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 ***@soe.ucsc.edu if you have any further
questions.
---
Steve Heitner
UCSC Genome Bioinformatics Group
From: Edge Edge [mailto:***@yahoo.com]
Sent: Tuesday, June 26, 2012 8:37 PM
To: ***@soe.ucsc.edu; ***@soe.ucsc.edu
Subject: Re: [Genome] Help with extract rRNA, tRNA, 3'-UTR and 5'-UTR from
UCSC Genome Browser
Dear Professor,
hg19_knownGene_uc010nxq.1 range=chr1:11874-12189 5'pad=0 3'pad=0 strand=+ repeatMasking=none
CTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTG
CTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAG
GTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCA
GCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTT
TCCTGTGGAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATCTT
CTGGCCCCTGTTGTCTGCATGTAACTTAATACCACAACCAGGCATAGGGG
AAAGATTGGAGGAAAG
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 <***@soe.ucsc.edu>
To: 'Edge Edge' <***@yahoo.com>; ***@soe.ucsc.edu
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 ***@soe.ucsc.edu if you have any further
questions.
---
Steve Heitner
UCSC Genome Bioinformatics Group
-----Original Message-----
From: genome-***@soe.ucsc.edu [mailto:genome-***@soe.ucsc.edu] On
Behalf Of Edge Edge
Sent: Tuesday, June 26, 2012 8:41 AM
To: ***@soe.ucsc.edu
Cc: genome-***@soe.ucsc.edu
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 - ***@soe.ucsc.edu
https://lists.soe.ucsc.edu/mailman/listinfo/genome