Question: (Closed) How to get intron sequence from GFF format?
0
gravatar for vani2lasky99
10 months ago by
vani2lasky990 wrote:

Hello! I'm new in bioinformatics and undergraduate student in biology

I want to get intron sequence from GFF file. how can i get it?

gff-version 3

!gff-spec-version 1.21

!processor NCBI annotwriter

!genome-build GRCh38.p12

!genome-build-accession NCBI_Assembly:GCF_000001405.38

!annotation-source NCBI Homo sapiens Annotation Release 109

sequence-region NC_000001.11 1 248956422

species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9606

NC_000001.11 RefSeq region 1 248956422 . + . ID=id0;Dbxref=taxon:9606;Name=1;chromosome=1;gbkey=Src;genome=chromosome;mol_type=genomic DNA NC_000001.11 BestRefSeq pseudogene 11874 14409 . + . ID=gene0;Dbxref=GeneID:100287102,HGNC:HGNC:37102;Name=DDX11L1;description=DEAD/H-box helicase 11 like 1;gbkey=Gene;gene=DDX11L1;gene_biotype=transcribed_pseudogene;pseudo=true NC_000001.11 BestRefSeq transcript 11874 14409 . + . ID=rna0;Parent=gene0;Dbxref=GeneID:100287102,Genbank:NR_046018.2,HGNC:HGNC:37102;Name=NR_046018.2;gbkey=misc_RNA;gene=DDX11L1;product=DEAD/H-box helicase 11 like 1;transcript_id=NR_046018.2 NC_000001.11 BestRefSeq exon 11874 12227 . + . ID=id1;Parent=rna0;Dbxref=GeneID:100287102,Genbank:NR_046018.2,HGNC:HGNC:37102;gbkey=misc_RNA;gene=DDX11L1;product=DEAD/H-box helicase 11 like 1;transcript_id=NR_046018.2 NC_000001.11 BestRefSeq exon 12613 12721 . + . ID=id2;Parent=rna0;Dbxref=GeneID:100287102,Genbank:NR_046018.2,HGNC:HGNC:37102;gbkey=misc_RNA;gene=DDX11L1;product=DEAD/H-box helicase 11 like 1;transcript_id=NR_046018.2 NC_000001.11 BestRefSeq exon 13221 14409 . + . ID=id3;Parent=rna0;Dbxref=GeneID:100287102,Genbank:NR_046018.2,HGNC:HGNC:37102;gbkey=misc_RNA;gene=DDX11L1;product=DEAD/H-box helicase 11 like 1;transcript_id=NR_046018.2 NC_000001.11 BestRefSeq pseudogene 14362 29370 . - . ID=gene1;Dbxref=GeneID:653635,HGNC:HGNC:38034;Name=WASH7P;description=WAS protein family homolog 7 pseudogene;gbkey=Gene;gene=WASH7P;gene_biotype=transcribed_pseudogene;gene_synonym=FAM39F,WASH5P;pseudo=true NC_000001.11 BestRefSeq transcript 14362 29370 . - . ID=rna1;Parent=gene1;Dbxref=GeneID:653635,Genbank:NR_024540.1,HGNC:HGNC:38034;Name=NR_024540.1;gbkey=misc_RNA;gene=WASH7P;product=WAS protein family homolog 7 pseudogene;transcript_id=NR_024540.1 NC_000001.11 BestRefSeq exon 29321 29370 . - . ID=id4;Parent=rna1;Dbxref=GeneID:653635,Genbank:NR_024540.1,HGNC:HGNC:38034;gbkey=misc_RNA;gene=WASH7P;product=WAS protein family homolog 7 pseudogene;transcript_id=NR_024540.1 NC_000001.11 BestRefSeq exon 24738 24891 . - . ID=id5;Parent=rna1;Dbxref=GeneID:653635,Genbank:NR_024540.1,HGNC:HGNC:38034;gbkey=misc_RNA;gene=WASH7P;product=WAS protein family homolog 7 pseudogene;transcript_id=NR_024540.1 NC_000001.11 BestRefSeq exon 18268 18366 . - . ID=id6;Parent=rna1;Dbxref=GeneID:653635,Genbank:NR_024540.1,HGNC:HGNC:38034;gbkey=misc_RNA;gene=WASH7P;product=WAS protein family homolog 7 pseudogene;transcript_id=NR_024540.1 NC_000001.11 BestRefSeq exon 17915 18061 . - . ID=id7;Parent=rna1;Dbxref=GeneID:653635,Genbank:NR_024540.1,HGNC:HGNC:38034;gbkey=misc_RNA;gene=WASH7P;product=WAS protein family homolog 7 pseudogene;transcript_id=NR_024540.1 NC_000001.11 BestRefSeq exon 17606 17742 . - . ID=id8;Parent=rna1;Dbxref=GeneID:653635,Genbank:NR_024540.1,HGNC:HGNC:38034;gbkey=misc_RNA;gene=WASH7P;product=WAS protein family homolog 7 pseudogene;transcript_id=NR_024540.1 NC_000001.11 BestRefSeq exon 17233 17368 . - . ID=id9;Parent=rna1;Dbxref=GeneID:653635,Genbank:NR_024540.1,HGNC:HGNC:38034;gbkey=misc_RNA;gene=WASH7P;product=WAS protein family homolog 7 pseudogene;transcript_id=NR_024540.1 NC_000001.11 BestRefSeq exon 16858 17055 . - . ID=id10;Parent=rna1;Dbxref=GeneID:653635,Genbank:NR_024540.1,HGNC:HGNC:38034;gbkey=misc_RNA;gene=WASH7P;product=WAS protein family homolog 7 pseudogene;transcript_id=NR_024540.1 NC_000001.11 BestRefSeq exon 16607 16765 . - . ID=id11;Parent=rna1;Dbxref=GeneID:653635,Genbank:NR_024540.1,HGNC:HGNC:38034;gbkey=misc_RNA;gene=WASH7P;product=WAS protein family homolog 7 pseudogene;transcript_id=NR_024540.1

this is the gff file I have

sequence gfffile • 353 views
ADD COMMENTlink written 10 months ago by vani2lasky990

Hello vani2lasky99!

Please use the search function. This question has been answered multiple times, e.g.:

Get intronic and intergenic sequences based on gff file

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 10 months ago • written 10 months ago by ATpoint19k
Please log in to add an answer.
The thread is closed. No new answers may be added.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1108 users visited in the last hour