||
###
|
||||
1 irgsp gene 86211 88583 . - . ID=gene:Os01g0101850;biotype=protein_coding;description=Hypothetical protein. (Os01t0101850-00);gene_id=Os01g0101850;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 86211 88583 . - . ID=transcript:Os01t0101850-00;Parent=gene:Os01g0101850;biotype=protein_coding;transcript_id=Os01t0101850-00
|
||||
1 irgsp exon 86211 86277 . - . Parent=transcript:Os01t0101850-00;Name=Os01t0101850-00.exon4;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0101850-00.exon4;rank=4
|
||||
1 irgsp three_prime_UTR 86211 86277 . - . Parent=transcript:Os01t0101850-00
|
||||
1 irgsp three_prime_UTR 86384 87326 . - . Parent=transcript:Os01t0101850-00
|
||||
1 irgsp exon 86384 87694 . - . Parent=transcript:Os01t0101850-00;Name=Os01t0101850-00.exon3;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0101850-00.exon3;rank=3
|
||||
1 irgsp CDS 87327 87662 . - 0 ID=CDS:Os01t0101850-00;Parent=transcript:Os01t0101850-00;protein_id=Os01t0101850-00
|
||||
1 irgsp five_prime_UTR 87663 87694 . - . Parent=transcript:Os01t0101850-00
|
||||
1 irgsp exon 88308 88396 . - . Parent=transcript:Os01t0101850-00;Name=Os01t0101850-00.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0101850-00.exon2;rank=2
|
||||
1 irgsp five_prime_UTR 88308 88396 . - . Parent=transcript:Os01t0101850-00
|
||||
1 irgsp exon 88496 88583 . - . Parent=transcript:Os01t0101850-00;Name=Os01t0101850-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0101850-00.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 88496 88583 . - . Parent=transcript:Os01t0101850-00
|
||||
###
|
||||
1 irgsp gene 88883 89228 . - . ID=gene:Os01g0101900;biotype=protein_coding;description=Similar to OSIGBa0075F02.3 protein. (Os01t0101900-00);gene_id=Os01g0101900;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 88883 89228 . - . ID=transcript:Os01t0101900-00;Parent=gene:Os01g0101900;biotype=protein_coding;transcript_id=Os01t0101900-00
|
||||
1 irgsp three_prime_UTR 88883 88985 . - . Parent=transcript:Os01t0101900-00
|
||||
1 irgsp exon 88883 89228 . - . Parent=transcript:Os01t0101900-00;Name=Os01t0101900-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0101900-00.exon1;rank=1
|
||||
1 irgsp CDS 88986 89204 . - 0 ID=CDS:Os01t0101900-00;Parent=transcript:Os01t0101900-00;protein_id=Os01t0101900-00
|
||||
1 irgsp five_prime_UTR 89205 89228 . - . Parent=transcript:Os01t0101900-00
|
||||
###
|
||||
1 irgsp gene 89763 91465 . - . ID=gene:Os01g0102000;Name=NON-SPECIFIC PHOSPHOLIPASE C5;biotype=protein_coding;description=Phosphoesterase family protein. (Os01t0102000-01);gene_id=Os01g0102000;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 89763 91465 . - . ID=transcript:Os01t0102000-01;Parent=gene:Os01g0102000;biotype=protein_coding;transcript_id=Os01t0102000-01
|
||||
1 irgsp three_prime_UTR 89763 89824 . - . Parent=transcript:Os01t0102000-01
|
||||
1 irgsp exon 89763 91465 . - . Parent=transcript:Os01t0102000-01;Name=Os01t0102000-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0102000-01.exon1;rank=1
|
||||
1 irgsp CDS 89825 91411 . - 0 ID=CDS:Os01t0102000-01;Parent=transcript:Os01t0102000-01;protein_id=Os01t0102000-01
|
||||
1 irgsp five_prime_UTR 91412 91465 . - . Parent=transcript:Os01t0102000-01
|
||||
###
|
||||
1 irgsp gene 134300 135439 . + . ID=gene:Os01g0102300;Name=OsTLP27;biotype=protein_coding;description=Thylakoid lumen protein%2C Photosynthesis and chloroplast development (Os01t0102300-01);gene_id=Os01g0102300;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 134300 135439 . + . ID=transcript:Os01t0102300-01;Parent=gene:Os01g0102300;biotype=protein_coding;transcript_id=Os01t0102300-01
|
||||
1 irgsp five_prime_UTR 134300 134310 . + . Parent=transcript:Os01t0102300-01
|
||||
1 irgsp exon 134300 134615 . + . Parent=transcript:Os01t0102300-01;Name=Os01t0102300-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0102300-01.exon1;rank=1
|
||||
1 irgsp CDS 134311 134615 . + 0 ID=CDS:Os01t0102300-01;Parent=transcript:Os01t0102300-01;protein_id=Os01t0102300-01
|
||||
1 irgsp exon 134698 134824 . + . Parent=transcript:Os01t0102300-01;Name=Os01t0102300-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0102300-01.exon2;rank=2
|
||||
1 irgsp CDS 134698 134824 . + 1 ID=CDS:Os01t0102300-01;Parent=transcript:Os01t0102300-01;protein_id=Os01t0102300-01
|
||||
1 irgsp CDS 134912 135253 . + 0 ID=CDS:Os01t0102300-01;Parent=transcript:Os01t0102300-01;protein_id=Os01t0102300-01
|
||||
1 irgsp exon 134912 135439 . + . Parent=transcript:Os01t0102300-01;Name=Os01t0102300-01.exon3;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0102300-01.exon3;rank=3
|
||||
1 irgsp three_prime_UTR 135254 135439 . + . Parent=transcript:Os01t0102300-01
|
||||
###
|
||||
1 irgsp gene 139826 141555 . + . ID=gene:Os01g0102400;Name=HAP5H SUBUNIT OF CCAAT-BOX BINDING COMPLEX;biotype=protein_coding;description=Histone-fold domain containing protein. (Os01t0102400-01);gene_id=Os01g0102400;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 139826 141555 . + . ID=transcript:Os01t0102400-01;Parent=gene:Os01g0102400;biotype=protein_coding;transcript_id=Os01t0102400-01
|
||||
1 irgsp exon 139826 139906 . + . Parent=transcript:Os01t0102400-01;Name=Os01t0102400-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0102400-01.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 139826 139906 . + . Parent=transcript:Os01t0102400-01
|
||||
1 irgsp five_prime_UTR 140120 140149 . + . Parent=transcript:Os01t0102400-01
|
||||
1 irgsp exon 140120 141555 . + . Parent=transcript:Os01t0102400-01;Name=Os01t0102400-01.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0102400-01.exon2;rank=2
|
||||
1 irgsp CDS 140150 141415 . + 0 ID=CDS:Os01t0102400-01;Parent=transcript:Os01t0102400-01;protein_id=Os01t0102400-01
|
||||
1 irgsp three_prime_UTR 141416 141555 . + . Parent=transcript:Os01t0102400-01
|
||||
###
|
||||
1 irgsp gene 141959 144554 . + . ID=gene:Os01g0102500;biotype=protein_coding;description=Conserved hypothetical protein. (Os01t0102500-01);gene_id=Os01g0102500;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 141959 144554 . + . ID=transcript:Os01t0102500-01;Parent=gene:Os01g0102500;biotype=protein_coding;transcript_id=Os01t0102500-01
|
||||
1 irgsp five_prime_UTR 141959 142083 . + . Parent=transcript:Os01t0102500-01
|
||||
1 irgsp exon 141959 142631 . + . Parent=transcript:Os01t0102500-01;Name=Os01t0102500-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0102500-01.exon1;rank=1
|
||||
1 irgsp CDS 142084 142631 . + 0 ID=CDS:Os01t0102500-01;Parent=transcript:Os01t0102500-01;protein_id=Os01t0102500-01
|
||||
1 irgsp exon 143191 143431 . + . Parent=transcript:Os01t0102500-01;Name=Os01t0102500-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0102500-01.exon2;rank=2
|
||||
1 irgsp CDS 143191 143431 . + 1 ID=CDS:Os01t0102500-01;Parent=transcript:Os01t0102500-01;protein_id=Os01t0102500-01
|
||||
1 irgsp exon 143563 143680 . + . Parent=transcript:Os01t0102500-01;Name=Os01t0102500-01.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0102500-01.exon3;rank=3
|
||||
1 irgsp CDS 143563 143680 . + 0 ID=CDS:Os01t0102500-01;Parent=transcript:Os01t0102500-01;protein_id=Os01t0102500-01
|
||||
1 irgsp CDS 143817 143908 . + 2 ID=CDS:Os01t0102500-01;Parent=transcript:Os01t0102500-01;protein_id=Os01t0102500-01
|
||||
1 irgsp exon 143817 144554 . + . Parent=transcript:Os01t0102500-01;Name=Os01t0102500-01.exon4;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0102500-01.exon4;rank=4
|
||||
1 irgsp three_prime_UTR 143909 144554 . + . Parent=transcript:Os01t0102500-01
|
||||
###
|
||||
1 irgsp gene 145603 147847 . + . ID=gene:Os01g0102600;Name=Shikimate kinase 4;biotype=protein_coding;description=Shikimate kinase domain containing protein. (Os01t0102600-01)%3BSimilar to shikimate kinase family protein. (Os01t0102600-02);gene_id=Os01g0102600;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 145603 147847 . + . ID=transcript:Os01t0102600-01;Parent=gene:Os01g0102600;biotype=protein_coding;transcript_id=Os01t0102600-01
|
||||
1 irgsp five_prime_UTR 145603 145644 . + . Parent=transcript:Os01t0102600-01
|
||||
1 irgsp exon 145603 145786 . + . Parent=transcript:Os01t0102600-01;Name=Os01t0102600-01.exon1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0102600-01.exon1;rank=1
|
||||
1 irgsp CDS 145645 145786 . + 0 ID=CDS:Os01t0102600-01;Parent=transcript:Os01t0102600-01;protein_id=Os01t0102600-01
|
||||
1 irgsp exon 145905 145951 . + . Parent=transcript:Os01t0102600-01;Name=Os01t0102600-01.exon2;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0102600-01.exon2;rank=2
|
||||
1 irgsp CDS 145905 145951 . + 2 ID=CDS:Os01t0102600-01;Parent=transcript:Os01t0102600-01;protein_id=Os01t0102600-01
|
||||
1 irgsp exon 146028 146082 . + . Parent=transcript:Os01t0102600-01;Name=Os01t0102600-01.exon3;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0102600-01.exon3;rank=3
|
||||
1 irgsp CDS 146028 146082 . + 0 ID=CDS:Os01t0102600-01;Parent=transcript:Os01t0102600-01;protein_id=Os01t0102600-01
|
||||
1 irgsp exon 146179 146339 . + . Parent=transcript:Os01t0102600-01;Name=Os01t0102600-01.exon4;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0102600-01.exon4;rank=4
|
||||
1 irgsp CDS 146179 146339 . + 2 ID=CDS:Os01t0102600-01;Parent=transcript:Os01t0102600-01;protein_id=Os01t0102600-01
|
||||
1 irgsp exon 146450 146532 . + . Parent=transcript:Os01t0102600-01;Name=Os01t0102600-01.exon5;constitutive=0;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0102600-01.exon5;rank=5
|
||||
1 irgsp CDS 146450 146532 . + 0 ID=CDS:Os01t0102600-01;Parent=transcript:Os01t0102600-01;protein_id=Os01t0102600-01
|
||||
1 irgsp exon 146611 146719 . + . Parent=transcript:Os01t0102600-01;Name=Os01t0102600-01.exon6;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0102600-01.exon6;rank=6
|
||||
1 irgsp CDS 146611 146719 . + 1 ID=CDS:Os01t0102600-01;Parent=transcript:Os01t0102600-01;protein_id=Os01t0102600-01
|
||||
1 irgsp exon 147106 147184 . + . Parent=transcript:Os01t0102600-01;Name=Os01t0102600-01.exon7;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0102600-01.exon7;rank=7
|
||||
1 irgsp CDS 147106 147184 . + 0 ID=CDS:Os01t0102600-01;Parent=transcript:Os01t0102600-01;protein_id=Os01t0102600-01
|
||||
1 irgsp exon 147311 147375 . + . Parent=transcript:Os01t0102600-01;Name=Os01t0102600-02.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0102600-02.exon2;rank=8
|
||||
1 irgsp CDS 147311 147375 . + 2 ID=CDS:Os01t0102600-01;Parent=transcript:Os01t0102600-01;protein_id=Os01t0102600-01
|
||||
1 irgsp CDS 147507 147575 . + 0 ID=CDS:Os01t0102600-01;Parent=transcript:Os01t0102600-01;protein_id=Os01t0102600-01
|
||||
1 irgsp exon 147507 147847 . + . Parent=transcript:Os01t0102600-01;Name=Os01t0102600-01.exon9;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0102600-01.exon9;rank=9
|
||||
1 irgsp three_prime_UTR 147576 147847 . + . Parent=transcript:Os01t0102600-01
|
||||
1 irgsp mRNA 147104 147805 . + . ID=transcript:Os01t0102600-02;Parent=gene:Os01g0102600;biotype=protein_coding;transcript_id=Os01t0102600-02
|
||||
1 irgsp five_prime_UTR 147104 147105 . + . Parent=transcript:Os01t0102600-02
|
||||
1 irgsp exon 147104 147184 . + . Parent=transcript:Os01t0102600-02;Name=Os01t0102600-02.exon1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0102600-02.exon1;rank=1
|
||||
1 irgsp CDS 147106 147184 . + 0 ID=CDS:Os01t0102600-02;Parent=transcript:Os01t0102600-02;protein_id=Os01t0102600-02
|
||||
1 irgsp exon 147311 147375 . + . Parent=transcript:Os01t0102600-02;Name=Os01t0102600-02.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0102600-02.exon2;rank=2
|
||||
1 irgsp CDS 147311 147375 . + 2 ID=CDS:Os01t0102600-02;Parent=transcript:Os01t0102600-02;protein_id=Os01t0102600-02
|
||||
1 irgsp CDS 147507 147575 . + 0 ID=CDS:Os01t0102600-02;Parent=transcript:Os01t0102600-02;protein_id=Os01t0102600-02
|
||||
1 irgsp exon 147507 147805 . + . Parent=transcript:Os01t0102600-02;Name=Os01t0102600-02.exon3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0102600-02.exon3;rank=3
|
||||
1 irgsp three_prime_UTR 147576 147805 . + . Parent=transcript:Os01t0102600-02
|
||||
###
|
||||
1 irgsp gene 148085 150568 . + . ID=gene:Os01g0102700;biotype=protein_coding;description=Translocon-associated beta family protein. (Os01t0102700-01);gene_id=Os01g0102700;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 148085 150568 . + . ID=transcript:Os01t0102700-01;Parent=gene:Os01g0102700;biotype=protein_coding;transcript_id=Os01t0102700-01
|
||||
1 irgsp five_prime_UTR 148085 148146 . + . Parent=transcript:Os01t0102700-01
|
||||
1 irgsp exon 148085 148313 . + . Parent=transcript:Os01t0102700-01;Name=Os01t0102700-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0102700-01.exon1;rank=1
|
||||
1 irgsp CDS 148147 148313 . + 0 ID=CDS:Os01t0102700-01;Parent=transcript:Os01t0102700-01;protein_id=Os01t0102700-01
|
||||
1 irgsp exon 149450 149548 . + . Parent=transcript:Os01t0102700-01;Name=Os01t0102700-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0102700-01.exon2;rank=2
|
||||
1 irgsp CDS 149450 149548 . + 1 ID=CDS:Os01t0102700-01;Parent=transcript:Os01t0102700-01;protein_id=Os01t0102700-01
|
||||
1 irgsp exon 149634 149742 . + . Parent=transcript:Os01t0102700-01;Name=Os01t0102700-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0102700-01.exon3;rank=3
|
||||
1 irgsp CDS 149634 149742 . + 1 ID=CDS:Os01t0102700-01;Parent=transcript:Os01t0102700-01;protein_id=Os01t0102700-01
|
||||
1 irgsp exon 149856 149931 . + . Parent=transcript:Os01t0102700-01;Name=Os01t0102700-01.exon4;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0102700-01.exon4;rank=4
|
||||
1 irgsp CDS 149856 149931 . + 0 ID=CDS:Os01t0102700-01;Parent=transcript:Os01t0102700-01;protein_id=Os01t0102700-01
|
||||
1 irgsp CDS 150152 150318 . + 2 ID=CDS:Os01t0102700-01;Parent=transcript:Os01t0102700-01;protein_id=Os01t0102700-01
|
||||
1 irgsp exon 150152 150568 . + . Parent=transcript:Os01t0102700-01;Name=Os01t0102700-01.exon5;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0102700-01.exon5;rank=5
|
||||
1 irgsp three_prime_UTR 150319 150568 . + . Parent=transcript:Os01t0102700-01
|
||||
###
|
||||
1 irgsp gene 152853 156449 . + . ID=gene:Os01g0102800;Name=Cockayne syndrome WD-repeat protein;biotype=protein_coding;description=Similar to chromatin remodeling complex subunit. (Os01t0102800-01);gene_id=Os01g0102800;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 152853 156449 . + . ID=transcript:Os01t0102800-01;Parent=gene:Os01g0102800;biotype=protein_coding;transcript_id=Os01t0102800-01
|
||||
1 irgsp five_prime_UTR 152853 152853 . + . Parent=transcript:Os01t0102800-01
|
||||
1 irgsp exon 152853 153025 . + . Parent=transcript:Os01t0102800-01;Name=Os01t0102800-01.exon1;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0102800-01.exon1;rank=1
|
||||
1 irgsp CDS 152854 153025 . + 0 ID=CDS:Os01t0102800-01;Parent=transcript:Os01t0102800-01;protein_id=Os01t0102800-01
|
||||
1 irgsp exon 153178 154646 . + . Parent=transcript:Os01t0102800-01;Name=Os01t0102800-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0102800-01.exon2;rank=2
|
||||
1 irgsp CDS 153178 154646 . + 2 ID=CDS:Os01t0102800-01;Parent=transcript:Os01t0102800-01;protein_id=Os01t0102800-01
|
||||
1 irgsp exon 155010 155450 . + . Parent=transcript:Os01t0102800-01;Name=Os01t0102800-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0102800-01.exon3;rank=3
|
||||
1 irgsp CDS 155010 155450 . + 0 ID=CDS:Os01t0102800-01;Parent=transcript:Os01t0102800-01;protein_id=Os01t0102800-01
|
||||
1 irgsp CDS 155543 156214 . + 0 ID=CDS:Os01t0102800-01;Parent=transcript:Os01t0102800-01;protein_id=Os01t0102800-01
|
||||
1 irgsp exon 155543 156449 . + . Parent=transcript:Os01t0102800-01;Name=Os01t0102800-01.exon4;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0102800-01.exon4;rank=4
|
||||
1 irgsp three_prime_UTR 156215 156449 . + . Parent=transcript:Os01t0102800-01
|
||||
###
|
||||
1 irgsp gene 164577 168921 . + . ID=gene:Os01g0102850;biotype=protein_coding;description=Similar to nitrilase 2. (Os01t0102850-00);gene_id=Os01g0102850;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 164577 168921 . + . ID=transcript:Os01t0102850-00;Parent=gene:Os01g0102850;biotype=protein_coding;transcript_id=Os01t0102850-00
|
||||
1 irgsp exon 164577 164905 . + . Parent=transcript:Os01t0102850-00;Name=Os01t0102850-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0102850-00.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 164577 164905 . + . Parent=transcript:Os01t0102850-00
|
||||
1 irgsp five_prime_UTR 168499 168804 . + . Parent=transcript:Os01t0102850-00
|
||||
1 irgsp exon 168499 168921 . + . Parent=transcript:Os01t0102850-00;Name=Os01t0102850-00.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0102850-00.exon2;rank=2
|
||||
1 irgsp CDS 168805 168921 . + 0 ID=CDS:Os01t0102850-00;Parent=transcript:Os01t0102850-00;protein_id=Os01t0102850-00
|
||||
###
|
||||
1 irgsp gene 169390 170316 . - . ID=gene:Os01g0102900;Name=LIGHT-REGULATED GENE 1;biotype=protein_coding;description=Light-regulated protein%2C Regulation of light-dependent attachment of LEAF-TYPE FERREDOXIN-NADP+ OXIDOREDUCTASE (LFNR) to the thylakoid membrane (Os01t0102900-01);gene_id=Os01g0102900;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 169390 170316 . - . ID=transcript:Os01t0102900-01;Parent=gene:Os01g0102900;biotype=protein_coding;transcript_id=Os01t0102900-01
|
||||
1 irgsp three_prime_UTR 169390 169598 . - . Parent=transcript:Os01t0102900-01
|
||||
1 irgsp exon 169390 169656 . - . Parent=transcript:Os01t0102900-01;Name=Os01t0102900-01.exon3;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0102900-01.exon3;rank=3
|
||||
1 irgsp CDS 169599 169656 . - 1 ID=CDS:Os01t0102900-01;Parent=transcript:Os01t0102900-01;protein_id=Os01t0102900-01
|
||||
1 irgsp exon 169751 169909 . - . Parent=transcript:Os01t0102900-01;Name=Os01t0102900-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0102900-01.exon2;rank=2
|
||||
1 irgsp CDS 169751 169909 . - 1 ID=CDS:Os01t0102900-01;Parent=transcript:Os01t0102900-01;protein_id=Os01t0102900-01
|
||||
1 irgsp CDS 170091 170260 . - 0 ID=CDS:Os01t0102900-01;Parent=transcript:Os01t0102900-01;protein_id=Os01t0102900-01
|
||||
1 irgsp exon 170091 170316 . - . Parent=transcript:Os01t0102900-01;Name=Os01t0102900-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0102900-01.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 170261 170316 . - . Parent=transcript:Os01t0102900-01
|
||||
###
|
||||
1 irgsp gene 170798 173144 . - . ID=gene:Os01g0103000;biotype=protein_coding;description=Snf7 family protein. (Os01t0103000-01);gene_id=Os01g0103000;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 170798 173144 . - . ID=transcript:Os01t0103000-01;Parent=gene:Os01g0103000;biotype=protein_coding;transcript_id=Os01t0103000-01
|
||||
1 irgsp three_prime_UTR 170798 171044 . - . Parent=transcript:Os01t0103000-01
|
||||
1 irgsp exon 170798 171095 . - . Parent=transcript:Os01t0103000-01;Name=Os01t0103000-01.exon7;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0103000-01.exon7;rank=7
|
||||
1 irgsp CDS 171045 171095 . - 0 ID=CDS:Os01t0103000-01;Parent=transcript:Os01t0103000-01;protein_id=Os01t0103000-01
|
||||
1 irgsp exon 171406 171554 . - . Parent=transcript:Os01t0103000-01;Name=Os01t0103000-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0103000-01.exon6;rank=6
|
||||
1 irgsp CDS 171406 171554 . - 2 ID=CDS:Os01t0103000-01;Parent=transcript:Os01t0103000-01;protein_id=Os01t0103000-01
|
||||
1 irgsp exon 171764 171875 . - . Parent=transcript:Os01t0103000-01;Name=Os01t0103000-01.exon5;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0103000-01.exon5;rank=5
|
||||
1 irgsp CDS 171764 171875 . - 0 ID=CDS:Os01t0103000-01;Parent=transcript:Os01t0103000-01;protein_id=Os01t0103000-01
|
||||
1 irgsp exon 172398 172469 . - . Parent=transcript:Os01t0103000-01;Name=Os01t0103000-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0103000-01.exon4;rank=4
|
||||
1 irgsp CDS 172398 172469 . - 0 ID=CDS:Os01t0103000-01;Parent=transcript:Os01t0103000-01;protein_id=Os01t0103000-01
|
||||
1 irgsp exon 172578 172671 . - . Parent=transcript:Os01t0103000-01;Name=Os01t0103000-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0103000-01.exon3;rank=3
|
||||
1 irgsp CDS 172578 172671 . - 1 ID=CDS:Os01t0103000-01;Parent=transcript:Os01t0103000-01;protein_id=Os01t0103000-01
|
||||
1 irgsp exon 172770 172921 . - . Parent=transcript:Os01t0103000-01;Name=Os01t0103000-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0103000-01.exon2;rank=2
|
||||
1 irgsp CDS 172770 172921 . - 0 ID=CDS:Os01t0103000-01;Parent=transcript:Os01t0103000-01;protein_id=Os01t0103000-01
|
||||
1 irgsp CDS 173004 173072 . - 0 ID=CDS:Os01t0103000-01;Parent=transcript:Os01t0103000-01;protein_id=Os01t0103000-01
|
||||
1 irgsp exon 173004 173144 . - . Parent=transcript:Os01t0103000-01;Name=Os01t0103000-01.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0103000-01.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 173073 173144 . - . Parent=transcript:Os01t0103000-01
|
||||
###
|
||||
1 irgsp gene 178607 180575 . + . ID=gene:Os01g0103100;biotype=protein_coding;description=TGF-beta receptor%2C type I/II extracellular region family protein. (Os01t0103100-01)%3BSimilar to predicted protein. (Os01t0103100-02);gene_id=Os01g0103100;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 178607 180548 . + . ID=transcript:Os01t0103100-01;Parent=gene:Os01g0103100;biotype=protein_coding;transcript_id=Os01t0103100-01
|
||||
1 irgsp five_prime_UTR 178607 178641 . + . Parent=transcript:Os01t0103100-01
|
||||
1 irgsp exon 178607 180548 . + . Parent=transcript:Os01t0103100-01;Name=Os01t0103100-01.exon1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0103100-01.exon1;rank=1
|
||||
1 irgsp CDS 178642 180462 . + 0 ID=CDS:Os01t0103100-01;Parent=transcript:Os01t0103100-01;protein_id=Os01t0103100-01
|
||||
1 irgsp three_prime_UTR 180463 180548 . + . Parent=transcript:Os01t0103100-01
|
||||
1 irgsp mRNA 178652 180575 . + . ID=transcript:Os01t0103100-02;Parent=gene:Os01g0103100;biotype=protein_coding;transcript_id=Os01t0103100-02
|
||||
1 irgsp five_prime_UTR 178652 178677 . + . Parent=transcript:Os01t0103100-02
|
||||
1 irgsp exon 178652 180575 . + . Parent=transcript:Os01t0103100-02;Name=Os01t0103100-02.exon1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0103100-02.exon1;rank=1
|
||||
1 irgsp CDS 178678 180462 . + 0 ID=CDS:Os01t0103100-02;Parent=transcript:Os01t0103100-02;protein_id=Os01t0103100-02
|
||||
1 irgsp three_prime_UTR 180463 180575 . + . Parent=transcript:Os01t0103100-02
|
||||
###
|
||||
1 irgsp gene 178815 180433 . - . ID=gene:Os01g0103075;biotype=protein_coding;description=Hypothetical protein. (Os01t0103075-00);gene_id=Os01g0103075;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 178815 180433 . - . ID=transcript:Os01t0103075-00;Parent=gene:Os01g0103075;biotype=protein_coding;transcript_id=Os01t0103075-00
|
||||
1 irgsp three_prime_UTR 178815 179511 . - . Parent=transcript:Os01t0103075-00
|
||||
1 irgsp exon 178815 180433 . - . Parent=transcript:Os01t0103075-00;Name=Os01t0103075-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0103075-00.exon1;rank=1
|
||||
1 irgsp CDS 179512 180054 . - 0 ID=CDS:Os01t0103075-00;Parent=transcript:Os01t0103075-00;protein_id=Os01t0103075-00
|
||||
1 irgsp five_prime_UTR 180055 180433 . - . Parent=transcript:Os01t0103075-00
|
||||
###
|
||||
1 Ensembl_Plants ncRNA_gene 182074 182154 . + . ID=gene:ENSRNA049442722;Name=tRNA-Leu;biotype=tRNA;description=tRNA-Leu for anticodon AAG;gene_id=ENSRNA049442722;logic_name=trnascan_gene
|
||||
1 Ensembl_Plants tRNA 182074 182154 . + . ID=transcript:ENSRNA049442722-T1;Parent=gene:ENSRNA049442722;biotype=tRNA;transcript_id=ENSRNA049442722-T1
|
||||
1 Ensembl_Plants exon 182074 182154 . + . Parent=transcript:ENSRNA049442722-T1;Name=ENSRNA049442722-E1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSRNA049442722-E1;rank=1
|
||||
###
|
||||
1 irgsp gene 185189 185828 . - . ID=gene:Os01g0103400;biotype=protein_coding;description=Hypothetical gene. (Os01t0103400-01);gene_id=Os01g0103400;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 185189 185828 . - . ID=transcript:Os01t0103400-01;Parent=gene:Os01g0103400;biotype=protein_coding;transcript_id=Os01t0103400-01
|
||||
1 irgsp three_prime_UTR 185189 185434 . - . Parent=transcript:Os01t0103400-01
|
||||
1 irgsp exon 185189 185828 . - . Parent=transcript:Os01t0103400-01;Name=Os01t0103400-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0103400-01.exon1;rank=1
|
||||
1 irgsp CDS 185435 185827 . - 0 ID=CDS:Os01t0103400-01;Parent=transcript:Os01t0103400-01;protein_id=Os01t0103400-01
|
||||
1 irgsp five_prime_UTR 185828 185828 . - . Parent=transcript:Os01t0103400-01
|
||||
###
|
||||
1 irgsp repeat_region 186000 186100 . + . ID=fakeRepeat2
|
||||
###
|
||||
1 irgsp gene 186250 190904 . - . ID=gene:Os01g0103600;biotype=protein_coding;description=Similar to sterol-8%2C7-isomerase. (Os01t0103600-01)%3BEmopamil-binding family protein. (Os01t0103600-02);gene_id=Os01g0103600;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 186250 190262 . - . ID=transcript:Os01t0103600-02;Parent=gene:Os01g0103600;biotype=protein_coding;transcript_id=Os01t0103600-02
|
||||
1 irgsp three_prime_UTR 186250 186515 . - . Parent=transcript:Os01t0103600-02
|
||||
1 irgsp exon 186250 186771 . - . Parent=transcript:Os01t0103600-02;Name=Os01t0103600-02.exon4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0103600-02.exon4;rank=4
|
||||
1 irgsp CDS 186516 186771 . - 1 ID=CDS:Os01t0103600-02;Parent=transcript:Os01t0103600-02;protein_id=Os01t0103600-02
|
||||
1 irgsp exon 189607 189715 . - . Parent=transcript:Os01t0103600-02;Name=Os01t0103600-02.exon3;constitutive=0;ensembl_end_phase=2;ensembl_phase=1;exon_id=Os01t0103600-02.exon3;rank=3
|
||||
1 irgsp CDS 189607 189715 . - 2 ID=CDS:Os01t0103600-02;Parent=transcript:Os01t0103600-02;protein_id=Os01t0103600-02
|
||||
1 irgsp exon 189841 189990 . - . Parent=transcript:Os01t0103600-02;Name=Os01t0103600-02.exon2;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0103600-02.exon2;rank=2
|
||||
1 irgsp CDS 189841 189990 . - 2 ID=CDS:Os01t0103600-02;Parent=transcript:Os01t0103600-02;protein_id=Os01t0103600-02
|
||||
1 irgsp CDS 190087 190231 . - 0 ID=CDS:Os01t0103600-02;Parent=transcript:Os01t0103600-02;protein_id=Os01t0103600-02
|
||||
1 irgsp exon 190087 190262 . - . Parent=transcript:Os01t0103600-02;Name=Os01t0103600-02.exon1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0103600-02.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 190232 190262 . - . Parent=transcript:Os01t0103600-02
|
||||
1 irgsp mRNA 187345 190904 . - . ID=transcript:Os01t0103600-01;Parent=gene:Os01g0103600;biotype=protein_coding;transcript_id=Os01t0103600-01
|
||||
1 irgsp three_prime_UTR 187345 189395 . - . Parent=transcript:Os01t0103600-01
|
||||
1 irgsp exon 187345 189715 . - . Parent=transcript:Os01t0103600-01;Name=Os01t0103600-01.exon3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0103600-01.exon3;rank=3
|
||||
1 irgsp CDS 189396 189715 . - 2 ID=CDS:Os01t0103600-01;Parent=transcript:Os01t0103600-01;protein_id=Os01t0103600-01
|
||||
1 irgsp exon 189841 189990 . - . Parent=transcript:Os01t0103600-01;Name=Os01t0103600-02.exon2;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0103600-02.exon2;rank=2
|
||||
1 irgsp CDS 189841 189990 . - 2 ID=CDS:Os01t0103600-01;Parent=transcript:Os01t0103600-01;protein_id=Os01t0103600-01
|
||||
1 irgsp CDS 190087 190231 . - 0 ID=CDS:Os01t0103600-01;Parent=transcript:Os01t0103600-01;protein_id=Os01t0103600-01
|
||||
1 irgsp exon 190087 190904 . - . Parent=transcript:Os01t0103600-01;Name=Os01t0103600-01.exon1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0103600-01.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 190232 190904 . - . Parent=transcript:Os01t0103600-01
|
||||
###
|
||||
1 irgsp gene 187545 188586 . + . ID=gene:Os01g0103650;biotype=protein_coding;description=Hypothetical gene. (Os01t0103650-00);gene_id=Os01g0103650;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 187545 188586 . + . ID=transcript:Os01t0103650-00;Parent=gene:Os01g0103650;biotype=protein_coding;transcript_id=Os01t0103650-00
|
||||
1 irgsp five_prime_UTR 187545 187546 . + . Parent=transcript:Os01t0103650-00
|
||||
1 irgsp exon 187545 188020 . + . Parent=transcript:Os01t0103650-00;Name=Os01t0103650-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0103650-00.exon1;rank=1
|
||||
1 irgsp CDS 187547 187768 . + 0 ID=CDS:Os01t0103650-00;Parent=transcript:Os01t0103650-00;protein_id=Os01t0103650-00
|
||||
1 irgsp three_prime_UTR 187769 188020 . + . Parent=transcript:Os01t0103650-00
|
||||
1 irgsp exon 188060 188385 . + . Parent=transcript:Os01t0103650-00;Name=Os01t0103650-00.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0103650-00.exon2;rank=2
|
||||
1 irgsp three_prime_UTR 188060 188385 . + . Parent=transcript:Os01t0103650-00
|
||||
1 irgsp exon 188455 188586 . + . Parent=transcript:Os01t0103650-00;Name=Os01t0103650-00.exon3;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0103650-00.exon3;rank=3
|
||||
1 irgsp three_prime_UTR 188455 188586 . + . Parent=transcript:Os01t0103650-00
|
||||
###
|
||||
1 irgsp gene 191037 196287 . + . ID=gene:Os01g0103700;biotype=protein_coding;description=Conserved hypothetical protein. (Os01t0103700-01);gene_id=Os01g0103700;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 191037 196287 . + . ID=transcript:Os01t0103700-01;Parent=gene:Os01g0103700;biotype=protein_coding;transcript_id=Os01t0103700-01
|
||||
1 irgsp exon 191037 191161 . + . Parent=transcript:Os01t0103700-01;Name=Os01t0103700-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0103700-01.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 191037 191161 . + . Parent=transcript:Os01t0103700-01
|
||||
1 irgsp five_prime_UTR 191625 191693 . + . Parent=transcript:Os01t0103700-01
|
||||
1 irgsp exon 191625 191705 . + . Parent=transcript:Os01t0103700-01;Name=Os01t0103700-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0103700-01.exon2;rank=2
|
||||
1 irgsp CDS 191694 191705 . + 0 ID=CDS:Os01t0103700-01;Parent=transcript:Os01t0103700-01;protein_id=Os01t0103700-01
|
||||
1 irgsp exon 192399 192506 . + . Parent=transcript:Os01t0103700-01;Name=Os01t0103700-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0103700-01.exon3;rank=3
|
||||
1 irgsp CDS 192399 192506 . + 0 ID=CDS:Os01t0103700-01;Parent=transcript:Os01t0103700-01;protein_id=Os01t0103700-01
|
||||
1 irgsp exon 192958 193161 . + . Parent=transcript:Os01t0103700-01;Name=Os01t0103700-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0103700-01.exon4;rank=4
|
||||
1 irgsp CDS 192958 193161 . + 0 ID=CDS:Os01t0103700-01;Parent=transcript:Os01t0103700-01;protein_id=Os01t0103700-01
|
||||
1 irgsp exon 193248 193356 . + . Parent=transcript:Os01t0103700-01;Name=Os01t0103700-01.exon5;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0103700-01.exon5;rank=5
|
||||
1 irgsp CDS 193248 193356 . + 0 ID=CDS:Os01t0103700-01;Parent=transcript:Os01t0103700-01;protein_id=Os01t0103700-01
|
||||
1 irgsp CDS 193434 193507 . + 2 ID=CDS:Os01t0103700-01;Parent=transcript:Os01t0103700-01;protein_id=Os01t0103700-01
|
||||
1 irgsp exon 193434 196287 . + . Parent=transcript:Os01t0103700-01;Name=Os01t0103700-01.exon6;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0103700-01.exon6;rank=6
|
||||
1 irgsp three_prime_UTR 193508 196287 . + . Parent=transcript:Os01t0103700-01
|
||||
###
|
||||
1 irgsp gene 197647 200803 . + . ID=gene:Os01g0103800;Name=OsDW1-01g;biotype=protein_coding;description=Conserved hypothetical protein. (Os01t0103800-01);gene_id=Os01g0103800;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 197647 200803 . + . ID=transcript:Os01t0103800-01;Parent=gene:Os01g0103800;biotype=protein_coding;transcript_id=Os01t0103800-01
|
||||
1 irgsp exon 197647 197838 . + . Parent=transcript:Os01t0103800-01;Name=Os01t0103800-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0103800-01.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 197647 197838 . + . Parent=transcript:Os01t0103800-01
|
||||
1 irgsp five_prime_UTR 198034 198129 . + . Parent=transcript:Os01t0103800-01
|
||||
1 irgsp exon 198034 198225 . + . Parent=transcript:Os01t0103800-01;Name=Os01t0103800-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0103800-01.exon2;rank=2
|
||||
1 irgsp CDS 198130 198225 . + 0 ID=CDS:Os01t0103800-01;Parent=transcript:Os01t0103800-01;protein_id=Os01t0103800-01
|
||||
1 irgsp exon 198830 200036 . + . Parent=transcript:Os01t0103800-01;Name=Os01t0103800-01.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0103800-01.exon3;rank=3
|
||||
1 irgsp CDS 198830 200036 . + 0 ID=CDS:Os01t0103800-01;Parent=transcript:Os01t0103800-01;protein_id=Os01t0103800-01
|
||||
1 irgsp CDS 200253 200479 . + 2 ID=CDS:Os01t0103800-01;Parent=transcript:Os01t0103800-01;protein_id=Os01t0103800-01
|
||||
1 irgsp exon 200253 200803 . + . Parent=transcript:Os01t0103800-01;Name=Os01t0103800-01.exon4;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0103800-01.exon4;rank=4
|
||||
1 irgsp three_prime_UTR 200480 200803 . + . Parent=transcript:Os01t0103800-01
|
||||
###
|
||||
1 irgsp gene 201944 206202 . + . ID=gene:Os01g0103900;biotype=protein_coding;description=Polynucleotidyl transferase%2C Ribonuclease H fold domain containing protein. (Os01t0103900-01);gene_id=Os01g0103900;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 201944 206202 . + . ID=transcript:Os01t0103900-01;Parent=gene:Os01g0103900;biotype=protein_coding;transcript_id=Os01t0103900-01
|
||||
1 irgsp five_prime_UTR 201944 202041 . + . Parent=transcript:Os01t0103900-01
|
||||
1 irgsp exon 201944 202110 . + . Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0103900-01.exon1;rank=1
|
||||
1 irgsp CDS 202042 202110 . + 0 ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
|
||||
1 irgsp exon 202252 202359 . + . Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0103900-01.exon2;rank=2
|
||||
1 irgsp CDS 202252 202359 . + 0 ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
|
||||
1 irgsp exon 203007 203127 . + . Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0103900-01.exon3;rank=3
|
||||
1 irgsp CDS 203007 203127 . + 0 ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
|
||||
1 irgsp exon 203302 203429 . + . Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0103900-01.exon4;rank=4
|
||||
1 irgsp CDS 203302 203429 . + 2 ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
|
||||
1 irgsp exon 203511 203658 . + . Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon5;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0103900-01.exon5;rank=5
|
||||
1 irgsp CDS 203511 203658 . + 0 ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
|
||||
1 irgsp exon 203760 203938 . + . Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0103900-01.exon6;rank=6
|
||||
1 irgsp CDS 203760 203938 . + 2 ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
|
||||
1 irgsp exon 204203 204440 . + . Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon7;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0103900-01.exon7;rank=7
|
||||
1 irgsp CDS 204203 204440 . + 0 ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
|
||||
1 irgsp exon 204543 204635 . + . Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon8;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0103900-01.exon8;rank=8
|
||||
1 irgsp CDS 204543 204635 . + 2 ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
|
||||
1 irgsp exon 204730 204875 . + . Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon9;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0103900-01.exon9;rank=9
|
||||
1 irgsp CDS 204730 204875 . + 2 ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
|
||||
1 irgsp exon 205042 205149 . + . Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon10;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0103900-01.exon10;rank=10
|
||||
1 irgsp CDS 205042 205149 . + 0 ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
|
||||
1 irgsp exon 205290 205378 . + . Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon11;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0103900-01.exon11;rank=11
|
||||
1 irgsp CDS 205290 205378 . + 0 ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
|
||||
1 irgsp CDS 205534 205543 . + 1 ID=CDS:Os01t0103900-01;Parent=transcript:Os01t0103900-01;protein_id=Os01t0103900-01
|
||||
1 irgsp exon 205534 206202 . + . Parent=transcript:Os01t0103900-01;Name=Os01t0103900-01.exon12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0103900-01.exon12;rank=12
|
||||
1 irgsp three_prime_UTR 205544 206202 . + . Parent=transcript:Os01t0103900-01
|
||||
###
|
||||
1 irgsp gene 206131 209606 . - . ID=gene:Os01g0104000;biotype=protein_coding;description=C-type lectin domain containing protein. (Os01t0104000-01)%3BSimilar to predicted protein. (Os01t0104000-02);gene_id=Os01g0104000;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 206131 209581 . - . ID=transcript:Os01t0104000-02;Parent=gene:Os01g0104000;biotype=protein_coding;transcript_id=Os01t0104000-02
|
||||
1 irgsp three_prime_UTR 206131 206449 . - . Parent=transcript:Os01t0104000-02
|
||||
1 irgsp exon 206131 207029 . - . Parent=transcript:Os01t0104000-02;Name=Os01t0104000-02.exon4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0104000-02.exon4;rank=4
|
||||
1 irgsp CDS 206450 207029 . - 1 ID=CDS:Os01t0104000-02;Parent=transcript:Os01t0104000-02;protein_id=Os01t0104000-02
|
||||
1 irgsp exon 207706 208273 . - . Parent=transcript:Os01t0104000-02;Name=Os01t0104000-02.exon3;constitutive=0;ensembl_end_phase=2;ensembl_phase=1;exon_id=Os01t0104000-02.exon3;rank=3
|
||||
1 irgsp CDS 207706 208273 . - 2 ID=CDS:Os01t0104000-02;Parent=transcript:Os01t0104000-02;protein_id=Os01t0104000-02
|
||||
1 irgsp exon 208408 208836 . - . Parent=transcript:Os01t0104000-02;Name=Os01t0104000-01.exon2;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0104000-01.exon2;rank=2
|
||||
1 irgsp CDS 208408 208836 . - 2 ID=CDS:Os01t0104000-02;Parent=transcript:Os01t0104000-02;protein_id=Os01t0104000-02
|
||||
1 irgsp CDS 209438 209525 . - 0 ID=CDS:Os01t0104000-02;Parent=transcript:Os01t0104000-02;protein_id=Os01t0104000-02
|
||||
1 irgsp exon 209438 209581 . - . Parent=transcript:Os01t0104000-02;Name=Os01t0104000-02.exon1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0104000-02.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 209526 209581 . - . Parent=transcript:Os01t0104000-02
|
||||
1 irgsp mRNA 206134 209606 . - . ID=transcript:Os01t0104000-01;Parent=gene:Os01g0104000;biotype=protein_coding;transcript_id=Os01t0104000-01
|
||||
1 irgsp three_prime_UTR 206134 206449 . - . Parent=transcript:Os01t0104000-01
|
||||
1 irgsp exon 206134 207029 . - . Parent=transcript:Os01t0104000-01;Name=Os01t0104000-01.exon4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0104000-01.exon4;rank=4
|
||||
1 irgsp CDS 206450 207029 . - 1 ID=CDS:Os01t0104000-01;Parent=transcript:Os01t0104000-01;protein_id=Os01t0104000-01
|
||||
1 irgsp exon 207706 208276 . - . Parent=transcript:Os01t0104000-01;Name=Os01t0104000-01.exon3;constitutive=0;ensembl_end_phase=2;ensembl_phase=1;exon_id=Os01t0104000-01.exon3;rank=3
|
||||
1 irgsp CDS 207706 208276 . - 2 ID=CDS:Os01t0104000-01;Parent=transcript:Os01t0104000-01;protein_id=Os01t0104000-01
|
||||
1 irgsp exon 208408 208836 . - . Parent=transcript:Os01t0104000-01;Name=Os01t0104000-01.exon2;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0104000-01.exon2;rank=2
|
||||
1 irgsp CDS 208408 208836 . - 2 ID=CDS:Os01t0104000-01;Parent=transcript:Os01t0104000-01;protein_id=Os01t0104000-01
|
||||
1 irgsp CDS 209438 209525 . - 0 ID=CDS:Os01t0104000-01;Parent=transcript:Os01t0104000-01;protein_id=Os01t0104000-01
|
||||
1 irgsp exon 209438 209606 . - . Parent=transcript:Os01t0104000-01;Name=Os01t0104000-01.exon1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0104000-01.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 209526 209606 . - . Parent=transcript:Os01t0104000-01
|
||||
###
|
||||
1 irgsp gene 209771 214173 . + . ID=gene:Os01g0104100;Name=cold-inducible%2C cold-inducible zinc finger protein;biotype=protein_coding;description=Similar to protein binding / zinc ion binding. (Os01t0104100-01)%3BSimilar to protein binding / zinc ion binding. (Os01t0104100-02);gene_id=Os01g0104100;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 209771 214173 . + . ID=transcript:Os01t0104100-01;Parent=gene:Os01g0104100;biotype=protein_coding;transcript_id=Os01t0104100-01
|
||||
1 irgsp exon 209771 209896 . + . Parent=transcript:Os01t0104100-01;Name=Os01t0104100-01.exon1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104100-01.exon1;rank=1
|
||||
1 irgsp CDS 209771 209896 . + 0 ID=CDS:Os01t0104100-01;Parent=transcript:Os01t0104100-01;protein_id=Os01t0104100-01
|
||||
1 irgsp exon 210244 210563 . + . Parent=transcript:Os01t0104100-01;Name=Os01t0104100-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0104100-01.exon2;rank=2
|
||||
1 irgsp CDS 210244 210563 . + 0 ID=CDS:Os01t0104100-01;Parent=transcript:Os01t0104100-01;protein_id=Os01t0104100-01
|
||||
1 irgsp exon 210659 210890 . + . Parent=transcript:Os01t0104100-01;Name=Os01t0104100-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104100-01.exon3;rank=3
|
||||
1 irgsp CDS 210659 210890 . + 1 ID=CDS:Os01t0104100-01;Parent=transcript:Os01t0104100-01;protein_id=Os01t0104100-01
|
||||
1 irgsp exon 211015 211160 . + . Parent=transcript:Os01t0104100-01;Name=Os01t0104100-01.exon4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0104100-01.exon4;rank=4
|
||||
1 irgsp CDS 211015 211160 . + 0 ID=CDS:Os01t0104100-01;Parent=transcript:Os01t0104100-01;protein_id=Os01t0104100-01
|
||||
1 irgsp exon 212265 212352 . + . Parent=transcript:Os01t0104100-01;Name=Os01t0104100-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104100-01.exon5;rank=5
|
||||
1 irgsp CDS 212265 212352 . + 1 ID=CDS:Os01t0104100-01;Parent=transcript:Os01t0104100-01;protein_id=Os01t0104100-01
|
||||
1 irgsp exon 212433 212579 . + . Parent=transcript:Os01t0104100-01;Name=Os01t0104100-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104100-01.exon6;rank=6
|
||||
1 irgsp CDS 212433 212579 . + 0 ID=CDS:Os01t0104100-01;Parent=transcript:Os01t0104100-01;protein_id=Os01t0104100-01
|
||||
1 irgsp exon 213490 213639 . + . Parent=transcript:Os01t0104100-01;Name=Os01t0104100-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104100-01.exon7;rank=7
|
||||
1 irgsp CDS 213490 213639 . + 0 ID=CDS:Os01t0104100-01;Parent=transcript:Os01t0104100-01;protein_id=Os01t0104100-01
|
||||
1 irgsp CDS 213741 213788 . + 0 ID=CDS:Os01t0104100-01;Parent=transcript:Os01t0104100-01;protein_id=Os01t0104100-01
|
||||
1 irgsp exon 213741 214173 . + . Parent=transcript:Os01t0104100-01;Name=Os01t0104100-01.exon8;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0104100-01.exon8;rank=8
|
||||
1 irgsp three_prime_UTR 213789 214173 . + . Parent=transcript:Os01t0104100-01
|
||||
1 irgsp mRNA 209794 214147 . + . ID=transcript:Os01t0104100-02;Parent=gene:Os01g0104100;biotype=protein_coding;transcript_id=Os01t0104100-02
|
||||
1 irgsp five_prime_UTR 209794 209794 . + . Parent=transcript:Os01t0104100-02
|
||||
1 irgsp exon 209794 209896 . + . Parent=transcript:Os01t0104100-02;Name=Os01t0104100-02.exon1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0104100-02.exon1;rank=1
|
||||
1 irgsp CDS 209795 209896 . + 0 ID=CDS:Os01t0104100-02;Parent=transcript:Os01t0104100-02;protein_id=Os01t0104100-02
|
||||
1 irgsp exon 210244 210563 . + . Parent=transcript:Os01t0104100-02;Name=Os01t0104100-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0104100-01.exon2;rank=2
|
||||
1 irgsp CDS 210244 210563 . + 0 ID=CDS:Os01t0104100-02;Parent=transcript:Os01t0104100-02;protein_id=Os01t0104100-02
|
||||
1 irgsp exon 210659 210890 . + . Parent=transcript:Os01t0104100-02;Name=Os01t0104100-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104100-01.exon3;rank=3
|
||||
1 irgsp CDS 210659 210890 . + 1 ID=CDS:Os01t0104100-02;Parent=transcript:Os01t0104100-02;protein_id=Os01t0104100-02
|
||||
1 irgsp exon 211015 211160 . + . Parent=transcript:Os01t0104100-02;Name=Os01t0104100-01.exon4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0104100-01.exon4;rank=4
|
||||
1 irgsp CDS 211015 211160 . + 0 ID=CDS:Os01t0104100-02;Parent=transcript:Os01t0104100-02;protein_id=Os01t0104100-02
|
||||
1 irgsp exon 212265 212352 . + . Parent=transcript:Os01t0104100-02;Name=Os01t0104100-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104100-01.exon5;rank=5
|
||||
1 irgsp CDS 212265 212352 . + 1 ID=CDS:Os01t0104100-02;Parent=transcript:Os01t0104100-02;protein_id=Os01t0104100-02
|
||||
1 irgsp exon 212433 212579 . + . Parent=transcript:Os01t0104100-02;Name=Os01t0104100-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104100-01.exon6;rank=6
|
||||
1 irgsp CDS 212433 212579 . + 0 ID=CDS:Os01t0104100-02;Parent=transcript:Os01t0104100-02;protein_id=Os01t0104100-02
|
||||
1 irgsp exon 213490 213639 . + . Parent=transcript:Os01t0104100-02;Name=Os01t0104100-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104100-01.exon7;rank=7
|
||||
1 irgsp CDS 213490 213639 . + 0 ID=CDS:Os01t0104100-02;Parent=transcript:Os01t0104100-02;protein_id=Os01t0104100-02
|
||||
1 irgsp CDS 213741 213788 . + 0 ID=CDS:Os01t0104100-02;Parent=transcript:Os01t0104100-02;protein_id=Os01t0104100-02
|
||||
1 irgsp exon 213741 214147 . + . Parent=transcript:Os01t0104100-02;Name=Os01t0104100-02.exon8;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0104100-02.exon8;rank=8
|
||||
1 irgsp three_prime_UTR 213789 214147 . + . Parent=transcript:Os01t0104100-02
|
||||
###
|
||||
1 irgsp gene 216212 217345 . + . ID=gene:Os01g0104200;Name=NAC DOMAIN-CONTAINING PROTEIN 16;biotype=protein_coding;description=No apical meristem (NAM) protein domain containing protein. (Os01t0104200-00);gene_id=Os01g0104200;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 216212 217345 . + . ID=transcript:Os01t0104200-00;Parent=gene:Os01g0104200;biotype=protein_coding;transcript_id=Os01t0104200-00
|
||||
1 irgsp exon 216212 216769 . + . Parent=transcript:Os01t0104200-00;Name=Os01t0104200-00.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104200-00.exon1;rank=1
|
||||
1 irgsp CDS 216212 216769 . + 0 ID=CDS:Os01t0104200-00;Parent=transcript:Os01t0104200-00;protein_id=Os01t0104200-00
|
||||
1 irgsp exon 216884 217345 . + . Parent=transcript:Os01t0104200-00;Name=Os01t0104200-00.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104200-00.exon2;rank=2
|
||||
1 irgsp CDS 216884 217345 . + 0 ID=CDS:Os01t0104200-00;Parent=transcript:Os01t0104200-00;protein_id=Os01t0104200-00
|
||||
###
|
||||
1 irgsp gene 226897 229301 . + . ID=gene:Os01g0104400;biotype=protein_coding;description=Ricin B-related lectin domain containing protein. (Os01t0104400-01)%3BRicin B-related lectin domain containing protein. (Os01t0104400-02)%3BRicin B-related lectin domain containing protein. (Os01t0104400-03);gene_id=Os01g0104400;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 226897 229229 . + . ID=transcript:Os01t0104400-01;Parent=gene:Os01g0104400;biotype=protein_coding;transcript_id=Os01t0104400-01
|
||||
1 irgsp five_prime_UTR 226897 227181 . + . Parent=transcript:Os01t0104400-01
|
||||
1 irgsp exon 226897 227634 . + . Parent=transcript:Os01t0104400-01;Name=Os01t0104400-01.exon1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0104400-01.exon1;rank=1
|
||||
1 irgsp CDS 227182 227634 . + 0 ID=CDS:Os01t0104400-01;Parent=transcript:Os01t0104400-01;protein_id=Os01t0104400-01
|
||||
1 irgsp exon 227742 227864 . + . Parent=transcript:Os01t0104400-01;Name=Os01t0104400-03.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104400-03.exon2;rank=2
|
||||
1 irgsp CDS 227742 227864 . + 0 ID=CDS:Os01t0104400-01;Parent=transcript:Os01t0104400-01;protein_id=Os01t0104400-01
|
||||
1 irgsp exon 228557 228785 . + . Parent=transcript:Os01t0104400-01;Name=Os01t0104400-03.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0104400-03.exon3;rank=3
|
||||
1 irgsp CDS 228557 228785 . + 0 ID=CDS:Os01t0104400-01;Parent=transcript:Os01t0104400-01;protein_id=Os01t0104400-01
|
||||
1 irgsp CDS 228930 228931 . + 2 ID=CDS:Os01t0104400-01;Parent=transcript:Os01t0104400-01;protein_id=Os01t0104400-01
|
||||
1 irgsp exon 228930 229229 . + . Parent=transcript:Os01t0104400-01;Name=Os01t0104400-01.exon4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0104400-01.exon4;rank=4
|
||||
1 irgsp three_prime_UTR 228932 229229 . + . Parent=transcript:Os01t0104400-01
|
||||
1 irgsp mRNA 227139 229301 . + . ID=transcript:Os01t0104400-02;Parent=gene:Os01g0104400;biotype=protein_coding;transcript_id=Os01t0104400-02
|
||||
1 irgsp five_prime_UTR 227139 227181 . + . Parent=transcript:Os01t0104400-02
|
||||
1 irgsp exon 227139 227634 . + . Parent=transcript:Os01t0104400-02;Name=Os01t0104400-02.exon1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0104400-02.exon1;rank=1
|
||||
1 irgsp CDS 227182 227634 . + 0 ID=CDS:Os01t0104400-02;Parent=transcript:Os01t0104400-02;protein_id=Os01t0104400-02
|
||||
1 irgsp exon 227742 227864 . + . Parent=transcript:Os01t0104400-02;Name=Os01t0104400-03.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104400-03.exon2;rank=2
|
||||
1 irgsp CDS 227742 227864 . + 0 ID=CDS:Os01t0104400-02;Parent=transcript:Os01t0104400-02;protein_id=Os01t0104400-02
|
||||
1 irgsp exon 228557 228785 . + . Parent=transcript:Os01t0104400-02;Name=Os01t0104400-03.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0104400-03.exon3;rank=3
|
||||
1 irgsp CDS 228557 228785 . + 0 ID=CDS:Os01t0104400-02;Parent=transcript:Os01t0104400-02;protein_id=Os01t0104400-02
|
||||
1 irgsp CDS 228930 228931 . + 2 ID=CDS:Os01t0104400-02;Parent=transcript:Os01t0104400-02;protein_id=Os01t0104400-02
|
||||
1 irgsp exon 228930 229301 . + . Parent=transcript:Os01t0104400-02;Name=Os01t0104400-02.exon4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0104400-02.exon4;rank=4
|
||||
1 irgsp three_prime_UTR 228932 229301 . + . Parent=transcript:Os01t0104400-02
|
||||
1 irgsp mRNA 227179 229214 . + . ID=transcript:Os01t0104400-03;Parent=gene:Os01g0104400;biotype=protein_coding;transcript_id=Os01t0104400-03
|
||||
1 irgsp five_prime_UTR 227179 227181 . + . Parent=transcript:Os01t0104400-03
|
||||
1 irgsp exon 227179 227634 . + . Parent=transcript:Os01t0104400-03;Name=Os01t0104400-03.exon1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0104400-03.exon1;rank=1
|
||||
1 irgsp CDS 227182 227634 . + 0 ID=CDS:Os01t0104400-03;Parent=transcript:Os01t0104400-03;protein_id=Os01t0104400-03
|
||||
1 irgsp exon 227742 227864 . + . Parent=transcript:Os01t0104400-03;Name=Os01t0104400-03.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104400-03.exon2;rank=2
|
||||
1 irgsp CDS 227742 227864 . + 0 ID=CDS:Os01t0104400-03;Parent=transcript:Os01t0104400-03;protein_id=Os01t0104400-03
|
||||
1 irgsp exon 228557 228785 . + . Parent=transcript:Os01t0104400-03;Name=Os01t0104400-03.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0104400-03.exon3;rank=3
|
||||
1 irgsp CDS 228557 228785 . + 0 ID=CDS:Os01t0104400-03;Parent=transcript:Os01t0104400-03;protein_id=Os01t0104400-03
|
||||
1 irgsp CDS 228930 228931 . + 2 ID=CDS:Os01t0104400-03;Parent=transcript:Os01t0104400-03;protein_id=Os01t0104400-03
|
||||
1 irgsp exon 228930 229214 . + . Parent=transcript:Os01t0104400-03;Name=Os01t0104400-03.exon4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0104400-03.exon4;rank=4
|
||||
1 irgsp three_prime_UTR 228932 229214 . + . Parent=transcript:Os01t0104400-03
|
||||
###
|
||||
1 irgsp gene 241680 243440 . + . ID=gene:Os01g0104500;Name=NAC DOMAIN-CONTAINING PROTEIN 20;biotype=protein_coding;description=No apical meristem (NAM) protein domain containing protein. (Os01t0104500-01);gene_id=Os01g0104500;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 241680 243440 . + . ID=transcript:Os01t0104500-01;Parent=gene:Os01g0104500;biotype=protein_coding;transcript_id=Os01t0104500-01
|
||||
1 irgsp exon 241680 241702 . + . Parent=transcript:Os01t0104500-01;Name=Os01t0104500-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0104500-01.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 241680 241702 . + . Parent=transcript:Os01t0104500-01
|
||||
1 irgsp five_prime_UTR 241866 241907 . + . Parent=transcript:Os01t0104500-01
|
||||
1 irgsp exon 241866 242091 . + . Parent=transcript:Os01t0104500-01;Name=Os01t0104500-01.exon2;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0104500-01.exon2;rank=2
|
||||
1 irgsp CDS 241908 242091 . + 0 ID=CDS:Os01t0104500-01;Parent=transcript:Os01t0104500-01;protein_id=Os01t0104500-01
|
||||
1 irgsp CDS 242199 242977 . + 2 ID=CDS:Os01t0104500-01;Parent=transcript:Os01t0104500-01;protein_id=Os01t0104500-01
|
||||
1 irgsp exon 242199 243440 . + . Parent=transcript:Os01t0104500-01;Name=Os01t0104500-01.exon3;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0104500-01.exon3;rank=3
|
||||
1 irgsp three_prime_UTR 242978 243440 . + . Parent=transcript:Os01t0104500-01
|
||||
###
|
||||
1 irgsp gene 248828 256872 . - . ID=gene:Os01g0104600;Name=DE-ETIOLATED1;biotype=protein_coding;description=Homolog of Arabidopsis DE-ETIOLATED1 (DET1)%2C Modulation of the ABA signaling pathway and ABA biosynthesis%2C Regulation of chlorophyll content (Os01t0104600-01)%3BSimilar to Light-mediated development protein DET1 (Deetiolated1 homolog) (tDET1) (High pigmentation protein 2) (Protein dark green). (Os01t0104600-02);gene_id=Os01g0104600;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 248828 256571 . - . ID=transcript:Os01t0104600-02;Parent=gene:Os01g0104600;biotype=protein_coding;transcript_id=Os01t0104600-02
|
||||
1 irgsp three_prime_UTR 248828 248970 . - . Parent=transcript:Os01t0104600-02
|
||||
1 irgsp exon 248828 249107 . - . Parent=transcript:Os01t0104600-02;Name=Os01t0104600-01.exon11;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0104600-01.exon11;rank=11
|
||||
1 irgsp CDS 248971 249107 . - 2 ID=CDS:Os01t0104600-02;Parent=transcript:Os01t0104600-02;protein_id=Os01t0104600-02
|
||||
1 irgsp exon 249369 249468 . - . Parent=transcript:Os01t0104600-02;Name=Os01t0104600-01.exon10;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0104600-01.exon10;rank=10
|
||||
1 irgsp CDS 249369 249468 . - 0 ID=CDS:Os01t0104600-02;Parent=transcript:Os01t0104600-02;protein_id=Os01t0104600-02
|
||||
1 irgsp exon 249861 249956 . - . Parent=transcript:Os01t0104600-02;Name=Os01t0104600-01.exon9;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon9;rank=9
|
||||
1 irgsp CDS 249861 249956 . - 0 ID=CDS:Os01t0104600-02;Parent=transcript:Os01t0104600-02;protein_id=Os01t0104600-02
|
||||
1 irgsp exon 250617 250781 . - . Parent=transcript:Os01t0104600-02;Name=Os01t0104600-01.exon8;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon8;rank=8
|
||||
1 irgsp CDS 250617 250781 . - 0 ID=CDS:Os01t0104600-02;Parent=transcript:Os01t0104600-02;protein_id=Os01t0104600-02
|
||||
1 irgsp exon 250860 250940 . - . Parent=transcript:Os01t0104600-02;Name=Os01t0104600-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon7;rank=7
|
||||
1 irgsp CDS 250860 250940 . - 0 ID=CDS:Os01t0104600-02;Parent=transcript:Os01t0104600-02;protein_id=Os01t0104600-02
|
||||
1 irgsp exon 251026 251082 . - . Parent=transcript:Os01t0104600-02;Name=Os01t0104600-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon6;rank=6
|
||||
1 irgsp CDS 251026 251082 . - 0 ID=CDS:Os01t0104600-02;Parent=transcript:Os01t0104600-02;protein_id=Os01t0104600-02
|
||||
1 irgsp exon 251316 251384 . - . Parent=transcript:Os01t0104600-02;Name=Os01t0104600-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon5;rank=5
|
||||
1 irgsp CDS 251316 251384 . - 0 ID=CDS:Os01t0104600-02;Parent=transcript:Os01t0104600-02;protein_id=Os01t0104600-02
|
||||
1 irgsp exon 251695 251790 . - . Parent=transcript:Os01t0104600-02;Name=Os01t0104600-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon4;rank=4
|
||||
1 irgsp CDS 251695 251790 . - 0 ID=CDS:Os01t0104600-02;Parent=transcript:Os01t0104600-02;protein_id=Os01t0104600-02
|
||||
1 irgsp exon 255325 255553 . - . Parent=transcript:Os01t0104600-02;Name=Os01t0104600-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104600-01.exon3;rank=3
|
||||
1 irgsp CDS 255325 255553 . - 1 ID=CDS:Os01t0104600-02;Parent=transcript:Os01t0104600-02;protein_id=Os01t0104600-02
|
||||
1 irgsp exon 255674 256098 . - . Parent=transcript:Os01t0104600-02;Name=Os01t0104600-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0104600-01.exon2;rank=2
|
||||
1 irgsp CDS 255674 256098 . - 0 ID=CDS:Os01t0104600-02;Parent=transcript:Os01t0104600-02;protein_id=Os01t0104600-02
|
||||
1 irgsp CDS 256361 256441 . - 0 ID=CDS:Os01t0104600-02;Parent=transcript:Os01t0104600-02;protein_id=Os01t0104600-02
|
||||
1 irgsp exon 256361 256571 . - . Parent=transcript:Os01t0104600-02;Name=Os01t0104600-02.exon1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0104600-02.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 256442 256571 . - . Parent=transcript:Os01t0104600-02
|
||||
1 irgsp mRNA 248828 256872 . - . ID=transcript:Os01t0104600-01;Parent=gene:Os01g0104600;biotype=protein_coding;transcript_id=Os01t0104600-01
|
||||
1 irgsp three_prime_UTR 248828 248970 . - . Parent=transcript:Os01t0104600-01
|
||||
1 irgsp exon 248828 249107 . - . Parent=transcript:Os01t0104600-01;Name=Os01t0104600-01.exon11;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0104600-01.exon11;rank=11
|
||||
1 irgsp CDS 248971 249107 . - 2 ID=CDS:Os01t0104600-01;Parent=transcript:Os01t0104600-01;protein_id=Os01t0104600-01
|
||||
1 irgsp exon 249369 249468 . - . Parent=transcript:Os01t0104600-01;Name=Os01t0104600-01.exon10;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0104600-01.exon10;rank=10
|
||||
1 irgsp CDS 249369 249468 . - 0 ID=CDS:Os01t0104600-01;Parent=transcript:Os01t0104600-01;protein_id=Os01t0104600-01
|
||||
1 irgsp exon 249861 249956 . - . Parent=transcript:Os01t0104600-01;Name=Os01t0104600-01.exon9;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon9;rank=9
|
||||
1 irgsp CDS 249861 249956 . - 0 ID=CDS:Os01t0104600-01;Parent=transcript:Os01t0104600-01;protein_id=Os01t0104600-01
|
||||
1 irgsp exon 250617 250781 . - . Parent=transcript:Os01t0104600-01;Name=Os01t0104600-01.exon8;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon8;rank=8
|
||||
1 irgsp CDS 250617 250781 . - 0 ID=CDS:Os01t0104600-01;Parent=transcript:Os01t0104600-01;protein_id=Os01t0104600-01
|
||||
1 irgsp exon 250860 250940 . - . Parent=transcript:Os01t0104600-01;Name=Os01t0104600-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon7;rank=7
|
||||
1 irgsp CDS 250860 250940 . - 0 ID=CDS:Os01t0104600-01;Parent=transcript:Os01t0104600-01;protein_id=Os01t0104600-01
|
||||
1 irgsp exon 251026 251082 . - . Parent=transcript:Os01t0104600-01;Name=Os01t0104600-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon6;rank=6
|
||||
1 irgsp CDS 251026 251082 . - 0 ID=CDS:Os01t0104600-01;Parent=transcript:Os01t0104600-01;protein_id=Os01t0104600-01
|
||||
1 irgsp exon 251316 251384 . - . Parent=transcript:Os01t0104600-01;Name=Os01t0104600-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon5;rank=5
|
||||
1 irgsp CDS 251316 251384 . - 0 ID=CDS:Os01t0104600-01;Parent=transcript:Os01t0104600-01;protein_id=Os01t0104600-01
|
||||
1 irgsp exon 251695 251790 . - . Parent=transcript:Os01t0104600-01;Name=Os01t0104600-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104600-01.exon4;rank=4
|
||||
1 irgsp CDS 251695 251790 . - 0 ID=CDS:Os01t0104600-01;Parent=transcript:Os01t0104600-01;protein_id=Os01t0104600-01
|
||||
1 irgsp exon 255325 255553 . - . Parent=transcript:Os01t0104600-01;Name=Os01t0104600-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104600-01.exon3;rank=3
|
||||
1 irgsp CDS 255325 255553 . - 1 ID=CDS:Os01t0104600-01;Parent=transcript:Os01t0104600-01;protein_id=Os01t0104600-01
|
||||
1 irgsp exon 255674 256098 . - . Parent=transcript:Os01t0104600-01;Name=Os01t0104600-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0104600-01.exon2;rank=2
|
||||
1 irgsp CDS 255674 256098 . - 0 ID=CDS:Os01t0104600-01;Parent=transcript:Os01t0104600-01;protein_id=Os01t0104600-01
|
||||
1 irgsp CDS 256361 256441 . - 0 ID=CDS:Os01t0104600-01;Parent=transcript:Os01t0104600-01;protein_id=Os01t0104600-01
|
||||
1 irgsp exon 256361 256872 . - . Parent=transcript:Os01t0104600-01;Name=Os01t0104600-01.exon1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0104600-01.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 256442 256872 . - . Parent=transcript:Os01t0104600-01
|
||||
###
|
||||
1 irgsp gene 261530 268145 . + . ID=gene:Os01g0104800;biotype=protein_coding;description=Sas10/Utp3 family protein. (Os01t0104800-01)%3BHypothetical conserved gene. (Os01t0104800-02);gene_id=Os01g0104800;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 261530 268145 . + . ID=transcript:Os01t0104800-01;Parent=gene:Os01g0104800;biotype=protein_coding;transcript_id=Os01t0104800-01
|
||||
1 irgsp five_prime_UTR 261530 261561 . + . Parent=transcript:Os01t0104800-01
|
||||
1 irgsp exon 261530 261661 . + . Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0104800-01.exon1;rank=1
|
||||
1 irgsp CDS 261562 261661 . + 0 ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
|
||||
1 irgsp exon 261767 261805 . + . Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon2;constitutive=0;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0104800-01.exon2;rank=2
|
||||
1 irgsp CDS 261767 261805 . + 2 ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
|
||||
1 irgsp exon 261895 261941 . + . Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon3;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0104800-01.exon3;rank=3
|
||||
1 irgsp CDS 261895 261941 . + 2 ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
|
||||
1 irgsp exon 262582 262681 . + . Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon4;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0104800-01.exon4;rank=4
|
||||
1 irgsp CDS 262582 262681 . + 0 ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
|
||||
1 irgsp exon 262925 263181 . + . Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon5;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0104800-01.exon5;rank=5
|
||||
1 irgsp CDS 262925 263181 . + 2 ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
|
||||
1 irgsp exon 263525 263640 . + . Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon6;constitutive=0;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0104800-01.exon6;rank=6
|
||||
1 irgsp CDS 263525 263640 . + 0 ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
|
||||
1 irgsp exon 264014 264098 . + . Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104800-01.exon7;rank=7
|
||||
1 irgsp CDS 264014 264098 . + 1 ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
|
||||
1 irgsp exon 265236 265415 . + . Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon8;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104800-01.exon8;rank=8
|
||||
1 irgsp CDS 265236 265415 . + 0 ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
|
||||
1 irgsp exon 265506 265649 . + . Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon9;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104800-01.exon9;rank=9
|
||||
1 irgsp CDS 265506 265649 . + 0 ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
|
||||
1 irgsp exon 265740 265817 . + . Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon10;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104800-01.exon10;rank=10
|
||||
1 irgsp CDS 265740 265817 . + 0 ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
|
||||
1 irgsp exon 265909 266045 . + . Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon11;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0104800-01.exon11;rank=11
|
||||
1 irgsp CDS 265909 266045 . + 0 ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
|
||||
1 irgsp exon 266138 266246 . + . Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon12;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104800-01.exon12;rank=12
|
||||
1 irgsp CDS 266138 266246 . + 1 ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
|
||||
1 irgsp exon 267237 267514 . + . Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon13;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0104800-01.exon13;rank=13
|
||||
1 irgsp CDS 267237 267514 . + 0 ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
|
||||
1 irgsp exon 267591 267657 . + . Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon14;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104800-01.exon14;rank=14
|
||||
1 irgsp CDS 267591 267657 . + 1 ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
|
||||
1 irgsp exon 267734 267802 . + . Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon15;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104800-01.exon15;rank=15
|
||||
1 irgsp CDS 267734 267802 . + 0 ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
|
||||
1 irgsp CDS 267880 268011 . + 0 ID=CDS:Os01t0104800-01;Parent=transcript:Os01t0104800-01;protein_id=Os01t0104800-01
|
||||
1 irgsp exon 267880 268145 . + . Parent=transcript:Os01t0104800-01;Name=Os01t0104800-01.exon16;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0104800-01.exon16;rank=16
|
||||
1 irgsp three_prime_UTR 268012 268145 . + . Parent=transcript:Os01t0104800-01
|
||||
1 irgsp mRNA 263523 268120 . + . ID=transcript:Os01t0104800-02;Parent=gene:Os01g0104800;biotype=protein_coding;transcript_id=Os01t0104800-02
|
||||
1 irgsp five_prime_UTR 263523 263524 . + . Parent=transcript:Os01t0104800-02
|
||||
1 irgsp exon 263523 263640 . + . Parent=transcript:Os01t0104800-02;Name=Os01t0104800-02.exon1;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0104800-02.exon1;rank=1
|
||||
1 irgsp CDS 263525 263640 . + 0 ID=CDS:Os01t0104800-02;Parent=transcript:Os01t0104800-02;protein_id=Os01t0104800-02
|
||||
1 irgsp exon 264014 264098 . + . Parent=transcript:Os01t0104800-02;Name=Os01t0104800-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104800-01.exon7;rank=2
|
||||
1 irgsp CDS 264014 264098 . + 1 ID=CDS:Os01t0104800-02;Parent=transcript:Os01t0104800-02;protein_id=Os01t0104800-02
|
||||
1 irgsp exon 265236 265415 . + . Parent=transcript:Os01t0104800-02;Name=Os01t0104800-01.exon8;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104800-01.exon8;rank=3
|
||||
1 irgsp CDS 265236 265415 . + 0 ID=CDS:Os01t0104800-02;Parent=transcript:Os01t0104800-02;protein_id=Os01t0104800-02
|
||||
1 irgsp exon 265506 265649 . + . Parent=transcript:Os01t0104800-02;Name=Os01t0104800-01.exon9;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104800-01.exon9;rank=4
|
||||
1 irgsp CDS 265506 265649 . + 0 ID=CDS:Os01t0104800-02;Parent=transcript:Os01t0104800-02;protein_id=Os01t0104800-02
|
||||
1 irgsp exon 265740 265817 . + . Parent=transcript:Os01t0104800-02;Name=Os01t0104800-01.exon10;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104800-01.exon10;rank=5
|
||||
1 irgsp CDS 265740 265817 . + 0 ID=CDS:Os01t0104800-02;Parent=transcript:Os01t0104800-02;protein_id=Os01t0104800-02
|
||||
1 irgsp exon 265909 266045 . + . Parent=transcript:Os01t0104800-02;Name=Os01t0104800-01.exon11;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0104800-01.exon11;rank=6
|
||||
1 irgsp CDS 265909 266045 . + 0 ID=CDS:Os01t0104800-02;Parent=transcript:Os01t0104800-02;protein_id=Os01t0104800-02
|
||||
1 irgsp exon 266138 266246 . + . Parent=transcript:Os01t0104800-02;Name=Os01t0104800-01.exon12;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104800-01.exon12;rank=7
|
||||
1 irgsp CDS 266138 266246 . + 1 ID=CDS:Os01t0104800-02;Parent=transcript:Os01t0104800-02;protein_id=Os01t0104800-02
|
||||
1 irgsp exon 267237 267514 . + . Parent=transcript:Os01t0104800-02;Name=Os01t0104800-01.exon13;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0104800-01.exon13;rank=8
|
||||
1 irgsp CDS 267237 267514 . + 0 ID=CDS:Os01t0104800-02;Parent=transcript:Os01t0104800-02;protein_id=Os01t0104800-02
|
||||
1 irgsp exon 267591 267657 . + . Parent=transcript:Os01t0104800-02;Name=Os01t0104800-01.exon14;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0104800-01.exon14;rank=9
|
||||
1 irgsp CDS 267591 267657 . + 1 ID=CDS:Os01t0104800-02;Parent=transcript:Os01t0104800-02;protein_id=Os01t0104800-02
|
||||
1 irgsp exon 267734 267802 . + . Parent=transcript:Os01t0104800-02;Name=Os01t0104800-01.exon15;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0104800-01.exon15;rank=10
|
||||
1 irgsp CDS 267734 267802 . + 0 ID=CDS:Os01t0104800-02;Parent=transcript:Os01t0104800-02;protein_id=Os01t0104800-02
|
||||
1 irgsp CDS 267880 268011 . + 0 ID=CDS:Os01t0104800-02;Parent=transcript:Os01t0104800-02;protein_id=Os01t0104800-02
|
||||
1 irgsp exon 267880 268120 . + . Parent=transcript:Os01t0104800-02;Name=Os01t0104800-02.exon11;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0104800-02.exon11;rank=11
|
||||
1 irgsp three_prime_UTR 268012 268120 . + . Parent=transcript:Os01t0104800-02
|
||||
###
|
||||
1 irgsp gene 270179 275084 . - . ID=gene:Os01g0104900;biotype=protein_coding;description=Transferase family protein. (Os01t0104900-01)%3BHypothetical conserved gene. (Os01t0104900-02);gene_id=Os01g0104900;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 270179 275084 . - . ID=transcript:Os01t0104900-01;Parent=gene:Os01g0104900;biotype=protein_coding;transcript_id=Os01t0104900-01
|
||||
1 irgsp three_prime_UTR 270179 270355 . - . Parent=transcript:Os01t0104900-01
|
||||
1 irgsp exon 270179 271333 . - . Parent=transcript:Os01t0104900-01;Name=Os01t0104900-01.exon2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0104900-01.exon2;rank=2
|
||||
1 irgsp CDS 270356 271333 . - 0 ID=CDS:Os01t0104900-01;Parent=transcript:Os01t0104900-01;protein_id=Os01t0104900-01
|
||||
1 irgsp CDS 274529 274957 . - 0 ID=CDS:Os01t0104900-01;Parent=transcript:Os01t0104900-01;protein_id=Os01t0104900-01
|
||||
1 irgsp exon 274529 275084 . - . Parent=transcript:Os01t0104900-01;Name=Os01t0104900-01.exon1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0104900-01.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 274958 275084 . - . Parent=transcript:Os01t0104900-01
|
||||
1 irgsp mRNA 270250 271518 . - . ID=transcript:Os01t0104900-02;Parent=gene:Os01g0104900;biotype=protein_coding;transcript_id=Os01t0104900-02
|
||||
1 irgsp three_prime_UTR 270250 270355 . - . Parent=transcript:Os01t0104900-02
|
||||
1 irgsp exon 270250 271333 . - . Parent=transcript:Os01t0104900-02;Name=Os01t0104900-02.exon2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0104900-02.exon2;rank=2
|
||||
1 irgsp CDS 270356 271309 . - 0 ID=CDS:Os01t0104900-02;Parent=transcript:Os01t0104900-02;protein_id=Os01t0104900-02
|
||||
1 irgsp five_prime_UTR 271310 271333 . - . Parent=transcript:Os01t0104900-02
|
||||
1 irgsp exon 271457 271518 . - . Parent=transcript:Os01t0104900-02;Name=Os01t0104900-02.exon1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0104900-02.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 271457 271518 . - . Parent=transcript:Os01t0104900-02
|
||||
###
|
||||
1 irgsp gene 284762 291892 . - . ID=gene:Os01g0105300;biotype=protein_coding;description=Similar to HAT family dimerisation domain containing protein%2C expressed. (Os01t0105300-01);gene_id=Os01g0105300;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 284762 291892 . - . ID=transcript:Os01t0105300-01;Parent=gene:Os01g0105300;biotype=protein_coding;transcript_id=Os01t0105300-01
|
||||
1 irgsp three_prime_UTR 284762 284930 . - . Parent=transcript:Os01t0105300-01
|
||||
1 irgsp exon 284762 287047 . - . Parent=transcript:Os01t0105300-01;Name=Os01t0105300-01.exon5;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105300-01.exon5;rank=5
|
||||
1 irgsp CDS 284931 285020 . - 0 ID=CDS:Os01t0105300-01;Parent=transcript:Os01t0105300-01;protein_id=Os01t0105300-01
|
||||
1 irgsp five_prime_UTR 285021 287047 . - . Parent=transcript:Os01t0105300-01
|
||||
1 irgsp exon 291398 291436 . - . Parent=transcript:Os01t0105300-01;Name=Os01t0105300-01.exon4;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105300-01.exon4;rank=4
|
||||
1 irgsp five_prime_UTR 291398 291436 . - . Parent=transcript:Os01t0105300-01
|
||||
1 irgsp exon 291520 291534 . - . Parent=transcript:Os01t0105300-01;Name=Os01t0105300-01.exon3;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105300-01.exon3;rank=3
|
||||
1 irgsp five_prime_UTR 291520 291534 . - . Parent=transcript:Os01t0105300-01
|
||||
1 irgsp exon 291678 291738 . - . Parent=transcript:Os01t0105300-01;Name=Os01t0105300-01.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105300-01.exon2;rank=2
|
||||
1 irgsp five_prime_UTR 291678 291738 . - . Parent=transcript:Os01t0105300-01
|
||||
1 irgsp exon 291838 291892 . - . Parent=transcript:Os01t0105300-01;Name=Os01t0105300-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105300-01.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 291838 291892 . - . Parent=transcript:Os01t0105300-01
|
||||
###
|
||||
1 irgsp gene 288372 292296 . + . ID=gene:Os01g0105400;biotype=protein_coding;description=Similar to Kinesin heavy chain. (Os01t0105400-01);gene_id=Os01g0105400;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 288372 292296 . + . ID=transcript:Os01t0105400-01;Parent=gene:Os01g0105400;biotype=protein_coding;transcript_id=Os01t0105400-01
|
||||
1 irgsp exon 288372 288846 . + . Parent=transcript:Os01t0105400-01;Name=Os01t0105400-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105400-01.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 288372 288846 . + . Parent=transcript:Os01t0105400-01
|
||||
1 irgsp exon 288950 289116 . + . Parent=transcript:Os01t0105400-01;Name=Os01t0105400-01.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105400-01.exon2;rank=2
|
||||
1 irgsp five_prime_UTR 288950 289116 . + . Parent=transcript:Os01t0105400-01
|
||||
1 irgsp exon 289202 289572 . + . Parent=transcript:Os01t0105400-01;Name=Os01t0105400-01.exon3;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105400-01.exon3;rank=3
|
||||
1 irgsp five_prime_UTR 289202 289572 . + . Parent=transcript:Os01t0105400-01
|
||||
1 irgsp exon 289661 289830 . + . Parent=transcript:Os01t0105400-01;Name=Os01t0105400-01.exon4;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105400-01.exon4;rank=4
|
||||
1 irgsp five_prime_UTR 289661 289830 . + . Parent=transcript:Os01t0105400-01
|
||||
1 irgsp five_prime_UTR 290395 290432 . + . Parent=transcript:Os01t0105400-01
|
||||
1 irgsp exon 290395 290512 . + . Parent=transcript:Os01t0105400-01;Name=Os01t0105400-01.exon5;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0105400-01.exon5;rank=5
|
||||
1 irgsp CDS 290433 290512 . + 0 ID=CDS:Os01t0105400-01;Parent=transcript:Os01t0105400-01;protein_id=Os01t0105400-01
|
||||
1 irgsp CDS 291372 291558 . + 1 ID=CDS:Os01t0105400-01;Parent=transcript:Os01t0105400-01;protein_id=Os01t0105400-01
|
||||
1 irgsp exon 291372 291574 . + . Parent=transcript:Os01t0105400-01;Name=Os01t0105400-01.exon6;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0105400-01.exon6;rank=6
|
||||
1 irgsp three_prime_UTR 291559 291574 . + . Parent=transcript:Os01t0105400-01
|
||||
1 irgsp exon 291648 291779 . + . Parent=transcript:Os01t0105400-01;Name=Os01t0105400-01.exon7;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105400-01.exon7;rank=7
|
||||
1 irgsp three_prime_UTR 291648 291779 . + . Parent=transcript:Os01t0105400-01
|
||||
1 irgsp exon 291859 291948 . + . Parent=transcript:Os01t0105400-01;Name=Os01t0105400-01.exon8;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105400-01.exon8;rank=8
|
||||
1 irgsp three_prime_UTR 291859 291948 . + . Parent=transcript:Os01t0105400-01
|
||||
1 irgsp exon 292073 292296 . + . Parent=transcript:Os01t0105400-01;Name=Os01t0105400-01.exon9;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105400-01.exon9;rank=9
|
||||
1 irgsp three_prime_UTR 292073 292296 . + . Parent=transcript:Os01t0105400-01
|
||||
###
|
||||
1 irgsp gene 303233 306736 . + . ID=gene:Os01g0105700;Name=basic helix-loop-helix protein 071;biotype=protein_coding;description=Basic helix-loop-helix dimerisation region bHLH domain containing protein. (Os01t0105700-01);gene_id=Os01g0105700;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 303233 306736 . + . ID=transcript:Os01t0105700-01;Parent=gene:Os01g0105700;biotype=protein_coding;transcript_id=Os01t0105700-01
|
||||
1 irgsp five_prime_UTR 303233 303328 . + . Parent=transcript:Os01t0105700-01
|
||||
1 irgsp exon 303233 303471 . + . Parent=transcript:Os01t0105700-01;Name=Os01t0105700-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0105700-01.exon1;rank=1
|
||||
1 irgsp CDS 303329 303471 . + 0 ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
|
||||
1 irgsp exon 303981 304509 . + . Parent=transcript:Os01t0105700-01;Name=Os01t0105700-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0105700-01.exon2;rank=2
|
||||
1 irgsp CDS 303981 304509 . + 1 ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
|
||||
1 irgsp exon 305572 305718 . + . Parent=transcript:Os01t0105700-01;Name=Os01t0105700-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105700-01.exon3;rank=3
|
||||
1 irgsp CDS 305572 305718 . + 0 ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
|
||||
1 irgsp exon 305834 305899 . + . Parent=transcript:Os01t0105700-01;Name=Os01t0105700-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105700-01.exon4;rank=4
|
||||
1 irgsp CDS 305834 305899 . + 0 ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
|
||||
1 irgsp exon 305993 306058 . + . Parent=transcript:Os01t0105700-01;Name=Os01t0105700-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105700-01.exon5;rank=5
|
||||
1 irgsp CDS 305993 306058 . + 0 ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
|
||||
1 irgsp exon 306171 306245 . + . Parent=transcript:Os01t0105700-01;Name=Os01t0105700-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105700-01.exon6;rank=6
|
||||
1 irgsp CDS 306171 306245 . + 0 ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
|
||||
1 irgsp CDS 306353 306493 . + 0 ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
|
||||
1 irgsp exon 306353 306736 . + . Parent=transcript:Os01t0105700-01;Name=Os01t0105700-01.exon7;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0105700-01.exon7;rank=7
|
||||
1 irgsp three_prime_UTR 306494 306736 . + . Parent=transcript:Os01t0105700-01
|
||||
###
|
||||
1 irgsp gene 306871 308842 . - . ID=gene:Os01g0105800;Name=IRON-SULFUR CLUSTER PROTEIN 9;biotype=protein_coding;description=Similar to Iron sulfur assembly protein 1. (Os01t0105800-01);gene_id=Os01g0105800;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 306871 308842 . - . ID=transcript:Os01t0105800-01;Parent=gene:Os01g0105800;biotype=protein_coding;transcript_id=Os01t0105800-01
|
||||
1 irgsp three_prime_UTR 306871 307123 . - . Parent=transcript:Os01t0105800-01
|
||||
1 irgsp exon 306871 307217 . - . Parent=transcript:Os01t0105800-01;Name=Os01t0105800-01.exon4;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0105800-01.exon4;rank=4
|
||||
1 irgsp CDS 307124 307217 . - 1 ID=CDS:Os01t0105800-01;Parent=transcript:Os01t0105800-01;protein_id=Os01t0105800-01
|
||||
1 irgsp exon 307296 307413 . - . Parent=transcript:Os01t0105800-01;Name=Os01t0105800-01.exon3;constitutive=1;ensembl_end_phase=2;ensembl_phase=1;exon_id=Os01t0105800-01.exon3;rank=3
|
||||
1 irgsp CDS 307296 307413 . - 2 ID=CDS:Os01t0105800-01;Parent=transcript:Os01t0105800-01;protein_id=Os01t0105800-01
|
||||
1 irgsp CDS 308397 308601 . - 0 ID=CDS:Os01t0105800-01;Parent=transcript:Os01t0105800-01;protein_id=Os01t0105800-01
|
||||
1 irgsp exon 308397 308626 . - . Parent=transcript:Os01t0105800-01;Name=Os01t0105800-01.exon2;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0105800-01.exon2;rank=2
|
||||
1 irgsp five_prime_UTR 308602 308626 . - . Parent=transcript:Os01t0105800-01
|
||||
1 irgsp exon 308703 308842 . - . Parent=transcript:Os01t0105800-01;Name=Os01t0105800-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105800-01.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 308703 308842 . - . Parent=transcript:Os01t0105800-01
|
||||
###
|
||||
1 irgsp gene 309520 313170 . - . ID=gene:Os01g0105900;biotype=protein_coding;description=Carbohydrate/purine kinase domain containing protein. (Os01t0105900-01);gene_id=Os01g0105900;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 309520 313170 . - . ID=transcript:Os01t0105900-01;Parent=gene:Os01g0105900;biotype=protein_coding;transcript_id=Os01t0105900-01
|
||||
1 irgsp three_prime_UTR 309520 309821 . - . Parent=transcript:Os01t0105900-01
|
||||
1 irgsp exon 309520 310070 . - . Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon8;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0105900-01.exon8;rank=8
|
||||
1 irgsp CDS 309822 310070 . - 0 ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
|
||||
1 irgsp exon 310256 310367 . - . Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0105900-01.exon7;rank=7
|
||||
1 irgsp CDS 310256 310367 . - 1 ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
|
||||
1 irgsp exon 310455 310552 . - . Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon6;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0105900-01.exon6;rank=6
|
||||
1 irgsp CDS 310455 310552 . - 0 ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
|
||||
1 irgsp exon 310632 310739 . - . Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105900-01.exon5;rank=5
|
||||
1 irgsp CDS 310632 310739 . - 0 ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
|
||||
1 irgsp exon 310880 310918 . - . Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105900-01.exon4;rank=4
|
||||
1 irgsp CDS 310880 310918 . - 0 ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
|
||||
1 irgsp exon 311002 311073 . - . Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105900-01.exon3;rank=3
|
||||
1 irgsp CDS 311002 311073 . - 0 ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
|
||||
1 irgsp exon 311163 311426 . - . Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105900-01.exon2;rank=2
|
||||
1 irgsp CDS 311163 311426 . - 0 ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
|
||||
1 irgsp CDS 312867 313064 . - 0 ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
|
||||
1 irgsp exon 312867 313170 . - . Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0105900-01.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 313065 313170 . - . Parent=transcript:Os01t0105900-01
|
||||
###
|
||||
1 irgsp gene 319754 322205 . + . ID=gene:Os01g0106200;biotype=protein_coding;description=Similar to RER1A protein (AtRER1A). (Os01t0106200-01);gene_id=Os01g0106200;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 319754 322205 . + . ID=transcript:Os01t0106200-01;Parent=gene:Os01g0106200;biotype=protein_coding;transcript_id=Os01t0106200-01
|
||||
1 irgsp five_prime_UTR 319754 319874 . + . Parent=transcript:Os01t0106200-01
|
||||
1 irgsp exon 319754 320236 . + . Parent=transcript:Os01t0106200-01;Name=Os01t0106200-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0106200-01.exon1;rank=1
|
||||
1 irgsp CDS 319875 320236 . + 0 ID=CDS:Os01t0106200-01;Parent=transcript:Os01t0106200-01;protein_id=Os01t0106200-01
|
||||
1 irgsp exon 321468 321648 . + . Parent=transcript:Os01t0106200-01;Name=Os01t0106200-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0106200-01.exon2;rank=2
|
||||
1 irgsp CDS 321468 321648 . + 1 ID=CDS:Os01t0106200-01;Parent=transcript:Os01t0106200-01;protein_id=Os01t0106200-01
|
||||
1 irgsp CDS 321928 321975 . + 0 ID=CDS:Os01t0106200-01;Parent=transcript:Os01t0106200-01;protein_id=Os01t0106200-01
|
||||
1 irgsp exon 321928 322205 . + . Parent=transcript:Os01t0106200-01;Name=Os01t0106200-01.exon3;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0106200-01.exon3;rank=3
|
||||
1 irgsp three_prime_UTR 321976 322205 . + . Parent=transcript:Os01t0106200-01
|
||||
###
|
||||
1 irgsp gene 322591 323923 . - . ID=gene:Os01g0106300;biotype=protein_coding;description=Similar to Isoflavone reductase homolog IRL (EC 1.3.1.-). (Os01t0106300-01);gene_id=Os01g0106300;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 322591 323923 . - . ID=transcript:Os01t0106300-01;Parent=gene:Os01g0106300;biotype=protein_coding;transcript_id=Os01t0106300-01
|
||||
1 irgsp three_prime_UTR 322591 322809 . - . Parent=transcript:Os01t0106300-01
|
||||
1 irgsp exon 322591 322973 . - . Parent=transcript:Os01t0106300-01;Name=Os01t0106300-01.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0106300-01.exon2;rank=2
|
||||
@@ -0,0 +1,881 @@
|
||||
seq_id source_tag primary_tag start end score strand frame Alias biotype constitutive description ensembl_end_phase ensembl_phase exon_id gene_id ID logic_name Name Parent protein_id rank transcript_id
|
||||
1 irgsp repeat_region 2000 2100 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A fakeRepeat1 N/A N/A N/A N/A N/A N/A
|
||||
1 irgsp gene 2983 10815 . 1 . N/A protein_coding N/A RabGAP/TBC domain containing protein. (Os01t0100100-01) N/A N/A N/A Os01g0100100 gene:Os01g0100100 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 2983 10815 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0100100-01 N/A N/A gene:Os01g0100100 N/A N/A Os01t0100100-01
|
||||
1 irgsp exon 2983 3268 . 1 . N/A N/A 1 N/A -1 -1 Os01t0100100-01.exon1 N/A Os01t0100100-01.exon1 N/A Os01t0100100-01.exon1 transcript:Os01t0100100-01 N/A 1 N/A
|
||||
1 irgsp exon 3354 3616 . 1 . N/A N/A 1 N/A 0 -1 Os01t0100100-01.exon2 N/A Os01t0100100-01.exon2 N/A Os01t0100100-01.exon2 transcript:Os01t0100100-01 N/A 2 N/A
|
||||
1 irgsp exon 4357 4455 . 1 . N/A N/A 1 N/A 0 0 Os01t0100100-01.exon3 N/A Os01t0100100-01.exon3 N/A Os01t0100100-01.exon3 transcript:Os01t0100100-01 N/A 3 N/A
|
||||
1 irgsp exon 5457 5560 . 1 . N/A N/A 1 N/A 2 0 Os01t0100100-01.exon4 N/A Os01t0100100-01.exon4 N/A Os01t0100100-01.exon4 transcript:Os01t0100100-01 N/A 4 N/A
|
||||
1 irgsp exon 7136 7944 . 1 . N/A N/A 1 N/A 1 2 Os01t0100100-01.exon5 N/A Os01t0100100-01.exon5 N/A Os01t0100100-01.exon5 transcript:Os01t0100100-01 N/A 5 N/A
|
||||
1 irgsp exon 8028 8150 . 1 . N/A N/A 1 N/A 1 1 Os01t0100100-01.exon6 N/A Os01t0100100-01.exon6 N/A Os01t0100100-01.exon6 transcript:Os01t0100100-01 N/A 6 N/A
|
||||
1 irgsp exon 8232 8320 . 1 . N/A N/A 1 N/A 0 1 Os01t0100100-01.exon7 N/A Os01t0100100-01.exon7 N/A Os01t0100100-01.exon7 transcript:Os01t0100100-01 N/A 7 N/A
|
||||
1 irgsp exon 8408 8608 . 1 . N/A N/A 1 N/A 0 0 Os01t0100100-01.exon8 N/A Os01t0100100-01.exon8 N/A Os01t0100100-01.exon8 transcript:Os01t0100100-01 N/A 8 N/A
|
||||
1 irgsp exon 9210 9615 . 1 . N/A N/A 1 N/A 1 0 Os01t0100100-01.exon9 N/A Os01t0100100-01.exon9 N/A Os01t0100100-01.exon9 transcript:Os01t0100100-01 N/A 9 N/A
|
||||
1 irgsp exon 10102 10187 . 1 . N/A N/A 1 N/A 0 1 Os01t0100100-01.exon10 N/A Os01t0100100-01.exon10 N/A Os01t0100100-01.exon10 transcript:Os01t0100100-01 N/A 10 N/A
|
||||
1 irgsp exon 10274 10430 . 1 . N/A N/A 1 N/A -1 0 Os01t0100100-01.exon11 N/A Os01t0100100-01.exon11 N/A Os01t0100100-01.exon11 transcript:Os01t0100100-01 N/A 11 N/A
|
||||
1 irgsp exon 10504 10815 . 1 . N/A N/A 1 N/A -1 -1 Os01t0100100-01.exon12 N/A Os01t0100100-01.exon12 N/A Os01t0100100-01.exon12 transcript:Os01t0100100-01 N/A 12 N/A
|
||||
1 irgsp CDS 3449 3616 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100100-01 N/A N/A transcript:Os01t0100100-01 Os01t0100100-01 N/A N/A
|
||||
1 irgsp CDS 4357 4455 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100100-01 N/A N/A transcript:Os01t0100100-01 Os01t0100100-01 N/A N/A
|
||||
1 irgsp CDS 5457 5560 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100100-01 N/A N/A transcript:Os01t0100100-01 Os01t0100100-01 N/A N/A
|
||||
1 irgsp CDS 7136 7944 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100100-01 N/A N/A transcript:Os01t0100100-01 Os01t0100100-01 N/A N/A
|
||||
1 irgsp CDS 8028 8150 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100100-01 N/A N/A transcript:Os01t0100100-01 Os01t0100100-01 N/A N/A
|
||||
1 irgsp CDS 8232 8320 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100100-01 N/A N/A transcript:Os01t0100100-01 Os01t0100100-01 N/A N/A
|
||||
1 irgsp CDS 8408 8608 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100100-01 N/A N/A transcript:Os01t0100100-01 Os01t0100100-01 N/A N/A
|
||||
1 irgsp CDS 9210 9615 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100100-01 N/A N/A transcript:Os01t0100100-01 Os01t0100100-01 N/A N/A
|
||||
1 irgsp CDS 10102 10187 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100100-01 N/A N/A transcript:Os01t0100100-01 Os01t0100100-01 N/A N/A
|
||||
1 irgsp CDS 10274 10297 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100100-01 N/A N/A transcript:Os01t0100100-01 Os01t0100100-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 2983 3268 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-1 N/A N/A transcript:Os01t0100100-01 N/A N/A N/A
|
||||
1 irgsp five_prime_UTR 3354 3448 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-2 N/A N/A transcript:Os01t0100100-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 10298 10430 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-1 N/A N/A transcript:Os01t0100100-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 10504 10815 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-2 N/A N/A transcript:Os01t0100100-01 N/A N/A N/A
|
||||
1 irgsp gene 11218 12435 . 1 . N/A protein_coding N/A Conserved hypothetical protein. (Os01t0100200-01) N/A N/A N/A Os01g0100200 gene:Os01g0100200 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 11218 12435 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0100200-01 N/A N/A gene:Os01g0100200 N/A N/A Os01t0100200-01
|
||||
1 irgsp exon 11218 12060 . 1 . N/A N/A 1 N/A 2 -1 Os01t0100200-01.exon1 N/A Os01t0100200-01.exon1 N/A Os01t0100200-01.exon1 transcript:Os01t0100200-01 N/A 1 N/A
|
||||
1 irgsp exon 12152 12435 . 1 . N/A N/A 1 N/A -1 2 Os01t0100200-01.exon2 N/A Os01t0100200-01.exon2 N/A Os01t0100200-01.exon2 transcript:Os01t0100200-01 N/A 2 N/A
|
||||
1 irgsp CDS 11798 12060 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100200-01 N/A N/A transcript:Os01t0100200-01 Os01t0100200-01 N/A N/A
|
||||
1 irgsp CDS 12152 12317 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100200-01 N/A N/A transcript:Os01t0100200-01 Os01t0100200-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 11218 11797 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-3 N/A N/A transcript:Os01t0100200-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 12318 12435 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-3 N/A N/A transcript:Os01t0100200-01 N/A N/A N/A
|
||||
1 irgsp gene 11372 12284 . -1 . N/A protein_coding N/A Cytochrome P450 domain containing protein. (Os01t0100300-00) N/A N/A N/A Os01g0100300 gene:Os01g0100300 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 11372 12284 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0100300-00 N/A N/A gene:Os01g0100300 N/A N/A Os01t0100300-00
|
||||
1 irgsp exon 11372 12042 . -1 . N/A N/A 1 N/A 0 1 Os01t0100300-00.exon2 N/A Os01t0100300-00.exon2 N/A Os01t0100300-00.exon2 transcript:Os01t0100300-00 N/A 2 N/A
|
||||
1 irgsp exon 12146 12284 . -1 . N/A N/A 1 N/A 1 0 Os01t0100300-00.exon1 N/A Os01t0100300-00.exon1 N/A Os01t0100300-00.exon1 transcript:Os01t0100300-00 N/A 1 N/A
|
||||
1 irgsp CDS 11372 12042 . -1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100300-00 N/A N/A transcript:Os01t0100300-00 Os01t0100300-00 N/A N/A
|
||||
1 irgsp CDS 12146 12284 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100300-00 N/A N/A transcript:Os01t0100300-00 Os01t0100300-00 N/A N/A
|
||||
1 irgsp gene 12721 15685 . 1 . N/A protein_coding N/A Similar to Pectinesterase-like protein. (Os01t0100400-01) N/A N/A N/A Os01g0100400 gene:Os01g0100400 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 12721 15685 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0100400-01 N/A N/A gene:Os01g0100400 N/A N/A Os01t0100400-01
|
||||
1 irgsp exon 12721 13813 . 1 . N/A N/A 1 N/A 2 -1 Os01t0100400-01.exon1 N/A Os01t0100400-01.exon1 N/A Os01t0100400-01.exon1 transcript:Os01t0100400-01 N/A 1 N/A
|
||||
1 irgsp exon 13906 14271 . 1 . N/A N/A 1 N/A 2 2 Os01t0100400-01.exon2 N/A Os01t0100400-01.exon2 N/A Os01t0100400-01.exon2 transcript:Os01t0100400-01 N/A 2 N/A
|
||||
1 irgsp exon 14359 14437 . 1 . N/A N/A 1 N/A 0 2 Os01t0100400-01.exon3 N/A Os01t0100400-01.exon3 N/A Os01t0100400-01.exon3 transcript:Os01t0100400-01 N/A 3 N/A
|
||||
1 irgsp exon 14969 15171 . 1 . N/A N/A 1 N/A 2 0 Os01t0100400-01.exon4 N/A Os01t0100400-01.exon4 N/A Os01t0100400-01.exon4 transcript:Os01t0100400-01 N/A 4 N/A
|
||||
1 irgsp exon 15266 15685 . 1 . N/A N/A 1 N/A -1 2 Os01t0100400-01.exon5 N/A Os01t0100400-01.exon5 N/A Os01t0100400-01.exon5 transcript:Os01t0100400-01 N/A 5 N/A
|
||||
1 irgsp CDS 12774 13813 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100400-01 N/A N/A transcript:Os01t0100400-01 Os01t0100400-01 N/A N/A
|
||||
1 irgsp CDS 13906 14271 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100400-01 N/A N/A transcript:Os01t0100400-01 Os01t0100400-01 N/A N/A
|
||||
1 irgsp CDS 14359 14437 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100400-01 N/A N/A transcript:Os01t0100400-01 Os01t0100400-01 N/A N/A
|
||||
1 irgsp CDS 14969 15171 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100400-01 N/A N/A transcript:Os01t0100400-01 Os01t0100400-01 N/A N/A
|
||||
1 irgsp CDS 15266 15359 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100400-01 N/A N/A transcript:Os01t0100400-01 Os01t0100400-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 12721 12773 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-4 N/A N/A transcript:Os01t0100400-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 15360 15685 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-4 N/A N/A transcript:Os01t0100400-01 N/A N/A N/A
|
||||
1 irgsp gene 12808 13978 . -1 . N/A protein_coding N/A Hypothetical protein. (Os01t0100466-00) N/A N/A N/A Os01g0100466 gene:Os01g0100466 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 12808 13978 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0100466-00 N/A N/A gene:Os01g0100466 N/A N/A Os01t0100466-00
|
||||
1 irgsp exon 12808 13782 . -1 . N/A N/A 1 N/A -1 -1 Os01t0100466-00.exon2 N/A Os01t0100466-00.exon2 N/A Os01t0100466-00.exon2 transcript:Os01t0100466-00 N/A 2 N/A
|
||||
1 irgsp exon 13880 13978 . -1 . N/A N/A 1 N/A -1 -1 Os01t0100466-00.exon1 N/A Os01t0100466-00.exon1 N/A Os01t0100466-00.exon1 transcript:Os01t0100466-00 N/A 1 N/A
|
||||
1 irgsp CDS 12869 13102 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100466-00 N/A N/A transcript:Os01t0100466-00 Os01t0100466-00 N/A N/A
|
||||
1 irgsp five_prime_UTR 13103 13782 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-5 N/A N/A transcript:Os01t0100466-00 N/A N/A N/A
|
||||
1 irgsp five_prime_UTR 13880 13978 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-6 N/A N/A transcript:Os01t0100466-00 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 12808 12868 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-5 N/A N/A transcript:Os01t0100466-00 N/A N/A N/A
|
||||
1 irgsp gene 16399 20144 . 1 . N/A protein_coding N/A Immunoglobulin-like domain containing protein. (Os01t0100500-01) N/A N/A N/A Os01g0100500 gene:Os01g0100500 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 16399 20144 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0100500-01 N/A N/A gene:Os01g0100500 N/A N/A Os01t0100500-01
|
||||
1 irgsp exon 16399 16976 . 1 . N/A N/A 1 N/A 0 -1 Os01t0100500-01.exon1 N/A Os01t0100500-01.exon1 N/A Os01t0100500-01.exon1 transcript:Os01t0100500-01 N/A 1 N/A
|
||||
1 irgsp exon 17383 17474 . 1 . N/A N/A 1 N/A 2 0 Os01t0100500-01.exon2 N/A Os01t0100500-01.exon2 N/A Os01t0100500-01.exon2 transcript:Os01t0100500-01 N/A 2 N/A
|
||||
1 irgsp exon 17558 18258 . 1 . N/A N/A 1 N/A 1 2 Os01t0100500-01.exon3 N/A Os01t0100500-01.exon3 N/A Os01t0100500-01.exon3 transcript:Os01t0100500-01 N/A 3 N/A
|
||||
1 irgsp exon 18501 18571 . 1 . N/A N/A 1 N/A 0 1 Os01t0100500-01.exon4 N/A Os01t0100500-01.exon4 N/A Os01t0100500-01.exon4 transcript:Os01t0100500-01 N/A 4 N/A
|
||||
1 irgsp exon 18968 19057 . 1 . N/A N/A 1 N/A 0 0 Os01t0100500-01.exon5 N/A Os01t0100500-01.exon5 N/A Os01t0100500-01.exon5 transcript:Os01t0100500-01 N/A 5 N/A
|
||||
1 irgsp exon 19142 19321 . 1 . N/A N/A 1 N/A 0 0 Os01t0100500-01.exon6 N/A Os01t0100500-01.exon6 N/A Os01t0100500-01.exon6 transcript:Os01t0100500-01 N/A 6 N/A
|
||||
1 irgsp exon 19531 19629 . 1 . N/A N/A 1 N/A -1 0 Os01t0100500-01.exon7 N/A Os01t0100500-01.exon7 N/A Os01t0100500-01.exon7 transcript:Os01t0100500-01 N/A 7 N/A
|
||||
1 irgsp exon 19734 20144 . 1 . N/A N/A 1 N/A -1 -1 Os01t0100500-01.exon8 N/A Os01t0100500-01.exon8 N/A Os01t0100500-01.exon8 transcript:Os01t0100500-01 N/A 8 N/A
|
||||
1 irgsp CDS 16599 16976 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100500-01 N/A N/A transcript:Os01t0100500-01 Os01t0100500-01 N/A N/A
|
||||
1 irgsp CDS 17383 17474 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100500-01 N/A N/A transcript:Os01t0100500-01 Os01t0100500-01 N/A N/A
|
||||
1 irgsp CDS 17558 18258 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100500-01 N/A N/A transcript:Os01t0100500-01 Os01t0100500-01 N/A N/A
|
||||
1 irgsp CDS 18501 18571 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100500-01 N/A N/A transcript:Os01t0100500-01 Os01t0100500-01 N/A N/A
|
||||
1 irgsp CDS 18968 19057 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100500-01 N/A N/A transcript:Os01t0100500-01 Os01t0100500-01 N/A N/A
|
||||
1 irgsp CDS 19142 19321 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100500-01 N/A N/A transcript:Os01t0100500-01 Os01t0100500-01 N/A N/A
|
||||
1 irgsp CDS 19531 19593 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100500-01 N/A N/A transcript:Os01t0100500-01 Os01t0100500-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 16399 16598 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-7 N/A N/A transcript:Os01t0100500-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 19594 19629 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-6 N/A N/A transcript:Os01t0100500-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 19734 20144 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-7 N/A N/A transcript:Os01t0100500-01 N/A N/A N/A
|
||||
1 irgsp gene 22841 26892 . 1 . N/A protein_coding N/A Single-stranded nucleic acid binding R3H domain containing protein. (Os01t0100600-01) N/A N/A N/A Os01g0100600 gene:Os01g0100600 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 22841 26892 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0100600-01 N/A N/A gene:Os01g0100600 N/A N/A Os01t0100600-01
|
||||
1 irgsp exon 22841 23281 . 1 . N/A N/A 1 N/A 2 -1 Os01t0100600-01.exon1 N/A Os01t0100600-01.exon1 N/A Os01t0100600-01.exon1 transcript:Os01t0100600-01 N/A 1 N/A
|
||||
1 irgsp exon 23572 23847 . 1 . N/A N/A 1 N/A 2 2 Os01t0100600-01.exon2 N/A Os01t0100600-01.exon2 N/A Os01t0100600-01.exon2 transcript:Os01t0100600-01 N/A 2 N/A
|
||||
1 irgsp exon 23962 24033 . 1 . N/A N/A 1 N/A 2 2 Os01t0100600-01.exon3 N/A Os01t0100600-01.exon3 N/A Os01t0100600-01.exon3 transcript:Os01t0100600-01 N/A 3 N/A
|
||||
1 irgsp exon 24492 24577 . 1 . N/A N/A 1 N/A 1 2 Os01t0100600-01.exon4 N/A Os01t0100600-01.exon4 N/A Os01t0100600-01.exon4 transcript:Os01t0100600-01 N/A 4 N/A
|
||||
1 irgsp exon 25445 25519 . 1 . N/A N/A 1 N/A 1 1 Os01t0100600-01.exon5 N/A Os01t0100600-01.exon5 N/A Os01t0100600-01.exon5 transcript:Os01t0100600-01 N/A 5 N/A
|
||||
1 irgsp exon 25883 26892 . 1 . N/A N/A 1 N/A -1 1 Os01t0100600-01.exon6 N/A Os01t0100600-01.exon6 N/A Os01t0100600-01.exon6 transcript:Os01t0100600-01 N/A 6 N/A
|
||||
1 irgsp CDS 23232 23281 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100600-01 N/A N/A transcript:Os01t0100600-01 Os01t0100600-01 N/A N/A
|
||||
1 irgsp CDS 23572 23847 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100600-01 N/A N/A transcript:Os01t0100600-01 Os01t0100600-01 N/A N/A
|
||||
1 irgsp CDS 23962 24033 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100600-01 N/A N/A transcript:Os01t0100600-01 Os01t0100600-01 N/A N/A
|
||||
1 irgsp CDS 24492 24577 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100600-01 N/A N/A transcript:Os01t0100600-01 Os01t0100600-01 N/A N/A
|
||||
1 irgsp CDS 25445 25519 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100600-01 N/A N/A transcript:Os01t0100600-01 Os01t0100600-01 N/A N/A
|
||||
1 irgsp CDS 25883 26391 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100600-01 N/A N/A transcript:Os01t0100600-01 Os01t0100600-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 22841 23231 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-8 N/A N/A transcript:Os01t0100600-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 26392 26892 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-8 N/A N/A transcript:Os01t0100600-01 N/A N/A N/A
|
||||
1 irgsp gene 25861 26424 . -1 . N/A protein_coding N/A Hypothetical gene. (Os01t0100650-00) N/A N/A N/A Os01g0100650 gene:Os01g0100650 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 25861 26424 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0100650-00 N/A N/A gene:Os01g0100650 N/A N/A Os01t0100650-00
|
||||
1 irgsp exon 25861 26424 . -1 . N/A N/A 1 N/A -1 -1 Os01t0100650-00.exon1 N/A Os01t0100650-00.exon1 N/A Os01t0100650-00.exon1 transcript:Os01t0100650-00 N/A 1 N/A
|
||||
1 irgsp CDS 26040 26423 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100650-00 N/A N/A transcript:Os01t0100650-00 Os01t0100650-00 N/A N/A
|
||||
1 irgsp five_prime_UTR 26424 26424 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-9 N/A N/A transcript:Os01t0100650-00 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 25861 26039 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-9 N/A N/A transcript:Os01t0100650-00 N/A N/A N/A
|
||||
1 irgsp gene 27143 28644 . 1 . N/A protein_coding N/A Similar to 40S ribosomal protein S5-1. (Os01t0100700-01) N/A N/A N/A Os01g0100700 gene:Os01g0100700 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 27143 28644 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0100700-01 N/A N/A gene:Os01g0100700 N/A N/A Os01t0100700-01
|
||||
1 irgsp exon 27143 27292 . 1 . N/A N/A 1 N/A 0 -1 Os01t0100700-01.exon1 N/A Os01t0100700-01.exon1 N/A Os01t0100700-01.exon1 transcript:Os01t0100700-01 N/A 1 N/A
|
||||
1 irgsp exon 27370 27641 . 1 . N/A N/A 1 N/A 2 0 Os01t0100700-01.exon2 N/A Os01t0100700-01.exon2 N/A Os01t0100700-01.exon2 transcript:Os01t0100700-01 N/A 2 N/A
|
||||
1 irgsp exon 28090 28293 . 1 . N/A N/A 1 N/A 2 2 Os01t0100700-01.exon3 N/A Os01t0100700-01.exon3 N/A Os01t0100700-01.exon3 transcript:Os01t0100700-01 N/A 3 N/A
|
||||
1 irgsp exon 28365 28644 . 1 . N/A N/A 1 N/A -1 2 Os01t0100700-01.exon4 N/A Os01t0100700-01.exon4 N/A Os01t0100700-01.exon4 transcript:Os01t0100700-01 N/A 4 N/A
|
||||
1 irgsp CDS 27221 27292 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100700-01 N/A N/A transcript:Os01t0100700-01 Os01t0100700-01 N/A N/A
|
||||
1 irgsp CDS 27370 27641 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100700-01 N/A N/A transcript:Os01t0100700-01 Os01t0100700-01 N/A N/A
|
||||
1 irgsp CDS 28090 28293 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100700-01 N/A N/A transcript:Os01t0100700-01 Os01t0100700-01 N/A N/A
|
||||
1 irgsp CDS 28365 28419 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100700-01 N/A N/A transcript:Os01t0100700-01 Os01t0100700-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 27143 27220 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-10 N/A N/A transcript:Os01t0100700-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 28420 28644 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-10 N/A N/A transcript:Os01t0100700-01 N/A N/A N/A
|
||||
1 irgsp gene 29818 34453 . 1 . N/A protein_coding N/A Protein of unknown function DUF1664 family protein. (Os01t0100800-01) N/A N/A N/A Os01g0100800 gene:Os01g0100800 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 29818 34453 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0100800-01 N/A N/A gene:Os01g0100800 N/A N/A Os01t0100800-01
|
||||
1 irgsp exon 29818 29976 . 1 . N/A N/A 1 N/A 1 -1 Os01t0100800-01.exon1 N/A Os01t0100800-01.exon1 N/A Os01t0100800-01.exon1 transcript:Os01t0100800-01 N/A 1 N/A
|
||||
1 irgsp exon 30146 30228 . 1 . N/A N/A 1 N/A 0 1 Os01t0100800-01.exon2 N/A Os01t0100800-01.exon2 N/A Os01t0100800-01.exon2 transcript:Os01t0100800-01 N/A 2 N/A
|
||||
1 irgsp exon 30735 30806 . 1 . N/A N/A 1 N/A 0 0 Os01t0100800-01.exon3 N/A Os01t0100800-01.exon3 N/A Os01t0100800-01.exon3 transcript:Os01t0100800-01 N/A 3 N/A
|
||||
1 irgsp exon 30885 30963 . 1 . N/A N/A 1 N/A 1 0 Os01t0100800-01.exon4 N/A Os01t0100800-01.exon4 N/A Os01t0100800-01.exon4 transcript:Os01t0100800-01 N/A 4 N/A
|
||||
1 irgsp exon 31258 31325 . 1 . N/A N/A 1 N/A 0 1 Os01t0100800-01.exon5 N/A Os01t0100800-01.exon5 N/A Os01t0100800-01.exon5 transcript:Os01t0100800-01 N/A 5 N/A
|
||||
1 irgsp exon 31505 31606 . 1 . N/A N/A 1 N/A 0 0 Os01t0100800-01.exon6 N/A Os01t0100800-01.exon6 N/A Os01t0100800-01.exon6 transcript:Os01t0100800-01 N/A 6 N/A
|
||||
1 irgsp exon 32377 32466 . 1 . N/A N/A 1 N/A 0 0 Os01t0100800-01.exon7 N/A Os01t0100800-01.exon7 N/A Os01t0100800-01.exon7 transcript:Os01t0100800-01 N/A 7 N/A
|
||||
1 irgsp exon 32542 32616 . 1 . N/A N/A 1 N/A 0 0 Os01t0100800-01.exon8 N/A Os01t0100800-01.exon8 N/A Os01t0100800-01.exon8 transcript:Os01t0100800-01 N/A 8 N/A
|
||||
1 irgsp exon 32712 32744 . 1 . N/A N/A 1 N/A 0 0 Os01t0100800-01.exon9 N/A Os01t0100800-01.exon9 N/A Os01t0100800-01.exon9 transcript:Os01t0100800-01 N/A 9 N/A
|
||||
1 irgsp exon 32828 32905 . 1 . N/A N/A 1 N/A 0 0 Os01t0100800-01.exon10 N/A Os01t0100800-01.exon10 N/A Os01t0100800-01.exon10 transcript:Os01t0100800-01 N/A 10 N/A
|
||||
1 irgsp exon 33274 33330 . 1 . N/A N/A 1 N/A 0 0 Os01t0100800-01.exon11 N/A Os01t0100800-01.exon11 N/A Os01t0100800-01.exon11 transcript:Os01t0100800-01 N/A 11 N/A
|
||||
1 irgsp exon 33400 33471 . 1 . N/A N/A 1 N/A 0 0 Os01t0100800-01.exon12 N/A Os01t0100800-01.exon12 N/A Os01t0100800-01.exon12 transcript:Os01t0100800-01 N/A 12 N/A
|
||||
1 irgsp exon 33543 33617 . 1 . N/A N/A 1 N/A 0 0 Os01t0100800-01.exon13 N/A Os01t0100800-01.exon13 N/A Os01t0100800-01.exon13 transcript:Os01t0100800-01 N/A 13 N/A
|
||||
1 irgsp exon 33975 34453 . 1 . N/A N/A 1 N/A -1 0 Os01t0100800-01.exon14 N/A Os01t0100800-01.exon14 N/A Os01t0100800-01.exon14 transcript:Os01t0100800-01 N/A 14 N/A
|
||||
1 irgsp CDS 29940 29976 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100800-01 N/A N/A transcript:Os01t0100800-01 Os01t0100800-01 N/A N/A
|
||||
1 irgsp CDS 30146 30228 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100800-01 N/A N/A transcript:Os01t0100800-01 Os01t0100800-01 N/A N/A
|
||||
1 irgsp CDS 30735 30806 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100800-01 N/A N/A transcript:Os01t0100800-01 Os01t0100800-01 N/A N/A
|
||||
1 irgsp CDS 30885 30963 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100800-01 N/A N/A transcript:Os01t0100800-01 Os01t0100800-01 N/A N/A
|
||||
1 irgsp CDS 31258 31325 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100800-01 N/A N/A transcript:Os01t0100800-01 Os01t0100800-01 N/A N/A
|
||||
1 irgsp CDS 31505 31606 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100800-01 N/A N/A transcript:Os01t0100800-01 Os01t0100800-01 N/A N/A
|
||||
1 irgsp CDS 32377 32466 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100800-01 N/A N/A transcript:Os01t0100800-01 Os01t0100800-01 N/A N/A
|
||||
1 irgsp CDS 32542 32616 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100800-01 N/A N/A transcript:Os01t0100800-01 Os01t0100800-01 N/A N/A
|
||||
1 irgsp CDS 32712 32744 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100800-01 N/A N/A transcript:Os01t0100800-01 Os01t0100800-01 N/A N/A
|
||||
1 irgsp CDS 32828 32905 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100800-01 N/A N/A transcript:Os01t0100800-01 Os01t0100800-01 N/A N/A
|
||||
1 irgsp CDS 33274 33330 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100800-01 N/A N/A transcript:Os01t0100800-01 Os01t0100800-01 N/A N/A
|
||||
1 irgsp CDS 33400 33471 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100800-01 N/A N/A transcript:Os01t0100800-01 Os01t0100800-01 N/A N/A
|
||||
1 irgsp CDS 33543 33617 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100800-01 N/A N/A transcript:Os01t0100800-01 Os01t0100800-01 N/A N/A
|
||||
1 irgsp CDS 33975 34124 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100800-01 N/A N/A transcript:Os01t0100800-01 Os01t0100800-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 29818 29939 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-11 N/A N/A transcript:Os01t0100800-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 34125 34453 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-11 N/A N/A transcript:Os01t0100800-01 N/A N/A N/A
|
||||
1 irgsp gene 35623 41136 . 1 . N/A protein_coding N/A Sphingosine-1-phosphate lyase, Disease resistance response (Os01t0100900-01) N/A N/A N/A Os01g0100900 gene:Os01g0100900 irgspv1.0-20170804-genes SPHINGOSINE-1-PHOSPHATE LYASE 1, Sphingosine-1-Phoshpate Lyase 1 N/A N/A N/A N/A
|
||||
1 irgsp mRNA 35623 41136 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0100900-01 N/A N/A gene:Os01g0100900 N/A N/A Os01t0100900-01
|
||||
1 irgsp exon 35623 35939 . 1 . N/A N/A 1 N/A 2 -1 Os01t0100900-01.exon1 N/A Os01t0100900-01.exon1 N/A Os01t0100900-01.exon1 transcript:Os01t0100900-01 N/A 1 N/A
|
||||
1 irgsp exon 36027 36072 . 1 . N/A N/A 1 N/A 0 2 Os01t0100900-01.exon2 N/A Os01t0100900-01.exon2 N/A Os01t0100900-01.exon2 transcript:Os01t0100900-01 N/A 2 N/A
|
||||
1 irgsp exon 36517 36668 . 1 . N/A N/A 1 N/A 2 0 Os01t0100900-01.exon3 N/A Os01t0100900-01.exon3 N/A Os01t0100900-01.exon3 transcript:Os01t0100900-01 N/A 3 N/A
|
||||
1 irgsp exon 36818 36877 . 1 . N/A N/A 1 N/A 2 2 Os01t0100900-01.exon4 N/A Os01t0100900-01.exon4 N/A Os01t0100900-01.exon4 transcript:Os01t0100900-01 N/A 4 N/A
|
||||
1 irgsp exon 37594 37818 . 1 . N/A N/A 1 N/A 2 2 Os01t0100900-01.exon5 N/A Os01t0100900-01.exon5 N/A Os01t0100900-01.exon5 transcript:Os01t0100900-01 N/A 5 N/A
|
||||
1 irgsp exon 37892 38033 . 1 . N/A N/A 1 N/A 0 2 Os01t0100900-01.exon6 N/A Os01t0100900-01.exon6 N/A Os01t0100900-01.exon6 transcript:Os01t0100900-01 N/A 6 N/A
|
||||
1 irgsp exon 38276 38326 . 1 . N/A N/A 1 N/A 0 0 Os01t0100900-01.exon7 N/A Os01t0100900-01.exon7 N/A Os01t0100900-01.exon7 transcript:Os01t0100900-01 N/A 7 N/A
|
||||
1 irgsp exon 38434 38525 . 1 . N/A N/A 1 N/A 2 0 Os01t0100900-01.exon8 N/A Os01t0100900-01.exon8 N/A Os01t0100900-01.exon8 transcript:Os01t0100900-01 N/A 8 N/A
|
||||
1 irgsp exon 39319 39445 . 1 . N/A N/A 1 N/A 0 2 Os01t0100900-01.exon9 N/A Os01t0100900-01.exon9 N/A Os01t0100900-01.exon9 transcript:Os01t0100900-01 N/A 9 N/A
|
||||
1 irgsp exon 39553 39568 . 1 . N/A N/A 1 N/A 1 0 Os01t0100900-01.exon10 N/A Os01t0100900-01.exon10 N/A Os01t0100900-01.exon10 transcript:Os01t0100900-01 N/A 10 N/A
|
||||
1 irgsp exon 39939 40046 . 1 . N/A N/A 1 N/A 1 1 Os01t0100900-01.exon11 N/A Os01t0100900-01.exon11 N/A Os01t0100900-01.exon11 transcript:Os01t0100900-01 N/A 11 N/A
|
||||
1 irgsp exon 40135 40189 . 1 . N/A N/A 1 N/A 2 1 Os01t0100900-01.exon12 N/A Os01t0100900-01.exon12 N/A Os01t0100900-01.exon12 transcript:Os01t0100900-01 N/A 12 N/A
|
||||
1 irgsp exon 40456 40602 . 1 . N/A N/A 1 N/A 2 2 Os01t0100900-01.exon13 N/A Os01t0100900-01.exon13 N/A Os01t0100900-01.exon13 transcript:Os01t0100900-01 N/A 13 N/A
|
||||
1 irgsp exon 40703 40781 . 1 . N/A N/A 1 N/A 0 2 Os01t0100900-01.exon14 N/A Os01t0100900-01.exon14 N/A Os01t0100900-01.exon14 transcript:Os01t0100900-01 N/A 14 N/A
|
||||
1 irgsp exon 40885 41136 . 1 . N/A N/A 1 N/A -1 0 Os01t0100900-01.exon15 N/A Os01t0100900-01.exon15 N/A Os01t0100900-01.exon15 transcript:Os01t0100900-01 N/A 15 N/A
|
||||
1 irgsp CDS 35743 35939 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100900-01 N/A N/A transcript:Os01t0100900-01 Os01t0100900-01 N/A N/A
|
||||
1 irgsp CDS 36027 36072 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100900-01 N/A N/A transcript:Os01t0100900-01 Os01t0100900-01 N/A N/A
|
||||
1 irgsp CDS 36517 36668 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100900-01 N/A N/A transcript:Os01t0100900-01 Os01t0100900-01 N/A N/A
|
||||
1 irgsp CDS 36818 36877 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100900-01 N/A N/A transcript:Os01t0100900-01 Os01t0100900-01 N/A N/A
|
||||
1 irgsp CDS 37594 37818 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100900-01 N/A N/A transcript:Os01t0100900-01 Os01t0100900-01 N/A N/A
|
||||
1 irgsp CDS 37892 38033 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100900-01 N/A N/A transcript:Os01t0100900-01 Os01t0100900-01 N/A N/A
|
||||
1 irgsp CDS 38276 38326 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100900-01 N/A N/A transcript:Os01t0100900-01 Os01t0100900-01 N/A N/A
|
||||
1 irgsp CDS 38434 38525 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100900-01 N/A N/A transcript:Os01t0100900-01 Os01t0100900-01 N/A N/A
|
||||
1 irgsp CDS 39319 39445 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100900-01 N/A N/A transcript:Os01t0100900-01 Os01t0100900-01 N/A N/A
|
||||
1 irgsp CDS 39553 39568 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100900-01 N/A N/A transcript:Os01t0100900-01 Os01t0100900-01 N/A N/A
|
||||
1 irgsp CDS 39939 40046 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100900-01 N/A N/A transcript:Os01t0100900-01 Os01t0100900-01 N/A N/A
|
||||
1 irgsp CDS 40135 40189 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100900-01 N/A N/A transcript:Os01t0100900-01 Os01t0100900-01 N/A N/A
|
||||
1 irgsp CDS 40456 40602 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100900-01 N/A N/A transcript:Os01t0100900-01 Os01t0100900-01 N/A N/A
|
||||
1 irgsp CDS 40703 40781 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100900-01 N/A N/A transcript:Os01t0100900-01 Os01t0100900-01 N/A N/A
|
||||
1 irgsp CDS 40885 41007 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0100900-01 N/A N/A transcript:Os01t0100900-01 Os01t0100900-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 35623 35742 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-12 N/A N/A transcript:Os01t0100900-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 41008 41136 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-12 N/A N/A transcript:Os01t0100900-01 N/A N/A N/A
|
||||
1 irgsp gene 58658 61090 . 1 . N/A protein_coding N/A Hypothetical conserved gene. (Os01t0101150-00) N/A N/A N/A Os01g0101150 gene:Os01g0101150 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 58658 61090 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0101150-00 N/A N/A gene:Os01g0101150 N/A N/A Os01t0101150-00
|
||||
1 irgsp exon 58658 61090 . 1 . N/A N/A 1 N/A 0 0 Os01t0101150-00.exon1 N/A Os01t0101150-00.exon1 N/A Os01t0101150-00.exon1 transcript:Os01t0101150-00 N/A 1 N/A
|
||||
1 irgsp CDS 58658 61090 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101150-00 N/A N/A transcript:Os01t0101150-00 Os01t0101150-00 N/A N/A
|
||||
1 irgsp gene 62060 65537 . 1 . N/A protein_coding N/A 2,3-diketo-5-methylthio-1-phosphopentane phosphatase domain containing protein. (Os01t0101200-01);2,3-diketo-5-methylthio-1-phosphopentane phosphatase domain containing protein. (Os01t0101200-02) N/A N/A N/A Os01g0101200 gene:Os01g0101200 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 62060 63576 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0101200-01 N/A N/A gene:Os01g0101200 N/A N/A Os01t0101200-01
|
||||
1 irgsp exon 62060 62295 . 1 . N/A N/A 0 N/A 0 -1 Os01t0101200-01.exon1 N/A Os01t0101200-01.exon1 N/A Os01t0101200-01.exon1 transcript:Os01t0101200-01 N/A 1 N/A
|
||||
1 irgsp exon 62385 62905 . 1 . N/A N/A 1 N/A 2 0 Os01t0101200-02.exon2 N/A Os01t0101200-02.exon2 N/A Os01t0101200-02.exon2 transcript:Os01t0101200-01 N/A 2 N/A
|
||||
1 irgsp exon 62996 63114 . 1 . N/A N/A 1 N/A 1 2 Os01t0101200-02.exon3 N/A Os01t0101200-02.exon3 N/A Os01t0101200-02.exon3 transcript:Os01t0101200-01 N/A 3 N/A
|
||||
1 irgsp exon 63248 63576 . 1 . N/A N/A 0 N/A -1 1 Os01t0101200-01.exon4 N/A Os01t0101200-01.exon4 N/A Os01t0101200-01.exon4 transcript:Os01t0101200-01 N/A 4 N/A
|
||||
1 irgsp CDS 62104 62295 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101200-01 N/A N/A transcript:Os01t0101200-01 Os01t0101200-01 N/A N/A
|
||||
1 irgsp CDS 62385 62905 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101200-01 N/A N/A transcript:Os01t0101200-01 Os01t0101200-01 N/A N/A
|
||||
1 irgsp CDS 62996 63114 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101200-01 N/A N/A transcript:Os01t0101200-01 Os01t0101200-01 N/A N/A
|
||||
1 irgsp CDS 63248 63345 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101200-01 N/A N/A transcript:Os01t0101200-01 Os01t0101200-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 62060 62103 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-13 N/A N/A transcript:Os01t0101200-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 63346 63576 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-13 N/A N/A transcript:Os01t0101200-01 N/A N/A N/A
|
||||
1 irgsp mRNA 62112 65537 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0101200-02 N/A N/A gene:Os01g0101200 N/A N/A Os01t0101200-02
|
||||
1 irgsp exon 62112 62295 . 1 . N/A N/A 0 N/A 0 -1 Os01t0101200-02.exon1 N/A Os01t0101200-02.exon1 N/A Os01t0101200-02.exon1 transcript:Os01t0101200-02 N/A 1 N/A
|
||||
1 irgsp exon 62385 62905 . 1 . N/A N/A 1 N/A 2 0 Os01t0101200-02.exon2 N/A agat-exon-1 N/A Os01t0101200-02.exon2 transcript:Os01t0101200-02 N/A 2 N/A
|
||||
1 irgsp exon 62996 63114 . 1 . N/A N/A 1 N/A 1 2 Os01t0101200-02.exon3 N/A agat-exon-2 N/A Os01t0101200-02.exon3 transcript:Os01t0101200-02 N/A 3 N/A
|
||||
1 irgsp exon 63248 65537 . 1 . N/A N/A 0 N/A -1 1 Os01t0101200-02.exon4 N/A Os01t0101200-02.exon4 N/A Os01t0101200-02.exon4 transcript:Os01t0101200-02 N/A 4 N/A
|
||||
1 irgsp CDS 62113 62295 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101200-02 N/A N/A transcript:Os01t0101200-02 Os01t0101200-02 N/A N/A
|
||||
1 irgsp CDS 62385 62905 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101200-02 N/A N/A transcript:Os01t0101200-02 Os01t0101200-02 N/A N/A
|
||||
1 irgsp CDS 62996 63114 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101200-02 N/A N/A transcript:Os01t0101200-02 Os01t0101200-02 N/A N/A
|
||||
1 irgsp CDS 63248 63345 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101200-02 N/A N/A transcript:Os01t0101200-02 Os01t0101200-02 N/A N/A
|
||||
1 irgsp five_prime_UTR 62112 62112 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-14 N/A N/A transcript:Os01t0101200-02 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 63346 65537 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-14 N/A N/A transcript:Os01t0101200-02 N/A N/A N/A
|
||||
1 irgsp gene 63350 66302 . -1 . N/A protein_coding N/A Similar to MRNA, partial cds, clone: RAFL22-26-L17. (Fragment). (Os01t0101300-01) N/A N/A N/A Os01g0101300 gene:Os01g0101300 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 63350 66302 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0101300-01 N/A N/A gene:Os01g0101300 N/A N/A Os01t0101300-01
|
||||
1 irgsp exon 63350 63783 . -1 . N/A N/A 1 N/A -1 0 Os01t0101300-01.exon7 N/A Os01t0101300-01.exon7 N/A Os01t0101300-01.exon7 transcript:Os01t0101300-01 N/A 7 N/A
|
||||
1 irgsp exon 63877 64020 . -1 . N/A N/A 1 N/A 0 0 Os01t0101300-01.exon6 N/A Os01t0101300-01.exon6 N/A Os01t0101300-01.exon6 transcript:Os01t0101300-01 N/A 6 N/A
|
||||
1 irgsp exon 64339 64431 . -1 . N/A N/A 1 N/A 0 0 Os01t0101300-01.exon5 N/A Os01t0101300-01.exon5 N/A Os01t0101300-01.exon5 transcript:Os01t0101300-01 N/A 5 N/A
|
||||
1 irgsp exon 64665 64779 . -1 . N/A N/A 1 N/A 0 2 Os01t0101300-01.exon4 N/A Os01t0101300-01.exon4 N/A Os01t0101300-01.exon4 transcript:Os01t0101300-01 N/A 4 N/A
|
||||
1 irgsp exon 64902 65152 . -1 . N/A N/A 1 N/A 2 0 Os01t0101300-01.exon3 N/A Os01t0101300-01.exon3 N/A Os01t0101300-01.exon3 transcript:Os01t0101300-01 N/A 3 N/A
|
||||
1 irgsp exon 65248 65431 . -1 . N/A N/A 1 N/A 0 2 Os01t0101300-01.exon2 N/A Os01t0101300-01.exon2 N/A Os01t0101300-01.exon2 transcript:Os01t0101300-01 N/A 2 N/A
|
||||
1 irgsp exon 65628 66302 . -1 . N/A N/A 1 N/A 2 -1 Os01t0101300-01.exon1 N/A Os01t0101300-01.exon1 N/A Os01t0101300-01.exon1 transcript:Os01t0101300-01 N/A 1 N/A
|
||||
1 irgsp CDS 63670 63783 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101300-01 N/A N/A transcript:Os01t0101300-01 Os01t0101300-01 N/A N/A
|
||||
1 irgsp CDS 63877 64020 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101300-01 N/A N/A transcript:Os01t0101300-01 Os01t0101300-01 N/A N/A
|
||||
1 irgsp CDS 64339 64431 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101300-01 N/A N/A transcript:Os01t0101300-01 Os01t0101300-01 N/A N/A
|
||||
1 irgsp CDS 64665 64779 . -1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101300-01 N/A N/A transcript:Os01t0101300-01 Os01t0101300-01 N/A N/A
|
||||
1 irgsp CDS 64902 65152 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101300-01 N/A N/A transcript:Os01t0101300-01 Os01t0101300-01 N/A N/A
|
||||
1 irgsp CDS 65248 65431 . -1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101300-01 N/A N/A transcript:Os01t0101300-01 Os01t0101300-01 N/A N/A
|
||||
1 irgsp CDS 65628 65950 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101300-01 N/A N/A transcript:Os01t0101300-01 Os01t0101300-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 65951 66302 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-15 N/A N/A transcript:Os01t0101300-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 63350 63669 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-15 N/A N/A transcript:Os01t0101300-01 N/A N/A N/A
|
||||
1 irgsp gene 72816 78349 . 1 . N/A protein_coding N/A Immunoglobulin-like fold domain containing protein. (Os01t0101600-01);Immunoglobulin-like fold domain containing protein. (Os01t0101600-02);Hypothetical conserved gene. (Os01t0101600-03) N/A N/A N/A Os01g0101600 gene:Os01g0101600 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 72816 78349 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0101600-01 N/A N/A gene:Os01g0101600 N/A N/A Os01t0101600-01
|
||||
1 irgsp exon 72816 73935 . 1 . N/A N/A 0 N/A 1 -1 Os01t0101600-01.exon1 N/A Os01t0101600-01.exon1 N/A Os01t0101600-01.exon1 transcript:Os01t0101600-01 N/A 1 N/A
|
||||
1 irgsp exon 74468 74981 . 1 . N/A N/A 0 N/A 2 1 Os01t0101600-02.exon2 N/A Os01t0101600-02.exon2 N/A Os01t0101600-02.exon2 transcript:Os01t0101600-01 N/A 2 N/A
|
||||
1 irgsp exon 75619 77205 . 1 . N/A N/A 0 N/A -1 2 Os01t0101600-01.exon3 N/A Os01t0101600-01.exon3 N/A Os01t0101600-01.exon3 transcript:Os01t0101600-01 N/A 3 N/A
|
||||
1 irgsp exon 77333 78349 . 1 . N/A N/A 0 N/A -1 -1 Os01t0101600-01.exon4 N/A Os01t0101600-01.exon4 N/A Os01t0101600-01.exon4 transcript:Os01t0101600-01 N/A 4 N/A
|
||||
1 irgsp CDS 72903 73935 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101600-01 N/A N/A transcript:Os01t0101600-01 Os01t0101600-01 N/A N/A
|
||||
1 irgsp CDS 74468 74981 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101600-01 N/A N/A transcript:Os01t0101600-01 Os01t0101600-01 N/A N/A
|
||||
1 irgsp CDS 75619 77008 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101600-01 N/A N/A transcript:Os01t0101600-01 Os01t0101600-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 72816 72902 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-16 N/A N/A transcript:Os01t0101600-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 77009 77205 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-16 N/A N/A transcript:Os01t0101600-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 77333 78349 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-17 N/A N/A transcript:Os01t0101600-01 N/A N/A N/A
|
||||
1 irgsp mRNA 72823 77699 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0101600-02 N/A N/A gene:Os01g0101600 N/A N/A Os01t0101600-02
|
||||
1 irgsp exon 72823 73935 . 1 . N/A N/A 0 N/A 1 -1 Os01t0101600-02.exon1 N/A Os01t0101600-02.exon1 N/A Os01t0101600-02.exon1 transcript:Os01t0101600-02 N/A 1 N/A
|
||||
1 irgsp exon 74468 74981 . 1 . N/A N/A 0 N/A 2 1 Os01t0101600-02.exon2 N/A agat-exon-3 N/A Os01t0101600-02.exon2 transcript:Os01t0101600-02 N/A 2 N/A
|
||||
1 irgsp exon 75619 77699 . 1 . N/A N/A 0 N/A -1 2 Os01t0101600-02.exon3 N/A Os01t0101600-02.exon3 N/A Os01t0101600-02.exon3 transcript:Os01t0101600-02 N/A 3 N/A
|
||||
1 irgsp CDS 72903 73935 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101600-02 N/A N/A transcript:Os01t0101600-02 Os01t0101600-02 N/A N/A
|
||||
1 irgsp CDS 74468 74981 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101600-02 N/A N/A transcript:Os01t0101600-02 Os01t0101600-02 N/A N/A
|
||||
1 irgsp CDS 75619 77008 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101600-02 N/A N/A transcript:Os01t0101600-02 Os01t0101600-02 N/A N/A
|
||||
1 irgsp five_prime_UTR 72823 72902 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-17 N/A N/A transcript:Os01t0101600-02 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 77009 77699 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-18 N/A N/A transcript:Os01t0101600-02 N/A N/A N/A
|
||||
1 irgsp mRNA 75942 77699 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0101600-03 N/A N/A gene:Os01g0101600 N/A N/A Os01t0101600-03
|
||||
1 irgsp exon 75942 77699 . 1 . N/A N/A 0 N/A -1 -1 Os01t0101600-03.exon1 N/A Os01t0101600-03.exon1 N/A Os01t0101600-03.exon1 transcript:Os01t0101600-03 N/A 1 N/A
|
||||
1 irgsp CDS 75944 77008 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101600-03 N/A N/A transcript:Os01t0101600-03 Os01t0101600-03 N/A N/A
|
||||
1 irgsp five_prime_UTR 75942 75943 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-18 N/A N/A transcript:Os01t0101600-03 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 77009 77699 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-19 N/A N/A transcript:Os01t0101600-03 N/A N/A N/A
|
||||
1 irgsp gene 82426 84095 . 1 . N/A protein_coding N/A Similar to chaperone protein dnaJ 20. (Os01t0101700-00) N/A N/A N/A Os01g0101700 gene:Os01g0101700 irgspv1.0-20170804-genes DnaJ domain protein C1, rice DJC26 homolog N/A N/A N/A N/A
|
||||
1 irgsp mRNA 82426 84095 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0101700-00 N/A N/A gene:Os01g0101700 N/A N/A Os01t0101700-00
|
||||
1 irgsp exon 82426 82932 . 1 . N/A N/A 1 N/A 0 -1 Os01t0101700-00.exon1 N/A Os01t0101700-00.exon1 N/A Os01t0101700-00.exon1 transcript:Os01t0101700-00 N/A 1 N/A
|
||||
1 irgsp exon 83724 84095 . 1 . N/A N/A 1 N/A -1 0 Os01t0101700-00.exon2 N/A Os01t0101700-00.exon2 N/A Os01t0101700-00.exon2 transcript:Os01t0101700-00 N/A 2 N/A
|
||||
1 irgsp CDS 82507 82932 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101700-00 N/A N/A transcript:Os01t0101700-00 Os01t0101700-00 N/A N/A
|
||||
1 irgsp CDS 83724 83864 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101700-00 N/A N/A transcript:Os01t0101700-00 Os01t0101700-00 N/A N/A
|
||||
1 irgsp five_prime_UTR 82426 82506 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-19 N/A N/A transcript:Os01t0101700-00 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 83865 84095 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-20 N/A N/A transcript:Os01t0101700-00 N/A N/A N/A
|
||||
1 irgsp gene 85337 88844 . 1 . N/A protein_coding N/A Conserved hypothetical protein. (Os01t0101800-01) N/A N/A N/A Os01g0101800 gene:Os01g0101800 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 85337 88844 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0101800-01 N/A N/A gene:Os01g0101800 N/A N/A Os01t0101800-01
|
||||
1 irgsp exon 85337 85600 . 1 . N/A N/A 1 N/A 0 -1 Os01t0101800-01.exon1 N/A Os01t0101800-01.exon1 N/A Os01t0101800-01.exon1 transcript:Os01t0101800-01 N/A 1 N/A
|
||||
1 irgsp exon 85737 85830 . 1 . N/A N/A 1 N/A 1 0 Os01t0101800-01.exon2 N/A Os01t0101800-01.exon2 N/A Os01t0101800-01.exon2 transcript:Os01t0101800-01 N/A 2 N/A
|
||||
1 irgsp exon 85935 86086 . 1 . N/A N/A 1 N/A 0 1 Os01t0101800-01.exon3 N/A Os01t0101800-01.exon3 N/A Os01t0101800-01.exon3 transcript:Os01t0101800-01 N/A 3 N/A
|
||||
1 irgsp exon 86212 86299 . 1 . N/A N/A 1 N/A 1 0 Os01t0101800-01.exon4 N/A Os01t0101800-01.exon4 N/A Os01t0101800-01.exon4 transcript:Os01t0101800-01 N/A 4 N/A
|
||||
1 irgsp exon 86399 87681 . 1 . N/A N/A 1 N/A 0 1 Os01t0101800-01.exon5 N/A Os01t0101800-01.exon5 N/A Os01t0101800-01.exon5 transcript:Os01t0101800-01 N/A 5 N/A
|
||||
1 irgsp exon 88291 88398 . 1 . N/A N/A 1 N/A 0 0 Os01t0101800-01.exon6 N/A Os01t0101800-01.exon6 N/A Os01t0101800-01.exon6 transcript:Os01t0101800-01 N/A 6 N/A
|
||||
1 irgsp exon 88500 88844 . 1 . N/A N/A 1 N/A -1 0 Os01t0101800-01.exon7 N/A Os01t0101800-01.exon7 N/A Os01t0101800-01.exon7 transcript:Os01t0101800-01 N/A 7 N/A
|
||||
1 irgsp CDS 85379 85600 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101800-01 N/A N/A transcript:Os01t0101800-01 Os01t0101800-01 N/A N/A
|
||||
1 irgsp CDS 85737 85830 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101800-01 N/A N/A transcript:Os01t0101800-01 Os01t0101800-01 N/A N/A
|
||||
1 irgsp CDS 85935 86086 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101800-01 N/A N/A transcript:Os01t0101800-01 Os01t0101800-01 N/A N/A
|
||||
1 irgsp CDS 86212 86299 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101800-01 N/A N/A transcript:Os01t0101800-01 Os01t0101800-01 N/A N/A
|
||||
1 irgsp CDS 86399 87681 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101800-01 N/A N/A transcript:Os01t0101800-01 Os01t0101800-01 N/A N/A
|
||||
1 irgsp CDS 88291 88398 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101800-01 N/A N/A transcript:Os01t0101800-01 Os01t0101800-01 N/A N/A
|
||||
1 irgsp CDS 88500 88583 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101800-01 N/A N/A transcript:Os01t0101800-01 Os01t0101800-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 85337 85378 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-20 N/A N/A transcript:Os01t0101800-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 88584 88844 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-21 N/A N/A transcript:Os01t0101800-01 N/A N/A N/A
|
||||
1 irgsp gene 86211 88583 . -1 . N/A protein_coding N/A Hypothetical protein. (Os01t0101850-00) N/A N/A N/A Os01g0101850 gene:Os01g0101850 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 86211 88583 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0101850-00 N/A N/A gene:Os01g0101850 N/A N/A Os01t0101850-00
|
||||
1 irgsp exon 86211 86277 . -1 . N/A N/A 1 N/A -1 -1 Os01t0101850-00.exon4 N/A Os01t0101850-00.exon4 N/A Os01t0101850-00.exon4 transcript:Os01t0101850-00 N/A 4 N/A
|
||||
1 irgsp exon 86384 87694 . -1 . N/A N/A 1 N/A -1 -1 Os01t0101850-00.exon3 N/A Os01t0101850-00.exon3 N/A Os01t0101850-00.exon3 transcript:Os01t0101850-00 N/A 3 N/A
|
||||
1 irgsp exon 88308 88396 . -1 . N/A N/A 1 N/A -1 -1 Os01t0101850-00.exon2 N/A Os01t0101850-00.exon2 N/A Os01t0101850-00.exon2 transcript:Os01t0101850-00 N/A 2 N/A
|
||||
1 irgsp exon 88496 88583 . -1 . N/A N/A 1 N/A -1 -1 Os01t0101850-00.exon1 N/A Os01t0101850-00.exon1 N/A Os01t0101850-00.exon1 transcript:Os01t0101850-00 N/A 1 N/A
|
||||
1 irgsp CDS 87327 87662 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101850-00 N/A N/A transcript:Os01t0101850-00 Os01t0101850-00 N/A N/A
|
||||
1 irgsp five_prime_UTR 87663 87694 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-21 N/A N/A transcript:Os01t0101850-00 N/A N/A N/A
|
||||
1 irgsp five_prime_UTR 88308 88396 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-22 N/A N/A transcript:Os01t0101850-00 N/A N/A N/A
|
||||
1 irgsp five_prime_UTR 88496 88583 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-23 N/A N/A transcript:Os01t0101850-00 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 86211 86277 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-22 N/A N/A transcript:Os01t0101850-00 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 86384 87326 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-23 N/A N/A transcript:Os01t0101850-00 N/A N/A N/A
|
||||
1 irgsp gene 88883 89228 . -1 . N/A protein_coding N/A Similar to OSIGBa0075F02.3 protein. (Os01t0101900-00) N/A N/A N/A Os01g0101900 gene:Os01g0101900 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 88883 89228 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0101900-00 N/A N/A gene:Os01g0101900 N/A N/A Os01t0101900-00
|
||||
1 irgsp exon 88883 89228 . -1 . N/A N/A 1 N/A -1 -1 Os01t0101900-00.exon1 N/A Os01t0101900-00.exon1 N/A Os01t0101900-00.exon1 transcript:Os01t0101900-00 N/A 1 N/A
|
||||
1 irgsp CDS 88986 89204 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0101900-00 N/A N/A transcript:Os01t0101900-00 Os01t0101900-00 N/A N/A
|
||||
1 irgsp five_prime_UTR 89205 89228 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-24 N/A N/A transcript:Os01t0101900-00 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 88883 88985 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-24 N/A N/A transcript:Os01t0101900-00 N/A N/A N/A
|
||||
1 irgsp gene 89763 91465 . -1 . N/A protein_coding N/A Phosphoesterase family protein. (Os01t0102000-01) N/A N/A N/A Os01g0102000 gene:Os01g0102000 irgspv1.0-20170804-genes NON-SPECIFIC PHOSPHOLIPASE C5 N/A N/A N/A N/A
|
||||
1 irgsp mRNA 89763 91465 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0102000-01 N/A N/A gene:Os01g0102000 N/A N/A Os01t0102000-01
|
||||
1 irgsp exon 89763 91465 . -1 . N/A N/A 1 N/A -1 -1 Os01t0102000-01.exon1 N/A Os01t0102000-01.exon1 N/A Os01t0102000-01.exon1 transcript:Os01t0102000-01 N/A 1 N/A
|
||||
1 irgsp CDS 89825 91411 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102000-01 N/A N/A transcript:Os01t0102000-01 Os01t0102000-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 91412 91465 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-25 N/A N/A transcript:Os01t0102000-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 89763 89824 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-25 N/A N/A transcript:Os01t0102000-01 N/A N/A N/A
|
||||
1 irgsp gene 134300 135439 . 1 . N/A protein_coding N/A Thylakoid lumen protein, Photosynthesis and chloroplast development (Os01t0102300-01) N/A N/A N/A Os01g0102300 gene:Os01g0102300 irgspv1.0-20170804-genes OsTLP27 N/A N/A N/A N/A
|
||||
1 irgsp mRNA 134300 135439 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0102300-01 N/A N/A gene:Os01g0102300 N/A N/A Os01t0102300-01
|
||||
1 irgsp exon 134300 134615 . 1 . N/A N/A 1 N/A 2 -1 Os01t0102300-01.exon1 N/A Os01t0102300-01.exon1 N/A Os01t0102300-01.exon1 transcript:Os01t0102300-01 N/A 1 N/A
|
||||
1 irgsp exon 134698 134824 . 1 . N/A N/A 1 N/A 0 2 Os01t0102300-01.exon2 N/A Os01t0102300-01.exon2 N/A Os01t0102300-01.exon2 transcript:Os01t0102300-01 N/A 2 N/A
|
||||
1 irgsp exon 134912 135439 . 1 . N/A N/A 1 N/A -1 0 Os01t0102300-01.exon3 N/A Os01t0102300-01.exon3 N/A Os01t0102300-01.exon3 transcript:Os01t0102300-01 N/A 3 N/A
|
||||
1 irgsp CDS 134311 134615 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102300-01 N/A N/A transcript:Os01t0102300-01 Os01t0102300-01 N/A N/A
|
||||
1 irgsp CDS 134698 134824 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102300-01 N/A N/A transcript:Os01t0102300-01 Os01t0102300-01 N/A N/A
|
||||
1 irgsp CDS 134912 135253 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102300-01 N/A N/A transcript:Os01t0102300-01 Os01t0102300-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 134300 134310 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-26 N/A N/A transcript:Os01t0102300-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 135254 135439 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-26 N/A N/A transcript:Os01t0102300-01 N/A N/A N/A
|
||||
1 irgsp gene 139826 141555 . 1 . N/A protein_coding N/A Histone-fold domain containing protein. (Os01t0102400-01) N/A N/A N/A Os01g0102400 gene:Os01g0102400 irgspv1.0-20170804-genes HAP5H SUBUNIT OF CCAAT-BOX BINDING COMPLEX N/A N/A N/A N/A
|
||||
1 irgsp mRNA 139826 141555 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0102400-01 N/A N/A gene:Os01g0102400 N/A N/A Os01t0102400-01
|
||||
1 irgsp exon 139826 139906 . 1 . N/A N/A 1 N/A -1 -1 Os01t0102400-01.exon1 N/A Os01t0102400-01.exon1 N/A Os01t0102400-01.exon1 transcript:Os01t0102400-01 N/A 1 N/A
|
||||
1 irgsp exon 140120 141555 . 1 . N/A N/A 1 N/A -1 -1 Os01t0102400-01.exon2 N/A Os01t0102400-01.exon2 N/A Os01t0102400-01.exon2 transcript:Os01t0102400-01 N/A 2 N/A
|
||||
1 irgsp CDS 140150 141415 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102400-01 N/A N/A transcript:Os01t0102400-01 Os01t0102400-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 139826 139906 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-27 N/A N/A transcript:Os01t0102400-01 N/A N/A N/A
|
||||
1 irgsp five_prime_UTR 140120 140149 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-28 N/A N/A transcript:Os01t0102400-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 141416 141555 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-27 N/A N/A transcript:Os01t0102400-01 N/A N/A N/A
|
||||
1 irgsp gene 141959 144554 . 1 . N/A protein_coding N/A Conserved hypothetical protein. (Os01t0102500-01) N/A N/A N/A Os01g0102500 gene:Os01g0102500 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 141959 144554 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0102500-01 N/A N/A gene:Os01g0102500 N/A N/A Os01t0102500-01
|
||||
1 irgsp exon 141959 142631 . 1 . N/A N/A 1 N/A 2 -1 Os01t0102500-01.exon1 N/A Os01t0102500-01.exon1 N/A Os01t0102500-01.exon1 transcript:Os01t0102500-01 N/A 1 N/A
|
||||
1 irgsp exon 143191 143431 . 1 . N/A N/A 1 N/A 0 2 Os01t0102500-01.exon2 N/A Os01t0102500-01.exon2 N/A Os01t0102500-01.exon2 transcript:Os01t0102500-01 N/A 2 N/A
|
||||
1 irgsp exon 143563 143680 . 1 . N/A N/A 1 N/A 1 0 Os01t0102500-01.exon3 N/A Os01t0102500-01.exon3 N/A Os01t0102500-01.exon3 transcript:Os01t0102500-01 N/A 3 N/A
|
||||
1 irgsp exon 143817 144554 . 1 . N/A N/A 1 N/A -1 1 Os01t0102500-01.exon4 N/A Os01t0102500-01.exon4 N/A Os01t0102500-01.exon4 transcript:Os01t0102500-01 N/A 4 N/A
|
||||
1 irgsp CDS 142084 142631 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102500-01 N/A N/A transcript:Os01t0102500-01 Os01t0102500-01 N/A N/A
|
||||
1 irgsp CDS 143191 143431 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102500-01 N/A N/A transcript:Os01t0102500-01 Os01t0102500-01 N/A N/A
|
||||
1 irgsp CDS 143563 143680 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102500-01 N/A N/A transcript:Os01t0102500-01 Os01t0102500-01 N/A N/A
|
||||
1 irgsp CDS 143817 143908 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102500-01 N/A N/A transcript:Os01t0102500-01 Os01t0102500-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 141959 142083 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-29 N/A N/A transcript:Os01t0102500-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 143909 144554 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-28 N/A N/A transcript:Os01t0102500-01 N/A N/A N/A
|
||||
1 irgsp gene 145603 147847 . 1 . N/A protein_coding N/A Shikimate kinase domain containing protein. (Os01t0102600-01);Similar to shikimate kinase family protein. (Os01t0102600-02) N/A N/A N/A Os01g0102600 gene:Os01g0102600 irgspv1.0-20170804-genes Shikimate kinase 4 N/A N/A N/A N/A
|
||||
1 irgsp mRNA 145603 147847 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0102600-01 N/A N/A gene:Os01g0102600 N/A N/A Os01t0102600-01
|
||||
1 irgsp exon 145603 145786 . 1 . N/A N/A 0 N/A 1 -1 Os01t0102600-01.exon1 N/A Os01t0102600-01.exon1 N/A Os01t0102600-01.exon1 transcript:Os01t0102600-01 N/A 1 N/A
|
||||
1 irgsp exon 145905 145951 . 1 . N/A N/A 0 N/A 0 1 Os01t0102600-01.exon2 N/A Os01t0102600-01.exon2 N/A Os01t0102600-01.exon2 transcript:Os01t0102600-01 N/A 2 N/A
|
||||
1 irgsp exon 146028 146082 . 1 . N/A N/A 0 N/A 1 0 Os01t0102600-01.exon3 N/A Os01t0102600-01.exon3 N/A Os01t0102600-01.exon3 transcript:Os01t0102600-01 N/A 3 N/A
|
||||
1 irgsp exon 146179 146339 . 1 . N/A N/A 0 N/A 0 1 Os01t0102600-01.exon4 N/A Os01t0102600-01.exon4 N/A Os01t0102600-01.exon4 transcript:Os01t0102600-01 N/A 4 N/A
|
||||
1 irgsp exon 146450 146532 . 1 . N/A N/A 0 N/A 2 0 Os01t0102600-01.exon5 N/A Os01t0102600-01.exon5 N/A Os01t0102600-01.exon5 transcript:Os01t0102600-01 N/A 5 N/A
|
||||
1 irgsp exon 146611 146719 . 1 . N/A N/A 0 N/A 0 2 Os01t0102600-01.exon6 N/A Os01t0102600-01.exon6 N/A Os01t0102600-01.exon6 transcript:Os01t0102600-01 N/A 6 N/A
|
||||
1 irgsp exon 147106 147184 . 1 . N/A N/A 0 N/A 1 0 Os01t0102600-01.exon7 N/A Os01t0102600-01.exon7 N/A Os01t0102600-01.exon7 transcript:Os01t0102600-01 N/A 7 N/A
|
||||
1 irgsp exon 147311 147375 . 1 . N/A N/A 1 N/A 0 1 Os01t0102600-02.exon2 N/A Os01t0102600-02.exon2 N/A Os01t0102600-02.exon2 transcript:Os01t0102600-01 N/A 8 N/A
|
||||
1 irgsp exon 147507 147847 . 1 . N/A N/A 0 N/A -1 0 Os01t0102600-01.exon9 N/A Os01t0102600-01.exon9 N/A Os01t0102600-01.exon9 transcript:Os01t0102600-01 N/A 9 N/A
|
||||
1 irgsp CDS 145645 145786 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102600-01 N/A N/A transcript:Os01t0102600-01 Os01t0102600-01 N/A N/A
|
||||
1 irgsp CDS 145905 145951 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102600-01 N/A N/A transcript:Os01t0102600-01 Os01t0102600-01 N/A N/A
|
||||
1 irgsp CDS 146028 146082 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102600-01 N/A N/A transcript:Os01t0102600-01 Os01t0102600-01 N/A N/A
|
||||
1 irgsp CDS 146179 146339 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102600-01 N/A N/A transcript:Os01t0102600-01 Os01t0102600-01 N/A N/A
|
||||
1 irgsp CDS 146450 146532 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102600-01 N/A N/A transcript:Os01t0102600-01 Os01t0102600-01 N/A N/A
|
||||
1 irgsp CDS 146611 146719 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102600-01 N/A N/A transcript:Os01t0102600-01 Os01t0102600-01 N/A N/A
|
||||
1 irgsp CDS 147106 147184 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102600-01 N/A N/A transcript:Os01t0102600-01 Os01t0102600-01 N/A N/A
|
||||
1 irgsp CDS 147311 147375 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102600-01 N/A N/A transcript:Os01t0102600-01 Os01t0102600-01 N/A N/A
|
||||
1 irgsp CDS 147507 147575 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102600-01 N/A N/A transcript:Os01t0102600-01 Os01t0102600-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 145603 145644 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-30 N/A N/A transcript:Os01t0102600-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 147576 147847 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-29 N/A N/A transcript:Os01t0102600-01 N/A N/A N/A
|
||||
1 irgsp mRNA 147104 147805 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0102600-02 N/A N/A gene:Os01g0102600 N/A N/A Os01t0102600-02
|
||||
1 irgsp exon 147104 147184 . 1 . N/A N/A 0 N/A 1 -1 Os01t0102600-02.exon1 N/A Os01t0102600-02.exon1 N/A Os01t0102600-02.exon1 transcript:Os01t0102600-02 N/A 1 N/A
|
||||
1 irgsp exon 147311 147375 . 1 . N/A N/A 1 N/A 0 1 Os01t0102600-02.exon2 N/A agat-exon-4 N/A Os01t0102600-02.exon2 transcript:Os01t0102600-02 N/A 2 N/A
|
||||
1 irgsp exon 147507 147805 . 1 . N/A N/A 0 N/A -1 0 Os01t0102600-02.exon3 N/A Os01t0102600-02.exon3 N/A Os01t0102600-02.exon3 transcript:Os01t0102600-02 N/A 3 N/A
|
||||
1 irgsp CDS 147106 147184 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102600-02 N/A N/A transcript:Os01t0102600-02 Os01t0102600-02 N/A N/A
|
||||
1 irgsp CDS 147311 147375 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102600-02 N/A N/A transcript:Os01t0102600-02 Os01t0102600-02 N/A N/A
|
||||
1 irgsp CDS 147507 147575 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102600-02 N/A N/A transcript:Os01t0102600-02 Os01t0102600-02 N/A N/A
|
||||
1 irgsp five_prime_UTR 147104 147105 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-31 N/A N/A transcript:Os01t0102600-02 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 147576 147805 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-30 N/A N/A transcript:Os01t0102600-02 N/A N/A N/A
|
||||
1 irgsp gene 148085 150568 . 1 . N/A protein_coding N/A Translocon-associated beta family protein. (Os01t0102700-01) N/A N/A N/A Os01g0102700 gene:Os01g0102700 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 148085 150568 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0102700-01 N/A N/A gene:Os01g0102700 N/A N/A Os01t0102700-01
|
||||
1 irgsp exon 148085 148313 . 1 . N/A N/A 1 N/A 2 -1 Os01t0102700-01.exon1 N/A Os01t0102700-01.exon1 N/A Os01t0102700-01.exon1 transcript:Os01t0102700-01 N/A 1 N/A
|
||||
1 irgsp exon 149450 149548 . 1 . N/A N/A 1 N/A 2 2 Os01t0102700-01.exon2 N/A Os01t0102700-01.exon2 N/A Os01t0102700-01.exon2 transcript:Os01t0102700-01 N/A 2 N/A
|
||||
1 irgsp exon 149634 149742 . 1 . N/A N/A 1 N/A 0 2 Os01t0102700-01.exon3 N/A Os01t0102700-01.exon3 N/A Os01t0102700-01.exon3 transcript:Os01t0102700-01 N/A 3 N/A
|
||||
1 irgsp exon 149856 149931 . 1 . N/A N/A 1 N/A 1 0 Os01t0102700-01.exon4 N/A Os01t0102700-01.exon4 N/A Os01t0102700-01.exon4 transcript:Os01t0102700-01 N/A 4 N/A
|
||||
1 irgsp exon 150152 150568 . 1 . N/A N/A 1 N/A -1 1 Os01t0102700-01.exon5 N/A Os01t0102700-01.exon5 N/A Os01t0102700-01.exon5 transcript:Os01t0102700-01 N/A 5 N/A
|
||||
1 irgsp CDS 148147 148313 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102700-01 N/A N/A transcript:Os01t0102700-01 Os01t0102700-01 N/A N/A
|
||||
1 irgsp CDS 149450 149548 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102700-01 N/A N/A transcript:Os01t0102700-01 Os01t0102700-01 N/A N/A
|
||||
1 irgsp CDS 149634 149742 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102700-01 N/A N/A transcript:Os01t0102700-01 Os01t0102700-01 N/A N/A
|
||||
1 irgsp CDS 149856 149931 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102700-01 N/A N/A transcript:Os01t0102700-01 Os01t0102700-01 N/A N/A
|
||||
1 irgsp CDS 150152 150318 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102700-01 N/A N/A transcript:Os01t0102700-01 Os01t0102700-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 148085 148146 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-32 N/A N/A transcript:Os01t0102700-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 150319 150568 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-31 N/A N/A transcript:Os01t0102700-01 N/A N/A N/A
|
||||
1 irgsp gene 152853 156449 . 1 . N/A protein_coding N/A Similar to chromatin remodeling complex subunit. (Os01t0102800-01) N/A N/A N/A Os01g0102800 gene:Os01g0102800 irgspv1.0-20170804-genes Cockayne syndrome WD-repeat protein N/A N/A N/A N/A
|
||||
1 irgsp mRNA 152853 156449 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0102800-01 N/A N/A gene:Os01g0102800 N/A N/A Os01t0102800-01
|
||||
1 irgsp exon 152853 153025 . 1 . N/A N/A 1 N/A 1 -1 Os01t0102800-01.exon1 N/A Os01t0102800-01.exon1 N/A Os01t0102800-01.exon1 transcript:Os01t0102800-01 N/A 1 N/A
|
||||
1 irgsp exon 153178 154646 . 1 . N/A N/A 1 N/A 0 1 Os01t0102800-01.exon2 N/A Os01t0102800-01.exon2 N/A Os01t0102800-01.exon2 transcript:Os01t0102800-01 N/A 2 N/A
|
||||
1 irgsp exon 155010 155450 . 1 . N/A N/A 1 N/A 0 0 Os01t0102800-01.exon3 N/A Os01t0102800-01.exon3 N/A Os01t0102800-01.exon3 transcript:Os01t0102800-01 N/A 3 N/A
|
||||
1 irgsp exon 155543 156449 . 1 . N/A N/A 1 N/A -1 0 Os01t0102800-01.exon4 N/A Os01t0102800-01.exon4 N/A Os01t0102800-01.exon4 transcript:Os01t0102800-01 N/A 4 N/A
|
||||
1 irgsp CDS 152854 153025 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102800-01 N/A N/A transcript:Os01t0102800-01 Os01t0102800-01 N/A N/A
|
||||
1 irgsp CDS 153178 154646 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102800-01 N/A N/A transcript:Os01t0102800-01 Os01t0102800-01 N/A N/A
|
||||
1 irgsp CDS 155010 155450 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102800-01 N/A N/A transcript:Os01t0102800-01 Os01t0102800-01 N/A N/A
|
||||
1 irgsp CDS 155543 156214 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102800-01 N/A N/A transcript:Os01t0102800-01 Os01t0102800-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 152853 152853 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-33 N/A N/A transcript:Os01t0102800-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 156215 156449 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-32 N/A N/A transcript:Os01t0102800-01 N/A N/A N/A
|
||||
1 irgsp gene 164577 168921 . 1 . N/A protein_coding N/A Similar to nitrilase 2. (Os01t0102850-00) N/A N/A N/A Os01g0102850 gene:Os01g0102850 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 164577 168921 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0102850-00 N/A N/A gene:Os01g0102850 N/A N/A Os01t0102850-00
|
||||
1 irgsp exon 164577 164905 . 1 . N/A N/A 1 N/A -1 -1 Os01t0102850-00.exon1 N/A Os01t0102850-00.exon1 N/A Os01t0102850-00.exon1 transcript:Os01t0102850-00 N/A 1 N/A
|
||||
1 irgsp exon 168499 168921 . 1 . N/A N/A 1 N/A 0 -1 Os01t0102850-00.exon2 N/A Os01t0102850-00.exon2 N/A Os01t0102850-00.exon2 transcript:Os01t0102850-00 N/A 2 N/A
|
||||
1 irgsp CDS 168805 168921 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102850-00 N/A N/A transcript:Os01t0102850-00 Os01t0102850-00 N/A N/A
|
||||
1 irgsp five_prime_UTR 164577 164905 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-34 N/A N/A transcript:Os01t0102850-00 N/A N/A N/A
|
||||
1 irgsp five_prime_UTR 168499 168804 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-35 N/A N/A transcript:Os01t0102850-00 N/A N/A N/A
|
||||
1 irgsp gene 169390 170316 . -1 . N/A protein_coding N/A Light-regulated protein, Regulation of light-dependent attachment of LEAF-TYPE FERREDOXIN-NADP+ OXIDOREDUCTASE (LFNR) to the thylakoid membrane (Os01t0102900-01) N/A N/A N/A Os01g0102900 gene:Os01g0102900 irgspv1.0-20170804-genes LIGHT-REGULATED GENE 1 N/A N/A N/A N/A
|
||||
1 irgsp mRNA 169390 170316 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0102900-01 N/A N/A gene:Os01g0102900 N/A N/A Os01t0102900-01
|
||||
1 irgsp exon 169390 169656 . -1 . N/A N/A 1 N/A -1 2 Os01t0102900-01.exon3 N/A Os01t0102900-01.exon3 N/A Os01t0102900-01.exon3 transcript:Os01t0102900-01 N/A 3 N/A
|
||||
1 irgsp exon 169751 169909 . -1 . N/A N/A 1 N/A 2 2 Os01t0102900-01.exon2 N/A Os01t0102900-01.exon2 N/A Os01t0102900-01.exon2 transcript:Os01t0102900-01 N/A 2 N/A
|
||||
1 irgsp exon 170091 170316 . -1 . N/A N/A 1 N/A 2 -1 Os01t0102900-01.exon1 N/A Os01t0102900-01.exon1 N/A Os01t0102900-01.exon1 transcript:Os01t0102900-01 N/A 1 N/A
|
||||
1 irgsp CDS 169599 169656 . -1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102900-01 N/A N/A transcript:Os01t0102900-01 Os01t0102900-01 N/A N/A
|
||||
1 irgsp CDS 169751 169909 . -1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102900-01 N/A N/A transcript:Os01t0102900-01 Os01t0102900-01 N/A N/A
|
||||
1 irgsp CDS 170091 170260 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0102900-01 N/A N/A transcript:Os01t0102900-01 Os01t0102900-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 170261 170316 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-36 N/A N/A transcript:Os01t0102900-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 169390 169598 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-33 N/A N/A transcript:Os01t0102900-01 N/A N/A N/A
|
||||
1 irgsp gene 170798 173144 . -1 . N/A protein_coding N/A Snf7 family protein. (Os01t0103000-01) N/A N/A N/A Os01g0103000 gene:Os01g0103000 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 170798 173144 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0103000-01 N/A N/A gene:Os01g0103000 N/A N/A Os01t0103000-01
|
||||
1 irgsp exon 170798 171095 . -1 . N/A N/A 1 N/A -1 0 Os01t0103000-01.exon7 N/A Os01t0103000-01.exon7 N/A Os01t0103000-01.exon7 transcript:Os01t0103000-01 N/A 7 N/A
|
||||
1 irgsp exon 171406 171554 . -1 . N/A N/A 1 N/A 0 1 Os01t0103000-01.exon6 N/A Os01t0103000-01.exon6 N/A Os01t0103000-01.exon6 transcript:Os01t0103000-01 N/A 6 N/A
|
||||
1 irgsp exon 171764 171875 . -1 . N/A N/A 1 N/A 1 0 Os01t0103000-01.exon5 N/A Os01t0103000-01.exon5 N/A Os01t0103000-01.exon5 transcript:Os01t0103000-01 N/A 5 N/A
|
||||
1 irgsp exon 172398 172469 . -1 . N/A N/A 1 N/A 0 0 Os01t0103000-01.exon4 N/A Os01t0103000-01.exon4 N/A Os01t0103000-01.exon4 transcript:Os01t0103000-01 N/A 4 N/A
|
||||
1 irgsp exon 172578 172671 . -1 . N/A N/A 1 N/A 0 2 Os01t0103000-01.exon3 N/A Os01t0103000-01.exon3 N/A Os01t0103000-01.exon3 transcript:Os01t0103000-01 N/A 3 N/A
|
||||
1 irgsp exon 172770 172921 . -1 . N/A N/A 1 N/A 2 0 Os01t0103000-01.exon2 N/A Os01t0103000-01.exon2 N/A Os01t0103000-01.exon2 transcript:Os01t0103000-01 N/A 2 N/A
|
||||
1 irgsp exon 173004 173144 . -1 . N/A N/A 1 N/A 0 -1 Os01t0103000-01.exon1 N/A Os01t0103000-01.exon1 N/A Os01t0103000-01.exon1 transcript:Os01t0103000-01 N/A 1 N/A
|
||||
1 irgsp CDS 171045 171095 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103000-01 N/A N/A transcript:Os01t0103000-01 Os01t0103000-01 N/A N/A
|
||||
1 irgsp CDS 171406 171554 . -1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103000-01 N/A N/A transcript:Os01t0103000-01 Os01t0103000-01 N/A N/A
|
||||
1 irgsp CDS 171764 171875 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103000-01 N/A N/A transcript:Os01t0103000-01 Os01t0103000-01 N/A N/A
|
||||
1 irgsp CDS 172398 172469 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103000-01 N/A N/A transcript:Os01t0103000-01 Os01t0103000-01 N/A N/A
|
||||
1 irgsp CDS 172578 172671 . -1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103000-01 N/A N/A transcript:Os01t0103000-01 Os01t0103000-01 N/A N/A
|
||||
1 irgsp CDS 172770 172921 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103000-01 N/A N/A transcript:Os01t0103000-01 Os01t0103000-01 N/A N/A
|
||||
1 irgsp CDS 173004 173072 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103000-01 N/A N/A transcript:Os01t0103000-01 Os01t0103000-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 173073 173144 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-37 N/A N/A transcript:Os01t0103000-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 170798 171044 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-34 N/A N/A transcript:Os01t0103000-01 N/A N/A N/A
|
||||
1 irgsp gene 178607 180575 . 1 . N/A protein_coding N/A TGF-beta receptor, type I/II extracellular region family protein. (Os01t0103100-01);Similar to predicted protein. (Os01t0103100-02) N/A N/A N/A Os01g0103100 gene:Os01g0103100 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 178607 180548 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0103100-01 N/A N/A gene:Os01g0103100 N/A N/A Os01t0103100-01
|
||||
1 irgsp exon 178607 180548 . 1 . N/A N/A 0 N/A -1 -1 Os01t0103100-01.exon1 N/A Os01t0103100-01.exon1 N/A Os01t0103100-01.exon1 transcript:Os01t0103100-01 N/A 1 N/A
|
||||
1 irgsp CDS 178642 180462 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103100-01 N/A N/A transcript:Os01t0103100-01 Os01t0103100-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 178607 178641 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-38 N/A N/A transcript:Os01t0103100-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 180463 180548 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-35 N/A N/A transcript:Os01t0103100-01 N/A N/A N/A
|
||||
1 irgsp mRNA 178652 180575 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0103100-02 N/A N/A gene:Os01g0103100 N/A N/A Os01t0103100-02
|
||||
1 irgsp exon 178652 180575 . 1 . N/A N/A 0 N/A -1 -1 Os01t0103100-02.exon1 N/A Os01t0103100-02.exon1 N/A Os01t0103100-02.exon1 transcript:Os01t0103100-02 N/A 1 N/A
|
||||
1 irgsp CDS 178678 180462 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103100-02 N/A N/A transcript:Os01t0103100-02 Os01t0103100-02 N/A N/A
|
||||
1 irgsp five_prime_UTR 178652 178677 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-39 N/A N/A transcript:Os01t0103100-02 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 180463 180575 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-36 N/A N/A transcript:Os01t0103100-02 N/A N/A N/A
|
||||
1 irgsp gene 178815 180433 . -1 . N/A protein_coding N/A Hypothetical protein. (Os01t0103075-00) N/A N/A N/A Os01g0103075 gene:Os01g0103075 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 178815 180433 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0103075-00 N/A N/A gene:Os01g0103075 N/A N/A Os01t0103075-00
|
||||
1 irgsp exon 178815 180433 . -1 . N/A N/A 1 N/A -1 -1 Os01t0103075-00.exon1 N/A Os01t0103075-00.exon1 N/A Os01t0103075-00.exon1 transcript:Os01t0103075-00 N/A 1 N/A
|
||||
1 irgsp CDS 179512 180054 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103075-00 N/A N/A transcript:Os01t0103075-00 Os01t0103075-00 N/A N/A
|
||||
1 irgsp five_prime_UTR 180055 180433 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-40 N/A N/A transcript:Os01t0103075-00 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 178815 179511 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-37 N/A N/A transcript:Os01t0103075-00 N/A N/A N/A
|
||||
1 Ensembl_Plants ncRNA_gene 182074 182154 . 1 . N/A tRNA N/A tRNA-Leu for anticodon AAG N/A N/A N/A ENSRNA049442722 gene:ENSRNA049442722 trnascan_gene tRNA-Leu N/A N/A N/A N/A
|
||||
1 Ensembl_Plants tRNA 182074 182154 . 1 . N/A tRNA N/A N/A N/A N/A N/A N/A transcript:ENSRNA049442722-T1 N/A N/A gene:ENSRNA049442722 N/A N/A ENSRNA049442722-T1
|
||||
1 Ensembl_Plants exon 182074 182154 . 1 . N/A N/A 1 N/A -1 -1 ENSRNA049442722-E1 N/A ENSRNA049442722-E1 N/A ENSRNA049442722-E1 transcript:ENSRNA049442722-T1 N/A 1 N/A
|
||||
1 irgsp gene 185189 185828 . -1 . N/A protein_coding N/A Hypothetical gene. (Os01t0103400-01) N/A N/A N/A Os01g0103400 gene:Os01g0103400 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 185189 185828 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0103400-01 N/A N/A gene:Os01g0103400 N/A N/A Os01t0103400-01
|
||||
1 irgsp exon 185189 185828 . -1 . N/A N/A 1 N/A -1 -1 Os01t0103400-01.exon1 N/A Os01t0103400-01.exon1 N/A Os01t0103400-01.exon1 transcript:Os01t0103400-01 N/A 1 N/A
|
||||
1 irgsp CDS 185435 185827 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103400-01 N/A N/A transcript:Os01t0103400-01 Os01t0103400-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 185828 185828 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-41 N/A N/A transcript:Os01t0103400-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 185189 185434 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-38 N/A N/A transcript:Os01t0103400-01 N/A N/A N/A
|
||||
1 irgsp repeat_region 186000 186100 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A fakeRepeat2 N/A N/A N/A N/A N/A N/A
|
||||
1 irgsp gene 186250 190904 . -1 . N/A protein_coding N/A Similar to sterol-8,7-isomerase. (Os01t0103600-01);Emopamil-binding family protein. (Os01t0103600-02) N/A N/A N/A Os01g0103600 gene:Os01g0103600 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 186250 190262 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0103600-02 N/A N/A gene:Os01g0103600 N/A N/A Os01t0103600-02
|
||||
1 irgsp exon 186250 186771 . -1 . N/A N/A 0 N/A -1 2 Os01t0103600-02.exon4 N/A Os01t0103600-02.exon4 N/A Os01t0103600-02.exon4 transcript:Os01t0103600-02 N/A 4 N/A
|
||||
1 irgsp exon 189607 189715 . -1 . N/A N/A 0 N/A 2 1 Os01t0103600-02.exon3 N/A Os01t0103600-02.exon3 N/A Os01t0103600-02.exon3 transcript:Os01t0103600-02 N/A 3 N/A
|
||||
1 irgsp exon 189841 189990 . -1 . N/A N/A 1 N/A 1 1 Os01t0103600-02.exon2 N/A Os01t0103600-02.exon2 N/A Os01t0103600-02.exon2 transcript:Os01t0103600-02 N/A 2 N/A
|
||||
1 irgsp exon 190087 190262 . -1 . N/A N/A 0 N/A 1 -1 Os01t0103600-02.exon1 N/A Os01t0103600-02.exon1 N/A Os01t0103600-02.exon1 transcript:Os01t0103600-02 N/A 1 N/A
|
||||
1 irgsp CDS 186516 186771 . -1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103600-02 N/A N/A transcript:Os01t0103600-02 Os01t0103600-02 N/A N/A
|
||||
1 irgsp CDS 189607 189715 . -1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103600-02 N/A N/A transcript:Os01t0103600-02 Os01t0103600-02 N/A N/A
|
||||
1 irgsp CDS 189841 189990 . -1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103600-02 N/A N/A transcript:Os01t0103600-02 Os01t0103600-02 N/A N/A
|
||||
1 irgsp CDS 190087 190231 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103600-02 N/A N/A transcript:Os01t0103600-02 Os01t0103600-02 N/A N/A
|
||||
1 irgsp five_prime_UTR 190232 190262 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-42 N/A N/A transcript:Os01t0103600-02 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 186250 186515 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-39 N/A N/A transcript:Os01t0103600-02 N/A N/A N/A
|
||||
1 irgsp mRNA 187345 190904 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0103600-01 N/A N/A gene:Os01g0103600 N/A N/A Os01t0103600-01
|
||||
1 irgsp exon 187345 189715 . -1 . N/A N/A 0 N/A -1 1 Os01t0103600-01.exon3 N/A Os01t0103600-01.exon3 N/A Os01t0103600-01.exon3 transcript:Os01t0103600-01 N/A 3 N/A
|
||||
1 irgsp exon 189841 189990 . -1 . N/A N/A 1 N/A 1 1 Os01t0103600-02.exon2 N/A agat-exon-5 N/A Os01t0103600-02.exon2 transcript:Os01t0103600-01 N/A 2 N/A
|
||||
1 irgsp exon 190087 190904 . -1 . N/A N/A 0 N/A 1 -1 Os01t0103600-01.exon1 N/A Os01t0103600-01.exon1 N/A Os01t0103600-01.exon1 transcript:Os01t0103600-01 N/A 1 N/A
|
||||
1 irgsp CDS 189396 189715 . -1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103600-01 N/A N/A transcript:Os01t0103600-01 Os01t0103600-01 N/A N/A
|
||||
1 irgsp CDS 189841 189990 . -1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103600-01 N/A N/A transcript:Os01t0103600-01 Os01t0103600-01 N/A N/A
|
||||
1 irgsp CDS 190087 190231 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103600-01 N/A N/A transcript:Os01t0103600-01 Os01t0103600-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 190232 190904 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-43 N/A N/A transcript:Os01t0103600-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 187345 189395 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-40 N/A N/A transcript:Os01t0103600-01 N/A N/A N/A
|
||||
1 irgsp gene 187545 188586 . 1 . N/A protein_coding N/A Hypothetical gene. (Os01t0103650-00) N/A N/A N/A Os01g0103650 gene:Os01g0103650 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 187545 188586 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0103650-00 N/A N/A gene:Os01g0103650 N/A N/A Os01t0103650-00
|
||||
1 irgsp exon 187545 188020 . 1 . N/A N/A 1 N/A -1 -1 Os01t0103650-00.exon1 N/A Os01t0103650-00.exon1 N/A Os01t0103650-00.exon1 transcript:Os01t0103650-00 N/A 1 N/A
|
||||
1 irgsp exon 188060 188385 . 1 . N/A N/A 1 N/A -1 -1 Os01t0103650-00.exon2 N/A Os01t0103650-00.exon2 N/A Os01t0103650-00.exon2 transcript:Os01t0103650-00 N/A 2 N/A
|
||||
1 irgsp exon 188455 188586 . 1 . N/A N/A 1 N/A -1 -1 Os01t0103650-00.exon3 N/A Os01t0103650-00.exon3 N/A Os01t0103650-00.exon3 transcript:Os01t0103650-00 N/A 3 N/A
|
||||
1 irgsp CDS 187547 187768 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103650-00 N/A N/A transcript:Os01t0103650-00 Os01t0103650-00 N/A N/A
|
||||
1 irgsp five_prime_UTR 187545 187546 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-44 N/A N/A transcript:Os01t0103650-00 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 187769 188020 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-41 N/A N/A transcript:Os01t0103650-00 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 188060 188385 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-42 N/A N/A transcript:Os01t0103650-00 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 188455 188586 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-43 N/A N/A transcript:Os01t0103650-00 N/A N/A N/A
|
||||
1 irgsp gene 191037 196287 . 1 . N/A protein_coding N/A Conserved hypothetical protein. (Os01t0103700-01) N/A N/A N/A Os01g0103700 gene:Os01g0103700 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 191037 196287 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0103700-01 N/A N/A gene:Os01g0103700 N/A N/A Os01t0103700-01
|
||||
1 irgsp exon 191037 191161 . 1 . N/A N/A 1 N/A -1 -1 Os01t0103700-01.exon1 N/A Os01t0103700-01.exon1 N/A Os01t0103700-01.exon1 transcript:Os01t0103700-01 N/A 1 N/A
|
||||
1 irgsp exon 191625 191705 . 1 . N/A N/A 1 N/A 0 -1 Os01t0103700-01.exon2 N/A Os01t0103700-01.exon2 N/A Os01t0103700-01.exon2 transcript:Os01t0103700-01 N/A 2 N/A
|
||||
1 irgsp exon 192399 192506 . 1 . N/A N/A 1 N/A 0 0 Os01t0103700-01.exon3 N/A Os01t0103700-01.exon3 N/A Os01t0103700-01.exon3 transcript:Os01t0103700-01 N/A 3 N/A
|
||||
1 irgsp exon 192958 193161 . 1 . N/A N/A 1 N/A 0 0 Os01t0103700-01.exon4 N/A Os01t0103700-01.exon4 N/A Os01t0103700-01.exon4 transcript:Os01t0103700-01 N/A 4 N/A
|
||||
1 irgsp exon 193248 193356 . 1 . N/A N/A 1 N/A 1 0 Os01t0103700-01.exon5 N/A Os01t0103700-01.exon5 N/A Os01t0103700-01.exon5 transcript:Os01t0103700-01 N/A 5 N/A
|
||||
1 irgsp exon 193434 196287 . 1 . N/A N/A 1 N/A -1 1 Os01t0103700-01.exon6 N/A Os01t0103700-01.exon6 N/A Os01t0103700-01.exon6 transcript:Os01t0103700-01 N/A 6 N/A
|
||||
1 irgsp CDS 191694 191705 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103700-01 N/A N/A transcript:Os01t0103700-01 Os01t0103700-01 N/A N/A
|
||||
1 irgsp CDS 192399 192506 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103700-01 N/A N/A transcript:Os01t0103700-01 Os01t0103700-01 N/A N/A
|
||||
1 irgsp CDS 192958 193161 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103700-01 N/A N/A transcript:Os01t0103700-01 Os01t0103700-01 N/A N/A
|
||||
1 irgsp CDS 193248 193356 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103700-01 N/A N/A transcript:Os01t0103700-01 Os01t0103700-01 N/A N/A
|
||||
1 irgsp CDS 193434 193507 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103700-01 N/A N/A transcript:Os01t0103700-01 Os01t0103700-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 191037 191161 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-45 N/A N/A transcript:Os01t0103700-01 N/A N/A N/A
|
||||
1 irgsp five_prime_UTR 191625 191693 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-46 N/A N/A transcript:Os01t0103700-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 193508 196287 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-44 N/A N/A transcript:Os01t0103700-01 N/A N/A N/A
|
||||
1 irgsp gene 197647 200803 . 1 . N/A protein_coding N/A Conserved hypothetical protein. (Os01t0103800-01) N/A N/A N/A Os01g0103800 gene:Os01g0103800 irgspv1.0-20170804-genes OsDW1-01g N/A N/A N/A N/A
|
||||
1 irgsp mRNA 197647 200803 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0103800-01 N/A N/A gene:Os01g0103800 N/A N/A Os01t0103800-01
|
||||
1 irgsp exon 197647 197838 . 1 . N/A N/A 1 N/A -1 -1 Os01t0103800-01.exon1 N/A Os01t0103800-01.exon1 N/A Os01t0103800-01.exon1 transcript:Os01t0103800-01 N/A 1 N/A
|
||||
1 irgsp exon 198034 198225 . 1 . N/A N/A 1 N/A 0 -1 Os01t0103800-01.exon2 N/A Os01t0103800-01.exon2 N/A Os01t0103800-01.exon2 transcript:Os01t0103800-01 N/A 2 N/A
|
||||
1 irgsp exon 198830 200036 . 1 . N/A N/A 1 N/A 1 0 Os01t0103800-01.exon3 N/A Os01t0103800-01.exon3 N/A Os01t0103800-01.exon3 transcript:Os01t0103800-01 N/A 3 N/A
|
||||
1 irgsp exon 200253 200803 . 1 . N/A N/A 1 N/A -1 1 Os01t0103800-01.exon4 N/A Os01t0103800-01.exon4 N/A Os01t0103800-01.exon4 transcript:Os01t0103800-01 N/A 4 N/A
|
||||
1 irgsp CDS 198130 198225 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103800-01 N/A N/A transcript:Os01t0103800-01 Os01t0103800-01 N/A N/A
|
||||
1 irgsp CDS 198830 200036 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103800-01 N/A N/A transcript:Os01t0103800-01 Os01t0103800-01 N/A N/A
|
||||
1 irgsp CDS 200253 200479 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103800-01 N/A N/A transcript:Os01t0103800-01 Os01t0103800-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 197647 197838 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-47 N/A N/A transcript:Os01t0103800-01 N/A N/A N/A
|
||||
1 irgsp five_prime_UTR 198034 198129 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-48 N/A N/A transcript:Os01t0103800-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 200480 200803 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-45 N/A N/A transcript:Os01t0103800-01 N/A N/A N/A
|
||||
1 irgsp gene 201944 206202 . 1 . N/A protein_coding N/A Polynucleotidyl transferase, Ribonuclease H fold domain containing protein. (Os01t0103900-01) N/A N/A N/A Os01g0103900 gene:Os01g0103900 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 201944 206202 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0103900-01 N/A N/A gene:Os01g0103900 N/A N/A Os01t0103900-01
|
||||
1 irgsp exon 201944 202110 . 1 . N/A N/A 1 N/A 0 -1 Os01t0103900-01.exon1 N/A Os01t0103900-01.exon1 N/A Os01t0103900-01.exon1 transcript:Os01t0103900-01 N/A 1 N/A
|
||||
1 irgsp exon 202252 202359 . 1 . N/A N/A 1 N/A 0 0 Os01t0103900-01.exon2 N/A Os01t0103900-01.exon2 N/A Os01t0103900-01.exon2 transcript:Os01t0103900-01 N/A 2 N/A
|
||||
1 irgsp exon 203007 203127 . 1 . N/A N/A 1 N/A 1 0 Os01t0103900-01.exon3 N/A Os01t0103900-01.exon3 N/A Os01t0103900-01.exon3 transcript:Os01t0103900-01 N/A 3 N/A
|
||||
1 irgsp exon 203302 203429 . 1 . N/A N/A 1 N/A 0 1 Os01t0103900-01.exon4 N/A Os01t0103900-01.exon4 N/A Os01t0103900-01.exon4 transcript:Os01t0103900-01 N/A 4 N/A
|
||||
1 irgsp exon 203511 203658 . 1 . N/A N/A 1 N/A 1 0 Os01t0103900-01.exon5 N/A Os01t0103900-01.exon5 N/A Os01t0103900-01.exon5 transcript:Os01t0103900-01 N/A 5 N/A
|
||||
1 irgsp exon 203760 203938 . 1 . N/A N/A 1 N/A 0 1 Os01t0103900-01.exon6 N/A Os01t0103900-01.exon6 N/A Os01t0103900-01.exon6 transcript:Os01t0103900-01 N/A 6 N/A
|
||||
1 irgsp exon 204203 204440 . 1 . N/A N/A 1 N/A 1 0 Os01t0103900-01.exon7 N/A Os01t0103900-01.exon7 N/A Os01t0103900-01.exon7 transcript:Os01t0103900-01 N/A 7 N/A
|
||||
1 irgsp exon 204543 204635 . 1 . N/A N/A 1 N/A 1 1 Os01t0103900-01.exon8 N/A Os01t0103900-01.exon8 N/A Os01t0103900-01.exon8 transcript:Os01t0103900-01 N/A 8 N/A
|
||||
1 irgsp exon 204730 204875 . 1 . N/A N/A 1 N/A 0 1 Os01t0103900-01.exon9 N/A Os01t0103900-01.exon9 N/A Os01t0103900-01.exon9 transcript:Os01t0103900-01 N/A 9 N/A
|
||||
1 irgsp exon 205042 205149 . 1 . N/A N/A 1 N/A 0 0 Os01t0103900-01.exon10 N/A Os01t0103900-01.exon10 N/A Os01t0103900-01.exon10 transcript:Os01t0103900-01 N/A 10 N/A
|
||||
1 irgsp exon 205290 205378 . 1 . N/A N/A 1 N/A 2 0 Os01t0103900-01.exon11 N/A Os01t0103900-01.exon11 N/A Os01t0103900-01.exon11 transcript:Os01t0103900-01 N/A 11 N/A
|
||||
1 irgsp exon 205534 206202 . 1 . N/A N/A 1 N/A -1 2 Os01t0103900-01.exon12 N/A Os01t0103900-01.exon12 N/A Os01t0103900-01.exon12 transcript:Os01t0103900-01 N/A 12 N/A
|
||||
1 irgsp CDS 202042 202110 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103900-01 N/A N/A transcript:Os01t0103900-01 Os01t0103900-01 N/A N/A
|
||||
1 irgsp CDS 202252 202359 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103900-01 N/A N/A transcript:Os01t0103900-01 Os01t0103900-01 N/A N/A
|
||||
1 irgsp CDS 203007 203127 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103900-01 N/A N/A transcript:Os01t0103900-01 Os01t0103900-01 N/A N/A
|
||||
1 irgsp CDS 203302 203429 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103900-01 N/A N/A transcript:Os01t0103900-01 Os01t0103900-01 N/A N/A
|
||||
1 irgsp CDS 203511 203658 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103900-01 N/A N/A transcript:Os01t0103900-01 Os01t0103900-01 N/A N/A
|
||||
1 irgsp CDS 203760 203938 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103900-01 N/A N/A transcript:Os01t0103900-01 Os01t0103900-01 N/A N/A
|
||||
1 irgsp CDS 204203 204440 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103900-01 N/A N/A transcript:Os01t0103900-01 Os01t0103900-01 N/A N/A
|
||||
1 irgsp CDS 204543 204635 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103900-01 N/A N/A transcript:Os01t0103900-01 Os01t0103900-01 N/A N/A
|
||||
1 irgsp CDS 204730 204875 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103900-01 N/A N/A transcript:Os01t0103900-01 Os01t0103900-01 N/A N/A
|
||||
1 irgsp CDS 205042 205149 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103900-01 N/A N/A transcript:Os01t0103900-01 Os01t0103900-01 N/A N/A
|
||||
1 irgsp CDS 205290 205378 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103900-01 N/A N/A transcript:Os01t0103900-01 Os01t0103900-01 N/A N/A
|
||||
1 irgsp CDS 205534 205543 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0103900-01 N/A N/A transcript:Os01t0103900-01 Os01t0103900-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 201944 202041 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-49 N/A N/A transcript:Os01t0103900-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 205544 206202 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-46 N/A N/A transcript:Os01t0103900-01 N/A N/A N/A
|
||||
1 irgsp gene 206131 209606 . -1 . N/A protein_coding N/A C-type lectin domain containing protein. (Os01t0104000-01);Similar to predicted protein. (Os01t0104000-02) N/A N/A N/A Os01g0104000 gene:Os01g0104000 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 206131 209581 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0104000-02 N/A N/A gene:Os01g0104000 N/A N/A Os01t0104000-02
|
||||
1 irgsp exon 206131 207029 . -1 . N/A N/A 0 N/A -1 2 Os01t0104000-02.exon4 N/A Os01t0104000-02.exon4 N/A Os01t0104000-02.exon4 transcript:Os01t0104000-02 N/A 4 N/A
|
||||
1 irgsp exon 207706 208273 . -1 . N/A N/A 0 N/A 2 1 Os01t0104000-02.exon3 N/A Os01t0104000-02.exon3 N/A Os01t0104000-02.exon3 transcript:Os01t0104000-02 N/A 3 N/A
|
||||
1 irgsp exon 208408 208836 . -1 . N/A N/A 1 N/A 1 1 Os01t0104000-01.exon2 N/A Os01t0104000-01.exon2 N/A Os01t0104000-01.exon2 transcript:Os01t0104000-02 N/A 2 N/A
|
||||
1 irgsp exon 209438 209581 . -1 . N/A N/A 0 N/A 1 -1 Os01t0104000-02.exon1 N/A Os01t0104000-02.exon1 N/A Os01t0104000-02.exon1 transcript:Os01t0104000-02 N/A 1 N/A
|
||||
1 irgsp CDS 206450 207029 . -1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104000-02 N/A N/A transcript:Os01t0104000-02 Os01t0104000-02 N/A N/A
|
||||
1 irgsp CDS 207706 208273 . -1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104000-02 N/A N/A transcript:Os01t0104000-02 Os01t0104000-02 N/A N/A
|
||||
1 irgsp CDS 208408 208836 . -1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104000-02 N/A N/A transcript:Os01t0104000-02 Os01t0104000-02 N/A N/A
|
||||
1 irgsp CDS 209438 209525 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104000-02 N/A N/A transcript:Os01t0104000-02 Os01t0104000-02 N/A N/A
|
||||
1 irgsp five_prime_UTR 209526 209581 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-50 N/A N/A transcript:Os01t0104000-02 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 206131 206449 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-47 N/A N/A transcript:Os01t0104000-02 N/A N/A N/A
|
||||
1 irgsp mRNA 206134 209606 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0104000-01 N/A N/A gene:Os01g0104000 N/A N/A Os01t0104000-01
|
||||
1 irgsp exon 206134 207029 . -1 . N/A N/A 0 N/A -1 2 Os01t0104000-01.exon4 N/A Os01t0104000-01.exon4 N/A Os01t0104000-01.exon4 transcript:Os01t0104000-01 N/A 4 N/A
|
||||
1 irgsp exon 207706 208276 . -1 . N/A N/A 0 N/A 2 1 Os01t0104000-01.exon3 N/A Os01t0104000-01.exon3 N/A Os01t0104000-01.exon3 transcript:Os01t0104000-01 N/A 3 N/A
|
||||
1 irgsp exon 208408 208836 . -1 . N/A N/A 1 N/A 1 1 Os01t0104000-01.exon2 N/A agat-exon-6 N/A Os01t0104000-01.exon2 transcript:Os01t0104000-01 N/A 2 N/A
|
||||
1 irgsp exon 209438 209606 . -1 . N/A N/A 0 N/A 1 -1 Os01t0104000-01.exon1 N/A Os01t0104000-01.exon1 N/A Os01t0104000-01.exon1 transcript:Os01t0104000-01 N/A 1 N/A
|
||||
1 irgsp CDS 206450 207029 . -1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104000-01 N/A N/A transcript:Os01t0104000-01 Os01t0104000-01 N/A N/A
|
||||
1 irgsp CDS 207706 208276 . -1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104000-01 N/A N/A transcript:Os01t0104000-01 Os01t0104000-01 N/A N/A
|
||||
1 irgsp CDS 208408 208836 . -1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104000-01 N/A N/A transcript:Os01t0104000-01 Os01t0104000-01 N/A N/A
|
||||
1 irgsp CDS 209438 209525 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104000-01 N/A N/A transcript:Os01t0104000-01 Os01t0104000-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 209526 209606 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-51 N/A N/A transcript:Os01t0104000-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 206134 206449 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-48 N/A N/A transcript:Os01t0104000-01 N/A N/A N/A
|
||||
1 irgsp gene 209771 214173 . 1 . N/A protein_coding N/A Similar to protein binding / zinc ion binding. (Os01t0104100-01);Similar to protein binding / zinc ion binding. (Os01t0104100-02) N/A N/A N/A Os01g0104100 gene:Os01g0104100 irgspv1.0-20170804-genes cold-inducible, cold-inducible zinc finger protein N/A N/A N/A N/A
|
||||
1 irgsp mRNA 209771 214173 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0104100-01 N/A N/A gene:Os01g0104100 N/A N/A Os01t0104100-01
|
||||
1 irgsp exon 209771 209896 . 1 . N/A N/A 0 N/A 0 0 Os01t0104100-01.exon1 N/A Os01t0104100-01.exon1 N/A Os01t0104100-01.exon1 transcript:Os01t0104100-01 N/A 1 N/A
|
||||
1 irgsp exon 210244 210563 . 1 . N/A N/A 1 N/A 2 0 Os01t0104100-01.exon2 N/A Os01t0104100-01.exon2 N/A Os01t0104100-01.exon2 transcript:Os01t0104100-01 N/A 2 N/A
|
||||
1 irgsp exon 210659 210890 . 1 . N/A N/A 1 N/A 0 2 Os01t0104100-01.exon3 N/A Os01t0104100-01.exon3 N/A Os01t0104100-01.exon3 transcript:Os01t0104100-01 N/A 3 N/A
|
||||
1 irgsp exon 211015 211160 . 1 . N/A N/A 1 N/A 2 0 Os01t0104100-01.exon4 N/A Os01t0104100-01.exon4 N/A Os01t0104100-01.exon4 transcript:Os01t0104100-01 N/A 4 N/A
|
||||
1 irgsp exon 212265 212352 . 1 . N/A N/A 1 N/A 0 2 Os01t0104100-01.exon5 N/A Os01t0104100-01.exon5 N/A Os01t0104100-01.exon5 transcript:Os01t0104100-01 N/A 5 N/A
|
||||
1 irgsp exon 212433 212579 . 1 . N/A N/A 1 N/A 0 0 Os01t0104100-01.exon6 N/A Os01t0104100-01.exon6 N/A Os01t0104100-01.exon6 transcript:Os01t0104100-01 N/A 6 N/A
|
||||
1 irgsp exon 213490 213639 . 1 . N/A N/A 1 N/A 0 0 Os01t0104100-01.exon7 N/A Os01t0104100-01.exon7 N/A Os01t0104100-01.exon7 transcript:Os01t0104100-01 N/A 7 N/A
|
||||
1 irgsp exon 213741 214173 . 1 . N/A N/A 0 N/A -1 0 Os01t0104100-01.exon8 N/A Os01t0104100-01.exon8 N/A Os01t0104100-01.exon8 transcript:Os01t0104100-01 N/A 8 N/A
|
||||
1 irgsp CDS 209771 209896 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104100-01 N/A N/A transcript:Os01t0104100-01 Os01t0104100-01 N/A N/A
|
||||
1 irgsp CDS 210244 210563 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104100-01 N/A N/A transcript:Os01t0104100-01 Os01t0104100-01 N/A N/A
|
||||
1 irgsp CDS 210659 210890 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104100-01 N/A N/A transcript:Os01t0104100-01 Os01t0104100-01 N/A N/A
|
||||
1 irgsp CDS 211015 211160 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104100-01 N/A N/A transcript:Os01t0104100-01 Os01t0104100-01 N/A N/A
|
||||
1 irgsp CDS 212265 212352 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104100-01 N/A N/A transcript:Os01t0104100-01 Os01t0104100-01 N/A N/A
|
||||
1 irgsp CDS 212433 212579 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104100-01 N/A N/A transcript:Os01t0104100-01 Os01t0104100-01 N/A N/A
|
||||
1 irgsp CDS 213490 213639 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104100-01 N/A N/A transcript:Os01t0104100-01 Os01t0104100-01 N/A N/A
|
||||
1 irgsp CDS 213741 213788 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104100-01 N/A N/A transcript:Os01t0104100-01 Os01t0104100-01 N/A N/A
|
||||
1 irgsp three_prime_UTR 213789 214173 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-49 N/A N/A transcript:Os01t0104100-01 N/A N/A N/A
|
||||
1 irgsp mRNA 209794 214147 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0104100-02 N/A N/A gene:Os01g0104100 N/A N/A Os01t0104100-02
|
||||
1 irgsp exon 209794 209896 . 1 . N/A N/A 0 N/A 0 -1 Os01t0104100-02.exon1 N/A Os01t0104100-02.exon1 N/A Os01t0104100-02.exon1 transcript:Os01t0104100-02 N/A 1 N/A
|
||||
1 irgsp exon 210244 210563 . 1 . N/A N/A 1 N/A 2 0 Os01t0104100-01.exon2 N/A agat-exon-7 N/A Os01t0104100-01.exon2 transcript:Os01t0104100-02 N/A 2 N/A
|
||||
1 irgsp exon 210659 210890 . 1 . N/A N/A 1 N/A 0 2 Os01t0104100-01.exon3 N/A agat-exon-8 N/A Os01t0104100-01.exon3 transcript:Os01t0104100-02 N/A 3 N/A
|
||||
1 irgsp exon 211015 211160 . 1 . N/A N/A 1 N/A 2 0 Os01t0104100-01.exon4 N/A agat-exon-9 N/A Os01t0104100-01.exon4 transcript:Os01t0104100-02 N/A 4 N/A
|
||||
1 irgsp exon 212265 212352 . 1 . N/A N/A 1 N/A 0 2 Os01t0104100-01.exon5 N/A agat-exon-10 N/A Os01t0104100-01.exon5 transcript:Os01t0104100-02 N/A 5 N/A
|
||||
1 irgsp exon 212433 212579 . 1 . N/A N/A 1 N/A 0 0 Os01t0104100-01.exon6 N/A agat-exon-11 N/A Os01t0104100-01.exon6 transcript:Os01t0104100-02 N/A 6 N/A
|
||||
1 irgsp exon 213490 213639 . 1 . N/A N/A 1 N/A 0 0 Os01t0104100-01.exon7 N/A agat-exon-12 N/A Os01t0104100-01.exon7 transcript:Os01t0104100-02 N/A 7 N/A
|
||||
1 irgsp exon 213741 214147 . 1 . N/A N/A 0 N/A -1 0 Os01t0104100-02.exon8 N/A Os01t0104100-02.exon8 N/A Os01t0104100-02.exon8 transcript:Os01t0104100-02 N/A 8 N/A
|
||||
1 irgsp CDS 209795 209896 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104100-02 N/A N/A transcript:Os01t0104100-02 Os01t0104100-02 N/A N/A
|
||||
1 irgsp CDS 210244 210563 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104100-02 N/A N/A transcript:Os01t0104100-02 Os01t0104100-02 N/A N/A
|
||||
1 irgsp CDS 210659 210890 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104100-02 N/A N/A transcript:Os01t0104100-02 Os01t0104100-02 N/A N/A
|
||||
1 irgsp CDS 211015 211160 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104100-02 N/A N/A transcript:Os01t0104100-02 Os01t0104100-02 N/A N/A
|
||||
1 irgsp CDS 212265 212352 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104100-02 N/A N/A transcript:Os01t0104100-02 Os01t0104100-02 N/A N/A
|
||||
1 irgsp CDS 212433 212579 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104100-02 N/A N/A transcript:Os01t0104100-02 Os01t0104100-02 N/A N/A
|
||||
1 irgsp CDS 213490 213639 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104100-02 N/A N/A transcript:Os01t0104100-02 Os01t0104100-02 N/A N/A
|
||||
1 irgsp CDS 213741 213788 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104100-02 N/A N/A transcript:Os01t0104100-02 Os01t0104100-02 N/A N/A
|
||||
1 irgsp five_prime_UTR 209794 209794 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-52 N/A N/A transcript:Os01t0104100-02 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 213789 214147 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-50 N/A N/A transcript:Os01t0104100-02 N/A N/A N/A
|
||||
1 irgsp gene 216212 217345 . 1 . N/A protein_coding N/A No apical meristem (NAM) protein domain containing protein. (Os01t0104200-00) N/A N/A N/A Os01g0104200 gene:Os01g0104200 irgspv1.0-20170804-genes NAC DOMAIN-CONTAINING PROTEIN 16 N/A N/A N/A N/A
|
||||
1 irgsp mRNA 216212 217345 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0104200-00 N/A N/A gene:Os01g0104200 N/A N/A Os01t0104200-00
|
||||
1 irgsp exon 216212 216769 . 1 . N/A N/A 1 N/A 0 0 Os01t0104200-00.exon1 N/A Os01t0104200-00.exon1 N/A Os01t0104200-00.exon1 transcript:Os01t0104200-00 N/A 1 N/A
|
||||
1 irgsp exon 216884 217345 . 1 . N/A N/A 1 N/A 0 0 Os01t0104200-00.exon2 N/A Os01t0104200-00.exon2 N/A Os01t0104200-00.exon2 transcript:Os01t0104200-00 N/A 2 N/A
|
||||
1 irgsp CDS 216212 216769 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104200-00 N/A N/A transcript:Os01t0104200-00 Os01t0104200-00 N/A N/A
|
||||
1 irgsp CDS 216884 217345 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104200-00 N/A N/A transcript:Os01t0104200-00 Os01t0104200-00 N/A N/A
|
||||
1 irgsp gene 226897 229301 . 1 . N/A protein_coding N/A Ricin B-related lectin domain containing protein. (Os01t0104400-01);Ricin B-related lectin domain containing protein. (Os01t0104400-02);Ricin B-related lectin domain containing protein. (Os01t0104400-03) N/A N/A N/A Os01g0104400 gene:Os01g0104400 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 226897 229229 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0104400-01 N/A N/A gene:Os01g0104400 N/A N/A Os01t0104400-01
|
||||
1 irgsp exon 226897 227634 . 1 . N/A N/A 0 N/A 0 -1 Os01t0104400-01.exon1 N/A Os01t0104400-01.exon1 N/A Os01t0104400-01.exon1 transcript:Os01t0104400-01 N/A 1 N/A
|
||||
1 irgsp exon 227742 227864 . 1 . N/A N/A 1 N/A 0 0 Os01t0104400-03.exon2 N/A Os01t0104400-03.exon2 N/A Os01t0104400-03.exon2 transcript:Os01t0104400-01 N/A 2 N/A
|
||||
1 irgsp exon 228557 228785 . 1 . N/A N/A 1 N/A 1 0 Os01t0104400-03.exon3 N/A Os01t0104400-03.exon3 N/A Os01t0104400-03.exon3 transcript:Os01t0104400-01 N/A 3 N/A
|
||||
1 irgsp exon 228930 229229 . 1 . N/A N/A 0 N/A -1 1 Os01t0104400-01.exon4 N/A Os01t0104400-01.exon4 N/A Os01t0104400-01.exon4 transcript:Os01t0104400-01 N/A 4 N/A
|
||||
1 irgsp CDS 227182 227634 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104400-01 N/A N/A transcript:Os01t0104400-01 Os01t0104400-01 N/A N/A
|
||||
1 irgsp CDS 227742 227864 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104400-01 N/A N/A transcript:Os01t0104400-01 Os01t0104400-01 N/A N/A
|
||||
1 irgsp CDS 228557 228785 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104400-01 N/A N/A transcript:Os01t0104400-01 Os01t0104400-01 N/A N/A
|
||||
1 irgsp CDS 228930 228931 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104400-01 N/A N/A transcript:Os01t0104400-01 Os01t0104400-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 226897 227181 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-53 N/A N/A transcript:Os01t0104400-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 228932 229229 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-51 N/A N/A transcript:Os01t0104400-01 N/A N/A N/A
|
||||
1 irgsp mRNA 227139 229301 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0104400-02 N/A N/A gene:Os01g0104400 N/A N/A Os01t0104400-02
|
||||
1 irgsp exon 227139 227634 . 1 . N/A N/A 0 N/A 0 -1 Os01t0104400-02.exon1 N/A Os01t0104400-02.exon1 N/A Os01t0104400-02.exon1 transcript:Os01t0104400-02 N/A 1 N/A
|
||||
1 irgsp exon 227742 227864 . 1 . N/A N/A 1 N/A 0 0 Os01t0104400-03.exon2 N/A agat-exon-13 N/A Os01t0104400-03.exon2 transcript:Os01t0104400-02 N/A 2 N/A
|
||||
1 irgsp exon 228557 228785 . 1 . N/A N/A 1 N/A 1 0 Os01t0104400-03.exon3 N/A agat-exon-14 N/A Os01t0104400-03.exon3 transcript:Os01t0104400-02 N/A 3 N/A
|
||||
1 irgsp exon 228930 229301 . 1 . N/A N/A 0 N/A -1 1 Os01t0104400-02.exon4 N/A Os01t0104400-02.exon4 N/A Os01t0104400-02.exon4 transcript:Os01t0104400-02 N/A 4 N/A
|
||||
1 irgsp CDS 227182 227634 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104400-02 N/A N/A transcript:Os01t0104400-02 Os01t0104400-02 N/A N/A
|
||||
1 irgsp CDS 227742 227864 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104400-02 N/A N/A transcript:Os01t0104400-02 Os01t0104400-02 N/A N/A
|
||||
1 irgsp CDS 228557 228785 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104400-02 N/A N/A transcript:Os01t0104400-02 Os01t0104400-02 N/A N/A
|
||||
1 irgsp CDS 228930 228931 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104400-02 N/A N/A transcript:Os01t0104400-02 Os01t0104400-02 N/A N/A
|
||||
1 irgsp five_prime_UTR 227139 227181 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-54 N/A N/A transcript:Os01t0104400-02 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 228932 229301 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-52 N/A N/A transcript:Os01t0104400-02 N/A N/A N/A
|
||||
1 irgsp mRNA 227179 229214 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0104400-03 N/A N/A gene:Os01g0104400 N/A N/A Os01t0104400-03
|
||||
1 irgsp exon 227179 227634 . 1 . N/A N/A 0 N/A 0 -1 Os01t0104400-03.exon1 N/A Os01t0104400-03.exon1 N/A Os01t0104400-03.exon1 transcript:Os01t0104400-03 N/A 1 N/A
|
||||
1 irgsp exon 227742 227864 . 1 . N/A N/A 1 N/A 0 0 Os01t0104400-03.exon2 N/A agat-exon-15 N/A Os01t0104400-03.exon2 transcript:Os01t0104400-03 N/A 2 N/A
|
||||
1 irgsp exon 228557 228785 . 1 . N/A N/A 1 N/A 1 0 Os01t0104400-03.exon3 N/A agat-exon-16 N/A Os01t0104400-03.exon3 transcript:Os01t0104400-03 N/A 3 N/A
|
||||
1 irgsp exon 228930 229214 . 1 . N/A N/A 0 N/A -1 1 Os01t0104400-03.exon4 N/A Os01t0104400-03.exon4 N/A Os01t0104400-03.exon4 transcript:Os01t0104400-03 N/A 4 N/A
|
||||
1 irgsp CDS 227182 227634 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104400-03 N/A N/A transcript:Os01t0104400-03 Os01t0104400-03 N/A N/A
|
||||
1 irgsp CDS 227742 227864 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104400-03 N/A N/A transcript:Os01t0104400-03 Os01t0104400-03 N/A N/A
|
||||
1 irgsp CDS 228557 228785 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104400-03 N/A N/A transcript:Os01t0104400-03 Os01t0104400-03 N/A N/A
|
||||
1 irgsp CDS 228930 228931 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104400-03 N/A N/A transcript:Os01t0104400-03 Os01t0104400-03 N/A N/A
|
||||
1 irgsp five_prime_UTR 227179 227181 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-55 N/A N/A transcript:Os01t0104400-03 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 228932 229214 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-53 N/A N/A transcript:Os01t0104400-03 N/A N/A N/A
|
||||
1 irgsp gene 241680 243440 . 1 . N/A protein_coding N/A No apical meristem (NAM) protein domain containing protein. (Os01t0104500-01) N/A N/A N/A Os01g0104500 gene:Os01g0104500 irgspv1.0-20170804-genes NAC DOMAIN-CONTAINING PROTEIN 20 N/A N/A N/A N/A
|
||||
1 irgsp mRNA 241680 243440 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0104500-01 N/A N/A gene:Os01g0104500 N/A N/A Os01t0104500-01
|
||||
1 irgsp exon 241680 241702 . 1 . N/A N/A 1 N/A -1 -1 Os01t0104500-01.exon1 N/A Os01t0104500-01.exon1 N/A Os01t0104500-01.exon1 transcript:Os01t0104500-01 N/A 1 N/A
|
||||
1 irgsp exon 241866 242091 . 1 . N/A N/A 1 N/A 1 -1 Os01t0104500-01.exon2 N/A Os01t0104500-01.exon2 N/A Os01t0104500-01.exon2 transcript:Os01t0104500-01 N/A 2 N/A
|
||||
1 irgsp exon 242199 243440 . 1 . N/A N/A 1 N/A -1 1 Os01t0104500-01.exon3 N/A Os01t0104500-01.exon3 N/A Os01t0104500-01.exon3 transcript:Os01t0104500-01 N/A 3 N/A
|
||||
1 irgsp CDS 241908 242091 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104500-01 N/A N/A transcript:Os01t0104500-01 Os01t0104500-01 N/A N/A
|
||||
1 irgsp CDS 242199 242977 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104500-01 N/A N/A transcript:Os01t0104500-01 Os01t0104500-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 241680 241702 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-56 N/A N/A transcript:Os01t0104500-01 N/A N/A N/A
|
||||
1 irgsp five_prime_UTR 241866 241907 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-57 N/A N/A transcript:Os01t0104500-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 242978 243440 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-54 N/A N/A transcript:Os01t0104500-01 N/A N/A N/A
|
||||
1 irgsp gene 248828 256872 . -1 . N/A protein_coding N/A Homolog of Arabidopsis DE-ETIOLATED1 (DET1), Modulation of the ABA signaling pathway and ABA biosynthesis, Regulation of chlorophyll content (Os01t0104600-01);Similar to Light-mediated development protein DET1 (Deetiolated1 homolog) (tDET1) (High pigmentation protein 2) (Protein dark green). (Os01t0104600-02) N/A N/A N/A Os01g0104600 gene:Os01g0104600 irgspv1.0-20170804-genes DE-ETIOLATED1 N/A N/A N/A N/A
|
||||
1 irgsp mRNA 248828 256571 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0104600-02 N/A N/A gene:Os01g0104600 N/A N/A Os01t0104600-02
|
||||
1 irgsp exon 248828 249107 . -1 . N/A N/A 1 N/A -1 1 Os01t0104600-01.exon11 N/A Os01t0104600-01.exon11 N/A Os01t0104600-01.exon11 transcript:Os01t0104600-02 N/A 11 N/A
|
||||
1 irgsp exon 249369 249468 . -1 . N/A N/A 1 N/A 1 0 Os01t0104600-01.exon10 N/A Os01t0104600-01.exon10 N/A Os01t0104600-01.exon10 transcript:Os01t0104600-02 N/A 10 N/A
|
||||
1 irgsp exon 249861 249956 . -1 . N/A N/A 1 N/A 0 0 Os01t0104600-01.exon9 N/A Os01t0104600-01.exon9 N/A Os01t0104600-01.exon9 transcript:Os01t0104600-02 N/A 9 N/A
|
||||
1 irgsp exon 250617 250781 . -1 . N/A N/A 1 N/A 0 0 Os01t0104600-01.exon8 N/A Os01t0104600-01.exon8 N/A Os01t0104600-01.exon8 transcript:Os01t0104600-02 N/A 8 N/A
|
||||
1 irgsp exon 250860 250940 . -1 . N/A N/A 1 N/A 0 0 Os01t0104600-01.exon7 N/A Os01t0104600-01.exon7 N/A Os01t0104600-01.exon7 transcript:Os01t0104600-02 N/A 7 N/A
|
||||
1 irgsp exon 251026 251082 . -1 . N/A N/A 1 N/A 0 0 Os01t0104600-01.exon6 N/A Os01t0104600-01.exon6 N/A Os01t0104600-01.exon6 transcript:Os01t0104600-02 N/A 6 N/A
|
||||
1 irgsp exon 251316 251384 . -1 . N/A N/A 1 N/A 0 0 Os01t0104600-01.exon5 N/A Os01t0104600-01.exon5 N/A Os01t0104600-01.exon5 transcript:Os01t0104600-02 N/A 5 N/A
|
||||
1 irgsp exon 251695 251790 . -1 . N/A N/A 1 N/A 0 0 Os01t0104600-01.exon4 N/A Os01t0104600-01.exon4 N/A Os01t0104600-01.exon4 transcript:Os01t0104600-02 N/A 4 N/A
|
||||
1 irgsp exon 255325 255553 . -1 . N/A N/A 1 N/A 0 2 Os01t0104600-01.exon3 N/A Os01t0104600-01.exon3 N/A Os01t0104600-01.exon3 transcript:Os01t0104600-02 N/A 3 N/A
|
||||
1 irgsp exon 255674 256098 . -1 . N/A N/A 1 N/A 2 0 Os01t0104600-01.exon2 N/A Os01t0104600-01.exon2 N/A Os01t0104600-01.exon2 transcript:Os01t0104600-02 N/A 2 N/A
|
||||
1 irgsp exon 256361 256571 . -1 . N/A N/A 0 N/A 0 -1 Os01t0104600-02.exon1 N/A Os01t0104600-02.exon1 N/A Os01t0104600-02.exon1 transcript:Os01t0104600-02 N/A 1 N/A
|
||||
1 irgsp CDS 248971 249107 . -1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104600-02 N/A N/A transcript:Os01t0104600-02 Os01t0104600-02 N/A N/A
|
||||
1 irgsp CDS 249369 249468 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104600-02 N/A N/A transcript:Os01t0104600-02 Os01t0104600-02 N/A N/A
|
||||
1 irgsp CDS 249861 249956 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104600-02 N/A N/A transcript:Os01t0104600-02 Os01t0104600-02 N/A N/A
|
||||
1 irgsp CDS 250617 250781 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104600-02 N/A N/A transcript:Os01t0104600-02 Os01t0104600-02 N/A N/A
|
||||
1 irgsp CDS 250860 250940 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104600-02 N/A N/A transcript:Os01t0104600-02 Os01t0104600-02 N/A N/A
|
||||
1 irgsp CDS 251026 251082 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104600-02 N/A N/A transcript:Os01t0104600-02 Os01t0104600-02 N/A N/A
|
||||
1 irgsp CDS 251316 251384 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104600-02 N/A N/A transcript:Os01t0104600-02 Os01t0104600-02 N/A N/A
|
||||
1 irgsp CDS 251695 251790 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104600-02 N/A N/A transcript:Os01t0104600-02 Os01t0104600-02 N/A N/A
|
||||
1 irgsp CDS 255325 255553 . -1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104600-02 N/A N/A transcript:Os01t0104600-02 Os01t0104600-02 N/A N/A
|
||||
1 irgsp CDS 255674 256098 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104600-02 N/A N/A transcript:Os01t0104600-02 Os01t0104600-02 N/A N/A
|
||||
1 irgsp CDS 256361 256441 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104600-02 N/A N/A transcript:Os01t0104600-02 Os01t0104600-02 N/A N/A
|
||||
1 irgsp five_prime_UTR 256442 256571 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-58 N/A N/A transcript:Os01t0104600-02 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 248828 248970 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-55 N/A N/A transcript:Os01t0104600-02 N/A N/A N/A
|
||||
1 irgsp mRNA 248828 256872 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0104600-01 N/A N/A gene:Os01g0104600 N/A N/A Os01t0104600-01
|
||||
1 irgsp exon 248828 249107 . -1 . N/A N/A 1 N/A -1 1 Os01t0104600-01.exon11 N/A agat-exon-17 N/A Os01t0104600-01.exon11 transcript:Os01t0104600-01 N/A 11 N/A
|
||||
1 irgsp exon 249369 249468 . -1 . N/A N/A 1 N/A 1 0 Os01t0104600-01.exon10 N/A agat-exon-18 N/A Os01t0104600-01.exon10 transcript:Os01t0104600-01 N/A 10 N/A
|
||||
1 irgsp exon 249861 249956 . -1 . N/A N/A 1 N/A 0 0 Os01t0104600-01.exon9 N/A agat-exon-19 N/A Os01t0104600-01.exon9 transcript:Os01t0104600-01 N/A 9 N/A
|
||||
1 irgsp exon 250617 250781 . -1 . N/A N/A 1 N/A 0 0 Os01t0104600-01.exon8 N/A agat-exon-20 N/A Os01t0104600-01.exon8 transcript:Os01t0104600-01 N/A 8 N/A
|
||||
1 irgsp exon 250860 250940 . -1 . N/A N/A 1 N/A 0 0 Os01t0104600-01.exon7 N/A agat-exon-21 N/A Os01t0104600-01.exon7 transcript:Os01t0104600-01 N/A 7 N/A
|
||||
1 irgsp exon 251026 251082 . -1 . N/A N/A 1 N/A 0 0 Os01t0104600-01.exon6 N/A agat-exon-22 N/A Os01t0104600-01.exon6 transcript:Os01t0104600-01 N/A 6 N/A
|
||||
1 irgsp exon 251316 251384 . -1 . N/A N/A 1 N/A 0 0 Os01t0104600-01.exon5 N/A agat-exon-23 N/A Os01t0104600-01.exon5 transcript:Os01t0104600-01 N/A 5 N/A
|
||||
1 irgsp exon 251695 251790 . -1 . N/A N/A 1 N/A 0 0 Os01t0104600-01.exon4 N/A agat-exon-24 N/A Os01t0104600-01.exon4 transcript:Os01t0104600-01 N/A 4 N/A
|
||||
1 irgsp exon 255325 255553 . -1 . N/A N/A 1 N/A 0 2 Os01t0104600-01.exon3 N/A agat-exon-25 N/A Os01t0104600-01.exon3 transcript:Os01t0104600-01 N/A 3 N/A
|
||||
1 irgsp exon 255674 256098 . -1 . N/A N/A 1 N/A 2 0 Os01t0104600-01.exon2 N/A agat-exon-26 N/A Os01t0104600-01.exon2 transcript:Os01t0104600-01 N/A 2 N/A
|
||||
1 irgsp exon 256361 256872 . -1 . N/A N/A 0 N/A 0 -1 Os01t0104600-01.exon1 N/A Os01t0104600-01.exon1 N/A Os01t0104600-01.exon1 transcript:Os01t0104600-01 N/A 1 N/A
|
||||
1 irgsp CDS 248971 249107 . -1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104600-01 N/A N/A transcript:Os01t0104600-01 Os01t0104600-01 N/A N/A
|
||||
1 irgsp CDS 249369 249468 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104600-01 N/A N/A transcript:Os01t0104600-01 Os01t0104600-01 N/A N/A
|
||||
1 irgsp CDS 249861 249956 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104600-01 N/A N/A transcript:Os01t0104600-01 Os01t0104600-01 N/A N/A
|
||||
1 irgsp CDS 250617 250781 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104600-01 N/A N/A transcript:Os01t0104600-01 Os01t0104600-01 N/A N/A
|
||||
1 irgsp CDS 250860 250940 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104600-01 N/A N/A transcript:Os01t0104600-01 Os01t0104600-01 N/A N/A
|
||||
1 irgsp CDS 251026 251082 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104600-01 N/A N/A transcript:Os01t0104600-01 Os01t0104600-01 N/A N/A
|
||||
1 irgsp CDS 251316 251384 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104600-01 N/A N/A transcript:Os01t0104600-01 Os01t0104600-01 N/A N/A
|
||||
1 irgsp CDS 251695 251790 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104600-01 N/A N/A transcript:Os01t0104600-01 Os01t0104600-01 N/A N/A
|
||||
1 irgsp CDS 255325 255553 . -1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104600-01 N/A N/A transcript:Os01t0104600-01 Os01t0104600-01 N/A N/A
|
||||
1 irgsp CDS 255674 256098 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104600-01 N/A N/A transcript:Os01t0104600-01 Os01t0104600-01 N/A N/A
|
||||
1 irgsp CDS 256361 256441 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104600-01 N/A N/A transcript:Os01t0104600-01 Os01t0104600-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 256442 256872 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-59 N/A N/A transcript:Os01t0104600-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 248828 248970 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-56 N/A N/A transcript:Os01t0104600-01 N/A N/A N/A
|
||||
1 irgsp gene 261530 268145 . 1 . N/A protein_coding N/A Sas10/Utp3 family protein. (Os01t0104800-01);Hypothetical conserved gene. (Os01t0104800-02) N/A N/A N/A Os01g0104800 gene:Os01g0104800 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 261530 268145 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0104800-01 N/A N/A gene:Os01g0104800 N/A N/A Os01t0104800-01
|
||||
1 irgsp exon 261530 261661 . 1 . N/A N/A 0 N/A 1 -1 Os01t0104800-01.exon1 N/A Os01t0104800-01.exon1 N/A Os01t0104800-01.exon1 transcript:Os01t0104800-01 N/A 1 N/A
|
||||
1 irgsp exon 261767 261805 . 1 . N/A N/A 0 N/A 1 1 Os01t0104800-01.exon2 N/A Os01t0104800-01.exon2 N/A Os01t0104800-01.exon2 transcript:Os01t0104800-01 N/A 2 N/A
|
||||
1 irgsp exon 261895 261941 . 1 . N/A N/A 0 N/A 0 1 Os01t0104800-01.exon3 N/A Os01t0104800-01.exon3 N/A Os01t0104800-01.exon3 transcript:Os01t0104800-01 N/A 3 N/A
|
||||
1 irgsp exon 262582 262681 . 1 . N/A N/A 0 N/A 1 0 Os01t0104800-01.exon4 N/A Os01t0104800-01.exon4 N/A Os01t0104800-01.exon4 transcript:Os01t0104800-01 N/A 4 N/A
|
||||
1 irgsp exon 262925 263181 . 1 . N/A N/A 0 N/A 0 1 Os01t0104800-01.exon5 N/A Os01t0104800-01.exon5 N/A Os01t0104800-01.exon5 transcript:Os01t0104800-01 N/A 5 N/A
|
||||
1 irgsp exon 263525 263640 . 1 . N/A N/A 0 N/A 2 0 Os01t0104800-01.exon6 N/A Os01t0104800-01.exon6 N/A Os01t0104800-01.exon6 transcript:Os01t0104800-01 N/A 6 N/A
|
||||
1 irgsp exon 264014 264098 . 1 . N/A N/A 1 N/A 0 2 Os01t0104800-01.exon7 N/A Os01t0104800-01.exon7 N/A Os01t0104800-01.exon7 transcript:Os01t0104800-01 N/A 7 N/A
|
||||
1 irgsp exon 265236 265415 . 1 . N/A N/A 1 N/A 0 0 Os01t0104800-01.exon8 N/A Os01t0104800-01.exon8 N/A Os01t0104800-01.exon8 transcript:Os01t0104800-01 N/A 8 N/A
|
||||
1 irgsp exon 265506 265649 . 1 . N/A N/A 1 N/A 0 0 Os01t0104800-01.exon9 N/A Os01t0104800-01.exon9 N/A Os01t0104800-01.exon9 transcript:Os01t0104800-01 N/A 9 N/A
|
||||
1 irgsp exon 265740 265817 . 1 . N/A N/A 1 N/A 0 0 Os01t0104800-01.exon10 N/A Os01t0104800-01.exon10 N/A Os01t0104800-01.exon10 transcript:Os01t0104800-01 N/A 10 N/A
|
||||
1 irgsp exon 265909 266045 . 1 . N/A N/A 1 N/A 2 0 Os01t0104800-01.exon11 N/A Os01t0104800-01.exon11 N/A Os01t0104800-01.exon11 transcript:Os01t0104800-01 N/A 11 N/A
|
||||
1 irgsp exon 266138 266246 . 1 . N/A N/A 1 N/A 0 2 Os01t0104800-01.exon12 N/A Os01t0104800-01.exon12 N/A Os01t0104800-01.exon12 transcript:Os01t0104800-01 N/A 12 N/A
|
||||
1 irgsp exon 267237 267514 . 1 . N/A N/A 1 N/A 2 0 Os01t0104800-01.exon13 N/A Os01t0104800-01.exon13 N/A Os01t0104800-01.exon13 transcript:Os01t0104800-01 N/A 13 N/A
|
||||
1 irgsp exon 267591 267657 . 1 . N/A N/A 1 N/A 0 2 Os01t0104800-01.exon14 N/A Os01t0104800-01.exon14 N/A Os01t0104800-01.exon14 transcript:Os01t0104800-01 N/A 14 N/A
|
||||
1 irgsp exon 267734 267802 . 1 . N/A N/A 1 N/A 0 0 Os01t0104800-01.exon15 N/A Os01t0104800-01.exon15 N/A Os01t0104800-01.exon15 transcript:Os01t0104800-01 N/A 15 N/A
|
||||
1 irgsp exon 267880 268145 . 1 . N/A N/A 0 N/A -1 0 Os01t0104800-01.exon16 N/A Os01t0104800-01.exon16 N/A Os01t0104800-01.exon16 transcript:Os01t0104800-01 N/A 16 N/A
|
||||
1 irgsp CDS 261562 261661 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-01 N/A N/A transcript:Os01t0104800-01 Os01t0104800-01 N/A N/A
|
||||
1 irgsp CDS 261767 261805 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-01 N/A N/A transcript:Os01t0104800-01 Os01t0104800-01 N/A N/A
|
||||
1 irgsp CDS 261895 261941 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-01 N/A N/A transcript:Os01t0104800-01 Os01t0104800-01 N/A N/A
|
||||
1 irgsp CDS 262582 262681 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-01 N/A N/A transcript:Os01t0104800-01 Os01t0104800-01 N/A N/A
|
||||
1 irgsp CDS 262925 263181 . 1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-01 N/A N/A transcript:Os01t0104800-01 Os01t0104800-01 N/A N/A
|
||||
1 irgsp CDS 263525 263640 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-01 N/A N/A transcript:Os01t0104800-01 Os01t0104800-01 N/A N/A
|
||||
1 irgsp CDS 264014 264098 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-01 N/A N/A transcript:Os01t0104800-01 Os01t0104800-01 N/A N/A
|
||||
1 irgsp CDS 265236 265415 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-01 N/A N/A transcript:Os01t0104800-01 Os01t0104800-01 N/A N/A
|
||||
1 irgsp CDS 265506 265649 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-01 N/A N/A transcript:Os01t0104800-01 Os01t0104800-01 N/A N/A
|
||||
1 irgsp CDS 265740 265817 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-01 N/A N/A transcript:Os01t0104800-01 Os01t0104800-01 N/A N/A
|
||||
1 irgsp CDS 265909 266045 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-01 N/A N/A transcript:Os01t0104800-01 Os01t0104800-01 N/A N/A
|
||||
1 irgsp CDS 266138 266246 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-01 N/A N/A transcript:Os01t0104800-01 Os01t0104800-01 N/A N/A
|
||||
1 irgsp CDS 267237 267514 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-01 N/A N/A transcript:Os01t0104800-01 Os01t0104800-01 N/A N/A
|
||||
1 irgsp CDS 267591 267657 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-01 N/A N/A transcript:Os01t0104800-01 Os01t0104800-01 N/A N/A
|
||||
1 irgsp CDS 267734 267802 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-01 N/A N/A transcript:Os01t0104800-01 Os01t0104800-01 N/A N/A
|
||||
1 irgsp CDS 267880 268011 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-01 N/A N/A transcript:Os01t0104800-01 Os01t0104800-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 261530 261561 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-60 N/A N/A transcript:Os01t0104800-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 268012 268145 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-57 N/A N/A transcript:Os01t0104800-01 N/A N/A N/A
|
||||
1 irgsp mRNA 263523 268120 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0104800-02 N/A N/A gene:Os01g0104800 N/A N/A Os01t0104800-02
|
||||
1 irgsp exon 263523 263640 . 1 . N/A N/A 0 N/A 2 -1 Os01t0104800-02.exon1 N/A Os01t0104800-02.exon1 N/A Os01t0104800-02.exon1 transcript:Os01t0104800-02 N/A 1 N/A
|
||||
1 irgsp exon 264014 264098 . 1 . N/A N/A 1 N/A 0 2 Os01t0104800-01.exon7 N/A agat-exon-27 N/A Os01t0104800-01.exon7 transcript:Os01t0104800-02 N/A 2 N/A
|
||||
1 irgsp exon 265236 265415 . 1 . N/A N/A 1 N/A 0 0 Os01t0104800-01.exon8 N/A agat-exon-28 N/A Os01t0104800-01.exon8 transcript:Os01t0104800-02 N/A 3 N/A
|
||||
1 irgsp exon 265506 265649 . 1 . N/A N/A 1 N/A 0 0 Os01t0104800-01.exon9 N/A agat-exon-29 N/A Os01t0104800-01.exon9 transcript:Os01t0104800-02 N/A 4 N/A
|
||||
1 irgsp exon 265740 265817 . 1 . N/A N/A 1 N/A 0 0 Os01t0104800-01.exon10 N/A agat-exon-30 N/A Os01t0104800-01.exon10 transcript:Os01t0104800-02 N/A 5 N/A
|
||||
1 irgsp exon 265909 266045 . 1 . N/A N/A 1 N/A 2 0 Os01t0104800-01.exon11 N/A agat-exon-31 N/A Os01t0104800-01.exon11 transcript:Os01t0104800-02 N/A 6 N/A
|
||||
1 irgsp exon 266138 266246 . 1 . N/A N/A 1 N/A 0 2 Os01t0104800-01.exon12 N/A agat-exon-32 N/A Os01t0104800-01.exon12 transcript:Os01t0104800-02 N/A 7 N/A
|
||||
1 irgsp exon 267237 267514 . 1 . N/A N/A 1 N/A 2 0 Os01t0104800-01.exon13 N/A agat-exon-33 N/A Os01t0104800-01.exon13 transcript:Os01t0104800-02 N/A 8 N/A
|
||||
1 irgsp exon 267591 267657 . 1 . N/A N/A 1 N/A 0 2 Os01t0104800-01.exon14 N/A agat-exon-34 N/A Os01t0104800-01.exon14 transcript:Os01t0104800-02 N/A 9 N/A
|
||||
1 irgsp exon 267734 267802 . 1 . N/A N/A 1 N/A 0 0 Os01t0104800-01.exon15 N/A agat-exon-35 N/A Os01t0104800-01.exon15 transcript:Os01t0104800-02 N/A 10 N/A
|
||||
1 irgsp exon 267880 268120 . 1 . N/A N/A 0 N/A -1 0 Os01t0104800-02.exon11 N/A Os01t0104800-02.exon11 N/A Os01t0104800-02.exon11 transcript:Os01t0104800-02 N/A 11 N/A
|
||||
1 irgsp CDS 263525 263640 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-02 N/A N/A transcript:Os01t0104800-02 Os01t0104800-02 N/A N/A
|
||||
1 irgsp CDS 264014 264098 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-02 N/A N/A transcript:Os01t0104800-02 Os01t0104800-02 N/A N/A
|
||||
1 irgsp CDS 265236 265415 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-02 N/A N/A transcript:Os01t0104800-02 Os01t0104800-02 N/A N/A
|
||||
1 irgsp CDS 265506 265649 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-02 N/A N/A transcript:Os01t0104800-02 Os01t0104800-02 N/A N/A
|
||||
1 irgsp CDS 265740 265817 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-02 N/A N/A transcript:Os01t0104800-02 Os01t0104800-02 N/A N/A
|
||||
1 irgsp CDS 265909 266045 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-02 N/A N/A transcript:Os01t0104800-02 Os01t0104800-02 N/A N/A
|
||||
1 irgsp CDS 266138 266246 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-02 N/A N/A transcript:Os01t0104800-02 Os01t0104800-02 N/A N/A
|
||||
1 irgsp CDS 267237 267514 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-02 N/A N/A transcript:Os01t0104800-02 Os01t0104800-02 N/A N/A
|
||||
1 irgsp CDS 267591 267657 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-02 N/A N/A transcript:Os01t0104800-02 Os01t0104800-02 N/A N/A
|
||||
1 irgsp CDS 267734 267802 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-02 N/A N/A transcript:Os01t0104800-02 Os01t0104800-02 N/A N/A
|
||||
1 irgsp CDS 267880 268011 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104800-02 N/A N/A transcript:Os01t0104800-02 Os01t0104800-02 N/A N/A
|
||||
1 irgsp five_prime_UTR 263523 263524 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-61 N/A N/A transcript:Os01t0104800-02 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 268012 268120 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-58 N/A N/A transcript:Os01t0104800-02 N/A N/A N/A
|
||||
1 irgsp gene 270179 275084 . -1 . N/A protein_coding N/A Transferase family protein. (Os01t0104900-01);Hypothetical conserved gene. (Os01t0104900-02) N/A N/A N/A Os01g0104900 gene:Os01g0104900 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 270179 275084 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0104900-01 N/A N/A gene:Os01g0104900 N/A N/A Os01t0104900-01
|
||||
1 irgsp exon 270179 271333 . -1 . N/A N/A 0 N/A -1 0 Os01t0104900-01.exon2 N/A Os01t0104900-01.exon2 N/A Os01t0104900-01.exon2 transcript:Os01t0104900-01 N/A 2 N/A
|
||||
1 irgsp exon 274529 275084 . -1 . N/A N/A 0 N/A 0 -1 Os01t0104900-01.exon1 N/A Os01t0104900-01.exon1 N/A Os01t0104900-01.exon1 transcript:Os01t0104900-01 N/A 1 N/A
|
||||
1 irgsp CDS 270356 271333 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104900-01 N/A N/A transcript:Os01t0104900-01 Os01t0104900-01 N/A N/A
|
||||
1 irgsp CDS 274529 274957 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104900-01 N/A N/A transcript:Os01t0104900-01 Os01t0104900-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 274958 275084 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-62 N/A N/A transcript:Os01t0104900-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 270179 270355 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-59 N/A N/A transcript:Os01t0104900-01 N/A N/A N/A
|
||||
1 irgsp mRNA 270250 271518 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0104900-02 N/A N/A gene:Os01g0104900 N/A N/A Os01t0104900-02
|
||||
1 irgsp exon 270250 271333 . -1 . N/A N/A 0 N/A -1 -1 Os01t0104900-02.exon2 N/A Os01t0104900-02.exon2 N/A Os01t0104900-02.exon2 transcript:Os01t0104900-02 N/A 2 N/A
|
||||
1 irgsp exon 271457 271518 . -1 . N/A N/A 0 N/A -1 -1 Os01t0104900-02.exon1 N/A Os01t0104900-02.exon1 N/A Os01t0104900-02.exon1 transcript:Os01t0104900-02 N/A 1 N/A
|
||||
1 irgsp CDS 270356 271309 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0104900-02 N/A N/A transcript:Os01t0104900-02 Os01t0104900-02 N/A N/A
|
||||
1 irgsp five_prime_UTR 271310 271333 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-63 N/A N/A transcript:Os01t0104900-02 N/A N/A N/A
|
||||
1 irgsp five_prime_UTR 271457 271518 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-64 N/A N/A transcript:Os01t0104900-02 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 270250 270355 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-60 N/A N/A transcript:Os01t0104900-02 N/A N/A N/A
|
||||
1 irgsp gene 284762 291892 . -1 . N/A protein_coding N/A Similar to HAT family dimerisation domain containing protein, expressed. (Os01t0105300-01) N/A N/A N/A Os01g0105300 gene:Os01g0105300 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 284762 291892 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0105300-01 N/A N/A gene:Os01g0105300 N/A N/A Os01t0105300-01
|
||||
1 irgsp exon 284762 287047 . -1 . N/A N/A 1 N/A -1 -1 Os01t0105300-01.exon5 N/A Os01t0105300-01.exon5 N/A Os01t0105300-01.exon5 transcript:Os01t0105300-01 N/A 5 N/A
|
||||
1 irgsp exon 291398 291436 . -1 . N/A N/A 1 N/A -1 -1 Os01t0105300-01.exon4 N/A Os01t0105300-01.exon4 N/A Os01t0105300-01.exon4 transcript:Os01t0105300-01 N/A 4 N/A
|
||||
1 irgsp exon 291520 291534 . -1 . N/A N/A 1 N/A -1 -1 Os01t0105300-01.exon3 N/A Os01t0105300-01.exon3 N/A Os01t0105300-01.exon3 transcript:Os01t0105300-01 N/A 3 N/A
|
||||
1 irgsp exon 291678 291738 . -1 . N/A N/A 1 N/A -1 -1 Os01t0105300-01.exon2 N/A Os01t0105300-01.exon2 N/A Os01t0105300-01.exon2 transcript:Os01t0105300-01 N/A 2 N/A
|
||||
1 irgsp exon 291838 291892 . -1 . N/A N/A 1 N/A -1 -1 Os01t0105300-01.exon1 N/A Os01t0105300-01.exon1 N/A Os01t0105300-01.exon1 transcript:Os01t0105300-01 N/A 1 N/A
|
||||
1 irgsp CDS 284931 285020 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0105300-01 N/A N/A transcript:Os01t0105300-01 Os01t0105300-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 285021 287047 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-65 N/A N/A transcript:Os01t0105300-01 N/A N/A N/A
|
||||
1 irgsp five_prime_UTR 291398 291436 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-66 N/A N/A transcript:Os01t0105300-01 N/A N/A N/A
|
||||
1 irgsp five_prime_UTR 291520 291534 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-67 N/A N/A transcript:Os01t0105300-01 N/A N/A N/A
|
||||
1 irgsp five_prime_UTR 291678 291738 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-68 N/A N/A transcript:Os01t0105300-01 N/A N/A N/A
|
||||
1 irgsp five_prime_UTR 291838 291892 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-69 N/A N/A transcript:Os01t0105300-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 284762 284930 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-61 N/A N/A transcript:Os01t0105300-01 N/A N/A N/A
|
||||
1 irgsp gene 288372 292296 . 1 . N/A protein_coding N/A Similar to Kinesin heavy chain. (Os01t0105400-01) N/A N/A N/A Os01g0105400 gene:Os01g0105400 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 288372 292296 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0105400-01 N/A N/A gene:Os01g0105400 N/A N/A Os01t0105400-01
|
||||
1 irgsp exon 288372 288846 . 1 . N/A N/A 1 N/A -1 -1 Os01t0105400-01.exon1 N/A Os01t0105400-01.exon1 N/A Os01t0105400-01.exon1 transcript:Os01t0105400-01 N/A 1 N/A
|
||||
1 irgsp exon 288950 289116 . 1 . N/A N/A 1 N/A -1 -1 Os01t0105400-01.exon2 N/A Os01t0105400-01.exon2 N/A Os01t0105400-01.exon2 transcript:Os01t0105400-01 N/A 2 N/A
|
||||
1 irgsp exon 289202 289572 . 1 . N/A N/A 1 N/A -1 -1 Os01t0105400-01.exon3 N/A Os01t0105400-01.exon3 N/A Os01t0105400-01.exon3 transcript:Os01t0105400-01 N/A 3 N/A
|
||||
1 irgsp exon 289661 289830 . 1 . N/A N/A 1 N/A -1 -1 Os01t0105400-01.exon4 N/A Os01t0105400-01.exon4 N/A Os01t0105400-01.exon4 transcript:Os01t0105400-01 N/A 4 N/A
|
||||
1 irgsp exon 290395 290512 . 1 . N/A N/A 1 N/A 2 -1 Os01t0105400-01.exon5 N/A Os01t0105400-01.exon5 N/A Os01t0105400-01.exon5 transcript:Os01t0105400-01 N/A 5 N/A
|
||||
1 irgsp exon 291372 291574 . 1 . N/A N/A 1 N/A -1 2 Os01t0105400-01.exon6 N/A Os01t0105400-01.exon6 N/A Os01t0105400-01.exon6 transcript:Os01t0105400-01 N/A 6 N/A
|
||||
1 irgsp exon 291648 291779 . 1 . N/A N/A 1 N/A -1 -1 Os01t0105400-01.exon7 N/A Os01t0105400-01.exon7 N/A Os01t0105400-01.exon7 transcript:Os01t0105400-01 N/A 7 N/A
|
||||
1 irgsp exon 291859 291948 . 1 . N/A N/A 1 N/A -1 -1 Os01t0105400-01.exon8 N/A Os01t0105400-01.exon8 N/A Os01t0105400-01.exon8 transcript:Os01t0105400-01 N/A 8 N/A
|
||||
1 irgsp exon 292073 292296 . 1 . N/A N/A 1 N/A -1 -1 Os01t0105400-01.exon9 N/A Os01t0105400-01.exon9 N/A Os01t0105400-01.exon9 transcript:Os01t0105400-01 N/A 9 N/A
|
||||
1 irgsp CDS 290433 290512 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0105400-01 N/A N/A transcript:Os01t0105400-01 Os01t0105400-01 N/A N/A
|
||||
1 irgsp CDS 291372 291558 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0105400-01 N/A N/A transcript:Os01t0105400-01 Os01t0105400-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 288372 288846 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-70 N/A N/A transcript:Os01t0105400-01 N/A N/A N/A
|
||||
1 irgsp five_prime_UTR 288950 289116 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-71 N/A N/A transcript:Os01t0105400-01 N/A N/A N/A
|
||||
1 irgsp five_prime_UTR 289202 289572 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-72 N/A N/A transcript:Os01t0105400-01 N/A N/A N/A
|
||||
1 irgsp five_prime_UTR 289661 289830 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-73 N/A N/A transcript:Os01t0105400-01 N/A N/A N/A
|
||||
1 irgsp five_prime_UTR 290395 290432 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-74 N/A N/A transcript:Os01t0105400-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 291559 291574 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-62 N/A N/A transcript:Os01t0105400-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 291648 291779 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-63 N/A N/A transcript:Os01t0105400-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 291859 291948 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-64 N/A N/A transcript:Os01t0105400-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 292073 292296 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-65 N/A N/A transcript:Os01t0105400-01 N/A N/A N/A
|
||||
1 irgsp gene 303233 306736 . 1 . N/A protein_coding N/A Basic helix-loop-helix dimerisation region bHLH domain containing protein. (Os01t0105700-01) N/A N/A N/A Os01g0105700 gene:Os01g0105700 irgspv1.0-20170804-genes basic helix-loop-helix protein 071 N/A N/A N/A N/A
|
||||
1 irgsp mRNA 303233 306736 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0105700-01 N/A N/A gene:Os01g0105700 N/A N/A Os01t0105700-01
|
||||
1 irgsp exon 303233 303471 . 1 . N/A N/A 1 N/A 2 -1 Os01t0105700-01.exon1 N/A Os01t0105700-01.exon1 N/A Os01t0105700-01.exon1 transcript:Os01t0105700-01 N/A 1 N/A
|
||||
1 irgsp exon 303981 304509 . 1 . N/A N/A 1 N/A 0 2 Os01t0105700-01.exon2 N/A Os01t0105700-01.exon2 N/A Os01t0105700-01.exon2 transcript:Os01t0105700-01 N/A 2 N/A
|
||||
1 irgsp exon 305572 305718 . 1 . N/A N/A 1 N/A 0 0 Os01t0105700-01.exon3 N/A Os01t0105700-01.exon3 N/A Os01t0105700-01.exon3 transcript:Os01t0105700-01 N/A 3 N/A
|
||||
1 irgsp exon 305834 305899 . 1 . N/A N/A 1 N/A 0 0 Os01t0105700-01.exon4 N/A Os01t0105700-01.exon4 N/A Os01t0105700-01.exon4 transcript:Os01t0105700-01 N/A 4 N/A
|
||||
1 irgsp exon 305993 306058 . 1 . N/A N/A 1 N/A 0 0 Os01t0105700-01.exon5 N/A Os01t0105700-01.exon5 N/A Os01t0105700-01.exon5 transcript:Os01t0105700-01 N/A 5 N/A
|
||||
1 irgsp exon 306171 306245 . 1 . N/A N/A 1 N/A 0 0 Os01t0105700-01.exon6 N/A Os01t0105700-01.exon6 N/A Os01t0105700-01.exon6 transcript:Os01t0105700-01 N/A 6 N/A
|
||||
1 irgsp exon 306353 306736 . 1 . N/A N/A 1 N/A -1 0 Os01t0105700-01.exon7 N/A Os01t0105700-01.exon7 N/A Os01t0105700-01.exon7 transcript:Os01t0105700-01 N/A 7 N/A
|
||||
1 irgsp CDS 303329 303471 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0105700-01 N/A N/A transcript:Os01t0105700-01 Os01t0105700-01 N/A N/A
|
||||
1 irgsp CDS 303981 304509 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0105700-01 N/A N/A transcript:Os01t0105700-01 Os01t0105700-01 N/A N/A
|
||||
1 irgsp CDS 305572 305718 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0105700-01 N/A N/A transcript:Os01t0105700-01 Os01t0105700-01 N/A N/A
|
||||
1 irgsp CDS 305834 305899 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0105700-01 N/A N/A transcript:Os01t0105700-01 Os01t0105700-01 N/A N/A
|
||||
1 irgsp CDS 305993 306058 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0105700-01 N/A N/A transcript:Os01t0105700-01 Os01t0105700-01 N/A N/A
|
||||
1 irgsp CDS 306171 306245 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0105700-01 N/A N/A transcript:Os01t0105700-01 Os01t0105700-01 N/A N/A
|
||||
1 irgsp CDS 306353 306493 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0105700-01 N/A N/A transcript:Os01t0105700-01 Os01t0105700-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 303233 303328 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-75 N/A N/A transcript:Os01t0105700-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 306494 306736 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-66 N/A N/A transcript:Os01t0105700-01 N/A N/A N/A
|
||||
1 irgsp gene 306871 308842 . -1 . N/A protein_coding N/A Similar to Iron sulfur assembly protein 1. (Os01t0105800-01) N/A N/A N/A Os01g0105800 gene:Os01g0105800 irgspv1.0-20170804-genes IRON-SULFUR CLUSTER PROTEIN 9 N/A N/A N/A N/A
|
||||
1 irgsp mRNA 306871 308842 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0105800-01 N/A N/A gene:Os01g0105800 N/A N/A Os01t0105800-01
|
||||
1 irgsp exon 306871 307217 . -1 . N/A N/A 1 N/A -1 2 Os01t0105800-01.exon4 N/A Os01t0105800-01.exon4 N/A Os01t0105800-01.exon4 transcript:Os01t0105800-01 N/A 4 N/A
|
||||
1 irgsp exon 307296 307413 . -1 . N/A N/A 1 N/A 2 1 Os01t0105800-01.exon3 N/A Os01t0105800-01.exon3 N/A Os01t0105800-01.exon3 transcript:Os01t0105800-01 N/A 3 N/A
|
||||
1 irgsp exon 308397 308626 . -1 . N/A N/A 1 N/A 1 -1 Os01t0105800-01.exon2 N/A Os01t0105800-01.exon2 N/A Os01t0105800-01.exon2 transcript:Os01t0105800-01 N/A 2 N/A
|
||||
1 irgsp exon 308703 308842 . -1 . N/A N/A 1 N/A -1 -1 Os01t0105800-01.exon1 N/A Os01t0105800-01.exon1 N/A Os01t0105800-01.exon1 transcript:Os01t0105800-01 N/A 1 N/A
|
||||
1 irgsp CDS 307124 307217 . -1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0105800-01 N/A N/A transcript:Os01t0105800-01 Os01t0105800-01 N/A N/A
|
||||
1 irgsp CDS 307296 307413 . -1 2 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0105800-01 N/A N/A transcript:Os01t0105800-01 Os01t0105800-01 N/A N/A
|
||||
1 irgsp CDS 308397 308601 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0105800-01 N/A N/A transcript:Os01t0105800-01 Os01t0105800-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 308602 308626 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-76 N/A N/A transcript:Os01t0105800-01 N/A N/A N/A
|
||||
1 irgsp five_prime_UTR 308703 308842 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-77 N/A N/A transcript:Os01t0105800-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 306871 307123 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-67 N/A N/A transcript:Os01t0105800-01 N/A N/A N/A
|
||||
1 irgsp gene 309520 313170 . -1 . N/A protein_coding N/A Carbohydrate/purine kinase domain containing protein. (Os01t0105900-01) N/A N/A N/A Os01g0105900 gene:Os01g0105900 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 309520 313170 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0105900-01 N/A N/A gene:Os01g0105900 N/A N/A Os01t0105900-01
|
||||
1 irgsp exon 309520 310070 . -1 . N/A N/A 1 N/A -1 0 Os01t0105900-01.exon8 N/A Os01t0105900-01.exon8 N/A Os01t0105900-01.exon8 transcript:Os01t0105900-01 N/A 8 N/A
|
||||
1 irgsp exon 310256 310367 . -1 . N/A N/A 1 N/A 0 2 Os01t0105900-01.exon7 N/A Os01t0105900-01.exon7 N/A Os01t0105900-01.exon7 transcript:Os01t0105900-01 N/A 7 N/A
|
||||
1 irgsp exon 310455 310552 . -1 . N/A N/A 1 N/A 2 0 Os01t0105900-01.exon6 N/A Os01t0105900-01.exon6 N/A Os01t0105900-01.exon6 transcript:Os01t0105900-01 N/A 6 N/A
|
||||
1 irgsp exon 310632 310739 . -1 . N/A N/A 1 N/A 0 0 Os01t0105900-01.exon5 N/A Os01t0105900-01.exon5 N/A Os01t0105900-01.exon5 transcript:Os01t0105900-01 N/A 5 N/A
|
||||
1 irgsp exon 310880 310918 . -1 . N/A N/A 1 N/A 0 0 Os01t0105900-01.exon4 N/A Os01t0105900-01.exon4 N/A Os01t0105900-01.exon4 transcript:Os01t0105900-01 N/A 4 N/A
|
||||
1 irgsp exon 311002 311073 . -1 . N/A N/A 1 N/A 0 0 Os01t0105900-01.exon3 N/A Os01t0105900-01.exon3 N/A Os01t0105900-01.exon3 transcript:Os01t0105900-01 N/A 3 N/A
|
||||
1 irgsp exon 311163 311426 . -1 . N/A N/A 1 N/A 0 0 Os01t0105900-01.exon2 N/A Os01t0105900-01.exon2 N/A Os01t0105900-01.exon2 transcript:Os01t0105900-01 N/A 2 N/A
|
||||
1 irgsp exon 312867 313170 . -1 . N/A N/A 1 N/A 0 -1 Os01t0105900-01.exon1 N/A Os01t0105900-01.exon1 N/A Os01t0105900-01.exon1 transcript:Os01t0105900-01 N/A 1 N/A
|
||||
1 irgsp CDS 309822 310070 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0105900-01 N/A N/A transcript:Os01t0105900-01 Os01t0105900-01 N/A N/A
|
||||
1 irgsp CDS 310256 310367 . -1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0105900-01 N/A N/A transcript:Os01t0105900-01 Os01t0105900-01 N/A N/A
|
||||
1 irgsp CDS 310455 310552 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0105900-01 N/A N/A transcript:Os01t0105900-01 Os01t0105900-01 N/A N/A
|
||||
1 irgsp CDS 310632 310739 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0105900-01 N/A N/A transcript:Os01t0105900-01 Os01t0105900-01 N/A N/A
|
||||
1 irgsp CDS 310880 310918 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0105900-01 N/A N/A transcript:Os01t0105900-01 Os01t0105900-01 N/A N/A
|
||||
1 irgsp CDS 311002 311073 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0105900-01 N/A N/A transcript:Os01t0105900-01 Os01t0105900-01 N/A N/A
|
||||
1 irgsp CDS 311163 311426 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0105900-01 N/A N/A transcript:Os01t0105900-01 Os01t0105900-01 N/A N/A
|
||||
1 irgsp CDS 312867 313064 . -1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0105900-01 N/A N/A transcript:Os01t0105900-01 Os01t0105900-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 313065 313170 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-78 N/A N/A transcript:Os01t0105900-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 309520 309821 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-68 N/A N/A transcript:Os01t0105900-01 N/A N/A N/A
|
||||
1 irgsp gene 319754 322205 . 1 . N/A protein_coding N/A Similar to RER1A protein (AtRER1A). (Os01t0106200-01) N/A N/A N/A Os01g0106200 gene:Os01g0106200 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 319754 322205 . 1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0106200-01 N/A N/A gene:Os01g0106200 N/A N/A Os01t0106200-01
|
||||
1 irgsp exon 319754 320236 . 1 . N/A N/A 1 N/A 2 -1 Os01t0106200-01.exon1 N/A Os01t0106200-01.exon1 N/A Os01t0106200-01.exon1 transcript:Os01t0106200-01 N/A 1 N/A
|
||||
1 irgsp exon 321468 321648 . 1 . N/A N/A 1 N/A 0 2 Os01t0106200-01.exon2 N/A Os01t0106200-01.exon2 N/A Os01t0106200-01.exon2 transcript:Os01t0106200-01 N/A 2 N/A
|
||||
1 irgsp exon 321928 322205 . 1 . N/A N/A 1 N/A -1 0 Os01t0106200-01.exon3 N/A Os01t0106200-01.exon3 N/A Os01t0106200-01.exon3 transcript:Os01t0106200-01 N/A 3 N/A
|
||||
1 irgsp CDS 319875 320236 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0106200-01 N/A N/A transcript:Os01t0106200-01 Os01t0106200-01 N/A N/A
|
||||
1 irgsp CDS 321468 321648 . 1 1 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0106200-01 N/A N/A transcript:Os01t0106200-01 Os01t0106200-01 N/A N/A
|
||||
1 irgsp CDS 321928 321975 . 1 0 N/A N/A N/A N/A N/A N/A N/A N/A CDS:Os01t0106200-01 N/A N/A transcript:Os01t0106200-01 Os01t0106200-01 N/A N/A
|
||||
1 irgsp five_prime_UTR 319754 319874 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-five_prime_utr-79 N/A N/A transcript:Os01t0106200-01 N/A N/A N/A
|
||||
1 irgsp three_prime_UTR 321976 322205 . 1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-69 N/A N/A transcript:Os01t0106200-01 N/A N/A N/A
|
||||
1 irgsp gene 322591 323923 . -1 . N/A protein_coding N/A Similar to Isoflavone reductase homolog IRL (EC 1.3.1.-). (Os01t0106300-01) N/A N/A N/A Os01g0106300 gene:Os01g0106300 irgspv1.0-20170804-genes N/A N/A N/A N/A N/A
|
||||
1 irgsp mRNA 322591 323923 . -1 . N/A protein_coding N/A N/A N/A N/A N/A N/A transcript:Os01t0106300-01 N/A N/A gene:Os01g0106300 N/A N/A Os01t0106300-01
|
||||
1 irgsp exon 322591 323923 . -1 . N/A N/A 1 N/A -1 1 Os01t0106300-01.exon2 N/A Os01t0106300-01.exon2 N/A Os01t0106300-01.exon2 transcript:Os01t0106300-01 N/A 2 N/A
|
||||
1 irgsp three_prime_UTR 322591 322809 . -1 . N/A N/A N/A N/A N/A N/A N/A N/A agat-three_prime_utr-70 N/A N/A transcript:Os01t0106300-01 N/A N/A N/A
|
||||
|
10
src/agat/agat_convert_sp_gff2tsv/test_data/script.sh
Executable file
10
src/agat/agat_convert_sp_gff2tsv/test_data/script.sh
Executable file
@@ -0,0 +1,10 @@
|
||||
#!/bin/bash
|
||||
|
||||
# clone repo
|
||||
if [ ! -d /tmp/agat_source ]; then
|
||||
git clone --depth 1 --single-branch --branch master https://github.com/NBISweden/AGAT /tmp/agat_source
|
||||
fi
|
||||
|
||||
# copy test data
|
||||
cp -r /tmp/agat_source/t/scripts_output/out/agat_convert_sp_gff2tsv_1.tsv src/agat/agat_convert_sp_gff2tsv/test_data
|
||||
cp -r /tmp/agat_source/t/scripts_output/in/1.gff src/agat/agat_convert_sp_gff2tsv/test_data
|
||||
75
src/agat/agat_convert_sp_gxf2gxf/config.vsh.yaml
Normal file
75
src/agat/agat_convert_sp_gxf2gxf/config.vsh.yaml
Normal file
@@ -0,0 +1,75 @@
|
||||
name: agat_convert_sp_gxf2gxf
|
||||
namespace: agat
|
||||
description: |
|
||||
This script fixes and/or standardizes any GTF/GFF file into full sorted
|
||||
GTF/GFF file. It AGAT parser removes duplicate features, fixes
|
||||
duplicated IDs, adds missing ID and/or Parent attributes, deflates
|
||||
factorized attributes (attributes with several parents are duplicated
|
||||
with uniq ID), add missing features when possible (e.g. add exon if only
|
||||
CDS described, add UTR if CDS and exon described), fix feature locations
|
||||
(e.g. check exon is embedded in the parent features mRNA, gene), etc...
|
||||
|
||||
All AGAT's scripts with the _sp_ prefix use the AGAT parser, before to
|
||||
perform any supplementary task. So, it is not necessary to run this
|
||||
script prior the use of any other _sp_ script.
|
||||
keywords: [gene annotations, GFF conversion]
|
||||
links:
|
||||
homepage: https://github.com/NBISweden/AGAT
|
||||
documentation: https://agat.readthedocs.io/en/latest/tools/agat_convert_sp_gxf2gxf.html
|
||||
issue_tracker: https://github.com/NBISweden/AGAT/issues
|
||||
repository: https://github.com/NBISweden/AGAT
|
||||
references:
|
||||
doi: 10.5281/zenodo.3552717
|
||||
license: GPL-3.0
|
||||
authors:
|
||||
- __merge__: /src/_authors/leila_paquay.yaml
|
||||
roles: [ author, maintainer ]
|
||||
|
||||
argument_groups:
|
||||
- name: Inputs
|
||||
arguments:
|
||||
- name: --gxf
|
||||
alternatives: [-g, --gtf, --gff]
|
||||
description: |
|
||||
String - Input GTF/GFF file. Compressed file with .gz extension is accepted.
|
||||
type: file
|
||||
required: true
|
||||
direction: input
|
||||
example: input.gff
|
||||
- name: Outputs
|
||||
arguments:
|
||||
- name: --output
|
||||
alternatives: [-o]
|
||||
description: |
|
||||
String - Output GFF file. If no output file is specified, the output will be written to STDOUT.
|
||||
type: file
|
||||
direction: output
|
||||
required: true
|
||||
example: output.gff
|
||||
- name: Arguments
|
||||
arguments:
|
||||
- name: --config
|
||||
alternatives: [-c]
|
||||
description: |
|
||||
String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
|
||||
type: file
|
||||
required: false
|
||||
example: custom_agat_config.yaml
|
||||
resources:
|
||||
- type: bash_script
|
||||
path: script.sh
|
||||
test_resources:
|
||||
- type: bash_script
|
||||
path: test.sh
|
||||
- type: file
|
||||
path: test_data
|
||||
engines:
|
||||
- type: docker
|
||||
image: quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0
|
||||
setup:
|
||||
- type: docker
|
||||
run: |
|
||||
agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.txt
|
||||
runners:
|
||||
- type: executable
|
||||
- type: nextflow
|
||||
73
src/agat/agat_convert_sp_gxf2gxf/help.txt
Normal file
73
src/agat/agat_convert_sp_gxf2gxf/help.txt
Normal file
@@ -0,0 +1,73 @@
|
||||
```sh
|
||||
agat_convert_sp_gxf2gxf.pl --help
|
||||
```
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
| Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0 |
|
||||
| https://github.com/NBISweden/AGAT |
|
||||
| National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se |
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
Name:
|
||||
agat_convert_sp_gxf2gxf.pl
|
||||
|
||||
Description:
|
||||
This script fixes and/or standardizes any GTF/GFF file into full sorted
|
||||
GTF/GFF file. It AGAT parser removes duplicate features, fixes
|
||||
duplicated IDs, adds missing ID and/or Parent attributes, deflates
|
||||
factorized attributes (attributes with several parents are duplicated
|
||||
with uniq ID), add missing features when possible (e.g. add exon if only
|
||||
CDS described, add UTR if CDS and exon described), fix feature locations
|
||||
(e.g. check exon is embedded in the parent features mRNA, gene), etc...
|
||||
|
||||
All AGAT's scripts with the _sp_ prefix use the AGAT parser, before to
|
||||
perform any supplementary task. So, it is not necessary to run this
|
||||
script prior the use of any other _sp_ script.
|
||||
|
||||
Usage:
|
||||
agat_convert_sp_gxf2gxf.pl -g infile.gff [ -o outfile ]
|
||||
agat_convert_sp_gxf2gxf.pl --help
|
||||
|
||||
Options:
|
||||
-g, --gtf, --gff or --gxf
|
||||
String - Input GTF/GFF file. Compressed file with .gz extension
|
||||
is accepted.
|
||||
|
||||
-o or --output
|
||||
String - Output GFF file. If no output file is specified, the
|
||||
output will be written to STDOUT.
|
||||
|
||||
-c or --config
|
||||
String - Input agat config file. By default AGAT takes as input
|
||||
agat_config.yaml file from the working directory if any,
|
||||
otherwise it takes the orignal agat_config.yaml shipped with
|
||||
AGAT. To get the agat_config.yaml locally type: "agat config
|
||||
--expose". The --config option gives you the possibility to use
|
||||
your own AGAT config file (located elsewhere or named
|
||||
differently).
|
||||
|
||||
-h or --help
|
||||
Boolean - Display this helpful text.
|
||||
|
||||
Feedback:
|
||||
Did you find a bug?:
|
||||
Do not hesitate to report bugs to help us keep track of the bugs and
|
||||
their resolution. Please use the GitHub issue tracking system available
|
||||
at this address:
|
||||
|
||||
https://github.com/NBISweden/AGAT/issues
|
||||
|
||||
Ensure that the bug was not already reported by searching under Issues.
|
||||
If you're unable to find an (open) issue addressing the problem, open a new one.
|
||||
Try as much as possible to include in the issue when relevant:
|
||||
- a clear description,
|
||||
- as much relevant information as possible,
|
||||
- the command used,
|
||||
- a data sample,
|
||||
- an explanation of the expected behaviour that is not occurring.
|
||||
|
||||
Do you want to contribute?:
|
||||
You are very welcome, visit this address for the Contributing
|
||||
guidelines:
|
||||
https://github.com/NBISweden/AGAT/blob/master/CONTRIBUTING.md
|
||||
9
src/agat/agat_convert_sp_gxf2gxf/script.sh
Normal file
9
src/agat/agat_convert_sp_gxf2gxf/script.sh
Normal file
@@ -0,0 +1,9 @@
|
||||
#!/bin/bash
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
agat_convert_sp_gxf2gxf.pl \
|
||||
-g "$par_gxf" \
|
||||
-o "$par_output" \
|
||||
${par_config:+--config "${par_config}"}
|
||||
28
src/agat/agat_convert_sp_gxf2gxf/test.sh
Normal file
28
src/agat/agat_convert_sp_gxf2gxf/test.sh
Normal file
@@ -0,0 +1,28 @@
|
||||
#!/bin/bash
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
test_dir="${meta_resources_dir}/test_data"
|
||||
out_dir="${meta_resources_dir}/out_data"
|
||||
|
||||
echo "> Run $meta_name with test data"
|
||||
"$meta_executable" \
|
||||
--gxf "$test_dir/0_test.gff" \
|
||||
--output "$out_dir/output.gff"
|
||||
|
||||
echo ">> Checking output"
|
||||
[ ! -f "$out_dir/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
|
||||
|
||||
echo ">> Check if output is empty"
|
||||
[ ! -s "$out_dir/output.gff" ] && echo "Output file output.gff is empty" && exit 1
|
||||
|
||||
|
||||
echo ">> Check if output matches expected output"
|
||||
diff "$out_dir/output.gff" "$test_dir/0_correct_output.gff"
|
||||
if [ $? -ne 0 ]; then
|
||||
echo "Output file output.gff does not match expected output"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
echo "> Test successful"
|
||||
@@ -0,0 +1,36 @@
|
||||
##gff-version 3
|
||||
scaffold625 maker gene 337818 343277 . + . ID=CLUHARG00000005458;Name=TUBB3_2
|
||||
scaffold625 maker mRNA 337818 343277 . + . ID=CLUHART00000008717;Parent=CLUHARG00000005458
|
||||
scaffold625 maker exon 337818 337971 . + . ID=CLUHART00000008717:exon:1404;Parent=CLUHART00000008717
|
||||
scaffold625 maker exon 340733 340841 . + . ID=CLUHART00000008717:exon:1405;Parent=CLUHART00000008717
|
||||
scaffold625 maker exon 341518 341628 . + . ID=CLUHART00000008717:exon:1406;Parent=CLUHART00000008717
|
||||
scaffold625 maker exon 341964 343277 . + . ID=CLUHART00000008717:exon:1407;Parent=CLUHART00000008717
|
||||
scaffold625 maker CDS 337915 337971 . + 0 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
|
||||
scaffold625 maker CDS 340733 340841 . + 0 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
|
||||
scaffold625 maker CDS 341518 341628 . + 2 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
|
||||
scaffold625 maker CDS 341964 343033 . + 2 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
|
||||
scaffold625 maker five_prime_UTR 337818 337914 . + . ID=CLUHART00000008717:five_prime_utr;Parent=CLUHART00000008717
|
||||
scaffold625 maker three_prime_UTR 343034 343277 . + . ID=CLUHART00000008717:three_prime_utr;Parent=CLUHART00000008717
|
||||
scaffold789 maker gene 558184 564780 . + . ID=CLUHARG00000003852;Name=PF11_0240
|
||||
scaffold789 maker mRNA 558184 564780 . + . ID=CLUHART00000006146;Parent=CLUHARG00000003852
|
||||
scaffold789 maker exon 558184 560123 . + . ID=CLUHART00000006146:exon:995;Parent=CLUHART00000006146
|
||||
scaffold789 maker exon 561401 561519 . + . ID=CLUHART00000006146:exon:996;Parent=CLUHART00000006146
|
||||
scaffold789 maker exon 564171 564235 . + . ID=CLUHART00000006146:exon:997;Parent=CLUHART00000006146
|
||||
scaffold789 maker exon 564372 564780 . + . ID=CLUHART00000006146:exon:998;Parent=CLUHART00000006146
|
||||
scaffold789 maker CDS 558191 560123 . + 0 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
|
||||
scaffold789 maker CDS 561401 561519 . + 2 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
|
||||
scaffold789 maker CDS 564171 564235 . + 0 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
|
||||
scaffold789 maker CDS 564372 564588 . + 1 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
|
||||
scaffold789 maker five_prime_UTR 558184 558190 . + . ID=CLUHART00000006146:five_prime_utr;Parent=CLUHART00000006146
|
||||
scaffold789 maker three_prime_UTR 564589 564780 . + . ID=CLUHART00000006146:three_prime_utr;Parent=CLUHART00000006146
|
||||
scaffold789 maker mRNA 558184 564780 . + . ID=CLUHART00000006147;Parent=CLUHARG00000003852
|
||||
scaffold789 maker exon 558184 560123 . + . ID=CLUHART00000006147:exon:997;Parent=CLUHART00000006147
|
||||
scaffold789 maker exon 561401 561519 . + . ID=CLUHART00000006147:exon:998;Parent=CLUHART00000006147
|
||||
scaffold789 maker exon 562057 562121 . + . ID=CLUHART00000006147:exon:999;Parent=CLUHART00000006147
|
||||
scaffold789 maker exon 564372 564780 . + . ID=CLUHART00000006147:exon:1000;Parent=CLUHART00000006147
|
||||
scaffold789 maker CDS 558191 560123 . + 0 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
|
||||
scaffold789 maker CDS 561401 561519 . + 2 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
|
||||
scaffold789 maker CDS 562057 562121 . + 0 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
|
||||
scaffold789 maker CDS 564372 564588 . + 1 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
|
||||
scaffold789 maker five_prime_UTR 558184 558190 . + . ID=CLUHART00000006147:five_prime_utr;Parent=CLUHART00000006147
|
||||
scaffold789 maker three_prime_UTR 564589 564780 . + . ID=CLUHART00000006147:three_prime_utr;Parent=CLUHART00000006147
|
||||
36
src/agat/agat_convert_sp_gxf2gxf/test_data/0_test.gff
Normal file
36
src/agat/agat_convert_sp_gxf2gxf/test_data/0_test.gff
Normal file
@@ -0,0 +1,36 @@
|
||||
##gff-version 3
|
||||
scaffold625 maker gene 337818 343277 . + . ID=CLUHARG00000005458;Name=TUBB3_2
|
||||
scaffold625 maker mRNA 337818 343277 . + . ID=CLUHART00000008717;Parent=CLUHARG00000005458
|
||||
scaffold625 maker exon 337818 337971 . + . ID=CLUHART00000008717:exon:1404;Parent=CLUHART00000008717
|
||||
scaffold625 maker exon 340733 340841 . + . ID=CLUHART00000008717:exon:1405;Parent=CLUHART00000008717
|
||||
scaffold625 maker exon 341518 341628 . + . ID=CLUHART00000008717:exon:1406;Parent=CLUHART00000008717
|
||||
scaffold625 maker exon 341964 343277 . + . ID=CLUHART00000008717:exon:1407;Parent=CLUHART00000008717
|
||||
scaffold625 maker CDS 337915 337971 . + 0 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
|
||||
scaffold625 maker CDS 340733 340841 . + 0 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
|
||||
scaffold625 maker CDS 341518 341628 . + 2 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
|
||||
scaffold625 maker CDS 341964 343033 . + 2 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
|
||||
scaffold625 maker five_prime_UTR 337818 337914 . + . ID=CLUHART00000008717:five_prime_utr;Parent=CLUHART00000008717
|
||||
scaffold625 maker three_prime_UTR 343034 343277 . + . ID=CLUHART00000008717:three_prime_utr;Parent=CLUHART00000008717
|
||||
scaffold789 maker gene 558184 564780 . + . ID=CLUHARG00000003852;Name=PF11_0240
|
||||
scaffold789 maker mRNA 558184 564780 . + . ID=CLUHART00000006146;Parent=CLUHARG00000003852
|
||||
scaffold789 maker exon 558184 560123 . + . ID=CLUHART00000006146:exon:995;Parent=CLUHART00000006146
|
||||
scaffold789 maker exon 561401 561519 . + . ID=CLUHART00000006146:exon:996;Parent=CLUHART00000006146
|
||||
scaffold789 maker exon 564171 564235 . + . ID=CLUHART00000006146:exon:997;Parent=CLUHART00000006146
|
||||
scaffold789 maker exon 564372 564780 . + . ID=CLUHART00000006146:exon:998;Parent=CLUHART00000006146
|
||||
scaffold789 maker CDS 558191 560123 . + 0 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
|
||||
scaffold789 maker CDS 561401 561519 . + 2 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
|
||||
scaffold789 maker CDS 564171 564235 . + 0 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
|
||||
scaffold789 maker CDS 564372 564588 . + 1 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
|
||||
scaffold789 maker five_prime_UTR 558184 558190 . + . ID=CLUHART00000006146:five_prime_utr;Parent=CLUHART00000006146
|
||||
scaffold789 maker three_prime_UTR 564589 564780 . + . ID=CLUHART00000006146:three_prime_utr;Parent=CLUHART00000006146
|
||||
scaffold789 maker mRNA 558184 564780 . + . ID=CLUHART00000006147;Parent=CLUHARG00000003852
|
||||
scaffold789 maker exon 558184 560123 . + . ID=CLUHART00000006147:exon:997;Parent=CLUHART00000006147
|
||||
scaffold789 maker exon 561401 561519 . + . ID=CLUHART00000006147:exon:998;Parent=CLUHART00000006147
|
||||
scaffold789 maker exon 562057 562121 . + . ID=CLUHART00000006147:exon:999;Parent=CLUHART00000006147
|
||||
scaffold789 maker exon 564372 564780 . + . ID=CLUHART00000006147:exon:1000;Parent=CLUHART00000006147
|
||||
scaffold789 maker CDS 558191 560123 . + 0 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
|
||||
scaffold789 maker CDS 561401 561519 . + 2 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
|
||||
scaffold789 maker CDS 562057 562121 . + 0 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
|
||||
scaffold789 maker CDS 564372 564588 . + 1 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
|
||||
scaffold789 maker five_prime_UTR 558184 558190 . + . ID=CLUHART00000006147:five_prime_utr;Parent=CLUHART00000006147
|
||||
scaffold789 maker three_prime_UTR 564589 564780 . + . ID=CLUHART00000006147:three_prime_utr;Parent=CLUHART00000006147
|
||||
10
src/agat/agat_convert_sp_gxf2gxf/test_data/script.sh
Executable file
10
src/agat/agat_convert_sp_gxf2gxf/test_data/script.sh
Executable file
@@ -0,0 +1,10 @@
|
||||
#!/bin/bash
|
||||
|
||||
# clone repo
|
||||
if [ ! -d /tmp/agat_source ]; then
|
||||
git clone --depth 1 --single-branch --branch master https://github.com/NBISweden/AGAT /tmp/agat_source
|
||||
fi
|
||||
|
||||
# copy test data
|
||||
cp -r /tmp/agat_source/t/gff_syntax/in/0_test.gff src/agat/agat_convert_sp_gxf2gxf/test_data
|
||||
cp -r /tmp/agat_source/t/gff_syntax/out/0_correct_output.gff src/agat/agat_convert_sp_gxf2gxf/test_data
|
||||
64
src/agat/agat_sp_add_introns/config.vsh.yaml
Normal file
64
src/agat/agat_sp_add_introns/config.vsh.yaml
Normal file
@@ -0,0 +1,64 @@
|
||||
name: agat_sp_add_introns
|
||||
namespace: agat
|
||||
description: |
|
||||
Add intronic elements to a gtf/gff file without intron features.
|
||||
keywords: [gene annotations, GTF conversion]
|
||||
links:
|
||||
homepage: https://github.com/NBISweden/AGAT
|
||||
documentation: https://agat.readthedocs.io/en/latest/tools/agat_sp_add_introns.html
|
||||
issue_tracker: https://github.com/NBISweden/AGAT/issues
|
||||
repository: https://github.com/NBISweden/AGAT
|
||||
references:
|
||||
doi: 10.5281/zenodo.3552717
|
||||
license: GPL-3.0
|
||||
requirements:
|
||||
commands: [agat]
|
||||
authors:
|
||||
- __merge__: /src/_authors/leila_paquay.yaml
|
||||
roles: [ author, maintainer ]
|
||||
|
||||
argument_groups:
|
||||
- name: Inputs
|
||||
arguments:
|
||||
- name: --gff
|
||||
alternatives: [-f, --ref, --reffile]
|
||||
description: Input GTF/GFF file.
|
||||
type: file
|
||||
required: true
|
||||
example: input.gff
|
||||
- name: Outputs
|
||||
arguments:
|
||||
- name: --output
|
||||
alternatives: [-o, --out, --outfile, --gtf]
|
||||
description: Output GFF3 file.
|
||||
type: file
|
||||
direction: output
|
||||
required: true
|
||||
example: output.gff
|
||||
- name: Arguments
|
||||
arguments:
|
||||
- name: --config
|
||||
alternatives: [-c]
|
||||
description: |
|
||||
AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. The `--config` option
|
||||
gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
|
||||
type: file
|
||||
example: custom_agat_config.yaml
|
||||
resources:
|
||||
- type: bash_script
|
||||
path: script.sh
|
||||
test_resources:
|
||||
- type: bash_script
|
||||
path: test.sh
|
||||
- type: file
|
||||
path: test_data
|
||||
engines:
|
||||
- type: docker
|
||||
image: quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0
|
||||
setup:
|
||||
- type: docker
|
||||
run: |
|
||||
agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.txt
|
||||
runners:
|
||||
- type: executable
|
||||
- type: nextflow
|
||||
62
src/agat/agat_sp_add_introns/help.txt
Normal file
62
src/agat/agat_sp_add_introns/help.txt
Normal file
@@ -0,0 +1,62 @@
|
||||
```sh
|
||||
agat_sp_add_introns.pl --help
|
||||
```
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
| Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0 |
|
||||
| https://github.com/NBISweden/AGAT |
|
||||
| National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se |
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
Name:
|
||||
agat_sp_add_introns.pl
|
||||
|
||||
Description:
|
||||
The script aims to add intron features to gtf/gff file without intron
|
||||
features.
|
||||
|
||||
Usage:
|
||||
agat_sp_add_introns.pl --gff infile --out outFile
|
||||
agat_sp_add_introns.pl --help
|
||||
|
||||
Options:
|
||||
--gff, -f, --ref or -reffile
|
||||
Input GTF/GFF file.
|
||||
|
||||
--out, --output or -o
|
||||
Output GFF3 file.
|
||||
|
||||
-c or --config
|
||||
String - Input agat config file. By default AGAT takes as input
|
||||
agat_config.yaml file from the working directory if any,
|
||||
otherwise it takes the orignal agat_config.yaml shipped with
|
||||
AGAT. To get the agat_config.yaml locally type: "agat config
|
||||
--expose". The --config option gives you the possibility to use
|
||||
your own AGAT config file (located elsewhere or named
|
||||
differently).
|
||||
|
||||
--help or -h
|
||||
Display this helpful text.
|
||||
|
||||
Feedback:
|
||||
Did you find a bug?:
|
||||
Do not hesitate to report bugs to help us keep track of the bugs and
|
||||
their resolution. Please use the GitHub issue tracking system available
|
||||
at this address:
|
||||
|
||||
https://github.com/NBISweden/AGAT/issues
|
||||
|
||||
Ensure that the bug was not already reported by searching under Issues.
|
||||
If you're unable to find an (open) issue addressing the problem, open a new one.
|
||||
Try as much as possible to include in the issue when relevant:
|
||||
- a clear description,
|
||||
- as much relevant information as possible,
|
||||
- the command used,
|
||||
- a data sample,
|
||||
- an explanation of the expected behaviour that is not occurring.
|
||||
|
||||
Do you want to contribute?:
|
||||
You are very welcome, visit this address for the Contributing
|
||||
guidelines:
|
||||
https://github.com/NBISweden/AGAT/blob/master/CONTRIBUTING.md
|
||||
11
src/agat/agat_sp_add_introns/script.sh
Normal file
11
src/agat/agat_sp_add_introns/script.sh
Normal file
@@ -0,0 +1,11 @@
|
||||
#!/bin/bash
|
||||
|
||||
set -eo pipefail
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
agat_sp_add_introns.pl \
|
||||
-f "$par_gff" \
|
||||
-o "$par_output" \
|
||||
${par_config:+--config "${par_config}"}
|
||||
34
src/agat/agat_sp_add_introns/test.sh
Normal file
34
src/agat/agat_sp_add_introns/test.sh
Normal file
@@ -0,0 +1,34 @@
|
||||
#!/bin/bash
|
||||
|
||||
set -eo pipefail
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
test_dir="${meta_resources_dir}/test_data"
|
||||
|
||||
# create temporary directory and clean up on exit
|
||||
TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXX")
|
||||
function clean_up {
|
||||
[[ -d "$TMPDIR" ]] && rm -rf "$TMPDIR"
|
||||
}
|
||||
trap clean_up EXIT
|
||||
|
||||
echo "> Run $meta_name with test data"
|
||||
"$meta_executable" \
|
||||
--gff "$test_dir/1_truncated.gff" \
|
||||
--output "$TMPDIR/output.gff"
|
||||
|
||||
echo ">> Checking output"
|
||||
[ ! -f "$TMPDIR/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
|
||||
|
||||
echo ">> Check if output is empty"
|
||||
[ ! -s "$TMPDIR/output.gff" ] && echo "Output file output.gff is empty" && exit 1
|
||||
|
||||
echo ">> Check if output matches expected output"
|
||||
diff "$TMPDIR/output.gff" "$test_dir/test_output.gff"
|
||||
if [ $? -ne 0 ]; then
|
||||
echo "Output file output.gff does not match expected output"
|
||||
exit 1
|
||||
fi
|
||||
echo "> Test successful"
|
||||
106
src/agat/agat_sp_add_introns/test_data/1_truncated.gff
Normal file
106
src/agat/agat_sp_add_introns/test_data/1_truncated.gff
Normal file
@@ -0,0 +1,106 @@
|
||||
##gff-version 3
|
||||
##sequence-region 1 1 43270923
|
||||
#!genome-build RAP-DB IRGSP-1.0
|
||||
#!genome-version IRGSP-1.0
|
||||
#!genome-date 2015-10
|
||||
#!genome-build-accession GCA_001433935.1
|
||||
1 RAP-DB chromosome 1 43270923 . . . ID=chromosome:1;Alias=Chr1,AP014957.1,NC_029256.1
|
||||
###
|
||||
1 irgsp repeat_region 2000 2100 . + . ID=fakeRepeat1
|
||||
###
|
||||
1 irgsp gene 2983 10815 . + . ID=gene:Os01g0100100;biotype=protein_coding;description=RabGAP/TBC domain containing protein. (Os01t0100100-01);gene_id=Os01g0100100;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 2983 10815 . + . ID=transcript:Os01t0100100-01;Parent=gene:Os01g0100100;biotype=protein_coding;transcript_id=Os01t0100100-01
|
||||
1 irgsp exon 2983 3268 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 2983 3268 . + . Parent=transcript:Os01t0100100-01
|
||||
1 irgsp five_prime_UTR 3354 3448 . + . Parent=transcript:Os01t0100100-01
|
||||
1 irgsp exon 3354 3616 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0100100-01.exon2;rank=2
|
||||
1 irgsp CDS 3449 3616 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 4357 4455 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100100-01.exon3;rank=3
|
||||
1 irgsp CDS 4357 4455 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 5457 5560 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100100-01.exon4;rank=4
|
||||
1 irgsp CDS 5457 5560 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 7136 7944 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon5;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0100100-01.exon5;rank=5
|
||||
1 irgsp CDS 7136 7944 . + 1 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 8028 8150 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon6;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0100100-01.exon6;rank=6
|
||||
1 irgsp CDS 8028 8150 . + 2 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 8232 8320 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100100-01.exon7;rank=7
|
||||
1 irgsp CDS 8232 8320 . + 2 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 8408 8608 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon8;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100100-01.exon8;rank=8
|
||||
1 irgsp CDS 8408 8608 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 9210 9615 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon9;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0100100-01.exon9;rank=9
|
||||
1 irgsp CDS 9210 9615 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 10102 10187 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon10;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100100-01.exon10;rank=10
|
||||
1 irgsp CDS 10102 10187 . + 2 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp CDS 10274 10297 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 10274 10430 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon11;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0100100-01.exon11;rank=11
|
||||
1 irgsp three_prime_UTR 10298 10430 . + . Parent=transcript:Os01t0100100-01
|
||||
1 irgsp exon 10504 10815 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon12;rank=12
|
||||
1 irgsp three_prime_UTR 10504 10815 . + . Parent=transcript:Os01t0100100-01
|
||||
###
|
||||
1 irgsp gene 11218 12435 . + . ID=gene:Os01g0100200;biotype=protein_coding;description=Conserved hypothetical protein. (Os01t0100200-01);gene_id=Os01g0100200;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 11218 12435 . + . ID=transcript:Os01t0100200-01;Parent=gene:Os01g0100200;biotype=protein_coding;transcript_id=Os01t0100200-01
|
||||
1 irgsp five_prime_UTR 11218 11797 . + . Parent=transcript:Os01t0100200-01
|
||||
1 irgsp exon 11218 12060 . + . Parent=transcript:Os01t0100200-01;Name=Os01t0100200-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100200-01.exon1;rank=1
|
||||
1 irgsp CDS 11798 12060 . + 0 ID=CDS:Os01t0100200-01;Parent=transcript:Os01t0100200-01;protein_id=Os01t0100200-01
|
||||
1 irgsp CDS 12152 12317 . + 1 ID=CDS:Os01t0100200-01;Parent=transcript:Os01t0100200-01;protein_id=Os01t0100200-01
|
||||
1 irgsp exon 12152 12435 . + . Parent=transcript:Os01t0100200-01;Name=Os01t0100200-01.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100200-01.exon2;rank=2
|
||||
1 irgsp three_prime_UTR 12318 12435 . + . Parent=transcript:Os01t0100200-01
|
||||
###
|
||||
1 irgsp gene 11372 12284 . - . ID=gene:Os01g0100300;biotype=protein_coding;description=Cytochrome P450 domain containing protein. (Os01t0100300-00);gene_id=Os01g0100300;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 11372 12284 . - . ID=transcript:Os01t0100300-00;Parent=gene:Os01g0100300;biotype=protein_coding;transcript_id=Os01t0100300-00
|
||||
1 irgsp exon 11372 12042 . - . Parent=transcript:Os01t0100300-00;Name=Os01t0100300-00.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100300-00.exon2;rank=2
|
||||
1 irgsp CDS 11372 12042 . - 2 ID=CDS:Os01t0100300-00;Parent=transcript:Os01t0100300-00;protein_id=Os01t0100300-00
|
||||
1 irgsp exon 12146 12284 . - . Parent=transcript:Os01t0100300-00;Name=Os01t0100300-00.exon1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0100300-00.exon1;rank=1
|
||||
1 irgsp CDS 12146 12284 . - 0 ID=CDS:Os01t0100300-00;Parent=transcript:Os01t0100300-00;protein_id=Os01t0100300-00
|
||||
###
|
||||
1 irgsp gene 12721 15685 . + . ID=gene:Os01g0100400;biotype=protein_coding;description=Similar to Pectinesterase-like protein. (Os01t0100400-01);gene_id=Os01g0100400;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 12721 15685 . + . ID=transcript:Os01t0100400-01;Parent=gene:Os01g0100400;biotype=protein_coding;transcript_id=Os01t0100400-01
|
||||
1 irgsp five_prime_UTR 12721 12773 . + . Parent=transcript:Os01t0100400-01
|
||||
1 irgsp exon 12721 13813 . + . Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100400-01.exon1;rank=1
|
||||
1 irgsp CDS 12774 13813 . + 0 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp exon 13906 14271 . + . Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100400-01.exon2;rank=2
|
||||
1 irgsp CDS 13906 14271 . + 1 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp exon 14359 14437 . + . Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0100400-01.exon3;rank=3
|
||||
1 irgsp CDS 14359 14437 . + 1 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp exon 14969 15171 . + . Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100400-01.exon4;rank=4
|
||||
1 irgsp CDS 14969 15171 . + 0 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp CDS 15266 15359 . + 1 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp exon 15266 15685 . + . Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon5;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100400-01.exon5;rank=5
|
||||
1 irgsp three_prime_UTR 15360 15685 . + . Parent=transcript:Os01t0100400-01
|
||||
###
|
||||
1 irgsp gene 12808 13978 . - . ID=gene:Os01g0100466;biotype=protein_coding;description=Hypothetical protein. (Os01t0100466-00);gene_id=Os01g0100466;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 12808 13978 . - . ID=transcript:Os01t0100466-00;Parent=gene:Os01g0100466;biotype=protein_coding;transcript_id=Os01t0100466-00
|
||||
1 irgsp three_prime_UTR 12808 12868 . - . Parent=transcript:Os01t0100466-00
|
||||
1 irgsp exon 12808 13782 . - . Parent=transcript:Os01t0100466-00;Name=Os01t0100466-00.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100466-00.exon2;rank=2
|
||||
1 irgsp CDS 12869 13102 . - 0 ID=CDS:Os01t0100466-00;Parent=transcript:Os01t0100466-00;protein_id=Os01t0100466-00
|
||||
1 irgsp five_prime_UTR 13103 13782 . - . Parent=transcript:Os01t0100466-00
|
||||
1 irgsp exon 13880 13978 . - . Parent=transcript:Os01t0100466-00;Name=Os01t0100466-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100466-00.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 13880 13978 . - . Parent=transcript:Os01t0100466-00
|
||||
###
|
||||
1 irgsp gene 16399 20144 . + . ID=gene:Os01g0100500;biotype=protein_coding;description=Immunoglobulin-like domain containing protein. (Os01t0100500-01);gene_id=Os01g0100500;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 16399 20144 . + . ID=transcript:Os01t0100500-01;Parent=gene:Os01g0100500;biotype=protein_coding;transcript_id=Os01t0100500-01
|
||||
1 irgsp five_prime_UTR 16399 16598 . + . Parent=transcript:Os01t0100500-01
|
||||
1 irgsp exon 16399 16976 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0100500-01.exon1;rank=1
|
||||
1 irgsp CDS 16599 16976 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp exon 17383 17474 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100500-01.exon2;rank=2
|
||||
1 irgsp CDS 17383 17474 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp exon 17558 18258 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0100500-01.exon3;rank=3
|
||||
1 irgsp CDS 17558 18258 . + 1 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp exon 18501 18571 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100500-01.exon4;rank=4
|
||||
1 irgsp CDS 18501 18571 . + 2 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp exon 18968 19057 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100500-01.exon5;rank=5
|
||||
1 irgsp CDS 18968 19057 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp exon 19142 19321 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100500-01.exon6;rank=6
|
||||
1 irgsp CDS 19142 19321 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp CDS 19531 19593 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp exon 19531 19629 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon7;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0100500-01.exon7;rank=7
|
||||
1 irgsp three_prime_UTR 19594 19629 . + . Parent=transcript:Os01t0100500-01
|
||||
1 irgsp exon 19734 20144 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon8;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100500-01.exon8;rank=8
|
||||
1 irgsp three_prime_UTR 19734 20144 . + . Parent=transcript:Os01t0100500-01
|
||||
###
|
||||
1 irgsp gene 22841 26892 . + . ID=gene:Os01g0100600;biotype=protein_coding;description=Single-stranded nucleic acid binding R3H domain containing protein. (Os01t0100600-01);gene_id=Os01g0100600;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 22841 26892 . + . ID=transcript:Os01t0100600-01;Parent=gene:Os01g0100600;biotype=protein_coding;transcript_id=Os01t0100600-01
|
||||
1 irgsp five_prime_UTR 22841 23231 . + . Parent=transcript:Os01t0100600-01
|
||||
1 irgsp exon 22841 23281 . + . Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100600-01.exon1;rank=1
|
||||
1 irgsp CDS 23232 23281 . + 0 ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
|
||||
1 irgsp exon 23572 23847 . + . Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100600-01.exon2;rank=2
|
||||
12
src/agat/agat_sp_add_introns/test_data/script.sh
Executable file
12
src/agat/agat_sp_add_introns/test_data/script.sh
Executable file
@@ -0,0 +1,12 @@
|
||||
#!/bin/bash
|
||||
|
||||
# clone repo
|
||||
if [ ! -d /tmp/agat_source ]; then
|
||||
git clone --depth 1 --single-branch --branch master https://github.com/NBISweden/AGAT /tmp/agat_source
|
||||
fi
|
||||
|
||||
# copy test data
|
||||
cp -r /tmp/agat_source/t/scripts_output/in/1.gff src/agat/agat_sp_add_introns/test_data
|
||||
cp -r /tmp/agat_source/t/scripts_output/out/agat_sp_add_introns_1.gff src/agat/agat_sp_add_introns/test_data
|
||||
|
||||
head -n 106 "src/agat/agat_sp_add_introns/test_data/1.gff" > "src/agat/agat_sp_add_introns/test_data/1_truncated.gff"
|
||||
125
src/agat/agat_sp_add_introns/test_data/test_output.gff
Normal file
125
src/agat/agat_sp_add_introns/test_data/test_output.gff
Normal file
@@ -0,0 +1,125 @@
|
||||
##gff-version 3
|
||||
##sequence-region 1 1 43270923
|
||||
#!genome-build RAP-DB IRGSP-1.0
|
||||
#!genome-version IRGSP-1.0
|
||||
#!genome-date 2015-10
|
||||
#!genome-build-accession GCA_001433935.1
|
||||
1 RAP-DB chromosome 1 43270923 . . . ID=chromosome:1;Alias=Chr1,AP014957.1,NC_029256.1
|
||||
1 irgsp repeat_region 2000 2100 . + . ID=fakeRepeat1
|
||||
1 irgsp gene 2983 10815 . + . ID=gene:Os01g0100100;biotype=protein_coding;description=RabGAP/TBC domain containing protein. (Os01t0100100-01);gene_id=Os01g0100100;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 2983 10815 . + . ID=transcript:Os01t0100100-01;Parent=gene:Os01g0100100;biotype=protein_coding;transcript_id=Os01t0100100-01
|
||||
1 irgsp exon 2983 3268 . + . ID=Os01t0100100-01.exon1;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon1;rank=1
|
||||
1 irgsp exon 3354 3616 . + . ID=Os01t0100100-01.exon2;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0100100-01.exon2;rank=2
|
||||
1 irgsp exon 4357 4455 . + . ID=Os01t0100100-01.exon3;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100100-01.exon3;rank=3
|
||||
1 irgsp exon 5457 5560 . + . ID=Os01t0100100-01.exon4;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100100-01.exon4;rank=4
|
||||
1 irgsp exon 7136 7944 . + . ID=Os01t0100100-01.exon5;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon5;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0100100-01.exon5;rank=5
|
||||
1 irgsp exon 8028 8150 . + . ID=Os01t0100100-01.exon6;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon6;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0100100-01.exon6;rank=6
|
||||
1 irgsp exon 8232 8320 . + . ID=Os01t0100100-01.exon7;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100100-01.exon7;rank=7
|
||||
1 irgsp exon 8408 8608 . + . ID=Os01t0100100-01.exon8;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon8;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100100-01.exon8;rank=8
|
||||
1 irgsp exon 9210 9615 . + . ID=Os01t0100100-01.exon9;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon9;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0100100-01.exon9;rank=9
|
||||
1 irgsp exon 10102 10187 . + . ID=Os01t0100100-01.exon10;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon10;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100100-01.exon10;rank=10
|
||||
1 irgsp exon 10274 10430 . + . ID=Os01t0100100-01.exon11;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon11;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0100100-01.exon11;rank=11
|
||||
1 irgsp exon 10504 10815 . + . ID=Os01t0100100-01.exon12;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon12;rank=12
|
||||
1 irgsp CDS 3449 3616 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp CDS 4357 4455 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp CDS 5457 5560 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp CDS 7136 7944 . + 1 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp CDS 8028 8150 . + 2 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp CDS 8232 8320 . + 2 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp CDS 8408 8608 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp CDS 9210 9615 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp CDS 10102 10187 . + 2 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp CDS 10274 10297 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp five_prime_UTR 2983 3268 . + . ID=agat-five_prime_utr-1;Parent=transcript:Os01t0100100-01
|
||||
1 irgsp five_prime_UTR 3354 3448 . + . ID=agat-five_prime_utr-2;Parent=transcript:Os01t0100100-01
|
||||
1 irgsp intron 3269 3353 . + . ID=intron_added-1;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon12;rank=12
|
||||
1 irgsp intron 3617 4356 . + . ID=intron_added-2;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon12;rank=12
|
||||
1 irgsp intron 4456 5456 . + . ID=intron_added-3;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon12;rank=12
|
||||
1 irgsp intron 5561 7135 . + . ID=intron_added-4;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon12;rank=12
|
||||
1 irgsp intron 7945 8027 . + . ID=intron_added-5;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon12;rank=12
|
||||
1 irgsp intron 8151 8231 . + . ID=intron_added-6;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon12;rank=12
|
||||
1 irgsp intron 8321 8407 . + . ID=intron_added-7;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon12;rank=12
|
||||
1 irgsp intron 8609 9209 . + . ID=intron_added-8;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon12;rank=12
|
||||
1 irgsp intron 9616 10101 . + . ID=intron_added-9;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon12;rank=12
|
||||
1 irgsp intron 10188 10273 . + . ID=intron_added-10;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon12;rank=12
|
||||
1 irgsp intron 10431 10503 . + . ID=intron_added-11;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon12;rank=12
|
||||
1 irgsp three_prime_UTR 10298 10430 . + . ID=agat-three_prime_utr-1;Parent=transcript:Os01t0100100-01
|
||||
1 irgsp three_prime_UTR 10504 10815 . + . ID=agat-three_prime_utr-2;Parent=transcript:Os01t0100100-01
|
||||
1 irgsp gene 11218 12435 . + . ID=gene:Os01g0100200;biotype=protein_coding;description=Conserved hypothetical protein. (Os01t0100200-01);gene_id=Os01g0100200;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 11218 12435 . + . ID=transcript:Os01t0100200-01;Parent=gene:Os01g0100200;biotype=protein_coding;transcript_id=Os01t0100200-01
|
||||
1 irgsp exon 11218 12060 . + . ID=Os01t0100200-01.exon1;Parent=transcript:Os01t0100200-01;Name=Os01t0100200-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100200-01.exon1;rank=1
|
||||
1 irgsp exon 12152 12435 . + . ID=Os01t0100200-01.exon2;Parent=transcript:Os01t0100200-01;Name=Os01t0100200-01.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100200-01.exon2;rank=2
|
||||
1 irgsp CDS 11798 12060 . + 0 ID=CDS:Os01t0100200-01;Parent=transcript:Os01t0100200-01;protein_id=Os01t0100200-01
|
||||
1 irgsp CDS 12152 12317 . + 1 ID=CDS:Os01t0100200-01;Parent=transcript:Os01t0100200-01;protein_id=Os01t0100200-01
|
||||
1 irgsp five_prime_UTR 11218 11797 . + . ID=agat-five_prime_utr-3;Parent=transcript:Os01t0100200-01
|
||||
1 irgsp intron 12061 12151 . + . ID=intron_added-12;Parent=transcript:Os01t0100200-01;Name=Os01t0100200-01.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100200-01.exon2;rank=2
|
||||
1 irgsp three_prime_UTR 12318 12435 . + . ID=agat-three_prime_utr-3;Parent=transcript:Os01t0100200-01
|
||||
1 irgsp gene 11372 12284 . - . ID=gene:Os01g0100300;biotype=protein_coding;description=Cytochrome P450 domain containing protein. (Os01t0100300-00);gene_id=Os01g0100300;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 11372 12284 . - . ID=transcript:Os01t0100300-00;Parent=gene:Os01g0100300;biotype=protein_coding;transcript_id=Os01t0100300-00
|
||||
1 irgsp exon 11372 12042 . - . ID=Os01t0100300-00.exon2;Parent=transcript:Os01t0100300-00;Name=Os01t0100300-00.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100300-00.exon2;rank=2
|
||||
1 irgsp exon 12146 12284 . - . ID=Os01t0100300-00.exon1;Parent=transcript:Os01t0100300-00;Name=Os01t0100300-00.exon1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0100300-00.exon1;rank=1
|
||||
1 irgsp CDS 11372 12042 . - 2 ID=CDS:Os01t0100300-00;Parent=transcript:Os01t0100300-00;protein_id=Os01t0100300-00
|
||||
1 irgsp CDS 12146 12284 . - 0 ID=CDS:Os01t0100300-00;Parent=transcript:Os01t0100300-00;protein_id=Os01t0100300-00
|
||||
1 irgsp intron 12043 12145 . - . ID=intron_added-13;Parent=transcript:Os01t0100300-00;Name=Os01t0100300-00.exon1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0100300-00.exon1;rank=1
|
||||
1 irgsp gene 12721 15685 . + . ID=gene:Os01g0100400;biotype=protein_coding;description=Similar to Pectinesterase-like protein. (Os01t0100400-01);gene_id=Os01g0100400;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 12721 15685 . + . ID=transcript:Os01t0100400-01;Parent=gene:Os01g0100400;biotype=protein_coding;transcript_id=Os01t0100400-01
|
||||
1 irgsp exon 12721 13813 . + . ID=Os01t0100400-01.exon1;Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100400-01.exon1;rank=1
|
||||
1 irgsp exon 13906 14271 . + . ID=Os01t0100400-01.exon2;Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100400-01.exon2;rank=2
|
||||
1 irgsp exon 14359 14437 . + . ID=Os01t0100400-01.exon3;Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0100400-01.exon3;rank=3
|
||||
1 irgsp exon 14969 15171 . + . ID=Os01t0100400-01.exon4;Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100400-01.exon4;rank=4
|
||||
1 irgsp exon 15266 15685 . + . ID=Os01t0100400-01.exon5;Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon5;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100400-01.exon5;rank=5
|
||||
1 irgsp CDS 12774 13813 . + 0 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp CDS 13906 14271 . + 1 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp CDS 14359 14437 . + 1 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp CDS 14969 15171 . + 0 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp CDS 15266 15359 . + 1 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp five_prime_UTR 12721 12773 . + . ID=agat-five_prime_utr-4;Parent=transcript:Os01t0100400-01
|
||||
1 irgsp intron 13814 13905 . + . ID=intron_added-14;Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon5;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100400-01.exon5;rank=5
|
||||
1 irgsp intron 14272 14358 . + . ID=intron_added-15;Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon5;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100400-01.exon5;rank=5
|
||||
1 irgsp intron 14438 14968 . + . ID=intron_added-16;Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon5;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100400-01.exon5;rank=5
|
||||
1 irgsp intron 15172 15265 . + . ID=intron_added-17;Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon5;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100400-01.exon5;rank=5
|
||||
1 irgsp three_prime_UTR 15360 15685 . + . ID=agat-three_prime_utr-4;Parent=transcript:Os01t0100400-01
|
||||
1 irgsp gene 12808 13978 . - . ID=gene:Os01g0100466;biotype=protein_coding;description=Hypothetical protein. (Os01t0100466-00);gene_id=Os01g0100466;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 12808 13978 . - . ID=transcript:Os01t0100466-00;Parent=gene:Os01g0100466;biotype=protein_coding;transcript_id=Os01t0100466-00
|
||||
1 irgsp exon 12808 13782 . - . ID=Os01t0100466-00.exon2;Parent=transcript:Os01t0100466-00;Name=Os01t0100466-00.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100466-00.exon2;rank=2
|
||||
1 irgsp exon 13880 13978 . - . ID=Os01t0100466-00.exon1;Parent=transcript:Os01t0100466-00;Name=Os01t0100466-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100466-00.exon1;rank=1
|
||||
1 irgsp CDS 12869 13102 . - 0 ID=CDS:Os01t0100466-00;Parent=transcript:Os01t0100466-00;protein_id=Os01t0100466-00
|
||||
1 irgsp five_prime_UTR 13103 13782 . - . ID=agat-five_prime_utr-5;Parent=transcript:Os01t0100466-00
|
||||
1 irgsp five_prime_UTR 13880 13978 . - . ID=agat-five_prime_utr-6;Parent=transcript:Os01t0100466-00
|
||||
1 irgsp intron 13783 13879 . - . ID=intron_added-18;Parent=transcript:Os01t0100466-00;Name=Os01t0100466-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100466-00.exon1;rank=1
|
||||
1 irgsp three_prime_UTR 12808 12868 . - . ID=agat-three_prime_utr-5;Parent=transcript:Os01t0100466-00
|
||||
1 irgsp gene 16399 20144 . + . ID=gene:Os01g0100500;biotype=protein_coding;description=Immunoglobulin-like domain containing protein. (Os01t0100500-01);gene_id=Os01g0100500;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 16399 20144 . + . ID=transcript:Os01t0100500-01;Parent=gene:Os01g0100500;biotype=protein_coding;transcript_id=Os01t0100500-01
|
||||
1 irgsp exon 16399 16976 . + . ID=Os01t0100500-01.exon1;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0100500-01.exon1;rank=1
|
||||
1 irgsp exon 17383 17474 . + . ID=Os01t0100500-01.exon2;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100500-01.exon2;rank=2
|
||||
1 irgsp exon 17558 18258 . + . ID=Os01t0100500-01.exon3;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0100500-01.exon3;rank=3
|
||||
1 irgsp exon 18501 18571 . + . ID=Os01t0100500-01.exon4;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100500-01.exon4;rank=4
|
||||
1 irgsp exon 18968 19057 . + . ID=Os01t0100500-01.exon5;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100500-01.exon5;rank=5
|
||||
1 irgsp exon 19142 19321 . + . ID=Os01t0100500-01.exon6;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100500-01.exon6;rank=6
|
||||
1 irgsp exon 19531 19629 . + . ID=Os01t0100500-01.exon7;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon7;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0100500-01.exon7;rank=7
|
||||
1 irgsp exon 19734 20144 . + . ID=Os01t0100500-01.exon8;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon8;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100500-01.exon8;rank=8
|
||||
1 irgsp CDS 16599 16976 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp CDS 17383 17474 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp CDS 17558 18258 . + 1 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp CDS 18501 18571 . + 2 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp CDS 18968 19057 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp CDS 19142 19321 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp CDS 19531 19593 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp five_prime_UTR 16399 16598 . + . ID=agat-five_prime_utr-7;Parent=transcript:Os01t0100500-01
|
||||
1 irgsp intron 16977 17382 . + . ID=intron_added-19;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon8;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100500-01.exon8;rank=8
|
||||
1 irgsp intron 17475 17557 . + . ID=intron_added-20;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon8;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100500-01.exon8;rank=8
|
||||
1 irgsp intron 18259 18500 . + . ID=intron_added-21;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon8;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100500-01.exon8;rank=8
|
||||
1 irgsp intron 18572 18967 . + . ID=intron_added-22;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon8;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100500-01.exon8;rank=8
|
||||
1 irgsp intron 19058 19141 . + . ID=intron_added-23;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon8;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100500-01.exon8;rank=8
|
||||
1 irgsp intron 19322 19530 . + . ID=intron_added-24;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon8;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100500-01.exon8;rank=8
|
||||
1 irgsp intron 19630 19733 . + . ID=intron_added-25;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon8;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100500-01.exon8;rank=8
|
||||
1 irgsp three_prime_UTR 19594 19629 . + . ID=agat-three_prime_utr-6;Parent=transcript:Os01t0100500-01
|
||||
1 irgsp three_prime_UTR 19734 20144 . + . ID=agat-three_prime_utr-7;Parent=transcript:Os01t0100500-01
|
||||
1 irgsp gene 22841 26892 . + . ID=gene:Os01g0100600;biotype=protein_coding;description=Single-stranded nucleic acid binding R3H domain containing protein. (Os01t0100600-01);gene_id=Os01g0100600;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 22841 26892 . + . ID=transcript:Os01t0100600-01;Parent=gene:Os01g0100600;biotype=protein_coding;transcript_id=Os01t0100600-01
|
||||
1 irgsp exon 22841 23281 . + . ID=Os01t0100600-01.exon1;Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100600-01.exon1;rank=1
|
||||
1 irgsp exon 23572 26892 . + . ID=Os01t0100600-01.exon2;Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100600-01.exon2;rank=2
|
||||
1 irgsp CDS 23232 23281 . + 0 ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
|
||||
1 irgsp five_prime_UTR 22841 23231 . + . ID=agat-five_prime_utr-8;Parent=transcript:Os01t0100600-01
|
||||
1 irgsp intron 23282 23571 . + . ID=intron_added-26;Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100600-01.exon2;rank=2
|
||||
1 AGAT three_prime_UTR 23572 26892 . + . ID=agat-three_prime_utr-8;Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100600-01.exon1;rank=1
|
||||
105
src/agat/agat_sp_filter_feature_from_kill_list/config.vsh.yaml
Normal file
105
src/agat/agat_sp_filter_feature_from_kill_list/config.vsh.yaml
Normal file
@@ -0,0 +1,105 @@
|
||||
name: agat_sp_filter_feature_from_kill_list
|
||||
namespace: agat
|
||||
description: |
|
||||
Remove features based on a kill list. The default behaviour is to look at the features's ID.
|
||||
If the feature has an ID (case insensitive) listed among the kill list it will be removed.
|
||||
Removing a level1 or level2 feature will automatically remove all linked subfeatures, and
|
||||
removing all children of a feature will automatically remove this feature too.
|
||||
keywords: [gene annotations, filtering, gff]
|
||||
links:
|
||||
homepage: https://github.com/NBISweden/AGAT
|
||||
documentation: https://agat.readthedocs.io/en/latest/tools/agat_sp_filter_feature_from_kill_list.html
|
||||
issue_tracker: https://github.com/NBISweden/AGAT/issues
|
||||
repository: https://github.com/NBISweden/AGAT
|
||||
references:
|
||||
doi: 10.5281/zenodo.3552717
|
||||
license: GPL-3.0
|
||||
requirements:
|
||||
- commands: [agat]
|
||||
authors:
|
||||
- __merge__: /src/_authors/leila_paquay.yaml
|
||||
roles: [ author, maintainer ]
|
||||
|
||||
argument_groups:
|
||||
- name: Inputs
|
||||
arguments:
|
||||
- name: --gff
|
||||
alternatives: [-f, --ref, --reffile]
|
||||
description: Input GFF3 file that will be read.
|
||||
type: file
|
||||
required: true
|
||||
- name: --kill_list
|
||||
alternatives: [--kl]
|
||||
description: Text file containing the kill list. One value per line.
|
||||
type: file
|
||||
required: true
|
||||
example: kill_list.txt
|
||||
- name: Outputs
|
||||
arguments:
|
||||
- name: --output
|
||||
alternatives: [-o, --out]
|
||||
description: |
|
||||
Path to the output GFF file that contains filtered features.
|
||||
type: file
|
||||
direction: output
|
||||
required: true
|
||||
- name: Arguments
|
||||
arguments:
|
||||
- name: --type
|
||||
alternatives: [-p, -l]
|
||||
description: |
|
||||
Primary tag option, case insensitive, list. Allow to specify the feature types that
|
||||
will be handled.
|
||||
|
||||
You can specify a specific feature by giving its primary tag name (column 3) as:
|
||||
|
||||
* cds
|
||||
* Gene
|
||||
* mRNA
|
||||
|
||||
You can specify directly all the feature of a particular
|
||||
level:
|
||||
|
||||
* level2=mRNA,ncRNA,tRNA,etc
|
||||
* level3=CDS,exon,UTR,etc.
|
||||
|
||||
By default all features are taken into account. Fill the option with the value "all" will
|
||||
have the same behaviour.
|
||||
type: string
|
||||
multiple: true
|
||||
- name: --attribute
|
||||
alternatives: [-a]
|
||||
description: |
|
||||
Attribute tag to specify the attribute to analyse. Case sensitive. Default: ID
|
||||
type: string
|
||||
example: ID
|
||||
- name: --config
|
||||
alternatives: [-c]
|
||||
description: |
|
||||
AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT.
|
||||
The `--config` option gives you the possibility to use your own AGAT config file (located
|
||||
elsewhere or named differently).
|
||||
type: file
|
||||
example: custom_agat_config.yaml
|
||||
- name: --verbose
|
||||
alternatives: [-v]
|
||||
description: Verbose option for debugging purpose.
|
||||
type: boolean_true
|
||||
resources:
|
||||
- type: bash_script
|
||||
path: script.sh
|
||||
test_resources:
|
||||
- type: bash_script
|
||||
path: test.sh
|
||||
- type: file
|
||||
path: test_data
|
||||
engines:
|
||||
- type: docker
|
||||
image: quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0
|
||||
setup:
|
||||
- type: docker
|
||||
run: |
|
||||
agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.txt
|
||||
runners:
|
||||
- type: executable
|
||||
- type: nextflow
|
||||
85
src/agat/agat_sp_filter_feature_from_kill_list/help.txt
Normal file
85
src/agat/agat_sp_filter_feature_from_kill_list/help.txt
Normal file
@@ -0,0 +1,85 @@
|
||||
```sh
|
||||
agat_sp_filter_feature_from_kill_list.pl --help
|
||||
```
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
| Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0 |
|
||||
| https://github.com/NBISweden/AGAT |
|
||||
| National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se |
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
Name:
|
||||
agat_sp_filter_feature_from_kill_list.pl
|
||||
|
||||
Description:
|
||||
The script aims to remove features based on a kill list. The default
|
||||
behaviour is to look at the features's ID. If the feature has an ID
|
||||
(case insensitive) listed among the kill list it will be removed. /!\
|
||||
Removing a level1 or level2 feature will automatically remove all linked
|
||||
subfeatures, and removing all children of a feature will automatically
|
||||
remove this feature too.
|
||||
|
||||
Usage:
|
||||
agat_sp_filter_feature_from_kill_list.pl --gff infile.gff --kill_list file.txt [ --output outfile ]
|
||||
agat_sp_filter_feature_from_kill_list.pl --help
|
||||
|
||||
Options:
|
||||
-f, --reffile, --gff or -ref
|
||||
Input GFF3 file that will be read
|
||||
|
||||
-p, --type or -l
|
||||
primary tag option, case insensitive, list. Allow to specied the
|
||||
feature types that will be handled. You can specified a specific
|
||||
feature by given its primary tag name (column 3) as: cds, Gene,
|
||||
MrNa You can specify directly all the feature of a particular
|
||||
level: level2=mRNA,ncRNA,tRNA,etc level3=CDS,exon,UTR,etc By
|
||||
default all feature are taking into account. fill the option by
|
||||
the value "all" will have the same behaviour.
|
||||
|
||||
--kl or --kill_list
|
||||
Kill list. One value per line.
|
||||
|
||||
-a or --attribute
|
||||
Attribute tag to specify the attribute to analyse. Case
|
||||
sensitive. Default: ID
|
||||
|
||||
-o or --output
|
||||
Output GFF file. If no output file is specified, the output will
|
||||
be written to STDOUT.
|
||||
|
||||
-v Verbose option for debugging purpose.
|
||||
|
||||
-c or --config
|
||||
String - Input agat config file. By default AGAT takes as input
|
||||
agat_config.yaml file from the working directory if any,
|
||||
otherwise it takes the orignal agat_config.yaml shipped with
|
||||
AGAT. To get the agat_config.yaml locally type: "agat config
|
||||
--expose". The --config option gives you the possibility to use
|
||||
your own AGAT config file (located elsewhere or named
|
||||
differently).
|
||||
|
||||
-h or --help
|
||||
Display this helpful text.
|
||||
|
||||
Feedback:
|
||||
Did you find a bug?:
|
||||
Do not hesitate to report bugs to help us keep track of the bugs and
|
||||
their resolution. Please use the GitHub issue tracking system available
|
||||
at this address:
|
||||
|
||||
https://github.com/NBISweden/AGAT/issues
|
||||
|
||||
Ensure that the bug was not already reported by searching under Issues.
|
||||
If you're unable to find an (open) issue addressing the problem, open a new one.
|
||||
Try as much as possible to include in the issue when relevant:
|
||||
- a clear description,
|
||||
- as much relevant information as possible,
|
||||
- the command used,
|
||||
- a data sample,
|
||||
- an explanation of the expected behaviour that is not occurring.
|
||||
|
||||
Do you want to contribute?:
|
||||
You are very welcome, visit this address for the Contributing
|
||||
guidelines:
|
||||
https://github.com/NBISweden/AGAT/blob/master/CONTRIBUTING.md
|
||||
22
src/agat/agat_sp_filter_feature_from_kill_list/script.sh
Normal file
22
src/agat/agat_sp_filter_feature_from_kill_list/script.sh
Normal file
@@ -0,0 +1,22 @@
|
||||
#!/bin/bash
|
||||
|
||||
set -eo pipefail
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
# unset flags
|
||||
[[ "$par_verbose" == "false" ]] && unset par_verbose
|
||||
|
||||
# convert par_type to comma separated list
|
||||
par_type=$(echo $par_type | tr ';' ',')
|
||||
|
||||
# run agat_sp_filter_feature_from_kill_list
|
||||
agat_sp_filter_feature_from_kill_list.pl \
|
||||
--gff "$par_gff" \
|
||||
--kill_list "$par_kill_list" \
|
||||
--output "$par_output" \
|
||||
${par_type:+--type "${par_type}"} \
|
||||
${par_attribute:+--attribute "${par_attribute}"} \
|
||||
${par_config:+--config "${par_config}"} \
|
||||
${par_verbose:+-v}
|
||||
36
src/agat/agat_sp_filter_feature_from_kill_list/test.sh
Normal file
36
src/agat/agat_sp_filter_feature_from_kill_list/test.sh
Normal file
@@ -0,0 +1,36 @@
|
||||
#!/bin/bash
|
||||
|
||||
set -eo pipefail
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
test_dir="${meta_resources_dir}/test_data"
|
||||
|
||||
# create temporary directory and clean up on exit
|
||||
TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXX")
|
||||
function clean_up {
|
||||
[[ -d "$TMPDIR" ]] && rm -rf "$TMPDIR"
|
||||
}
|
||||
#trap clean_up EXIT
|
||||
|
||||
echo "> Run $meta_name with test data"
|
||||
"$meta_executable" \
|
||||
--gff "$test_dir/1_truncated.gff" \
|
||||
--kill_list "$test_dir/kill_list.txt" \
|
||||
--output "$TMPDIR/output.gff"
|
||||
|
||||
echo ">> Checking output"
|
||||
[ ! -f "$TMPDIR/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
|
||||
|
||||
echo ">> Check if output is empty"
|
||||
[ ! -s "$TMPDIR/output.gff" ] && echo "Output file output.gff is empty" && exit 1
|
||||
|
||||
echo ">> Check if output matches expected output"
|
||||
diff "$TMPDIR/output.gff" "$test_dir/test_output.gff"
|
||||
if [ $? -ne 0 ]; then
|
||||
echo "Output file output.gff does not match expected output"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
echo "> Test successful"
|
||||
@@ -0,0 +1,123 @@
|
||||
##gff-version 3
|
||||
##sequence-region 1 1 43270923
|
||||
#!genome-build RAP-DB IRGSP-1.0
|
||||
#!genome-version IRGSP-1.0
|
||||
#!genome-date 2015-10
|
||||
#!genome-build-accession GCA_001433935.1
|
||||
1 RAP-DB chromosome 1 43270923 . . . ID=chromosome:1;Alias=Chr1,AP014957.1,NC_029256.1
|
||||
###
|
||||
1 irgsp repeat_region 2000 2100 . + . ID=fakeRepeat1
|
||||
###
|
||||
1 irgsp gene 2983 10815 . + . ID=gene:Os01g0100100;biotype=protein_coding;description=RabGAP/TBC domain containing protein. (Os01t0100100-01);gene_id=Os01g0100100;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 2983 10815 . + . ID=transcript:Os01t0100100-01;Parent=gene:Os01g0100100;biotype=protein_coding;transcript_id=Os01t0100100-01
|
||||
1 irgsp exon 2983 3268 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 2983 3268 . + . Parent=transcript:Os01t0100100-01
|
||||
1 irgsp five_prime_UTR 3354 3448 . + . Parent=transcript:Os01t0100100-01
|
||||
1 irgsp exon 3354 3616 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0100100-01.exon2;rank=2
|
||||
1 irgsp CDS 3449 3616 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 4357 4455 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100100-01.exon3;rank=3
|
||||
1 irgsp CDS 4357 4455 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 5457 5560 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100100-01.exon4;rank=4
|
||||
1 irgsp CDS 5457 5560 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 7136 7944 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon5;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0100100-01.exon5;rank=5
|
||||
1 irgsp CDS 7136 7944 . + 1 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 8028 8150 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon6;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0100100-01.exon6;rank=6
|
||||
1 irgsp CDS 8028 8150 . + 2 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 8232 8320 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100100-01.exon7;rank=7
|
||||
1 irgsp CDS 8232 8320 . + 2 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 8408 8608 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon8;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100100-01.exon8;rank=8
|
||||
1 irgsp CDS 8408 8608 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 9210 9615 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon9;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0100100-01.exon9;rank=9
|
||||
1 irgsp CDS 9210 9615 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 10102 10187 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon10;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100100-01.exon10;rank=10
|
||||
1 irgsp CDS 10102 10187 . + 2 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp CDS 10274 10297 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 10274 10430 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon11;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0100100-01.exon11;rank=11
|
||||
1 irgsp three_prime_UTR 10298 10430 . + . Parent=transcript:Os01t0100100-01
|
||||
1 irgsp exon 10504 10815 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon12;rank=12
|
||||
1 irgsp three_prime_UTR 10504 10815 . + . Parent=transcript:Os01t0100100-01
|
||||
###
|
||||
1 irgsp gene 11218 12435 . + . ID=gene:Os01g0100200;biotype=protein_coding;description=Conserved hypothetical protein. (Os01t0100200-01);gene_id=Os01g0100200;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 11218 12435 . + . ID=transcript:Os01t0100200-01;Parent=gene:Os01g0100200;biotype=protein_coding;transcript_id=Os01t0100200-01
|
||||
1 irgsp five_prime_UTR 11218 11797 . + . Parent=transcript:Os01t0100200-01
|
||||
1 irgsp exon 11218 12060 . + . Parent=transcript:Os01t0100200-01;Name=Os01t0100200-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100200-01.exon1;rank=1
|
||||
1 irgsp CDS 11798 12060 . + 0 ID=CDS:Os01t0100200-01;Parent=transcript:Os01t0100200-01;protein_id=Os01t0100200-01
|
||||
1 irgsp CDS 12152 12317 . + 1 ID=CDS:Os01t0100200-01;Parent=transcript:Os01t0100200-01;protein_id=Os01t0100200-01
|
||||
1 irgsp exon 12152 12435 . + . Parent=transcript:Os01t0100200-01;Name=Os01t0100200-01.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100200-01.exon2;rank=2
|
||||
1 irgsp three_prime_UTR 12318 12435 . + . Parent=transcript:Os01t0100200-01
|
||||
###
|
||||
1 irgsp gene 11372 12284 . - . ID=gene:Os01g0100300;biotype=protein_coding;description=Cytochrome P450 domain containing protein. (Os01t0100300-00);gene_id=Os01g0100300;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 11372 12284 . - . ID=transcript:Os01t0100300-00;Parent=gene:Os01g0100300;biotype=protein_coding;transcript_id=Os01t0100300-00
|
||||
1 irgsp exon 11372 12042 . - . Parent=transcript:Os01t0100300-00;Name=Os01t0100300-00.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100300-00.exon2;rank=2
|
||||
1 irgsp CDS 11372 12042 . - 2 ID=CDS:Os01t0100300-00;Parent=transcript:Os01t0100300-00;protein_id=Os01t0100300-00
|
||||
1 irgsp exon 12146 12284 . - . Parent=transcript:Os01t0100300-00;Name=Os01t0100300-00.exon1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0100300-00.exon1;rank=1
|
||||
1 irgsp CDS 12146 12284 . - 0 ID=CDS:Os01t0100300-00;Parent=transcript:Os01t0100300-00;protein_id=Os01t0100300-00
|
||||
###
|
||||
1 irgsp gene 12721 15685 . + . ID=gene:Os01g0100400;biotype=protein_coding;description=Similar to Pectinesterase-like protein. (Os01t0100400-01);gene_id=Os01g0100400;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 12721 15685 . + . ID=transcript:Os01t0100400-01;Parent=gene:Os01g0100400;biotype=protein_coding;transcript_id=Os01t0100400-01
|
||||
1 irgsp five_prime_UTR 12721 12773 . + . Parent=transcript:Os01t0100400-01
|
||||
1 irgsp exon 12721 13813 . + . Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100400-01.exon1;rank=1
|
||||
1 irgsp CDS 12774 13813 . + 0 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp exon 13906 14271 . + . Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100400-01.exon2;rank=2
|
||||
1 irgsp CDS 13906 14271 . + 1 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp exon 14359 14437 . + . Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0100400-01.exon3;rank=3
|
||||
1 irgsp CDS 14359 14437 . + 1 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp exon 14969 15171 . + . Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100400-01.exon4;rank=4
|
||||
1 irgsp CDS 14969 15171 . + 0 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp CDS 15266 15359 . + 1 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp exon 15266 15685 . + . Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon5;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100400-01.exon5;rank=5
|
||||
1 irgsp three_prime_UTR 15360 15685 . + . Parent=transcript:Os01t0100400-01
|
||||
###
|
||||
1 irgsp gene 12808 13978 . - . ID=gene:Os01g0100466;biotype=protein_coding;description=Hypothetical protein. (Os01t0100466-00);gene_id=Os01g0100466;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 12808 13978 . - . ID=transcript:Os01t0100466-00;Parent=gene:Os01g0100466;biotype=protein_coding;transcript_id=Os01t0100466-00
|
||||
1 irgsp three_prime_UTR 12808 12868 . - . Parent=transcript:Os01t0100466-00
|
||||
1 irgsp exon 12808 13782 . - . Parent=transcript:Os01t0100466-00;Name=Os01t0100466-00.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100466-00.exon2;rank=2
|
||||
1 irgsp CDS 12869 13102 . - 0 ID=CDS:Os01t0100466-00;Parent=transcript:Os01t0100466-00;protein_id=Os01t0100466-00
|
||||
1 irgsp five_prime_UTR 13103 13782 . - . Parent=transcript:Os01t0100466-00
|
||||
1 irgsp exon 13880 13978 . - . Parent=transcript:Os01t0100466-00;Name=Os01t0100466-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100466-00.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 13880 13978 . - . Parent=transcript:Os01t0100466-00
|
||||
###
|
||||
1 irgsp gene 16399 20144 . + . ID=gene:Os01g0100500;biotype=protein_coding;description=Immunoglobulin-like domain containing protein. (Os01t0100500-01);gene_id=Os01g0100500;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 16399 20144 . + . ID=transcript:Os01t0100500-01;Parent=gene:Os01g0100500;biotype=protein_coding;transcript_id=Os01t0100500-01
|
||||
1 irgsp five_prime_UTR 16399 16598 . + . Parent=transcript:Os01t0100500-01
|
||||
1 irgsp exon 16399 16976 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0100500-01.exon1;rank=1
|
||||
1 irgsp CDS 16599 16976 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp exon 17383 17474 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100500-01.exon2;rank=2
|
||||
1 irgsp CDS 17383 17474 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp exon 17558 18258 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0100500-01.exon3;rank=3
|
||||
1 irgsp CDS 17558 18258 . + 1 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp exon 18501 18571 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100500-01.exon4;rank=4
|
||||
1 irgsp CDS 18501 18571 . + 2 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp exon 18968 19057 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100500-01.exon5;rank=5
|
||||
1 irgsp CDS 18968 19057 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp exon 19142 19321 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100500-01.exon6;rank=6
|
||||
1 irgsp CDS 19142 19321 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp CDS 19531 19593 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp exon 19531 19629 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon7;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0100500-01.exon7;rank=7
|
||||
1 irgsp three_prime_UTR 19594 19629 . + . Parent=transcript:Os01t0100500-01
|
||||
1 irgsp exon 19734 20144 . + . Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon8;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100500-01.exon8;rank=8
|
||||
1 irgsp three_prime_UTR 19734 20144 . + . Parent=transcript:Os01t0100500-01
|
||||
###
|
||||
1 irgsp gene 22841 26892 . + . ID=gene:Os01g0100600;biotype=protein_coding;description=Single-stranded nucleic acid binding R3H domain containing protein. (Os01t0100600-01);gene_id=Os01g0100600;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 22841 26892 . + . ID=transcript:Os01t0100600-01;Parent=gene:Os01g0100600;biotype=protein_coding;transcript_id=Os01t0100600-01
|
||||
1 irgsp five_prime_UTR 22841 23231 . + . Parent=transcript:Os01t0100600-01
|
||||
1 irgsp exon 22841 23281 . + . Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100600-01.exon1;rank=1
|
||||
1 irgsp CDS 23232 23281 . + 0 ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
|
||||
1 irgsp exon 23572 23847 . + . Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100600-01.exon2;rank=2
|
||||
1 irgsp CDS 23572 23847 . + 1 ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
|
||||
1 irgsp exon 23962 24033 . + . Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon3;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100600-01.exon3;rank=3
|
||||
1 irgsp CDS 23962 24033 . + 1 ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
|
||||
1 irgsp exon 24492 24577 . + . Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon4;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0100600-01.exon4;rank=4
|
||||
1 irgsp CDS 24492 24577 . + 1 ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
|
||||
1 irgsp exon 25445 25519 . + . Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon5;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0100600-01.exon5;rank=5
|
||||
1 irgsp CDS 25445 25519 . + 2 ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
|
||||
1 irgsp CDS 25883 26391 . + 2 ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
|
||||
1 irgsp exon 25883 26892 . + . Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon6;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0100600-01.exon6;rank=6
|
||||
1 irgsp three_prime_UTR 26392 26892 . + . Parent=transcript:Os01t0100600-01
|
||||
###
|
||||
1 irgsp gene 25861 26424 . - . ID=gene:Os01g0100650;biotype=protein_coding;description=Hypothetical gene. (Os01t0100650-00);gene_id=Os01g0100650;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 25861 26424 . - . ID=transcript:Os01t0100650-00;Parent=gene:Os01g0100650;biotype=protein_coding;transcript_id=Os01t0100650-00
|
||||
1 irgsp three_prime_UTR 25861 26039 . - . Parent=transcript:Os01t0100650-00
|
||||
1 irgsp exon 25861 26424 . - . Parent=transcript:Os01t0100650-00;Name=Os01t0100650-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100650-00.exon1;rank=1
|
||||
1 irgsp CDS 26040 26423 . - 0 ID=CDS:Os01t0100650-00;Parent=transcript:Os01t0100650-00;protein_id=Os01t0100650-00
|
||||
1 irgsp five_prime_UTR 26424 26424 . - . Parent=transcript:Os01t0100650-00
|
||||
@@ -0,0 +1,3 @@
|
||||
gene:Os01g0100700
|
||||
CDS:Os01t0100650-00
|
||||
transcript:Os01t0102700-01
|
||||
13
src/agat/agat_sp_filter_feature_from_kill_list/test_data/script.sh
Executable file
13
src/agat/agat_sp_filter_feature_from_kill_list/test_data/script.sh
Executable file
@@ -0,0 +1,13 @@
|
||||
#!/bin/bash
|
||||
|
||||
# clone repo
|
||||
if [ ! -d /tmp/agat_source ]; then
|
||||
git clone --depth 1 --single-branch --branch master https://github.com/NBISweden/AGAT /tmp/agat_source
|
||||
fi
|
||||
|
||||
# copy test data
|
||||
cp -r /tmp/agat_source/t/scripts_output/in/1.gff src/agat/agat_sp_filter_feature_from_kill_list/test_data
|
||||
cp -r /tmp/agat_source/t/scripts_output/out/agat_sp_filter_feature_from_kill_list_1.gff src/agat/agat_sp_filter_feature_from_kill_list/test_data
|
||||
cp -r /tmp/agat_source/t/scripts_output/in/kill_list.txt src/agat/agat_sp_filter_feature_from_kill_list/test_data
|
||||
|
||||
head -n 123 src/agat/agat_sp_filter_feature_from_kill_list/test_data/1.gff > src/agat/agat_sp_filter_feature_from_kill_list/test_data/1_truncated.gff
|
||||
@@ -0,0 +1,113 @@
|
||||
##gff-version 3
|
||||
##sequence-region 1 1 43270923
|
||||
#!genome-build RAP-DB IRGSP-1.0
|
||||
#!genome-version IRGSP-1.0
|
||||
#!genome-date 2015-10
|
||||
#!genome-build-accession GCA_001433935.1
|
||||
1 RAP-DB chromosome 1 43270923 . . . ID=chromosome:1;Alias=Chr1,AP014957.1,NC_029256.1
|
||||
1 irgsp repeat_region 2000 2100 . + . ID=fakeRepeat1
|
||||
1 irgsp gene 2983 10815 . + . ID=gene:Os01g0100100;biotype=protein_coding;description=RabGAP/TBC domain containing protein. (Os01t0100100-01);gene_id=Os01g0100100;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 2983 10815 . + . ID=transcript:Os01t0100100-01;Parent=gene:Os01g0100100;biotype=protein_coding;transcript_id=Os01t0100100-01
|
||||
1 irgsp exon 2983 3268 . + . ID=Os01t0100100-01.exon1;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon1;rank=1
|
||||
1 irgsp exon 3354 3616 . + . ID=Os01t0100100-01.exon2;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0100100-01.exon2;rank=2
|
||||
1 irgsp exon 4357 4455 . + . ID=Os01t0100100-01.exon3;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100100-01.exon3;rank=3
|
||||
1 irgsp exon 5457 5560 . + . ID=Os01t0100100-01.exon4;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100100-01.exon4;rank=4
|
||||
1 irgsp exon 7136 7944 . + . ID=Os01t0100100-01.exon5;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon5;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0100100-01.exon5;rank=5
|
||||
1 irgsp exon 8028 8150 . + . ID=Os01t0100100-01.exon6;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon6;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0100100-01.exon6;rank=6
|
||||
1 irgsp exon 8232 8320 . + . ID=Os01t0100100-01.exon7;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100100-01.exon7;rank=7
|
||||
1 irgsp exon 8408 8608 . + . ID=Os01t0100100-01.exon8;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon8;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100100-01.exon8;rank=8
|
||||
1 irgsp exon 9210 9615 . + . ID=Os01t0100100-01.exon9;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon9;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0100100-01.exon9;rank=9
|
||||
1 irgsp exon 10102 10187 . + . ID=Os01t0100100-01.exon10;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon10;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100100-01.exon10;rank=10
|
||||
1 irgsp exon 10274 10430 . + . ID=Os01t0100100-01.exon11;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon11;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0100100-01.exon11;rank=11
|
||||
1 irgsp exon 10504 10815 . + . ID=Os01t0100100-01.exon12;Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon12;rank=12
|
||||
1 irgsp CDS 3449 3616 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp CDS 4357 4455 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp CDS 5457 5560 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp CDS 7136 7944 . + 1 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp CDS 8028 8150 . + 2 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp CDS 8232 8320 . + 2 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp CDS 8408 8608 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp CDS 9210 9615 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp CDS 10102 10187 . + 2 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp CDS 10274 10297 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp five_prime_UTR 2983 3268 . + . ID=agat-five_prime_utr-1;Parent=transcript:Os01t0100100-01
|
||||
1 irgsp five_prime_UTR 3354 3448 . + . ID=agat-five_prime_utr-2;Parent=transcript:Os01t0100100-01
|
||||
1 irgsp three_prime_UTR 10298 10430 . + . ID=agat-three_prime_utr-1;Parent=transcript:Os01t0100100-01
|
||||
1 irgsp three_prime_UTR 10504 10815 . + . ID=agat-three_prime_utr-2;Parent=transcript:Os01t0100100-01
|
||||
1 irgsp gene 11218 12435 . + . ID=gene:Os01g0100200;biotype=protein_coding;description=Conserved hypothetical protein. (Os01t0100200-01);gene_id=Os01g0100200;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 11218 12435 . + . ID=transcript:Os01t0100200-01;Parent=gene:Os01g0100200;biotype=protein_coding;transcript_id=Os01t0100200-01
|
||||
1 irgsp exon 11218 12060 . + . ID=Os01t0100200-01.exon1;Parent=transcript:Os01t0100200-01;Name=Os01t0100200-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100200-01.exon1;rank=1
|
||||
1 irgsp exon 12152 12435 . + . ID=Os01t0100200-01.exon2;Parent=transcript:Os01t0100200-01;Name=Os01t0100200-01.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100200-01.exon2;rank=2
|
||||
1 irgsp CDS 11798 12060 . + 0 ID=CDS:Os01t0100200-01;Parent=transcript:Os01t0100200-01;protein_id=Os01t0100200-01
|
||||
1 irgsp CDS 12152 12317 . + 1 ID=CDS:Os01t0100200-01;Parent=transcript:Os01t0100200-01;protein_id=Os01t0100200-01
|
||||
1 irgsp five_prime_UTR 11218 11797 . + . ID=agat-five_prime_utr-3;Parent=transcript:Os01t0100200-01
|
||||
1 irgsp three_prime_UTR 12318 12435 . + . ID=agat-three_prime_utr-3;Parent=transcript:Os01t0100200-01
|
||||
1 irgsp gene 11372 12284 . - . ID=gene:Os01g0100300;biotype=protein_coding;description=Cytochrome P450 domain containing protein. (Os01t0100300-00);gene_id=Os01g0100300;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 11372 12284 . - . ID=transcript:Os01t0100300-00;Parent=gene:Os01g0100300;biotype=protein_coding;transcript_id=Os01t0100300-00
|
||||
1 irgsp exon 11372 12042 . - . ID=Os01t0100300-00.exon2;Parent=transcript:Os01t0100300-00;Name=Os01t0100300-00.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100300-00.exon2;rank=2
|
||||
1 irgsp exon 12146 12284 . - . ID=Os01t0100300-00.exon1;Parent=transcript:Os01t0100300-00;Name=Os01t0100300-00.exon1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0100300-00.exon1;rank=1
|
||||
1 irgsp CDS 11372 12042 . - 2 ID=CDS:Os01t0100300-00;Parent=transcript:Os01t0100300-00;protein_id=Os01t0100300-00
|
||||
1 irgsp CDS 12146 12284 . - 0 ID=CDS:Os01t0100300-00;Parent=transcript:Os01t0100300-00;protein_id=Os01t0100300-00
|
||||
1 irgsp gene 12721 15685 . + . ID=gene:Os01g0100400;biotype=protein_coding;description=Similar to Pectinesterase-like protein. (Os01t0100400-01);gene_id=Os01g0100400;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 12721 15685 . + . ID=transcript:Os01t0100400-01;Parent=gene:Os01g0100400;biotype=protein_coding;transcript_id=Os01t0100400-01
|
||||
1 irgsp exon 12721 13813 . + . ID=Os01t0100400-01.exon1;Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100400-01.exon1;rank=1
|
||||
1 irgsp exon 13906 14271 . + . ID=Os01t0100400-01.exon2;Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100400-01.exon2;rank=2
|
||||
1 irgsp exon 14359 14437 . + . ID=Os01t0100400-01.exon3;Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0100400-01.exon3;rank=3
|
||||
1 irgsp exon 14969 15171 . + . ID=Os01t0100400-01.exon4;Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100400-01.exon4;rank=4
|
||||
1 irgsp exon 15266 15685 . + . ID=Os01t0100400-01.exon5;Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon5;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100400-01.exon5;rank=5
|
||||
1 irgsp CDS 12774 13813 . + 0 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp CDS 13906 14271 . + 1 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp CDS 14359 14437 . + 1 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp CDS 14969 15171 . + 0 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp CDS 15266 15359 . + 1 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp five_prime_UTR 12721 12773 . + . ID=agat-five_prime_utr-4;Parent=transcript:Os01t0100400-01
|
||||
1 irgsp three_prime_UTR 15360 15685 . + . ID=agat-three_prime_utr-4;Parent=transcript:Os01t0100400-01
|
||||
1 irgsp gene 12808 13978 . - . ID=gene:Os01g0100466;biotype=protein_coding;description=Hypothetical protein. (Os01t0100466-00);gene_id=Os01g0100466;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 12808 13978 . - . ID=transcript:Os01t0100466-00;Parent=gene:Os01g0100466;biotype=protein_coding;transcript_id=Os01t0100466-00
|
||||
1 irgsp exon 12808 13782 . - . ID=Os01t0100466-00.exon2;Parent=transcript:Os01t0100466-00;Name=Os01t0100466-00.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100466-00.exon2;rank=2
|
||||
1 irgsp exon 13880 13978 . - . ID=Os01t0100466-00.exon1;Parent=transcript:Os01t0100466-00;Name=Os01t0100466-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100466-00.exon1;rank=1
|
||||
1 irgsp CDS 12869 13102 . - 0 ID=CDS:Os01t0100466-00;Parent=transcript:Os01t0100466-00;protein_id=Os01t0100466-00
|
||||
1 irgsp five_prime_UTR 13103 13782 . - . ID=agat-five_prime_utr-5;Parent=transcript:Os01t0100466-00
|
||||
1 irgsp five_prime_UTR 13880 13978 . - . ID=agat-five_prime_utr-6;Parent=transcript:Os01t0100466-00
|
||||
1 irgsp three_prime_UTR 12808 12868 . - . ID=agat-three_prime_utr-5;Parent=transcript:Os01t0100466-00
|
||||
1 irgsp gene 16399 20144 . + . ID=gene:Os01g0100500;biotype=protein_coding;description=Immunoglobulin-like domain containing protein. (Os01t0100500-01);gene_id=Os01g0100500;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 16399 20144 . + . ID=transcript:Os01t0100500-01;Parent=gene:Os01g0100500;biotype=protein_coding;transcript_id=Os01t0100500-01
|
||||
1 irgsp exon 16399 16976 . + . ID=Os01t0100500-01.exon1;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0100500-01.exon1;rank=1
|
||||
1 irgsp exon 17383 17474 . + . ID=Os01t0100500-01.exon2;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100500-01.exon2;rank=2
|
||||
1 irgsp exon 17558 18258 . + . ID=Os01t0100500-01.exon3;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0100500-01.exon3;rank=3
|
||||
1 irgsp exon 18501 18571 . + . ID=Os01t0100500-01.exon4;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100500-01.exon4;rank=4
|
||||
1 irgsp exon 18968 19057 . + . ID=Os01t0100500-01.exon5;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100500-01.exon5;rank=5
|
||||
1 irgsp exon 19142 19321 . + . ID=Os01t0100500-01.exon6;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100500-01.exon6;rank=6
|
||||
1 irgsp exon 19531 19629 . + . ID=Os01t0100500-01.exon7;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon7;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0100500-01.exon7;rank=7
|
||||
1 irgsp exon 19734 20144 . + . ID=Os01t0100500-01.exon8;Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon8;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100500-01.exon8;rank=8
|
||||
1 irgsp CDS 16599 16976 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp CDS 17383 17474 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp CDS 17558 18258 . + 1 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp CDS 18501 18571 . + 2 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp CDS 18968 19057 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp CDS 19142 19321 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp CDS 19531 19593 . + 0 ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
|
||||
1 irgsp five_prime_UTR 16399 16598 . + . ID=agat-five_prime_utr-7;Parent=transcript:Os01t0100500-01
|
||||
1 irgsp three_prime_UTR 19594 19629 . + . ID=agat-three_prime_utr-6;Parent=transcript:Os01t0100500-01
|
||||
1 irgsp three_prime_UTR 19734 20144 . + . ID=agat-three_prime_utr-7;Parent=transcript:Os01t0100500-01
|
||||
1 irgsp gene 22841 26892 . + . ID=gene:Os01g0100600;biotype=protein_coding;description=Single-stranded nucleic acid binding R3H domain containing protein. (Os01t0100600-01);gene_id=Os01g0100600;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 22841 26892 . + . ID=transcript:Os01t0100600-01;Parent=gene:Os01g0100600;biotype=protein_coding;transcript_id=Os01t0100600-01
|
||||
1 irgsp exon 22841 23281 . + . ID=Os01t0100600-01.exon1;Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100600-01.exon1;rank=1
|
||||
1 irgsp exon 23572 23847 . + . ID=Os01t0100600-01.exon2;Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100600-01.exon2;rank=2
|
||||
1 irgsp exon 23962 24033 . + . ID=Os01t0100600-01.exon3;Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon3;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100600-01.exon3;rank=3
|
||||
1 irgsp exon 24492 24577 . + . ID=Os01t0100600-01.exon4;Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon4;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0100600-01.exon4;rank=4
|
||||
1 irgsp exon 25445 25519 . + . ID=Os01t0100600-01.exon5;Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon5;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0100600-01.exon5;rank=5
|
||||
1 irgsp exon 25883 26892 . + . ID=Os01t0100600-01.exon6;Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon6;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Os01t0100600-01.exon6;rank=6
|
||||
1 irgsp CDS 23232 23281 . + 0 ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
|
||||
1 irgsp CDS 23572 23847 . + 1 ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
|
||||
1 irgsp CDS 23962 24033 . + 1 ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
|
||||
1 irgsp CDS 24492 24577 . + 1 ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
|
||||
1 irgsp CDS 25445 25519 . + 2 ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
|
||||
1 irgsp CDS 25883 26391 . + 2 ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
|
||||
1 irgsp five_prime_UTR 22841 23231 . + . ID=agat-five_prime_utr-8;Parent=transcript:Os01t0100600-01
|
||||
1 irgsp three_prime_UTR 26392 26892 . + . ID=agat-three_prime_utr-8;Parent=transcript:Os01t0100600-01
|
||||
1 irgsp gene 25861 26424 . - . ID=gene:Os01g0100650;biotype=protein_coding;description=Hypothetical gene. (Os01t0100650-00);gene_id=Os01g0100650;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 25861 26424 . - . ID=transcript:Os01t0100650-00;Parent=gene:Os01g0100650;biotype=protein_coding;transcript_id=Os01t0100650-00
|
||||
1 irgsp exon 25861 26424 . - . ID=Os01t0100650-00.exon1;Parent=transcript:Os01t0100650-00;Name=Os01t0100650-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100650-00.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 26424 26424 . - . ID=agat-five_prime_utr-9;Parent=transcript:Os01t0100650-00
|
||||
1 irgsp three_prime_UTR 25861 26039 . - . ID=agat-three_prime_utr-9;Parent=transcript:Os01t0100650-00
|
||||
67
src/agat/agat_sp_merge_annotations/config.vsh.yaml
Normal file
67
src/agat/agat_sp_merge_annotations/config.vsh.yaml
Normal file
@@ -0,0 +1,67 @@
|
||||
name: agat_sp_merge_annotations
|
||||
namespace: agat
|
||||
description: |
|
||||
Merge different gff annotation files into one. It uses the AGAT parser that takes care of
|
||||
duplicated names and fixes other oddities met in those files.
|
||||
keywords: [gene annotations, merge, gff]
|
||||
links:
|
||||
homepage: https://github.com/NBISweden/AGAT
|
||||
documentation: https://agat.readthedocs.io/en/latest/tools/agat_sp_merge_annotations.html
|
||||
issue_tracker: https://github.com/NBISweden/AGAT/issues
|
||||
repository: https://github.com/NBISweden/AGAT
|
||||
references:
|
||||
doi: 10.5281/zenodo.3552717
|
||||
license: GPL-3.0
|
||||
requirements:
|
||||
commands: [agat]
|
||||
authors:
|
||||
- __merge__: /src/_authors/leila_paquay.yaml
|
||||
roles: [ author, maintainer ]
|
||||
argument_groups:
|
||||
- name: Inputs
|
||||
arguments:
|
||||
- name: --gff
|
||||
alternatives: [-f]
|
||||
description: |
|
||||
Input GTF/GFF file(s).
|
||||
type: file
|
||||
multiple: true
|
||||
required: true
|
||||
example: input1.gff;input2.gff
|
||||
- name: Outputs
|
||||
arguments:
|
||||
- name: --output
|
||||
alternatives: [-o, --out]
|
||||
description: Output gff3 file where the gene incriminated will be writen.
|
||||
type: file
|
||||
direction: output
|
||||
required: true
|
||||
example: output.gff
|
||||
- name: Arguments
|
||||
arguments:
|
||||
- name: --config
|
||||
alternatives: [-c]
|
||||
description: |
|
||||
AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT.
|
||||
The `--config` option gives you the possibility to use your own AGAT config file (located
|
||||
elsewhere or named differently).
|
||||
type: file
|
||||
example: custom_agat_config.yaml
|
||||
resources:
|
||||
- type: bash_script
|
||||
path: script.sh
|
||||
test_resources:
|
||||
- type: bash_script
|
||||
path: test.sh
|
||||
- type: file
|
||||
path: test_data
|
||||
engines:
|
||||
- type: docker
|
||||
image: quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0
|
||||
setup:
|
||||
- type: docker
|
||||
run: |
|
||||
agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.txt
|
||||
runners:
|
||||
- type: executable
|
||||
- type: nextflow
|
||||
64
src/agat/agat_sp_merge_annotations/help.txt
Normal file
64
src/agat/agat_sp_merge_annotations/help.txt
Normal file
@@ -0,0 +1,64 @@
|
||||
```sh
|
||||
agat_sp_merge_annotations.pl --help
|
||||
```
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
| Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0 |
|
||||
| https://github.com/NBISweden/AGAT |
|
||||
| National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se |
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
Name:
|
||||
agat_sp_merge_annotations.pl
|
||||
|
||||
Description:
|
||||
This script merge different gff annotation files in one. It uses the
|
||||
AGAT parser that takes care of duplicated names and fixes other oddities
|
||||
met in those files.
|
||||
|
||||
Usage:
|
||||
agat_sp_merge_annotations.pl --gff infile1 --gff infile2 --out outFile
|
||||
agat_sp_merge_annotations.pl --help
|
||||
|
||||
Options:
|
||||
--gff or -f
|
||||
Input GTF/GFF file(s). You can specify as much file you want
|
||||
like so: -f file1 -f file2 -f file3
|
||||
|
||||
--out, --output or -o
|
||||
Output gff3 file where the gene incriminated will be write.
|
||||
|
||||
-c or --config
|
||||
String - Input agat config file. By default AGAT takes as input
|
||||
agat_config.yaml file from the working directory if any,
|
||||
otherwise it takes the orignal agat_config.yaml shipped with
|
||||
AGAT. To get the agat_config.yaml locally type: "agat config
|
||||
--expose". The --config option gives you the possibility to use
|
||||
your own AGAT config file (located elsewhere or named
|
||||
differently).
|
||||
|
||||
--help or -h
|
||||
Display this helpful text.
|
||||
|
||||
Feedback:
|
||||
Did you find a bug?:
|
||||
Do not hesitate to report bugs to help us keep track of the bugs and
|
||||
their resolution. Please use the GitHub issue tracking system available
|
||||
at this address:
|
||||
|
||||
https://github.com/NBISweden/AGAT/issues
|
||||
|
||||
Ensure that the bug was not already reported by searching under Issues.
|
||||
If you're unable to find an (open) issue addressing the problem, open a new one.
|
||||
Try as much as possible to include in the issue when relevant:
|
||||
- a clear description,
|
||||
- as much relevant information as possible,
|
||||
- the command used,
|
||||
- a data sample,
|
||||
- an explanation of the expected behaviour that is not occurring.
|
||||
|
||||
Do you want to contribute?:
|
||||
You are very welcome, visit this address for the Contributing
|
||||
guidelines:
|
||||
https://github.com/NBISweden/AGAT/blob/master/CONTRIBUTING.md
|
||||
19
src/agat/agat_sp_merge_annotations/script.sh
Normal file
19
src/agat/agat_sp_merge_annotations/script.sh
Normal file
@@ -0,0 +1,19 @@
|
||||
#!/bin/bash
|
||||
|
||||
set -eo pipefail
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
# Convert a list of file names to multiple -gff arguments
|
||||
input_files=""
|
||||
IFS=";" read -ra file_names <<< "$par_gff"
|
||||
for file in "${file_names[@]}"; do
|
||||
input_files+="--gff $file "
|
||||
done
|
||||
|
||||
# run agat_sp_merge_annotations
|
||||
agat_sp_merge_annotations.pl \
|
||||
$input_files \
|
||||
-o "$par_output" \
|
||||
${par_config:+--config "${par_config}"}
|
||||
56
src/agat/agat_sp_merge_annotations/test.sh
Normal file
56
src/agat/agat_sp_merge_annotations/test.sh
Normal file
@@ -0,0 +1,56 @@
|
||||
#!/bin/bash
|
||||
|
||||
set -eo pipefail
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
test_dir="${meta_resources_dir}/test_data"
|
||||
|
||||
# create temporary directory and clean up on exit
|
||||
TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXX")
|
||||
function clean_up {
|
||||
[[ -d "$TMPDIR" ]] && rm -rf "$TMPDIR"
|
||||
}
|
||||
trap clean_up EXIT
|
||||
|
||||
echo "> Run $meta_name with test data 1"
|
||||
"$meta_executable" \
|
||||
--gff "$test_dir/file1.gff;$test_dir/file2.gff" \
|
||||
--output "$TMPDIR/output.gff"
|
||||
|
||||
echo ">> Checking output"
|
||||
[ ! -f "$TMPDIR/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
|
||||
|
||||
echo ">> Check if output is empty"
|
||||
[ ! -s "$TMPDIR/output.gff" ] && echo "Output file output.gff is empty" && exit 1
|
||||
|
||||
echo ">> Check if output matches expected output"
|
||||
diff "$TMPDIR/output.gff" "$test_dir/agat_sp_merge_annotations_1.gff"
|
||||
if [ $? -ne 0 ]; then
|
||||
echo "Output file output.gff does not match expected output"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
echo ">> cleanup"
|
||||
rm -rf "$TMPDIR/output.gff"
|
||||
|
||||
echo "> Run $meta_name with test data 2"
|
||||
"$meta_executable" \
|
||||
--gff "$test_dir/fileA.gff;$test_dir/fileB.gff" \
|
||||
--output "$TMPDIR/output.gff"
|
||||
|
||||
echo ">> Checking output"
|
||||
[ ! -f "$TMPDIR/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
|
||||
|
||||
echo ">> Check if output is empty"
|
||||
[ ! -s "$TMPDIR/output.gff" ] && echo "Output file output.gff is empty" && exit 1
|
||||
|
||||
echo ">> Check if output matches expected output"
|
||||
diff "$TMPDIR/output.gff" "$test_dir/agat_sp_merge_annotations_2.gff"
|
||||
if [ $? -ne 0 ]; then
|
||||
echo "Output file output.gff does not match expected output"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
echo "> Test successful"
|
||||
@@ -0,0 +1,13 @@
|
||||
##gff-version 3
|
||||
chr10 BestRefSeq gene 123237824 123357992 . - . ID=gene-FGFR2;ontology=G0222
|
||||
chr10 BestRefSeq mRNA 123237824 123357992 . - . ID=rna-NM_022970.3;Parent=gene-FGFR2;ontology=G0222;merged_ID=IDmodified-mrna-1;merged_Ontology=G0333;merged_Parent=IDmodified-gene-1
|
||||
chr10 BestRefSeq exon 123237824 123239535 . - . ID=exon-NM_022970.3-18;Parent=rna-NM_022970.3
|
||||
chr10 BestRefSeq exon 123243212 123243317 . - . ID=exon-NM_022970.3-17;Parent=rna-NM_022970.3
|
||||
chr10 BestRefSeq exon 123353223 123353481 . - . ID=exon-NM_022970.3-2;Parent=rna-NM_022970.3
|
||||
chr10 BestRefSeq exon 123357476 123357992 . - . ID=exon-NM_022970.3-1;Parent=rna-NM_022970.3
|
||||
chr10 BestRefSeq CDS 123239371 123239535 . - 0 ID=cds-NP_075259.4;Parent=rna-NM_022970.3
|
||||
chr10 BestRefSeq CDS 123243212 123243317 . - 1 ID=cds-NP_075259.4;Parent=rna-NM_022970.3
|
||||
chr10 BestRefSeq CDS 123353223 123353331 . - 0 ID=cds-NP_075259.4;Parent=rna-NM_022970.3
|
||||
chr10 BestRefSeq five_prime_UTR 123353332 123353481 . - . ID=agat-five_prime_utr-54403;Parent=rna-NM_022970.3
|
||||
chr10 BestRefSeq five_prime_UTR 123357476 123357992 . - . ID=agat-five_prime_utr-54403;Parent=rna-NM_022970.3
|
||||
chr10 BestRefSeq three_prime_UTR 123237824 123239370 . - . ID=agat-three_prime_utr-54427;Parent=rna-NM_022970.3
|
||||
@@ -0,0 +1,3 @@
|
||||
##gff-version 3
|
||||
chr1 AUGUSTUS gene 1000424 1039237 . + . ID=A
|
||||
chr1 AUGUSTUS mRNA 1000424 1039237 . + . ID=A.t1;Parent=A;merged_ID=B.t1;merged_Parent=B
|
||||
14
src/agat/agat_sp_merge_annotations/test_data/file1.gff
Normal file
14
src/agat/agat_sp_merge_annotations/test_data/file1.gff
Normal file
@@ -0,0 +1,14 @@
|
||||
chr10 BestRefSeq gene 123237824 123357992 . - . ID=gene-FGFR2;Ontology=G0222;
|
||||
chr10 BestRefSeq mRNA 123237824 123357992 . - . ID=rna-NM_022970.3;Parent=gene-FGFR2;Ontology=G0222;
|
||||
chr10 BestRefSeq exon 123237824 123239535 . - . ID=exon-NM_022970.3-18;Parent=rna-NM_022970.3;
|
||||
chr10 BestRefSeq exon 123243212 123243317 . - . ID=exon-NM_022970.3-17;Parent=rna-NM_022970.3;
|
||||
chr10 BestRefSeq exon 123353223 123353481 . - . ID=exon-NM_022970.3-2;Parent=rna-NM_022970.3;
|
||||
chr10 BestRefSeq exon 123357476 123357992 . - . ID=exon-NM_022970.3-1;Parent=rna-NM_022970.3;
|
||||
chr10 BestRefSeq CDS 123239371 123239535 . - 0 ID=cds-NP_075259.4;Parent=rna-NM_022970.3;
|
||||
chr10 BestRefSeq CDS 123243212 123243317 . - 1 ID=cds-NP_075259.4;Parent=rna-NM_022970.3;
|
||||
chr10 BestRefSeq CDS 123353223 123353331 . - 0 ID=cds-NP_075259.4;Parent=rna-NM_022970.3;
|
||||
chr10 BestRefSeq five_prime_UTR 123353332 123353481 . - . ID=agat-five_prime_utr-54403;Parent=rna-NM_022970.3;
|
||||
chr10 BestRefSeq five_prime_UTR 123357476 123357992 . - . ID=agat-five_prime_utr-54403;Parent=rna-NM_022970.3;
|
||||
chr10 BestRefSeq three_prime_UTR 123237824 123239370 . - . ID=agat-three_prime_utr-54427;Parent=rna-NM_022970.3;
|
||||
|
||||
|
||||
12
src/agat/agat_sp_merge_annotations/test_data/file2.gff
Normal file
12
src/agat/agat_sp_merge_annotations/test_data/file2.gff
Normal file
@@ -0,0 +1,12 @@
|
||||
chr10 BestRefSeq gene 123237824 123357992 . - . ID=gene-FGFR2;Ontology=G0222;
|
||||
chr10 BestRefSeq mRNA 123237824 123357992 . - . ID=rna-NM_022970.3;Parent=gene-FGFR2;Ontology=G0333;
|
||||
chr10 BestRefSeq exon 123237824 123239535 . - . ID=exon-NM_022970.3-18;Parent=rna-NM_022970.3;
|
||||
chr10 BestRefSeq exon 123243212 123243317 . - . ID=exon-NM_022970.3-17;Parent=rna-NM_022970.3;
|
||||
chr10 BestRefSeq exon 123353223 123353481 . - . ID=exon-NM_022970.3-2;Parent=rna-NM_022970.3;
|
||||
chr10 BestRefSeq exon 123357476 123357992 . - . ID=exon-NM_022970.3-1;Parent=rna-NM_022970.3;
|
||||
chr10 BestRefSeq CDS 123239371 123239535 . - 0 ID=cds-NP_075259.4;Parent=rna-NM_022970.3;
|
||||
chr10 BestRefSeq CDS 123243212 123243317 . - 1 ID=cds-NP_075259.4;Parent=rna-NM_022970.3;
|
||||
chr10 BestRefSeq CDS 123353223 123353331 . - 0 ID=cds-NP_075259.4;Parent=rna-NM_022970.3;
|
||||
chr10 BestRefSeq five_prime_UTR 123353332 123353481 . - . ID=agat-five_prime_utr-54403;Parent=rna-NM_022970.3;
|
||||
chr10 BestRefSeq five_prime_UTR 123357476 123357992 . - . ID=agat-five_prime_utr-54403;Parent=rna-NM_022970.3;
|
||||
chr10 BestRefSeq three_prime_UTR 123237824 123239370 . - . ID=agat-three_prime_utr-54427;Parent=rna-NM_022970.3;
|
||||
2
src/agat/agat_sp_merge_annotations/test_data/fileA.gff
Normal file
2
src/agat/agat_sp_merge_annotations/test_data/fileA.gff
Normal file
@@ -0,0 +1,2 @@
|
||||
chr1 AUGUSTUS gene 1000424 1039237 . + . ID=A;
|
||||
chr1 AUGUSTUS mRNA 1000424 1039237 . + . ID=A.t1;Parent=A;
|
||||
2
src/agat/agat_sp_merge_annotations/test_data/fileB.gff
Normal file
2
src/agat/agat_sp_merge_annotations/test_data/fileB.gff
Normal file
@@ -0,0 +1,2 @@
|
||||
chr1 AUGUSTUS gene 1000424 1039237 . + . ID=B;
|
||||
chr1 AUGUSTUS mRNA 1000424 1039237 . + . ID=B.t1;Parent=B;
|
||||
15
src/agat/agat_sp_merge_annotations/test_data/script.sh
Executable file
15
src/agat/agat_sp_merge_annotations/test_data/script.sh
Executable file
@@ -0,0 +1,15 @@
|
||||
#!/bin/bash
|
||||
|
||||
# clone repo
|
||||
if [ ! -d /tmp/agat_source ]; then
|
||||
git clone --depth 1 --single-branch --branch master https://github.com/NBISweden/AGAT /tmp/agat_source
|
||||
fi
|
||||
|
||||
# copy test data
|
||||
cp -r /tmp/agat_source/t/scripts_output/in/agat_sp_merge_annotations/file1.gff src/agat/agat_sp_merge_annotations/test_data
|
||||
cp -r /tmp/agat_source/t/scripts_output/in/agat_sp_merge_annotations/file2.gff src/agat/agat_sp_merge_annotations/test_data
|
||||
cp -r /tmp/agat_source/t/scripts_output/out/agat_sp_merge_annotations_1.gff src/agat/agat_sp_merge_annotations/test_data
|
||||
|
||||
cp -r /tmp/agat_source/t/scripts_output/in/agat_sp_merge_annotations/fileA.gff src/agat/agat_sp_merge_annotations/test_data
|
||||
cp -r /tmp/agat_source/t/scripts_output/in/agat_sp_merge_annotations/fileB.gff src/agat/agat_sp_merge_annotations/test_data
|
||||
cp -r /tmp/agat_source/t/scripts_output/out/agat_sp_merge_annotations_2.gff src/agat/agat_sp_merge_annotations/test_data
|
||||
93
src/agat/agat_sp_statistics/config.vsh.yaml
Normal file
93
src/agat/agat_sp_statistics/config.vsh.yaml
Normal file
@@ -0,0 +1,93 @@
|
||||
name: agat_sp_statistics
|
||||
namespace: agat
|
||||
description: |
|
||||
The script provides exhaustive statistics of a gft/gff file.
|
||||
|
||||
If you have isoforms in your file, even if correct, some values calculated
|
||||
might sounds incoherent: e.g. total length mRNA can be superior than the
|
||||
genome size. Because all isoforms length is added... It is why by
|
||||
default we always compute the statistics twice when there are isoforms,
|
||||
once with the isoforms, once without (In that case we keep the longest
|
||||
isoform per locus).
|
||||
keywords: [gene annotations, statistics, gff]
|
||||
links:
|
||||
homepage: https://github.com/NBISweden/AGAT
|
||||
documentation: https://agat.readthedocs.io/en/latest/tools/agat_sp_statistics.html
|
||||
issue_tracker: https://github.com/NBISweden/AGAT/issues
|
||||
repository: https://github.com/NBISweden/AGAT
|
||||
references:
|
||||
doi: 10.5281/zenodo.3552717
|
||||
license: GPL-3.0
|
||||
requirements:
|
||||
- commands: [agat]
|
||||
authors:
|
||||
- __merge__: /src/_authors/leila_paquay.yaml
|
||||
roles: [ author, maintainer ]
|
||||
|
||||
argument_groups:
|
||||
- name: Inputs
|
||||
arguments:
|
||||
- name: --gff
|
||||
alternatives: [-i]
|
||||
description: Input GTF/GFF file.
|
||||
type: file
|
||||
required: true
|
||||
example: input.gff
|
||||
- name: --gs_fasta
|
||||
description: |
|
||||
Genome size directly from a fasta file to compute more statistics.
|
||||
type: file
|
||||
example: genome.fasta
|
||||
- name: Outputs
|
||||
arguments:
|
||||
- name: --output
|
||||
alternatives: [-o]
|
||||
description: |
|
||||
The file where the results will be written.
|
||||
type: file
|
||||
direction: output
|
||||
required: true
|
||||
example: output.txt
|
||||
- name: Options
|
||||
arguments:
|
||||
- name: --plot
|
||||
alternatives: [-p, -d]
|
||||
description: |
|
||||
When this option is used, an histogram of distribution of the features will be printed in pdf files.
|
||||
type: boolean_true
|
||||
- name: --gs_size
|
||||
description: |
|
||||
Genome size in nucleotides to compute more statistics.
|
||||
type: integer
|
||||
example: 1000000
|
||||
- name: --verbose
|
||||
alternatives: [-v]
|
||||
description: |
|
||||
Verbose option. To modify verbosity. Default is 1. 0 is quiet, 2 and 3 are increasing verbosity.
|
||||
type: integer
|
||||
example: 1
|
||||
- name: --config
|
||||
alternatives: [-c]
|
||||
description: |
|
||||
AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. The `--config`
|
||||
option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
|
||||
type: file
|
||||
example: custom_agat_config.yaml
|
||||
resources:
|
||||
- type: bash_script
|
||||
path: script.sh
|
||||
test_resources:
|
||||
- type: bash_script
|
||||
path: test.sh
|
||||
- type: file
|
||||
path: test_data
|
||||
engines:
|
||||
- type: docker
|
||||
image: quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0
|
||||
setup:
|
||||
- type: docker
|
||||
run: |
|
||||
agat --version | sed 's/.*v\.//; s/\s.*//' | sed 's/^/AGAT: /' > /var/software_versions.txt
|
||||
runners:
|
||||
- type: executable
|
||||
- type: nextflow
|
||||
60
src/agat/agat_sp_statistics/help.txt
Normal file
60
src/agat/agat_sp_statistics/help.txt
Normal file
@@ -0,0 +1,60 @@
|
||||
```sh
|
||||
agat_sp_statistics.pl --help
|
||||
```
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
| Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0 |
|
||||
| https://github.com/NBISweden/AGAT |
|
||||
| National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se |
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
Name:
|
||||
agat_sp_statistics.pl
|
||||
|
||||
Description:
|
||||
The script provides exhaustive statistics of a gft/gff file. /!\ If you
|
||||
have isoforms in your file, even if correct, some values calculated
|
||||
might sounds incoherent: e.g. total length mRNA can be superior than the
|
||||
genome size. Because all isoforms length is added... It is why by
|
||||
default we always compute the statistics twice when there are isoforms,
|
||||
once with the isoforms, once without (In that case we keep the longest
|
||||
isoform per locus).
|
||||
|
||||
Usage:
|
||||
agat_sp_statistics.pl --gff file.gff [ -o outfile ]
|
||||
agat_sp_statistics.pl --help
|
||||
|
||||
Options:
|
||||
--gff or -i
|
||||
Input GTF/GFF file.
|
||||
|
||||
--gs, -f or -g
|
||||
This option inform about the genome size in oder to compute more
|
||||
statistics. You can give the size in Nucleotide or directly the
|
||||
fasta file.
|
||||
|
||||
-d or -p
|
||||
When this option is used, an histogram of distribution of the
|
||||
features will be printed in pdf files. (d means distribution, p
|
||||
means plot).
|
||||
|
||||
-v or --verbose
|
||||
Verbose option. To modify verbosity. Default is 1. 0 is quiet, 2
|
||||
and 3 are increasing verbosity.
|
||||
|
||||
--output or -o
|
||||
File where will be written the result. If no output file is
|
||||
specified, the output will be written to STDOUT.
|
||||
|
||||
-c or --config
|
||||
String - Input agat config file. By default AGAT takes as input
|
||||
agat_config.yaml file from the working directory if any,
|
||||
otherwise it takes the orignal agat_config.yaml shipped with
|
||||
AGAT. To get the agat_config.yaml locally type: "agat config
|
||||
--expose". The --config option gives you the possibility to use
|
||||
your own AGAT config file (located elsewhere or named
|
||||
differently).
|
||||
|
||||
-h or --help
|
||||
Display this helpful text.
|
||||
26
src/agat/agat_sp_statistics/script.sh
Normal file
26
src/agat/agat_sp_statistics/script.sh
Normal file
@@ -0,0 +1,26 @@
|
||||
#!/bin/bash
|
||||
|
||||
set -eo pipefail
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
# unset flags
|
||||
[[ "$par_d" == "false" ]] && unset par_d
|
||||
|
||||
if [[ -n "$par_gs_size" && -n "$par_gs_fasta" ]]; then
|
||||
echo "[error] Please provide only one of the following options to set genome size: --gs_size or --gs_fasta"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
# run agat_sp_statistics
|
||||
agat_sp_statistics.pl \
|
||||
-i "$par_gff" \
|
||||
-o "$par_output" \
|
||||
${par_plot:+-d} \
|
||||
${par_gs_size:+--gs "${par_gs_size}"} \
|
||||
${par_gs_fasta:+--gs "${par_gs_fasta}"} \
|
||||
${par_verbose:+--verbose "${par_verbose}"} \
|
||||
${par_config:+--config "${par_config}"}
|
||||
|
||||
|
||||
65
src/agat/agat_sp_statistics/test.sh
Normal file
65
src/agat/agat_sp_statistics/test.sh
Normal file
@@ -0,0 +1,65 @@
|
||||
#!/bin/bash
|
||||
|
||||
set -eo pipefail
|
||||
|
||||
test_dir="${meta_resources_dir}/test_data"
|
||||
|
||||
# create temporary directory and clean up on exit
|
||||
TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXX")
|
||||
function clean_up {
|
||||
[[ -d "$TMPDIR" ]] && rm -rf "$TMPDIR"
|
||||
}
|
||||
trap clean_up EXIT
|
||||
|
||||
cd "$TMPDIR"
|
||||
|
||||
mkdir test1
|
||||
pushd test1
|
||||
|
||||
echo "> Run $meta_name with test data and --emblmygff3"
|
||||
"$meta_executable" \
|
||||
--gff "$test_dir/1.gff" \
|
||||
--output "output.txt" \
|
||||
|
||||
echo ">> Checking output"
|
||||
[ ! -f "output.txt" ] && echo "Output file output.txt does not exist" && exit 1
|
||||
|
||||
echo ">> Check if output is empty"
|
||||
[ ! -s "output.txt" ] && echo "Output file output.txt is empty" && exit 1
|
||||
|
||||
echo ">> Check if output matches expected output"
|
||||
diff "output.txt" "$test_dir/stats_out.txt"
|
||||
if [ $? -ne 0 ]; then
|
||||
echo "Output file output.txt does not match expected output"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
echo "> Test successful"
|
||||
|
||||
|
||||
popd
|
||||
mkdir test2
|
||||
pushd test2
|
||||
|
||||
cat <<EOF > genome.fasta
|
||||
>sample_sequence
|
||||
ATGCGTACGTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGC
|
||||
EOF
|
||||
|
||||
echo "> Run $meta_name with both gs_size and gs_fasta"
|
||||
error_message=$("$meta_executable" \
|
||||
--gff "$test_dir/1.gff" \
|
||||
--output "output.txt" \
|
||||
--gs_size "1000000" \
|
||||
--gs_fasta "genome.fasta" 2>&1 || true)
|
||||
|
||||
expected_error="[error] Please provide only one of the following options to set genome size: --gs_size or --gs_fasta"
|
||||
if [[ "$error_message" != *"$expected_error"* ]]; then
|
||||
echo "Output error message: $error_message does not match expected error message: $expected_error"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
echo "> Error test successful"
|
||||
|
||||
echo "---- All tests succeeded! ----"
|
||||
exit 0
|
||||
78
src/agat/agat_sp_statistics/test_data/1.gff
Normal file
78
src/agat/agat_sp_statistics/test_data/1.gff
Normal file
@@ -0,0 +1,78 @@
|
||||
##gff-version 3
|
||||
##sequence-region 1 1 43270923
|
||||
#!genome-build RAP-DB IRGSP-1.0
|
||||
#!genome-version IRGSP-1.0
|
||||
#!genome-date 2015-10
|
||||
#!genome-build-accession GCA_001433935.1
|
||||
1 RAP-DB chromosome 1 43270923 . . . ID=chromosome:1;Alias=Chr1,AP014957.1,NC_029256.1
|
||||
###
|
||||
1 irgsp repeat_region 2000 2100 . + . ID=fakeRepeat1
|
||||
###
|
||||
1 irgsp gene 2983 10815 . + . ID=gene:Os01g0100100;biotype=protein_coding;description=RabGAP/TBC domain containing protein. (Os01t0100100-01);gene_id=Os01g0100100;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 2983 10815 . + . ID=transcript:Os01t0100100-01;Parent=gene:Os01g0100100;biotype=protein_coding;transcript_id=Os01t0100100-01
|
||||
1 irgsp exon 2983 3268 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 2983 3268 . + . Parent=transcript:Os01t0100100-01
|
||||
1 irgsp five_prime_UTR 3354 3448 . + . Parent=transcript:Os01t0100100-01
|
||||
1 irgsp exon 3354 3616 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0100100-01.exon2;rank=2
|
||||
1 irgsp CDS 3449 3616 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 4357 4455 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100100-01.exon3;rank=3
|
||||
1 irgsp CDS 4357 4455 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 5457 5560 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100100-01.exon4;rank=4
|
||||
1 irgsp CDS 5457 5560 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 7136 7944 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon5;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0100100-01.exon5;rank=5
|
||||
1 irgsp CDS 7136 7944 . + 1 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 8028 8150 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon6;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0100100-01.exon6;rank=6
|
||||
1 irgsp CDS 8028 8150 . + 2 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 8232 8320 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100100-01.exon7;rank=7
|
||||
1 irgsp CDS 8232 8320 . + 2 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 8408 8608 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon8;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100100-01.exon8;rank=8
|
||||
1 irgsp CDS 8408 8608 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 9210 9615 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon9;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0100100-01.exon9;rank=9
|
||||
1 irgsp CDS 9210 9615 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 10102 10187 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon10;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100100-01.exon10;rank=10
|
||||
1 irgsp CDS 10102 10187 . + 2 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp CDS 10274 10297 . + 0 ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
|
||||
1 irgsp exon 10274 10430 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon11;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0100100-01.exon11;rank=11
|
||||
1 irgsp three_prime_UTR 10298 10430 . + . Parent=transcript:Os01t0100100-01
|
||||
1 irgsp exon 10504 10815 . + . Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon12;rank=12
|
||||
1 irgsp three_prime_UTR 10504 10815 . + . Parent=transcript:Os01t0100100-01
|
||||
###
|
||||
1 irgsp gene 11218 12435 . + . ID=gene:Os01g0100200;biotype=protein_coding;description=Conserved hypothetical protein. (Os01t0100200-01);gene_id=Os01g0100200;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 11218 12435 . + . ID=transcript:Os01t0100200-01;Parent=gene:Os01g0100200;biotype=protein_coding;transcript_id=Os01t0100200-01
|
||||
1 irgsp five_prime_UTR 11218 11797 . + . Parent=transcript:Os01t0100200-01
|
||||
1 irgsp exon 11218 12060 . + . Parent=transcript:Os01t0100200-01;Name=Os01t0100200-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100200-01.exon1;rank=1
|
||||
1 irgsp CDS 11798 12060 . + 0 ID=CDS:Os01t0100200-01;Parent=transcript:Os01t0100200-01;protein_id=Os01t0100200-01
|
||||
1 irgsp CDS 12152 12317 . + 1 ID=CDS:Os01t0100200-01;Parent=transcript:Os01t0100200-01;protein_id=Os01t0100200-01
|
||||
1 irgsp exon 12152 12435 . + . Parent=transcript:Os01t0100200-01;Name=Os01t0100200-01.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100200-01.exon2;rank=2
|
||||
1 irgsp three_prime_UTR 12318 12435 . + . Parent=transcript:Os01t0100200-01
|
||||
###
|
||||
1 irgsp gene 11372 12284 . - . ID=gene:Os01g0100300;biotype=protein_coding;description=Cytochrome P450 domain containing protein. (Os01t0100300-00);gene_id=Os01g0100300;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 11372 12284 . - . ID=transcript:Os01t0100300-00;Parent=gene:Os01g0100300;biotype=protein_coding;transcript_id=Os01t0100300-00
|
||||
1 irgsp exon 11372 12042 . - . Parent=transcript:Os01t0100300-00;Name=Os01t0100300-00.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100300-00.exon2;rank=2
|
||||
1 irgsp CDS 11372 12042 . - 2 ID=CDS:Os01t0100300-00;Parent=transcript:Os01t0100300-00;protein_id=Os01t0100300-00
|
||||
1 irgsp exon 12146 12284 . - . Parent=transcript:Os01t0100300-00;Name=Os01t0100300-00.exon1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0100300-00.exon1;rank=1
|
||||
1 irgsp CDS 12146 12284 . - 0 ID=CDS:Os01t0100300-00;Parent=transcript:Os01t0100300-00;protein_id=Os01t0100300-00
|
||||
###
|
||||
1 irgsp gene 12721 15685 . + . ID=gene:Os01g0100400;biotype=protein_coding;description=Similar to Pectinesterase-like protein. (Os01t0100400-01);gene_id=Os01g0100400;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 12721 15685 . + . ID=transcript:Os01t0100400-01;Parent=gene:Os01g0100400;biotype=protein_coding;transcript_id=Os01t0100400-01
|
||||
1 irgsp five_prime_UTR 12721 12773 . + . Parent=transcript:Os01t0100400-01
|
||||
1 irgsp exon 12721 13813 . + . Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100400-01.exon1;rank=1
|
||||
1 irgsp CDS 12774 13813 . + 0 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp exon 13906 14271 . + . Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100400-01.exon2;rank=2
|
||||
1 irgsp CDS 13906 14271 . + 1 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp exon 14359 14437 . + . Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0100400-01.exon3;rank=3
|
||||
1 irgsp CDS 14359 14437 . + 1 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp exon 14969 15171 . + . Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100400-01.exon4;rank=4
|
||||
1 irgsp CDS 14969 15171 . + 0 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp CDS 15266 15359 . + 1 ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
|
||||
1 irgsp exon 15266 15685 . + . Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon5;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100400-01.exon5;rank=5
|
||||
1 irgsp three_prime_UTR 15360 15685 . + . Parent=transcript:Os01t0100400-01
|
||||
###
|
||||
1 irgsp gene 12808 13978 . - . ID=gene:Os01g0100466;biotype=protein_coding;description=Hypothetical protein. (Os01t0100466-00);gene_id=Os01g0100466;logic_name=irgspv1.0-20170804-genes
|
||||
1 irgsp mRNA 12808 13978 . - . ID=transcript:Os01t0100466-00;Parent=gene:Os01g0100466;biotype=protein_coding;transcript_id=Os01t0100466-00
|
||||
1 irgsp three_prime_UTR 12808 12868 . - . Parent=transcript:Os01t0100466-00
|
||||
1 irgsp exon 12808 13782 . - . Parent=transcript:Os01t0100466-00;Name=Os01t0100466-00.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100466-00.exon2;rank=2
|
||||
1 irgsp CDS 12869 13102 . - 0 ID=CDS:Os01t0100466-00;Parent=transcript:Os01t0100466-00;protein_id=Os01t0100466-00
|
||||
1 irgsp five_prime_UTR 13103 13782 . - . Parent=transcript:Os01t0100466-00
|
||||
1 irgsp exon 13880 13978 . - . Parent=transcript:Os01t0100466-00;Name=Os01t0100466-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100466-00.exon1;rank=1
|
||||
1 irgsp five_prime_UTR 13880 13978 . - . Parent=transcript:Os01t0100466-00
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user