Hello Idit, The Table Browser retrieves information for the entire gene (or genes) that overlaps the region specified in the "position" box. The sequence you obtained corresponds to the coding exons of the two genes that overlap your region (uc001jav.2 and uc001jau.2).
The chromosome range you are looking at (chr10:43224544-43224585 on the hg18 browser) contains a 5' UTR exon. To include this sequence in your result from the Table Browser, be sure to select "5' UTR Exons" from the sequence retrieval options. I hope this is helpful. If you have further questions, please feel free to write back to the mailing list. -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/21/09 03:22, Idit Kosti wrote: > Hello, > I was searching for the area on chr10 between 43224544-43224585 on the - > strand. According to the browser I can clearly seen an exon and intro > there, but there's no what I'm getting from the knowngene table. > here is what I got with the same query: > >> hg18_knownGene_uc001jav.2 range=chr10:43202091-43203338 5'pad=0 3'pad=0 >> strand=- repeatMasking=none > ATGATGCTGGGCCCTGAGGGAGGTGAAGGCTTTGTGGTCAAGCTCCGTGG > CCTGCCCTGGTCCTGCTCTGTTGAGGACGTGCAGAACTTCCTCTCTGACT > GCACGATTCATGATGGGGCCGCAGGTGTCCATTTCATCTACACTAGAGAG > GGCAGGCAGAGTGGTGAGGCTTTTGTTGAACTTGGATCAGAAGATGATGT > AAAAATGGCCCTGAAAAAAGACAGGGAAAGCATGGGACACCGGTACATTG > AGGTGTTCAAGTCCCACAGAACCGAGATGGATTGGGTGTTGAAGCACAGT > GGTCCCAACAGTGCCGACAGCGCCAACGATGGCTTCGTGCGGCTTCGAGG > ACTCCCATTTGGATGCACAAAGGAAGAAATTGTTCAGTTCTTCTCAGGGT > TGGAAATTGTGCCAAACGGGATCACATTGCCTGTGGACCCCGAAGGCAAG > ATTACAGGGGAAGCGTTCGTGCAGTTTGCCTCGCAGGAGTTAGCTGAGAA > GGCTCTAGGGAAACACAAGGAGAGGATAGGGCACAGGTACATTGAGGTGT > TTAAGAGCAGCCAGGAGGAAGTTAGGTCATACTCAGATCCCCCTCTGAAG > TTCATGTCCGTGCAGCGGCCAGGGCCCTATGACCGGCCCGGGACTGCCAG > GAGGTACATTGGCATCGTGAAGCAGGCAGGCCTGGAAAGGATGAGGCCTG > GTGCCTACAGCACAGGCTACGGGGGCTACGAGGAGTACAGTGGCCTCAGT > GATGGCTACGGCTTCACCACCGACCTGTTCGGGAGAGACCTCAGCTACTG > TCTCTCCGGAATGTATGACCACAGATACGGCGACAGTGAGTTCACAGTGC > AGAGCACCACAGGCCACTGTGTCCACATGAGGGGCCTGCCGTACAAAGCG > ACCGAGAACGACATTTACAACTTCTTCTCTCCTCTCAACCCTGTGAGAGT > CCATATTGAGATTGGCCCAGATGGAAGAGTGACGGGTGAAGCAGATGTTG > AGTTTGCTACTCATGAAGAAGCTGTGGCAGCTATGTCCAAAGACAGGGCC > AATATGCAGCACAGATATATAGAACTCTTCTTGAATTCAACAACAGGGGC > CAGCAATGGGGCGTATAGCAGCCAGGTGATGCAAGGCATGGGGGTGTCTG > CTGCCCAGGCCACTTACAGTGGCCTGGAGAGCCAGTCAGTGAGTGGCTGT > TACGGGGCCGGCTACAGTGGGCAGAACAGCATGGGTGGCTATGACTAG >> hg18_knownGene_uc001jau.2 range=chr10:43202091-43203338 5'pad=0 3'pad=0 >> strand=- repeatMasking=none > ATGATGCTGGGCCCTGAGGGAGGTGAAGGCTTTGTGGTCAAGCTCCGTGG > CCTGCCCTGGTCCTGCTCTGTTGAGGACGTGCAGAACTTCCTCTCTGACT > GCACGATTCATGATGGGGCCGCAGGTGTCCATTTCATCTACACTAGAGAG > GGCAGGCAGAGTGGTGAGGCTTTTGTTGAACTTGGATCAGAAGATGATGT > AAAAATGGCCCTGAAAAAAGACAGGGAAAGCATGGGACACCGGTACATTG > AGGTGTTCAAGTCCCACAGAACCGAGATGGATTGGGTGTTGAAGCACAGT > GGTCCCAACAGTGCCGACAGCGCCAACGATGGCTTCGTGCGGCTTCGAGG > ACTCCCATTTGGATGCACAAAGGAAGAAATTGTTCAGTTCTTCTCAGGGT > TGGAAATTGTGCCAAACGGGATCACATTGCCTGTGGACCCCGAAGGCAAG > ATTACAGGGGAAGCGTTCGTGCAGTTTGCCTCGCAGGAGTTAGCTGAGAA > GGCTCTAGGGAAACACAAGGAGAGGATAGGGCACAGGTACATTGAGGTGT > TTAAGAGCAGCCAGGAGGAAGTTAGGTCATACTCAGATCCCCCTCTGAAG > TTCATGTCCGTGCAGCGGCCAGGGCCCTATGACCGGCCCGGGACTGCCAG > GAGGTACATTGGCATCGTGAAGCAGGCAGGCCTGGAAAGGATGAGGCCTG > GTGCCTACAGCACAGGCTACGGGGGCTACGAGGAGTACAGTGGCCTCAGT > GATGGCTACGGCTTCACCACCGACCTGTTCGGGAGAGACCTCAGCTACTG > TCTCTCCGGAATGTATGACCACAGATACGGCGACAGTGAGTTCACAGTGC > AGAGCACCACAGGCCACTGTGTCCACATGAGGGGCCTGCCGTACAAAGCG > ACCGAGAACGACATTTACAACTTCTTCTCTCCTCTCAACCCTGTGAGAGT > CCATATTGAGATTGGCCCAGATGGAAGAGTGACGGGTGAAGCAGATGTTG > AGTTTGCTACTCATGAAGAAGCTGTGGCAGCTATGTCCAAAGACAGGGCC > AATATGCAGCACAGATATATAGAACTCTTCTTGAATTCAACAACAGGGGC > CAGCAATGGGGCGTATAGCAGCCAGGTGATGCAAGGCATGGGGGTGTCTG > CTGCCCAGGCCACTTACAGTGGCCTGGAGAGCCAGTCAGTGAGTGGCTGT > TACGGGGCCGGCTACAGTGGGCAGAACAGCATGGGTGGCTATGACTAG > > > Any idea what is the problem? > > Thanks, > Idit > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
