Need help finding sequence - (Aug/23/2005 )

Hello I'm looking for the complete map of introns and exons for soluble guanylyl cyclase Beta-1.

I have been on the NCBI site and I was trying to BLAST the mRNA to find a complete sequence and map out the regions.

The problem is the clone that this was made from has not been completely mapped out and arranged and right now I'm without a clue. Could anyone help out.

-gungrave-

Please let us know what organism you are interested in.

-sage-

QUOTE (gungrave @ Aug 23 2005, 01:38 PM)

... the clone that this was made from has not been completely mapped out and arranged ...

Do you mean you cannot get a good alignment of the clone to the genomic sequence?

-cyberpostdoc-

Thanks for all your replies. We are trying to find the exon sequences in mus muscularis (mice). We were going to try aligning the mRNA sequence accession# AF297083 with the gene located on chrom. 3 Accession # NC_000069. The problem is that this sequence is not complete as it has a lot of "N" in its report. Could anyone assist, thanks a bunch.

-gungrave-

Have you tried UCSC genome browser? Here is where AF297083 mapped to
http://genome.ucsc.edu/cgi-bin/hgTracks?cl...1&Submit=submit

Then click "Tables" on the top bar and you will be able to export any sequence related to the gene.

-pcrman-

N's doesn't nessesarily mean that its not complete (in the sense you sequenc is missing)

It could just mean that for the NC sequence, the direction of a piece has not been determined yet.

If you try to align, you don't care directions, so just go ahead to align, as long as there is not so many repeatative sequence elements, you should be able to get a pretty good alignment.

-cyberpostdoc-