Mary, Is it possible to obtain NCBI annotations I referred to in previous email? I want it in the genome browser. Thank you Ammar
On Fri, Oct 29, 2010 at 2:45 PM, Mary Goldman <[email protected]> wrote: > Hi Ammar, > > Thank you for your patience. I believe the phenomena you are describing stems > from the way we construct the RefSeq track. We construct this track by taking > the entire mRNA sequence from Genbank and aligning it to the genome using > Blat (for more information see the details page here: > http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=refGene). In other words, > we do not use the RefSeq produced annotations. > > Very small exons, like those you have pointed out, are quite difficult for > computer algorithms, such as blat, to align correctly to the genome. These > small exons are often included in next exon, as is demonstrated here: > http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Marygoldman&hgS_otherUserSessionName=hg18RefSeqExon. > Hand curated tracks, such as Gencode, have a higher probability of aligning > these very small exons correctly (see > http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Marygoldman&hgS_otherUserSessionName=hg18GenecodeExon). > > I hope this information is helpful. Please feel free to contact the mail list > again if you require further assistance. > > Best, > Mary > > ----- Original Message ----- > From: "Ammar Husami" <[email protected]> > To: [email protected], [email protected] > Sent: Tuesday, October 26, 2010 2:47:02 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] CDH23 exon 33 of 3bps > > Hi Venessa, > Regarding my initial note to SOE community, AAG corresponds to hg18 > coordinates Chr10:73164419-73164421 its clearly an exon in gene records you > can view it here > http://www.ncbi.nlm.nih.gov//nuccore/NM_022124.4?report=graph > Please let me know if you still not convinced. There is another exon as well > you can see it there too its exons 11 and 33. > They are very small exons but there are there. > Anyone else can confirm this besides me? > > Ammar > > On Mon, Oct 25, 2010 at 5:06 PM, Vanessa Kirkup Swing > <[email protected]>wrote: > >> Hi Ammar, >> >> Thank you for your question. In order to receive an answer in the timeliest >> manner and for the benefit of all of our users, for whom we try to have the >> most comprehensive archives, I would appreciate it if you resent your email >> to [email protected]. Thank you for your understanding in this matter. >> >> Much thanks, >> Vanessa >> >> ----- Original Message ----- >> From: "Ammar Husami" <[email protected]> >> To: "Vanessa Kirkup Swing" <[email protected]> >> Sent: Monday, October 25, 2010 1:49:52 PM GMT -08:00 US/Canada Pacific >> Subject: Re: [Genome] CDH23 exon 33 of 3bps >> >> its exons 11 and 33 I apologize. >> >> >> On Mon, Oct 25, 2010 at 4:47 PM, Ammar Husami < [email protected] > >> wrote: >> >> >> Hi Venessa, >> I don't know what RefSeq you referring to its clearly an exon in gene >> records you can view it here >> http://www.ncbi.nlm.nih.gov//nuccore/NM_022124.4?report=graph >> Please let me know if you still not convinced. There is another exon as >> well you can see it there too its exon 3. >> They are very small exons but there are there. >> >> >> >> >> >> On Fri, Oct 22, 2010 at 7:23 PM, Vanessa Kirkup Swing < >> [email protected] > wrote: >> >> >> Dear Ammar, >> >> UCSC Genes is based mostly on RefSeq and there is not an exon displayed in >> RefSeq for that given location. Can you tell us why you think there should >> be an exon there? Thanks. >> >> >> Vanessa Kirkup Swing >> UCSC Genome Bioinformatics Group >> >> ----- Original Message ----- >> From: "Ammar Husami" < [email protected] > >> >> >> >> To: "Vanessa Kirkup Swing" < [email protected] > >> Sent: Friday, October 22, 2010 9:44:27 AM GMT -08:00 US/Canada Pacific >> Subject: Re: [Genome] CDH23 exon 33 of 3bps >> >> Yes, AAG corresponds to hg18 coordinates Chr10:73164419-73164421. >> Please email me back, I want to see this issue fixed. >> >> Thanks you >> >> >> On Fri, Oct 22, 2010 at 12:20 PM, Vanessa Kirkup Swing < >> [email protected] > wrote: >> >> >> Dear Ammar, >> >> Can you please send us the exact coordinates of the AAG that you are >> describing? Thanks! >> >> Vanessa Kirkup Swing >> UCSC Genome Bioinformatics Group >> >> >> >> >> ----- Original Message ----- >> From: "Ammar Husami" < [email protected] > >> To: [email protected] >> Sent: Thursday, October 21, 2010 8:11:11 AM GMT -08:00 US/Canada Pacific >> Subject: [Genome] CDH23 exon 33 of 3bps >> >> Dear Community of SOE, >> I am noticing that there is an exon in CDH23 gene of 3 nucleotides >> specifically AAG and one amino acid K that is not able to find in the >> genome >> hg18. The region encompassing this exon is chr10:73163920-73164440. You can >> see this small exon in graphical view here scroll to exon 34. >> Thank you >> >> >> Ammar Husami >> Application Specialist >> Molecular Diagnostics Lab >> Department of Human Genetics >> Cincinnati Childrens Hospital Medical Center >> Cincinnati, Ohio 45229 >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> >> >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
