Hi, This is Vidya, Jr research Associate. I have a doubt regarding the sequence retrieval of a gene. e.g. I want the sequence for chromosome 1: 179846800 to 179847000, when I am giving the gene name, the coordinates given by UCSC is 179809102 to 179846941. This sequence has 59 nucleotides less at the end when compared to my query. Please suggest me whether I should add the nucleotides by checking promoter/upstream checkbox or downstream checkbox? When I check on the upstream checkbox, the nucleotides are added in the beginning of the sequence but the position number changes at the end. why is it so? Below I am giving the sequences retrieved; 1.Original gene sequence >hg19_knownGene_uc001gnl.3 range=chr1:179809102-179846941 5'pad=0 3'pad=0 strand=- repeatMasking=none GACATTCGGGCCGCGGCGGCCGCTGGGTGCAGCCGAGCGGTGTGGAGCGG AGAGAATACTCGAAGGGCTCTCCTGATACTAACAGTTTTACGATTTAAAA CTTCGCCAGAATTTgtaagtaaacaaaatgactatgcagcttttccatgt tttagtattgaaactgatatcttgaatttttgaaaaggactttcagaaac ggtccctccccacccccaccttcgtaccgcacaaatggtatttttatttt
2. Sequence got when I checked upstream checkbox with addition of 59 nucleotides. >hg19_knownGene_uc001gnl.3 range=chr1:179809102-179847000 5'pad=0 3'pad=0 strand=- repeatMasking=none aggattccacgggcgccttccggcggaaagtgtttgtcatatgggcgggg accctggacGACATTCGGGCCGCGGCGGCCGCTGGGTGCAGCCGAGCGGT GTGGAGCGGAGAGAATACTCGAAGGGCTCTCCTGATACTAACAGTTTTAC GATTTAAAACTTCGCCAGAATTTgtaagtaaacaaaatgactatgcagct tttccatgttttagtattgaaactgatatcttgaatttttgaaaaggact Please resolve the problem for which I would be grateful. Regards H.K.VIDYA PGDB-10-10-33 ----------------------------------------- Institute of Bioinformatics and Applied Biotechnology, Bangalore _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
