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Get all the translation start site for human genome

Hi there,

I want to get all the positions of the translation start sites for the human genes. Note it is different from the transcription start sites (TSSs). protein translates at the codon ATG.

For all TSSs, GENCODE gff file and refGENE file from UCSC have the information.

my questions is, can I look at every gene sequences start from the TSS to the TES(transcription end site), and look for the first ATG, and assume it is the translation start site.

Alternative start codon is rare in eukaryotic genomes, but may still exist.

What's your suggestions?

Thanks,
Ming

translation gene
• 6,497 views • link
updated by Ram Ram • written by Ming Tommy Tang Ming Tommy Tang

2 answers

Hi Ming. ENSEMBL GTF files have the position of the "CDS" (coding sequence) in addition to "gene" and "transcript". It should be straightforward to extract the start of the CDS belonging to exon 1 of each protein coding gene. Just be careful to account for orientation of genes on the minus strand.

• 0 views • link
written by mark.ziemann mark.ziemann

Thanks! Mark. by the way, I found your blog very helpful :)

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updated by Ram Ram • written by Ming Tommy Tang Ming Tommy Tang

Actually, the GENCODE gtf file has a feature for start_codon. Even nicer for me :)

• 0 views • link
written by Ming Tommy Tang Ming Tommy Tang
Hi Ming, You can also use Ensembl's biomart and UCSC's table browser to get this information. In biomart for instance you select next to gene and transcript id the transcript start. Cheers, Michael
• 0 views • link
written by michael.ante michael.ante

I want the translation start sites which are different from the transcription start sites.

• 0 views • link
updated by Ram Ram • written by Ming Tommy Tang Ming Tommy Tang

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