Get all the translation start site for human genome

Question

[Ming Tommy Tang]

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

Answer 1

[mark.ziemann]

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.

[Ming Tommy Tang]

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

[Ming Tommy Tang]

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

Answer 2

[michael.ante]

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

[Ming Tommy Tang]

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