Hi Ammar, I'm sorry but we don't currently have a track with NCBI's annotations in the browser. One option would be to obtain the annotations from NCBI (ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/) and make a custom track. Please keep in mind that the NCBI annotation format is fairly different from any of our supported custom track formats. Thus, it would require some work to be able to visualize the annotations in the browser. Another option would be to use a manually curated track like Gencode Genes (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeSangerGencode).
I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ----------- Mary Goldman UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Ammar Husami" <[email protected]> To: "Mary Goldman" <[email protected]> Cc: [email protected], [email protected] Sent: Tuesday, November 2, 2010 7:11:40 AM GMT -08:00 US/Canada Pacific Subject: Re: [Genome] CDH23 exon 33 of 3bps 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
