> 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 >
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