[Genome] update frequency of RefGene.txt

[Rachel Harte]

Phoenix,

There are several RefGene tables. If you click on the "Tables" link on the
top blue bar and then select the Genome and assembly of interest and
"Genes and Gene Prediction Tracks" as the group and "RefSeq Genes" as the
track, then you will see the list of tables on the pull-down menu for
tables. If you select a table and then press the "describe table schema"
button then you will see a description of the type of data in each table
and also a list of related tables.
refFlat and refSeqAli contain the alignment information for BLAT
alignments of the RefSeqs against the genome. Some of the other tables
are:
refSeqStatus - gives the status for each RefSeq e.g.
Unknown','Reviewed','Validated','Provisional','Predicted','Inferred'

refSeqSummary - contains the completeness and the summary from the COMMENT
section of the GenBank record.

gbCdnaInfo - contains information for all GenBank mRNAs and RefSeqs such
as the version, type, direction, source, organism etc. so this is some of
the data that you see in the GenBank record.

refLink - links the RefSeq to other database identifiers such as gene
name, protein accession, Entrez Gene Id (locusLinkId) and OMIM ID etc.

I hope that this helps you. Please let us know if you have further
questions.

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Tue, 19 Dec 2006, Phoenix Kwan wrote:

> Hi Kayla,
>
> We are interested in knowing the positions of exon-exon junctions. We
> use the RefSeq data to update our database every odd-numbered month, so
> we want to know if your refGene table incorporates the data from RefSeq.
>
>
> Thank you for your help.
>
> Phoenix Kwan
>
> -----Original Message-----
> From: Kayla Smith [mailto:kayla at soe.ucsc.edu]
> Sent: Tuesday, December 19, 2006 10:37 AM
> To: Phoenix Kwan
> Cc: genome at soe.ucsc.edu
> Subject: Re: [Genome] update frequency of RefGene.txt
>
>
> Phoenix,
>
> The refGene table is updated daily, however, the version available for
> download on our website is from a database dump and is about 1 day
> behind what you'll see on our browser.
>
> Here is a link to to this data for the hg18 assembly:
> http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/
>
> I hope this answers your question.  Please don't hesitate to contact us
> again if you have further questions.
>
> Kayla Smith
> UCSC Genome Bioinformatics Group
>
>
> Phoenix Kwan wrote:
> > Dear Sir or Madam,
> >
> >
> >
> > I am interested in using the annotation data in RefGene.txt. I'd like
> to
> > know how frequently this file is updated.
> >
> >
> >
> > Thank you for your time.
> >
> >
> >
> > Sincerely,
> >
> > Phoenix Kwan
> >
> > _______________________________________________
> > Genome maillist  -  Genome at soe.ucsc.edu
> > http://www.soe.ucsc.edu/mailman/listinfo/genome
>
>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>