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Old 01-27-2012, 11:12 AM   #1
Location: CA

Join Date: May 2011
Posts: 31
Default gene location on UCSC vs NCBI

Hello All,

The location of a specific gene on a chromosome differs between UCSC and NCBI. It should not be difference since both are using the same assembly. is it difference in length or gap ..etc? Does any one have idea?

E.g mm9 on : chr1:38,053,731-38,054,342 (Txndc9)

nguyendofx is offline   Reply With Quote
Old 01-28-2012, 12:49 PM   #2
Location: one does not simply approximate location

Join Date: Dec 2011
Posts: 10

I think NCBI is using newer version (has patch) and UCSC is the older.

What UCSC uses: GRCh37

What NCBI uses: GRCh37.3

Look at how many patches since the GRCh37 assembly (UCSC uses)
mitochy is offline   Reply With Quote
Old 01-28-2012, 02:39 PM   #3
Richard Finney
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Location: bethesda

Join Date: Feb 2009
Posts: 700

Can you check again?

You report : chr1:38,053,731-38,054,342

NCBI reports : 38040712..38054053 (NC_000067.5 Reference MGSCv37 C57BL/6J)
scroll to RefSeqs of Annotated Genomes: Build 37.2, first entry about 1/2 into the webpage

UCSC reports : chr1:38040712-38054053

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