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Old 01-27-2012, 11:12 AM   #1
nguyendofx
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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)

Thanks,
Ng
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Old 01-28-2012, 12:49 PM   #2
mitochy
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I think NCBI is using newer version (has patch) and UCSC is the older.

What UCSC uses: GRCh37 http://www.ncbi.nlm.nih.gov/genome/assembly/2758/

What NCBI uses: GRCh37.3 http://www.ncbi.nlm.nih.gov/mapview/...build=37&ver=3

Look at how many patches since the GRCh37 assembly (UCSC uses)
http://www.ncbi.nlm.nih.gov/genome/a...homo%20sapiens
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Old 01-28-2012, 02:39 PM   #3
Richard Finney
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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
from http://www.ncbi.nlm.nih.gov/sites/en...ence-sequences

UCSC reports : chr1:38040712-38054053

from http://genome.ucsc.edu/cgi-bin/hgc?o...8054053&db=mm9
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