[Genome] problem with ABCC6 proteome entry

[Fan Hsu]

Hi Tim,

I looked into this case and found that at the time 
when we created the annotation for UCSC Known Genes and 
UCSC Proteome Browser, the RefSeq NM_001171.1 had 99.5% 
identity when aligned to the base genome.  Our gene-check
logic raised two error flags (badFrame and noStop), thus
this RefSeq did not make it to the KG candidate genes list.

I noticed that the latest version of NM_001171,
(NM_001171.3) has 100% identity with base genome.
I expect it would be picked up by our future
UCSC Known Genes update, which I anticipate to
happen within next few months.

Fan.
-----Original Message-----
From: genome-bounces at soe.ucsc.edu [mailto:genome-bounces at soe.ucsc.edu]On
Behalf Of Tim Hefferon
Sent: Wednesday, December 06, 2006 1:43 PM
To: genome at soe.ucsc.edu
Subject: [Genome] problem with ABCC6 proteome entry


Hi,

There appears to be a problem with the Proteome Browser entry for the  
human gene, ABCC6. The PB returns [Q8TCY8 Up-regulated gene 7 (ABCC6  
protein)]. This is a severely truncated isoform of the full-length  
protein.

NCBI's EntrezGene RefSeq entry for the full-length mRNA and protein  
is: [NM_001171.3→NP_001162.3 ATP-binding cassette, sub-family C,  
member 6 isoform 1].

The protein that is currently pulled up on the PB is the other RefSeq  
entry, [NM_001079528.1→NP_001072996.1 ATP-binding cassette, sub- 
family C, member 6 isoform 2].

Please resolve this issue if possible; there is a research community  
that works with this gene and would greatly appreciate it!

Thank you,

Tim Hefferon


_______________________________________________
Genome maillist  -  Genome at soe.ucsc.edu
http://www.soe.ucsc.edu/mailman/listinfo/genome

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