I have been looking for the position of intronic SNP rs3093024 in different transcript variants of CCR6 but unable to find. I also need a source from where i can get complete sequence of the mRNA along with all introns and exons for CCR6.
Hi Mehran
whatever you want you won't find an intronise variant in a transcript (mRNA) since introns are spliced to give transcript.
if you want to see the environment of your SNP, go to the UCSC website (http://genome-euro.ucsc.edu/cgi-bin/hgGateway?redirect=manual&source=genome.ucsc.edu), just type the rs number and when arriving on the genome browser, you'll have enough interesting tracks to search around your target.
fred
Thank you Frederic for your positive response. that link you have provided is helpful.
Yeah I got it. Actually I meant that I need complete sequence of CCR6 including all introns and exons with clear differences (that from where to where is exon and same for introns). Then I will locate my intended SNP in that sequence. I got FASTA from NCBI but couldn't differentiate in introns and exons
In the UCSC genome browser, just type on the name (at left of the browser) of your gene, and a new page opens with all you'll have the sequence with exon in upper case and introns in lower.
just try that (http://genome-euro.ucsc.edu/cgi-bin/hgc?hgsid=231400417_4MIzak2mCZXopWO72h0bQbBVWM4m&g=htcDnaNearGene&i=uc003qvl.3&c=chr6&l=167412815&r=167552629&o=knownGene&boolshad.hgSeq.promoter=0&hgSeq.promoterSize=1000&hgSeq.utrExon5=on&boolshad.hgSeq.utrExon5=0&hgSeq.cdsExon=on&boolshad.hgSeq.cdsExon=0&hgSeq.utrExon3=on&boolshad.hgSeq.utrExon3=0&hgSeq.intron=on&boolshad.hgSeq.intron=0&boolshad.hgSeq.downstream=0&hgSeq.downstreamSize=1000&hgSeq.granularity=gene&hgSeq.padding5=0&hgSeq.padding3=0&boolshad.hgSeq.splitCDSUTR=0&hgSeq.casing=exon&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&submit=submit).
fred
Thank you sooo much for help... it is really helpful. I got it. I was searching in Ensemble and NCBI but had not looked into UCSC genome browser.
Thank you once again.
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