Mismatch between UCSC and NCBI inforamtion
Imke Tammen
Dear UCSC team,
I am the curator of Online Mendelian Inheritance in Animals – OMIA – and recently received an enquiry in relation to a mismatch between c. and p. coordinates for a canine variant when comparing UCSC and NCBI data. We used the same genomic coordinates in the same reference genome CanFam3.1.
NCBI lists NC_006591.3:g.55282762C>A as having the consequence: NM_001131049.1:c.767G>T and NP_001124521.1:p.(R256L)
The UCSC Browser lists the protein coordinates as p.249?
I was hoping that you could clarify for us why there is a difference between the two genome viewers when we are using the same reference genome / transcripts?
Kind regards,
Imke
Associate Professor Imke Tammen
|
Academic Lead – Outcome Assessment Sydney School of Veterinary Science
The University of Sydney
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Gerardo Perez
Hello, Imke.
Thank you for reporting this mismatch, and sorry for the delay in responding.
The reason you are seeing a difference is that the UCSC Genome Browser's protein coordinate, p.249, comes from counting codons along the genome sequence, while NCBI counts along the transcript's own sequence. This transcript has 21 extra bases that the CanFam3.1 genome assembly does not have, so counting along the genome gives a different codon number (249) than counting along the transcript (256) from that point on.
On our development server, we updated the RefSeq gene tracks so that when this happens, the affected codon is shown in orange with an exclamation point, and its mouseover text shows both numbers along with a short note and a link to more information on our FAQ page. You can see it here: https://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=canFam3&position=chr9:55282743-55282778&refSeqComposite=full. This is still a development server and the display may change, but we would welcome any feedback you have on how it looks or reads.
One thing we're curious about: the note ends with a plain word link, "Help". Below it, in the same mouseover, there's a "?" icon next to "Codon phase". If the "?" were there instead of the Help link, would you have known to click it?
Thank you again for bringing this to our attention. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on a publicly accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Gerardo Perez
UCSC Genomics Institute
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