Off topic:How to get intron sequence from GFF format?
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2.6 years ago

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 • 1.5k views
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