Description of fasta file from human transcriptom Gencode
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0
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3.7 years ago

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

gencode • 1.1k views
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Thank you very much! I downloaded it from enter link description here

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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

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That was what i was looking for) Thank You!

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3.7 years ago
Ben_Ensembl ★ 2.3k

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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