Hello, Edge.
The UCSC Genes track is produced by UCSC while the RefSeq Genes track comes from NCBI. Many of the items from these tracks correspond with each other, but the RefSeq Genes track is updated nightly while the UCSC Genes track is updated less often, so you will find that some of the newer items in the RefSeq Genes track will not be present in the UCSC Genes track. This is almost certainly the case with NR_046235 as the Genbank page at http://www.ncbi.nlm.nih.gov/nucleotide/374429547?report=genbank reports that this is the first revision and it was released on 13-May-2012. To find the date that a track was last updated, go to that track's description page by clicking the vertical gray bar at the left side of the Browser's graphical display or by clicking the track name in the track listing below the graphical display. You will see "Data last updated" near the top of the page. For your question regarding uc001aaa.3 and uc010nxr.1 from the UCSC Genes track, if you browse to h19 coordinates chr1:11,874-14,409, you will see that these are both transcript variants of the same gene, DDX11L1 (http://www.ncbi.nlm.nih.gov/nuccore/NR_046018?report=GenBank). Similar to the above question, the 5' UTR and 3' UTR sequences you refer to belong to different transcript variants. If you again browse to hg19 chr1:11,874-14,409 here, you will see that uc010nxq.1 has only one 5' UTR on exon 1 and only one 3' UTR on exon 3. With uc001aaa.3, the entire region is untranslated and thus the entire transcript is considered 3' UTR. This is why you see overlap between the 5' UTR of uc010nxq.1 and the 3' UTR of uc001aaa.3 and this is perfectly fine. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group From: Edge Edge [mailto:[email protected]] Sent: Tuesday, June 26, 2012 8:37 PM To: [email protected]; [email protected] Subject: Re: [Genome] Help with extract rRNA, tRNA, 3'-UTR and 5'-UTR from UCSC Genome Browser Dear Professor, Below is the sequence of 5'UTR which I extracted out from UCSC: >hg19_knownGene_uc010nxq.1 range=chr1:11874-12189 5'pad=0 3'pad=0 strand=+ repeatMasking=none CTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTG CTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAG GTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCA GCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTT TCCTGTGGAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATCTT CTGGCCCCTGTTGTCTGCATGTAACTTAATACCACAACCAGGCATAGGGG AAAGATTGGAGGAAAG Below is the sequence of 3'UTR which I extracted out from UCSC: >hg19_knownGene_uc001aaa.3 range=chr1:11874-14409 5'pad=0 3'pad=0 strand=+ repeatMasking=none CTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTG CTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAG GTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCA GCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTT TCCTGTGGAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATCTT CTGGCCCCTGTTGTCTGCATGTAACTTAATACCACAACCAGGCATAGGGG AAAGATTGGAGGAAAGATGAGTGAGAGCATCAACTTCTCTCACAACCTAG GCCAGTGTGTGGTGATGCCAGGCATGCCCTTCCCCAGCATCAGGTCTCCA GAGCTGCAGAAGACGACGGCCGACTTGGATCACACTCTTGTGAGTGTCCC CAGTGTTGCAGAGGCAGGGCCATCAGGCACCAAAGGGATTCTGCCAGCAT AGTGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGACACGCTGT TGGCCTGGATCTGAGCCCTGGTGGAGGTCAAAGCCACCTTTGGTTCTGCC ATTGCTGCTGTGTGGAAGTTCACTCCTGCCTTTTCCTTTCCCTAGAGCCT CCACCACCCCGAGATCACATTTCTCACTGCCTTTTGTCTGCCCAGTTTCA CCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGGCGCTG TGCCCTTCCTTTGCTCTGCCCGCTGGAGACGGTGTTTGTCATGGGCCTGG TCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGGAGAGTGTGGAGTCCA GAGTGTTGCCAGGACCCAGGCACAGGCATTAGTGCCCGTTGGAGAAAACA GGGGAATCCCGAAGAAATGGTGGGTCCTGGCCATCCGTGAGATCTTCCCA GGGCAGCTCCCCTCTGTGGAATCCAATCTGTCTTCCATCCTGCGTGGCCG AGGGCCAGGCTTCTCACTGGGCCTCTGCAGGAGGCTGCCATTTGTCCTGC CCACCTTCTTAGAAGCGAGACGGAGCAGACCCATCTGCTACTGCCCTTTC TATAATAACTAAAGTTAGCTGCCCTGGACTATTCACCCCCTAGTCTCAAT TTAAGAAGATCCCCATGGCCACAGGGCCCCTGCCTGGGGGCTTGTCACCT CCCCCACCTTCTTCCTGAGTCATTCCTGCAGCCTTGCTCCCTAACCTGCC CCACAGCCTTGCCTGGATTTCTATCTCCCTGGCTTGGTGCCAGTTCCTCC AAGTCGATGGCACCTCCCTCCCTCTCAACCACTTGAGCAAACTCCAAGAC ATCTTCTACCCCAACACCAGCAATTGTGCCAAGGGCCATTAGGCTCTCAG CATGACTATTTTTAGAGACCCCGTGTCTGTCACTGAAACCTTTTTTGTGG GAGACTATTCCTCCCATCTGCAACAGCTGCCCCTGCTGACTGCCCTTCTC TCCTCCCTCTCATCCCAGAGAAACAGGTCAGCTGGGAGCTTCTGCCCCCA CTGCCTAGGGACCAACAGGGGCAGGAGGCAGTCACTGACCCCGAGACGTT TGCATCCTGCACAGCTAGAGATCCTTTATTAAAAGCACACTGTTGGTTTC TG My problem is that how come 3'-UTR and 5'-UTR can be at the same region in human genome? Do you have any distinguish which part is the 3'-UTR and 5'-UTR? Based on my understanding, the human genome structure should be promoter-5'-UTR-exon-intron-3'UTR-terminator Thus I confused that the region of 3'-UTR and 5'-UTR is fall within the same region. Many thanks for advice to solve my doubts. best regards Edge Research Student _____ From: Steve Heitner <[email protected]> To: 'Edge Edge' <[email protected]>; [email protected] Sent: Wednesday, June 27, 2012 2:16 AM Subject: RE: [Genome] Help with extract rRNA, tRNA, 3'-UTR and 5'-UTR from UCSC Genome Browser Hello, Edge. I repeated the steps you provided and I did not encounter a discrepancy between the coordinates of the two queries. I would also like to add that you do not need to set "group" to "All Tables" in order to use the rmsk table. You can set "group" to "Variation and Repeats" and set "track" to "RepeatMasker". If you would like the coordinates of 5' UTR and 3' UTR regions, you will need to use a gene track like UCSC Genes or RefSeq Genes. You can do so by performing the following steps: 1. Set the following options: Group: Genes and Gene Prediction Tracks Track: UCSC Genes Table: knownGene Output format: sequence 2. Click the "get output" button 3. Select "genomic" and click the "submit" button 4. Check the "5' UTR Exons" and "3' UTR Exons" checkboxes and select any other options you desire 5. Click the "get sequence" button Note that the output here will not distinguish 5' UTR sequences from 3' UTR sequences. If you want to distinguish 5' UTR sequences from 3' UTR sequences, you will want to make two separate queries. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Edge Edge Sent: Tuesday, June 26, 2012 8:41 AM To: [email protected] Cc: [email protected] Subject: [Genome] Help with extract rRNA, tRNA, 3'-UTR and 5'-UTR from UCSC Genome Browser Dear Professor, Can I know that how to extract the information (such as chromosome number, position start and position ) of human hg19 3'-UTR, 5'-UTR, rRNA, tRNA from UCSC Genome Browser? I got extract rRNA and tRNA by using the following method: * Select "All Tables" from the group drop-down list * Select the "rmsk" table from the table drop-down list * Choose "GTF" as the output format / Choose "Sequence" as the output format * Type a filename in "output file" so your browser downloads the result * Click "create" next to filter * Next to "repClass," type rRNA * Next to free-form query, select "OR" and type repClass = "tRNA" * Click submit on that page, then get output on the main page However, when I check the position of rRNA and tRNA in GTF format and Sequence format. It shown difference nucleotide. Can I know how to solve this issue? I just wanna to make sure the position of rRNA and tRNA in GTF format is tally with the position and chromosome shown in Sequence format. Can I know how to get all the info regarding human hg19 3'-UTR, 5'-UTR, rRNA, tRNA from UCSC Genome Browser? Many thanks for any advice. best regards Edge Research Student _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
