How to find genomic location for genes in batch mode

[Seyed Mehdi Iranmanesh]

Dear Sir/Madam, 

I have 6000 genes. I have Gene symbol and gene accession bank for these 6000 genes. I need to find genomic location of these genes. I used gene sorter to find the genomic location of these genes. But, I could find the genomic location for just 1000 genes. How should I find the genomic location for the rest of them. Is it a better way to do it?

 Thank in advance and I am looking forward to hearing from you. 

Best Regards, 

Mehdi Iranmanesh

Ph.D. candidate, West Virginia Universiry

[Brooke Rhead]

Hi Mehdi,

Instead of using the Gene Sorter to find your genes, try the Table
Browser: http://genome.ucsc.edu/cgi-bin/hgTables. You can select a
gene track, and then use the "identifiers (names/accessions): paste
list" button (or the "upload list" button) to add your 6,000
identifiers. Make sure "region: genome" is specified.

Many of the gene tracks that we host will accept a list of either a gene
symbol or an accession, but the accessions you can enter will be
specific to each gene track. What do your accessions look like? Some
common formats and their corresponding tracks are:

uc004eqj.1 - UCSC Genes
NM_053284 - RefSeq Genes
ENST00000458747 - Ensembl Genes

If you know what Gene track your accessions belong to, I suggest
selecting that track in the Table Browser to retrieve locations. (If
you paste gene symbols instead, you will likely get more than one
isoform returned for each symbol.)

I hope this information helps you get started. If you have further
questions, please reply to gen...@soe.ucsc.edu.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

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[Seyed Mehdi Iranmanesh]

Dear Sir/ Madam, 

Thanks for your kind reply. I Have genbank accession number (which is like NM_053284 - RefSeq Genes) and I have gene symbol for these 6000 genes. But I don't have Ensemble or UCSC identifier. I tried both methods (Table Browser and Gene sorter). Each time I tried both Identifier (Refseq and Gene symbol). In the best case, I could find genome position for 1657 genes out of 6000 genes. So, still there are more than 4000 genes which I don't have genomic position for them. So, how can I get the genomic position for these genes as well?

Thanks in advance and I am looking forward to hearing from you. 

[Brooke Rhead]

Hi Mehdi,

Do you know if all of your RefSeq identifiers are specific to human?  If an identifier comes from another organism, such as mouse or rat, it won't show up in the "RefSeq Genes" track on the human assembly. However, it might be in the "Other RefSeq" track (table: xenoRefGene). The Other RefSeq track contains RefSeq genes in organisms other than human aligned to the human genome (see the track description here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=xenoRefGene).

--

Brooke Rhead

UCSC Genome Bioinformatics Group

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