[Genome] CD24 gene on chromosome 6

[Kayla Smith]

Alain,

Alignment of CD24 on the genome happens by BLATing the sequences that we 
get from 3rd party sources.  The reason CD24 is showing up on chromosome 
Y is because of how well it BLATs there.

Here are some details on this, under the "Methods" section:
http://genome.ucsc.edu/cgi-bin/hgGene?hgg_do_kgMethod=1&hgg_type=knownGene

I poked around a little bit and found the following:

Ensembl lists this gene as being on chrY:
http://www.ensembl.org/Homo_sapiens/geneview?transcript=ENST00000382840

Entrez lists this gene as being on chr6:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=934

Copying and BLATing the ncbi sequence into the genome browser gives hits 
on chrY, not chr6:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&term=NM_013230&doptcmdl=GenBank&tool=genome.ucsc.edu

I hope this helps to elucidate how we do things at the UCSC Genome 
Browser.  Please don't hesitate to contact us again if you require more 
assistance.

Kayla Smith
UCSC Genome Bioinformatics Group

Nganga, Alain wrote:
> Hello 
> 
> I am a post-Doc at roswellpark cancer Institute (Buffalo, NY) and I am intersted to find the CD24 genomic sequence.
> Can you help me to localize the CD24 gene on Chromosome 6, please ?
> Because the only CD24 Chromosome map I am getting is fom the chromosome Y using 6q21 CD24 mRNA as query.
> 
> Thank you very much
> 
> Alain
> 
> 
> 
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