[Genome] REFSEQ and table searching

[Archana Thakkapallayil]

Hello Jonathan,

I tried these two examples, refSeq: NM_001013203,NM_001034941 for the 
Rat (rn4) assembly and was able to reteive the 3'UTR and 1.5 kb 
downstream sequences. I am not sure which table you are looking at. The 
table that gives this information is called "refGene" under the "group: 
Genes and Gene Prediction Tracks", "track: RefSeq Genes". You can then 
paste or upload your list of refSeq identifiers by clicking on the 
paste/upload list button. Make sure that you select the "genome" radio 
button.

Also, the "refLink" and "kgXref" table (found in the table list 
associated with the RefSeq Genes and Known Gene track) provides a good 
cross-reference among the gene identifiers.

I hope this information is helpful to you. Please let us know if you 
have further questions.

Regards,

Archana
UCSC Genome Bioinformatics Group

We invite you to give us your feedback on the UCSC Genome Browser 
through May 31, 2007: http://www.surveymonkey.com/s.asp?U=881163743177


Cohen, Jonathan (NIH/NICHD) [F] wrote:
> I am currently using the UCSC genome browser to obtain 3'UTR and 1.5 kb downstream seuqences for human, mouse, rat to perform motif anaylsis on sets of differentially regulated genes.  IN doing this, I have had to convert unigene symbols and/or accession numbers into reference sequence accessions using DAVID (http://david.abcc.ncifcrf.gov/) .  However, when I submit the REFSEQ to UCSC, I dont not get back a matching list of genes.  Wouldnt the fact that these are REFSEQs mean that they have their 3'UTR in the database? Here are 2 examples: 
>
> Gene name       Trim44 
> Cluster Rn.8005
> LLID    362172
> GENE NAME       TRIPARTITE MOTIF-CONTAINING 44
> REFSEQ  NM_001013203   
> SPECIES 10116:RATTUS NORVEGICUS
>
> When I try to retrive 3'UTR and 1.5 kb using the table browser, nothing
> comes back.  If I BLAT it, there is a REFSEQ entry which I can click on
> to retrieve 3' sequence.  Antoher example is
>
> Gene name       Tarbp2
> Cluster Rn.17227
> LLID            363006
> GENE NAME       TAR (HIV) RNA BINDING PROTEIN 2
> REFSEQ  NM_001034941
> SPECIES 10116:RATTUS NORVEGICUS
>
> Has anyone had this problem?
>
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