[ensembl-dev] human transcripts with non 'AUG' start

Paila, Uma Devi (udp3f) udp3f at eservices.virginia.edu
Thu Sep 12 20:37:38 BST 2013


Hi,
 I would greatly appreciated if anybody could tell me what it means by an initiator codon in ENSEMBL? If it refers to the translational start site, why some of the HUMAN transcripts in ENSEMBL  show an initiator codon other than 'AUG' ? Considering this example, http://www.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?g=ENSG00005917;r=2:20449625-20512017;t=ENST00000440577;transcript=ENST0000044057, this transcript shows a translation with 'R' as the first amino acid whereas you would expect to see a 'M' as in this example http://www.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?db=core;g=ENSG00000055917;r=2:20449625-20512017;t=ENST00000442400

I see the first example shows its CDS as incomplete. Does that mean it is actually missing some transcript info? My other question is, how is the initiator_codon_variant defined? Does this mean a variation in the translational start or the transcription start site?

regards,
uma
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