Hello,
I'd like to know the full description of header of transcript. It is from https://www.gencodegenes.org/pages/data_format.html.
>ENST00000335137.4|ENSG00000186092.6|OTTHUMG00000001094.4|-|OR4F5-201|OR4F5|1054|UTR5:1-36|CDS:37-954|UTR3:955-1054|
ENST00000335137.4 - transcript_id
|ENSG00000186092.6 - gene id
OTTHUMG00000001094.4 - havana_gene
"
-
OR4F5-201
OR4F5
1054
UTR5:1-36
CDS:37-95
UTR3:955-1054"
I haven't work with transcriptome before, maybe full description should be in Ensembl.
A lot of thanks, Valery
1 answer
Hi v.shapovalova1,
I'm not sure where you found this header or where it comes from.
However, OR4F5-201 - transcript name OR4F5 - gene name 1054 - transcript length (base pairs) UTR5:1-36 - coordinates of 5' UTR relative to transcript CDS:37-95 - coordinates of CDS relative to transcript UTR3:955-1054 - coordinates of 3' UTR relative to transcript
The information can be found on the transcript tab in the Ensembl browser: https://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000186092;r=1:65419-71585;t=ENST00000335137
Best wishes
Ben
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Thank you very much! I downloaded it from enter link description here
No problem - I think you mean the FASTA file of transcript sequences from here: https://www.gencodegenes.org/human/
In that case, you can refer to my description above. More information about the header content can be found in the README on the FTP site: ftp://ftp.ebi.ac.uk/pub/databases/gencode/_README.TXT
Best wishes
Ben
That was what i was looking for) Thank You!