Hi Pauline, The point of our original e-mail was to point out that block 3 of NM_001001432 was mismapped by BLAT and should correspond to the position of block 3 in NM_000364. The error appears to stem from the incorrect mapping of a single GG repeat at the beginning of this block that results in the entire exon being positioned incorrectly. This may also apply to the mapping of GenBank mRNA X79861. We believe this to be an erroneous BLAT alignment that should be fixed in the UCSC RefGene track entry for this gene.
In case the formatting of our original diagram was lost through e-mail, I have attached a PDF version. - Trevor -----Original Message----- From: Pauline Fujita [mailto:[email protected]] Sent: Monday, November 15, 2010 5:35 PM To: Pugh, Trevor Cc: [email protected]; Duffy, Elizabeth Subject: Re: [Genome] Mismapping of TNNT2 isoforms in RefGene track Hello Trevor, One of our developers had this to say about your issue: NM_001001432 block 3 is at different chromosomal coordinates than NM_000364 block 3. These blocks are generated by blat alignment. It appears that NM_001001432 block 3 doesn't annotate a reference genome exon and I suspect this is a polymorphism with the reference genome. While it is only support by one GenBank mRNA X79861, the mRNA and EST tracks show evidence of structural polymorphisms in this genome. The block structure of the two alignments in this region, in positive strand, zero-based coordinates are: NM_001001432 end start size block 2 201342340 201342396 56 block 3 201338460 201338470 10 block 4 201337289 201337355 66 NM_000364 end start size block 2 201342341 201342396 55 block 3 201341272 201341283 11 block 4 201341154 201341169 15 If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 11/11/10 11:41, Pugh, Trevor wrote: >> Dear UCSC Curators, >> >> We have been examining the mapping of various transcript models of TNNT2 and >> appear to have uncovered a mapping error of NM_001001432 in the UCSC RefGene >> Track, hg19 build. The track lists block 3 as mapping to a genomic region >> lacking splice donor and acceptor sites and to be inconsistent with other >> transcript models with similar mRNA sequence such as NM_000364. This appears >> to be due to a mismapping of the 5' GG of block 3 which is correctly mapped in >> NM_000364 but is broken across blocks 2 and 3 in NM_001001432. We have >> included a diagram of this phenomenon below. Blue denotes exonic sequence, >> cyan denotes the mismapped GG, and pink denotes the splice recognition >> locations. >> >> We bring this to your attention so that you may evaluate the mapping of the >> transcript yourself and a correction be made, if warranted. Please let us know >> if you require additional information. >> >> Thank you, >> >> Trevor Pugh and Beth Duffy >> Laboratory for Molecular Medicine >> Partners Healthcare Center for Personalized Genetic Medicine >> Cambridge, MA >> >> Block 2+3 from NM_001001432 (note: no donor/acceptor sites) >> atcagcaggt ggccttgctg ccatgtgggt gtcactatct cccccagcag 201342556 >> gggagaaaac aggctttttg ttgcaggtca cacagctcat gaggggtgga 201342506 >> actagattca ccctaggcct cgctgatctc tgtacaacgg gggccagagc 201342456 >> tcttctgagg aaggcaggct tccctttgta cctgcactga cttttttctc 201342406 >> cttttggagG GAGAGCAGAG ACCATGTCTG ACATAGAAGA GGTGGTGGAA 201342356 >> GAGTACGAGG AGGAGtgagt atctggagca tcttgcctga gtggggtcct 201342306 >> ctcccgccgc tgccctgaca cctggtccag gagcctccca gctgtccctc 201342256 >> ... >> gcaccaagca gggtggccag gtgttggttg gggggtctgg ggacagagtc 201338506 >> ctctggagag cagccaggga gactggaaat agccaGAGCA GGAAGgacat 201338456 >> gacgtcagcc ttcagatgcg ccctgctgat ggggagcaca ggaccaaggc 201338406 >> aagggagtga gaccagggct taattttaga aagtgcgttc tgacagctat 201338356 >> >> >> CDS NM_001001432.1 >> 1 atgtctgaca tagaagaggt ggtggaagag tacgaggagg aggagcagga agagcaggag >> 61 gaggcagcgg aagaggatgc tgaagcagag gctgagaccg aggagaccag ggcagaagaa >> >> _______________________________________________________________________ >> >> Block 2+3 from NM_000364 (note: correct splice sites) >> cttttggagG GAGAGCAGAG ACCATGTCTG ACATAGAAGA GGTGGTGGAA 201342356 >> GAGTACGAGG AGGAgtgagt atctggagca tcttgcctga gtggggtcct 201342306 >> ctcccgccgc tgccctgaca cctggtccag gagcctccca gctgtccctc 201342256 >> ggattctggg tagaagtagc tgtgtgtgtt ttgggcaccc cgaggagaga 201342206 >> ... >> ctagtgggtg tcattgcaag gtgggcaggg cagcgtggac tccactaggc 201341406 >> aacaagggaa aagaaagggg gattatcttt ggggaaaggc cagtgtgtgc 201341356 >> atgtgtgtgc aggcgtgtgt gtttgcatgt gcttgtgtgc gagctactga 201341306 >> cagtgtttcc tgttgctctc agGGAGCAGG AAGgtaagcg taaacgtgtg 201341256 >> tactcatttg gatcaaagac agcctggttc gaaactgacc cacctcttct 201341206 >> >> CDS NM_000364 >> 1 atgtctgaca tagaagaggt ggtggaagag tacgaggagg aggagcagga agaagcagct >> 61 gttgaagaag aggaggactg gagagaggac gaagacgagc aggaggaggc agcggaagag >> > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome
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