[Genome] update of the UCSC data

[Brooke Rhead]

Hello Juliette,

You are correct: we do update our refGene and refLink tables nightly.
We get information for our tables from the NCBI records, searchable 
here: http://www.ncbi.nlm.nih.gov/sites/entrez?db=nucleotide .

In our refGene and refLink tables, we have three entries for 
INF2/C14orf151 genes (with three separate RefSeq "NM_" identifiers):

INF2
RefSeq: NM_001031714.3
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=149999377

INF2
RefSeq: NM_022489.3
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=149999379

C14orf151
RefSeq: NM_032714.1
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=14249315

The third RefSeq Gene, NM_032714.1, is still listed at NCBI as having 
the name "C14orf151" at NCBI (look for the line: /gene="C14orf151" in 
the NCBI record).

I hope this explanation helps.  If you have further questions, please 
feel free to write back to the mailing list.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Juliette Aury Landas wrote:
> Good morning,
> 
> I have some questions about the update of the UCSC data.
> 
> You wrote me that you use the most recent RefSeq entry at NCBI, and you 
> update your refGene and refLink tables nightly for every assembly for 
> which you have a browser.
> 
> In refFlat and refLink file I still find that C14orf151 and INF2 are 2 
> distinct genes with 2 GeneID. In the other databank like the NCBI, 
> C14orf151 is an aliases (previous name) of INF2. I first thought that 
> the 2 databases (UCSC and NCBI) were not synchronized. That is why I 
> waited 10 days before comparing them again. But they still differ. Do 
> you know why ?
> 
> Thanks in advance,
> Juliette
>