Hi Luigi,
If you click on either of those genes in the browser display, you are
taken to a details page. Under the section mRNA/Genomic Alignments,
you'll see:
BROWSER | SIZE IDENTITY CHROMOSOME STRAND START END QUERY
START END TOTAL
-----------------------------------------------------------------------------------------------------
browser
<http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=240495993&db=mm9&position=chr14%3A56629129-56630317>
| 1189 100.0% 14 - 56629129 56630317 NR_002889
1 1189 1189
<http://genome.ucsc.edu/cgi-bin/hgc?hgsid=240495993&g=htcCdnaAli&i=NR_002889&c=chr14&l=56629128&r=56630317&o=56629128&aliTable=refSeqAli&table=refGene>
browser
<http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=240495993&db=mm9&position=chr4%3A155320362-155331710>
| 1181 99.1% 4 + 155320362 155331710 NR_002889
1 1189 1189
<http://genome.ucsc.edu/cgi-bin/hgc?hgsid=240495993&g=htcCdnaAli&i=NR_002889&c=chr4&l=56629128&r=56630317&o=155320361&aliTable=refSeqAli&table=refGene>
...showing both alignments. Lower down in the Methods section, it
explains how this track was created:
" RefSeq RNAs were aligned against the mouse genome using blat; those
with an alignment of less than 15% were discarded. When a single RNA
aligned in multiple places, the alignment having the highest base
identity was identified. Only alignments having a base identity level
within 0.1% of the best and at least 96% base identity with the genomic
sequence were kept."
Please let us know if you have any additional questions: [email protected]
-
Greg Roe
UCSC Genome Bioinformatics Group
On 1/30/12 9:48 AM, Luigi Grassi wrote:
> Dear All,
>
> I'm observing something strange about the RefSeq Genes track. In
> detail the gene NR_002889 (a predicted pseudogene) maps on two
> different locations: chr14:56629129-56630317 and
> chr4:155320362-155331710; looking this gene in RefSeq i found that
> only one location is right whilst the other is the location of the
> corresponding functional gene. It is the same for NR_002883. How is
> this possible?
>
> Thanks in advance
> Luigi
>
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