I am referring to (http://www.ncbi.nlm.nih.gov//nuccore/NM_022124.5?report=graph)
On Tue, Nov 2, 2010 at 10:03 AM, Ammar Husami <[email protected]> wrote: > 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
