[Genome] [UCSC Genome Browser] Origin of RefSeq mRNA sequences

[Fan Hsu]

Hi ChangHee,

RefSeq data are part of the Genbank data we download nightly from NCBI.

There is a table, refSeqAli, has detailed RefSeq alignment data, including
qStarts and tStarts.

For example:

mysql> select qStarts, tStarts from refSeqAli where qName like 'NM_020644';
+------------------------+------------------------------------------+
| qStarts                | tStarts                                  |
+------------------------+------------------------------------------+
| 0,1183,1318,1427,1519, | 8925415,8931325,8934312,8940214,8942331, |
+------------------------+------------------------------------------+

Fan.
-----Original Message-----
From: genome-bounces at soe.ucsc.edu [mailto:genome-bounces at soe.ucsc.edu]On
Behalf Of ChangHee Lee
Sent: Wednesday, May 30, 2007 7:10 AM
To: genome at soe.ucsc.edu
Subject: [Genome] [UCSC Genome Browser] Origin of RefSeq mRNA sequences


Dear UCSC genome administrator,

I'm wondering where the RefSeq mRNA sequences (which claims it could be
different from the genomic sequences) come from. I was trying to search by
Table Browser, and apparently, although mrnaRefSeq table does hold some mrna
identifiers, the one with the same refseq name did not retrieve any results
from all_mrna.

Example :
Looking the mRNA identifier for NM_020644 in hg18 database. It results in 12
different "mrna" query names one of which is "NM_020644" itself. But
querying that to all_mrna table, it yields no results.

I'm trying this because I need the qStarts, tStarts coordinates of the
RefSeq mRNA, which I see as a column in all_mrna table. But I couldn't find
the mRNA of RefSeq.

Hope I can get an answer,

Best wishes,
ChangHee Lee
2007. 05. 30. (Wed)
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