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Question: Refseq accessions - getting gene function and GO terms for each one
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11 months ago
Biogeek • 350

Can someone please let me know how I can get access to refseq gene names/functions and GO (CC,BP,MF) information for each gene using information gained from refseq accessions / information within the gff3.

Many thanks.

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0

Which gff do you have? Please paste some entries from it, and wrap the output with the 101 010 button

ADD REPLYlink 11 months ago
Kevin Blighe
43k
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GFF3 version 1.21

NW_018384101.1  RefSeq  region  1   1835033 .   +   .   ID=id0;Dbxref=taxon:1720309;Name=Unknown;chromosome=Unknown;collection-date=Mar-2014;country=Saudi Arabia: KAUST;gbkey=Src;genome=genomic;isolate=CC7;isolation-source=whole animal;mol_type=genomic DNA
NW_018384101.1  Gnomon  gene    12260   37834   .   +   .   ID=gene0;Dbxref=GeneID:110245770;Name=LOC110245770;gbkey=Gene;gene=LOC110245770;gene_biotype=protein_coding;partial=true
NW_018384101.1  Gnomon  mRNA    12260   37834   .   +   .   ID=rna0;Parent=gene0;Dbxref=GeneID:110245770,Genbank:XM_021052419.1;Name=XM_021052419.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 142 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC110245770;inference=similar to RNA sequence%2C mRNA (same species):INSD:JV120934.1;model_evidence=Supporting evidence includes similarity to: 1 Protein%2C and 98%25 coverage of the annotated genomic feature by RNAseq alignments;partial=true;product=DNA-binding protein RFX6-like;transcript_id=XM_021052419.1
NW_018384101.1  Gnomon  exon    12260   12660   .   +   .   ID=id1;Parent=rna0;Dbxref=GeneID:110245770,Genbank:XM_021052419.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 142 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC110245770;inference=similar to RNA sequence%2C mRNA (same species):INSD:JV120934.1;partial=true;product=DNA-binding protein RFX6-like;transcript_id=XM_021052419.1
 

ADD REPLYlink 11 months ago
Biogeek
• 350
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It appears that this particular organism does not have GO annotation. It does not appear in the list of organisms in geneontology.org.

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vkkodali
♦ 1.1k

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