Introns - Not in databases (Apr/13/2008 )
Hello,
I have trouble looking for intron sequences in databases. Currently I'm looking for the A. thaliana RTM intron and based on the genomic sequence and a paper on the cloning of this gene I've been able to work out the sequence of the intron, however, I'd like to confirm I've got the right sequence. Is there a special database for this or a special way to look for it? I've tried ncbi and tair but I only get the genomic sequence.
Thanks a lot. 
I have trouble looking for intron sequences in databases. Currently I'm looking for the A. thaliana RTM intron and based on the genomic sequence and a paper on the cloning of this gene I've been able to work out the sequence of the intron, however, I'd like to confirm I've got the right sequence. Is there a special database for this or a special way to look for it? I've tried ncbi and tair but I only get the genomic sequence.
Thanks a lot.
try ensembl (www.ensembl.org)
I have trouble looking for intron sequences in databases. Currently I'm looking for the A. thaliana RTM intron and based on the genomic sequence and a paper on the cloning of this gene I've been able to work out the sequence of the intron, however, I'd like to confirm I've got the right sequence. Is there a special database for this or a special way to look for it? I've tried ncbi and tair but I only get the genomic sequence.
Thanks a lot.
What is your At number? If you go to the sequence viewer on the TAIR website, the intron/exon structure should be mapped out. You would then need to confirm if with cDNAs.
I have trouble looking for intron sequences in databases. Currently I'm looking for the A. thaliana RTM intron and based on the genomic sequence and a paper on the cloning of this gene I've been able to work out the sequence of the intron, however, I'd like to confirm I've got the right sequence. Is there a special database for this or a special way to look for it? I've tried ncbi and tair but I only get the genomic sequence.
Thanks a lot.
What is your At number? If you go to the sequence viewer on the TAIR website, the intron/exon structure should be mapped out. You would then need to confirm if with cDNAs.
I have trouble looking for intron sequences in databases. Currently I'm looking for the A. thaliana RTM intron and based on the genomic sequence and a paper on the cloning of this gene I've been able to work out the sequence of the intron, however, I'd like to confirm I've got the right sequence. Is there a special database for this or a special way to look for it? I've tried ncbi and tair but I only get the genomic sequence.
Thanks a lot.
What is your At number? If you go to the sequence viewer on the TAIR website, the intron/exon structure should be mapped out. You would then need to confirm if with cDNAs.
My apologies for not replying to your post sooner. I left work early on friday and didn't check the forum until just now. If you are still having trouble finding your sequences then post again and I will try to help you. BTW - your gene name for the accession number you gave is At1g05760. It can be helpful to know this because it tells you positional information - the chromosome and location on the chromosome.
Cheers,
smu
Coming soon: GeneSplicer: complete list of intron/exons in all assemblies
[~/projects/GeneSplicer $] ./GeneSplicer.exe 837084
837084 RTM1 (Arabidopsis thaliana) NM_100456.2 Exon 1 NC_003070.6 1724233 1724485 - 253
837084 RTM1 (Arabidopsis thaliana) NM_100456.2 Intron 1 NC_003070.6 1724114 1724232 - 119
837084 RTM1 (Arabidopsis thaliana) NM_100456.2 Exon 2 NC_003070.6 1723733 1724113 - 381