Hello,
I have a query regarding downloading 3'UTR for ensembl genes for Homo sapien. I am trying to download 3'UTR for all genes of ensembl (hg19) for Human >From the UCSC table I do the following: Clade: mammal: Genome: human assembly: GRCh37 Group: Genes and gene Predictions tracks track: ensemble genes Table: ensGene Region:genome Output format: sequence >From Ensembl Genes genomic Sequence browser Sequence Retreival Region Options I choose: 3'UTR exons One FASTA record per gene When I download the sequence and compare one FASTA sequence for gene ENST00000327299 with the 3'UTR sequence of the same gene downloaded from ensembl, I see the lengths are different. The UCSC sequence appears to a subset of the ensemble downloaded 3'UTR sequence. (See below the two sequences) QUESTION: 1. Am I doing the steps right to download the entire 3'UTR sequence from UCSC table or am I just downloading a part of the 3'UTR region? See below: FROM UCSC: >hg19_ensGene_ENST00000327299 range=chr1:65691861-65693173 5'pad=0 3'pad=0 strand=+ repeatMasking=none CCCTGCCCAATGGAAGAACCAGGAAGATGTGGTCATTCATTCAATAGTGT GTGTAGTATTGGTGCTGTGTCCAAATTAGAAGCTAGCTGAGGTAGCTTGC AGCATCTTTTCTAGTTGAAATGGTGAACTGATAGGAAAACAAATGAGTAG AAAGAGTTCATGAAGAGGCCCTCCTCTGCCTTTCAAAAGGCTGGTCACCT ACACATGTTTAAGGTGTCTCTGCACATGTCTCAAGCCCATCACAAGAAAG CAAGTACAGTGTGGATTTCAAATGGTGTGTAACTTCAGCTCCAGCTGGTT TTTGACAGCTGTTGCTGTGGTAATATTTTTGACATGTGATGGTGATAGTC TCTGGTTCTCCCCATCCCCACAAAGGCTGTTGAACCACAGCACCAGGAAG CCTGAGAATGAATCCTGAGGGCTCTAGCCCAGGCTTTGTCCCAGGCTTTC TGGTGTGTGCCCTCCTGGTAACAGTGAAATTGAAGCTACTTACTCATAGT GGTTGTTTCTCTGGTCTTGAGTGACTGTGTCCACAGTTCATTTTTTTCCG GTAGGAATAACTCCTTTTCTACATCCACGCTCCATAGAGTCTCTCCTTTT CAGACATCCTGGGATGAAAGAATTTGGCTTTTTTTTTTCTTTTTTTTTTT GGACATCTGTTTTCACTCTTAGGCTTTTAAACAATAGTTATTGCTTTTAT CCCTCTCAGATTCTAATAACTGAGAGCGATGGGGCTATATTGAATCTCTG TATGCACTGAGAACTGAGCTATGAAGAGGATCTTATTAAACTGCTGGTCT GACTTTATGGATTGACACTGTTCCTTTCTTTTATTGTGAAAAAAAAAAAA AACCCTGAAAGTCTTGGGAACCCCCTAAAGTCTTTTGGGAATCCTCAAAA AGCATGGGAAGTTAAGTATTTAGCTACATAAATGTTGTAAGATCATATCT TATGTATAGAAGTAATAAGACCATTTGGAATTACTGGACTAATTGAATAG TTAAGGTTTCTATTCGGGACAATAAAATGTATTTTGAAAGTGCTGCTAAC TATTGATGCTGACAGTGTTTCACTCCTATGAGTGACCCAAACATATTATA AATATGTGGTAAAGGGAATGGAGCCTGTGGGGTTGAGCAGAATGTTGTAC TAGCTGTGCCTGGACTGAGTATAACAGCTTTATGATTATGAGAAAACAAA TTCTTTATTTTTTTTTTCTGTTCCAAAGATTCATCCTATGGGGTGGCCAT AAAGTCTAGAATTAGATACTAATATTTTGTCATTCATTATAACATATCAA TAAACCATTTGTT FROM ENSEMBL >ENSG00000162433|ENST00000327299 CCCTGCCCAATGGAAGAACCAGGAAGATGTGGTCATTCATTCAATAGTGTGTGTAGTATT GGTGCTGTGTCCAAATTAGAAGCTAGCTGAGGTAGCTTGCAGCATCTTTTCTAGTTGAAA TGGTGAACTGATAGGAAAACAAATGAGTAGAAAGAGTTCATGAAGAGGCCCTCCTCTGCC TTTCAAAAGGCTGGTCACCTACACATGTTTAAGGTGTCTCTGCACATGTCTCAAGCCCAT CACAAGAAAGCAAGTACAGTGTGGATTTCAAATGGTGTGTAACTTCAGCTCCAGCTGGTT TTTGACAGCTGTTGCTGTGGTAATATTTTTGACATGTGATGGTGATAGTCTCTGGTTCTC CCCATCCCCACAAAGGCTGTTGAACCACAGCACCAGGAAGCCTGAGAATGAATCCTGAGG GCTCTAGCCCAGGCTTTGTCCCAGGCTTTCTGGTGTGTGCCCTCCTGGTAACAGTGAAAT TGAAGCTACTTACTCATAGTGGTTGTTTCTCTGGTCTTGAGTGACTGTGTCCACAGTTCA TTTTTTTCCGGTAGGAATAACTCCTTTTCTACATCCACGCTCCATAGAGTCTCTCCTTTT CAGACATCCTGGGATGAAAGAATTTGGCTTTTTTTTTTCTTTTTTTTTTTGGACATCTGT TTTCACTCTTAGGCTTTTAAACAATAGTTATTGCTTTTATCCCTCTCAGATTCTAATAAC TGAGAGCGATGGGGCTATATTGAATCTCTGTATGCACTGAGAACTGAGCTATGAAGAGGA TCTTATTAAACTGCTGGTCTGACTTTATGGATTGACACTGTTCCTTTCTTTTATTGTGAA AAAAAAAAAAAACCCTGAAAGTCTTGGGAACCCCCTAAAGTCTTTTGGGAATCCTCAAAA AGCATGGGAAGTTAAGTATTTAGCTACATAAATGTTGTAAGATCATATCTTATGTATAGA AGTAATAAGACCATTTGGAATTACTGGACTAATTGAATAGTTAAGGTTTCTATTCGGGAC AATAAAATGTATTTTGAAAGTGCTGCTAACTATTGATGCTGACAGTGTTTCACTCCTATG AGTGACCCAAACATATTATAAATATGTGGTAAAGGGAATGGAGCCTGTGGGGTTGAGCAG AATGTTGTACTAGCTGTGCCTGGACTGAGTATAACAGCTTTATGATTATGAGAAAACAAA TTCTTTATTTTTTTTTTCTGTTCCAAAGATTCATCCTATGGGGTGGCCATAAAGTCTAGA ATTAGATACTAATATTTTGTCATTCATTATAACATATCAATAAACCATTTGTTAAAAGAT TTGCCTGGTTTCCAGACTTGGTGGCCACCTTGAATAATTCTTGCTGTCTTCTGGGAAGGA TGATGAAATTTATTCCTGCTGCCTTAAAAATATGTATCCCTTCTTCACCCATCATGACTG TCCCCAGTGAGTGTCCTTTACTATTCTTGGGAGTGACTCCTGTCTAACTTTTCATACTGG CGAGAAGAAAAGAAGCCTATTTTAACACTTTAGTGGTGTTGAAACACATTACTTACTTTC TGAAGATGTCCCAGTGAATCCTCTGTCAATTCACTGCCATATGTAATCTATATGATAAGG AATGCATCTTCCTTCTAAGTACTGCCCAAACTCTTGCCAGCTCCTCTCCCATTGTCCCTT CATGTGAATATTTCTTGGCTACCTTAGTGGAAATATAGATCAGTTTTCTCCCCATCCATC CTCTCAAACATAATGAGATTGTTTACTTTTTAGATTTATGCAGTGAAAATGCCCAGTCAG GTCTGAATCGTCAGTGCATTATATTGACTCTGAGCACTTTAGAATTTAGAGTTGCAATTG AATGCCAGCTGTGGAGATGGGGTGCATATCAGATATATAAATAAAGCTCAGGTTTGCTAG GGAACCAGGTATAGAGAAAAATAAGTCTGATATGAGGAAAATTGCACAATTTAGAGTAGT TATGCCGTAGAGAAAATTTCCACAAACTAGGAAATGTAGAGAGTTATTCTATAGAATACT CAAAAGAGGAAAGTATGTGATTTTTGGAAACAGGAAAATCTTCAAACTTCTTTCTTCACT TCCCTTTGTGTTTAGCTGACCCTCCAATGTGATCATTGCCTTTGGAGTTTGGGAGAGGTA CGGGAAGTGGCCTGATCCCTGCTTCCATACTTCACTCCTCCATCCATCCTTCCCTCCCTC TTCCCCTCCAGCTAAATGGACAATTCTAGCCAACATTGAGTCACTCAATAAGTCTCAACA GTGGGTGTGTTTGCTGAGATTGTCCAGCGGTTGAGCAGTTTGGTCTCACCTCCCTCGCTA GTTGAGACCAAAAAGAGACAAATAACTTTTTCATGGTCTTTGAAACATAATGCTTATTTC GTGGTCAATGGCTTTAAAAAAATCTGTTTCTTGTTTTCTTCAACAAACTCACTAGTTTTC CCTTAAATGATATTGTAAAAATTAAAGTAATCTTGAAAATGTTTTGACAAAAGTAAAATT AAAGGGACATCTTTTCTTGTTTTGTTTTTTTTTTTTCTATTGCCACACATGACCGTTCCT TCACCTTTAAGCAAAGAGAGTGGTTCAGATGGTTTCTAAGATGCCAACCTGACCTCGCAT TCTGTCATTCTACCCAGCTCTTAATTCAATTTGCTTCCATTATCCTAACAGGCTTCTTTC TTACTTAGAACTTGGAAAGGCTGCTGTATTTAATACCCTCCAACACTAACGCAGACTTAA GATAGGTACTGTTTATTGAAAACCTACTGAGTGAAATGTGCGGTTTTAGGACCTTCATAA ACATCTCATTTAATCTTTCTAGCATCCTGTGAAACAGCCATGATTTCACGTTGATAAACA AAGAAGACAGGGGTCCCAGGGATGTGAAGCATCTTGCCCAGGCTTCTGCTGCTGGTGACC AGTGTAGCCAGGACTCCAGCCCAGGTTTTCCTGACTCAGAAGACTGAGCTTTTTCCTGGA TGTTATTAATAGCTAATTGTGTCCAAGCAACCAAGGGCCTTGAGTCTGCTTGGTTCTGCT TATGGCCTCACATCAAGAAATGGAGCTAGTCCATGTCTGTAGTCCCAATGCTTTGGGAAG CCATGATGGGAAGGTTGTCGGAGGCCAAAAGTTCAAGACCAGGCTGGGCAATATCACAAG ACTCCATCTCTACGGAAAAGTAAAAAATTAGCCAGTCATGGTGGTGTACACTTATGGTCC TAGTTACTCAGGAGACTTAGGCAGGAGGATTGCTTGATCCTAGGAATTCGAGGCTGCAGT GAGCTATGATTGCACCTCTGCACCCAAGCCTGGGCGACACAGCGAGACCCTCTCTCTTAA AAAAAAAAAATAGCAGAGCTCACCAAAGTGATGTTCACCTTTTTATGACATTCCTTTTTC TTAGCTTAAGAAAAGAAAGCTGCTAGATGAGAGTCTTAGTTTTCCTGCATAAGACCTCCT TTATGAATAGAATAAAAGACTGTCAAAGTAGGCTGGGCTTGGGCCCAGGCTAATCTATGA AGGAAGCAAGCTCGTGTTCCTTACCTATCCTTTTGGTGTCCATTGGATTGTGCCCCGAAG TGGCCTTTACCCTTGAGCCGTCCCCAGCCATGGTGCTCACACATAGGCTTTTGAGCTCCT TGGAGCTATCCAGATCCTGCTCACTTTTCCTTCCTGAGATCAGAACAAATCACCCCCTTA CTCCCACTCCAAACAAGGCCTTGATGATAAACTAATCCTTCCTAAAATGCTGGTAGGTAA ACAAGCAATGATGAAGCATTGAACACAGGTTAACTCCTGACTTTTGTACCATTGTCTATT CCATTACACATTAACATGACTCTGAATGCCAGATCCAAACCTTTGCCCACCATCTGCTTG TCGTGCAACAGTTGAGGCAGTAACCAGGGGAGATTCACTTCCTGTCTTGTCCTTCCCCAG GGATCACCCCCCTGCTGCCCTCTAGCAGCCAAACTCAGATGAGTTCCATTGTTACCCTAG GTGTGCCCATCTCTTTGGTAGGGAAGGAGAAAGGTAAGAATAGCCATCAGTGAGGAAGGA TTCTTGGAGCGAGGAGCCACTGTGGTTTTTCCTGCTATTTAAGATGTTGAGACCGGATAA CTTTAGAAAGATACCTGCACAAACCCATAAATAGTGCTTTTATAAAGTTTAGTTCACCGG AACCTGAGTTCAGTATTTGACATTAGCTTTTTGTCCAAAGAGTTGAAGCCTGCTGGAGGT CTTTGCTCAAATAATAAATACCACATATTTCCAAGTGTGTTCAGGTATAGGCACTAGGTA CTGTCTGTTTACTTCATGTTAGGCACATTACATGCATTGGCTAATCAAATCCTCATCAAT TACATATGTAATAATCTAAACTTGCCTCCTTGTATTATAAATGGAAATAATCCTGTTTAT TTAAACGGGTTTTCATGTACCTGTAGGGATTAGGAAACTCAAATGGCCTTTTTAATACCT TTCCCTAGTTTGAGCTCCCTGTTCTCTTTAACAGATAAAACAACATATTTGCTTCAGCCT GGAATCTGTTTTTGGTGCTTTGGTGCAGAGACAGGAAATGGGCACTCAGAGTCACACTGG TAGTTGCACACTGTATCTACAGAGGGCGTGTCTCATCTGTACTCTGCTGGGTTACAGGAT TTCAGTAGGTATTTGTGTCCACCTGAGAATTCTGTTTATTACCTTTCATTTGACAGTGTC TTTCCTTTCTGCAGTTGATTTTGCTAGAGAGGCAATTCATAAGGTGAGGTCCTGTTCATA GTATGACTTGCTTTCTCAATATCTCCTTCAATTTTTAGTAACTCTTGGTCTATTTGGTGT CTTTAAAAAAAATAACCTAGTAATAAAGACTTCTTTTAATGTGGAAATGTGGTCTGGTAG TAAGTTATTTCTTTCCACATGTAACTGACCCAATCTGGTTTCCAAATGAGAAGTGTGCAG GCCCCAGAGGTTGAGAAGCCATATTTCAACTGTGAAAAAAATCTGCTTCCTGCATCTGTT GAAATATAGTTGTTCATACTTGCCATCCCTTATCTTTCTTGTAACAATTTGCACAGTTCT TGCCAGAATAAATGCCATTATCTGTATGTTTCAGGGAGTTCCCCAATTTGATCATTTTTG TGTGTGTGTGGTGTGTGTGTGAGAGAGAGAGATACTGCAGTAAAACATTTCTAAAGGATG AAAGCTCTTGTATGGCATAGATATGAATTCCTTCCTCTGGTAATAATTAGGTTATTCCCA GAAGCACAGTGTCATTCTTTAAATAAAAGCTTTCCTGTTTAAAGCTTTTCAAAGGAGCAG ACCACCTTGAAGATTCCCCCTAGGGTTGATATGTGTCTAATTCATTTTATAAAAATTATT CTTGTCTTCATTTTAAAGCTTTGGCTATATAGTCAGAAATGTCCTAAATAACAAACTATT TTGTATTTAATTTAGGGAAGACTAAAGGGAAGAAAAATGAAAACTCAGTCTTTATGTAAG CTCCAAGGATATTAGGGCTTAAAGGGCTTTTCTAGTTTTATGAGAATTTGTACTACTGAT TTTTATATATTCCTGTTTTTGAGATGAACAGATCTCTGGGGAAATTGTTGAGTTACAATG GCATTTCACTGTGATCCCTCTCAAGCTCAGATCAGTTCTATAACCCAATGACAACCTGTC TCTTTGGTTTACTGTCCTGTGAAATGTCAGCTCAAGTTTCCCAGAAGTCGTGTGTTTATG ATGAGTCAGAGTGCTTTTCCTCGGTGGGACAGTTGCTGGCCCTCTTAATTTTGGTGTATG TGCTTCCAAGTATCTAAACCTCCAGTCTGATCTGTATATGCTATCCTAACTGTTAATTGT ATTATTGATTATGTTGATTATCTTGCTTGAAGGTTCATACTTTTCAATTTGATAGAAATA AAGTTTTTTTCTGCTTATA _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
