Hello, Peng,
I'd like to clarify something in Greg's reply. It is rare,
but there are a few places in the genome where a gene sequence
aligns in more than place. Because Vmn1r100 aligns in two
locations in the mouse mm9 assembly that do not overlap (a
repeat region on chr7), two entries are generated in the
knownCanonical table. The hgSuggest CGI that underlies the
"gene" entry box relies on this table and only takes one of these.
Greg's advice to use the Position box in this rare case is
the best way to go.
regards,
--b0b kuhn
ucsc genome bioinformatics group
On 4/30/2012 2:43 PM, Greg Roe wrote:
> Hi Peng,
>
> The Gene search box is only supposed to come up with one match, which I
> believe finds the match on the lowest chrom. We may change that in the
> future. But if you want to see all the results, use the search/position box.
>
> Please let us know if you have any additional questions: [email protected]
>
> -
> Greg Roe
> UCSC Genome Bioinformatics Group
>
>
> On 4/29/12 10:13 AM, Peng Yu wrote:
>> Hi,
>>
>> Vmn1r100 is mapped to the following two loci based on the mysql db.
>> But when I type Vmn1r100 in the "gene" box, it only shows one locus (I
>> know that "position/search" can return two loci). Should special care
>> be taken to make sure "gene" box returns two loci?
>>
>> +------------+------------+-------+--------+----------+----------+----------+----------+-----------+------------+-----------+--------------+------------+
>> | geneSymbol | name | chrom | strand | txStart | txEnd |
>> cdsStart | cdsEnd | exonCount | exonStarts | exonEnds | proteinID
>> | alignID |
>> +------------+------------+-------+--------+----------+----------+----------+----------+-----------+------------+-----------+--------------+------------+
>> | Vmn1r100 | uc012fbx.1 | chr7 | + | 21003290 | 21004214 |
>> 21003290 | 21004214 | 1 | 21003290, | 21004214, |
>> NP_001160316 | uc012fbx.1 |
>> | Vmn1r100 | uc009foa.1 | chr7 | + | 23197249 | 23199687 |
>> 23198601 | 23199525 | 1 | 23197249, | 23199687, |
>> NP_001160316 | uc009foa.1 |
>> +------------+------------+-------+--------+----------+----------+----------+----------+-----------+------------+-----------+--------------+------------+
>>
>>
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