Hi Pauline,
Thanks a lot for the reply. It's very helpful.
I have a doubt in the starting sequence range for the two coordinates of the
same gene . Even though we have the same coordinates (Upstream sequence) in
BCL2 gene i.e for chr18:60790579-60986613 and chr18:60790579-60986657, the UCSC
genome browser is showing two different sequence for the same start regions.
Please have a look, It would be great if you please let me know the Discrepancy
or probably, may be i am interpreting in a wrong way. Kindly clarify.
I have crossed checked the same with NCBI, where it shows common gene starting
sequence for both co-ordinates.( NCBI Reference Sequence: NG_009361.1 )
Ø >hg19_knownGene_uc002lit.1 range=chr18:60790579-60986613 5'pad=0 3'pad=0
strand=- repeatMasking=none
TTTCTGTGAAGCAGAAGTCTGGGAATCGATCTGGAAATCCTCCTAATTTT
TACTCCCTCTCCCCGCGACTCCTGATTCATTGGGAAGTTTCAAATCAGCT
ATAACTGGAGAGTGCTGAAGATTGATGGGATCGTTGCCTTATGCATTTGT
TTTGGTTTTACAAAAAGGAAACTTGACAGAGGATCATGCTGTACTTAAAA
Ø >hg19_knownGene_uc002liu.1 range=chr18:60790579-60986657 5'pad=0 3'pad=0
strand=- repeatMasking=none
CTCGAGCTCTTGAGATCTCCGGTTGGGATTCCTGCGGATTGACATTTCTG
TGAAGCAGAAGTCTGGGAATCGATCTGGAAATCCTCCTAATTTTTACTCC
CTCTCCCCGCGACTCCTGATTCATTGGGAAGTTTCAAATCAGCTATAACT
GGAGAGTGCTGAAGATTGATGGGATCGTTGCCTTATGCATTTGTTTTGGT
TTTACAAAAAGGAAACTTGACAGAGGATCATGCTGTACTTAAAAAATACA
For your reference i am sending you few reference sequences (splice variants)
wherein its perfectly fine.
I. VEGFA (uc021yzu.1) at chr6:43737946-43754223 - Homo sapiens
vascular endothelial growth factor A (VEGFA), transcript variant 9, mRNA.
II. VEGFA (uc010jyx.3) at chr6:43737946-43754223 - Homo sapiens
vascular endothelial growth factor A (VEGFA), transcript variant 8, mRNA.
III. VEGFA (uc003owk.3) at chr6:43745460-43754223 - Homo sapiens
vascular endothelial growth factor A (VEGFA), transcript variant 6, mRNA.
IV. VEGFA (uc003owj.3) at chr6:43737946-43754223 - Homo sapiens
vascular endothelial growth factor A (VEGFA), transcript variant 6, mRNA.
V. VEGFA (uc003owi.3) at chr6:43737946-43754223 - Homo sapiens
vascular endothelial growth factor A (VEGFA), transcript variant 7, mRNA.
VI. VEGFA (uc003owh.3) at chr6:43737946-43754223 - Homo sapiens
vascular endothelial growth factor A (VEGFA), transcript variant 1, mRNA.
VII. VEGFA (uc003owg.3) at chr6:43737946-43754223 - Homo sapiens
vascular endothelial growth factor A (VEGFA), transcript variant 3, mRNA.
VIII. VEGFA (uc003owf.3) at chr6:43737946-43754223 - Homo sapiens
vascular endothelial growth factor A (VEGFA), transcript variant 2, mRNA.
IX. VEGFA (uc003owe.3) at chr6:43737946-43754223 - Homo sapiens
vascular endothelial growth factor A (VEGFA), transcript variant 4, mRNA.
X. VEGFA (uc003owd.3) at chr6:43737946-43754223 - Homo sapiens
vascular endothelial growth factor A (VEGFA), transcript variant 5, mRNA.
XI. VEGFA (uc003owb.3) at chr6:43737946-43745562 - Homo sapiens
vascular endothelial growth factor A (VEGFA), transcript variant 8, mRNA.
XII. VEGFB (uc001nyx.3) at chr11:64002056-64006736 - Homo sapiens
vascular endothelial growth factor B (VEGFB), transcript variant VEGFB-167,
mRNA.
XIII. VEGFB (uc001nyw.3) at chr11:64002056-64006736 - Homo sapiens
vascular endothelial growth factor B (VEGFB), transcript variant VEGFB-186,
mRNA.
XIV. PDCD10 (uc003fez.3) at chr3:167401695-167452651 - Homo sapiens
programmed cell death 10 (PDCD10), transcript variant 3, mRNA.
XV. PDCD10 (uc003fey.3) at chr3:167401695-167452651 - Homo sapiens
programmed cell death 10 (PDCD10), transcript variant 2, mRNA.
XVI. PDCD10 (uc003fex.3) at chr3:167401695-167452594 - Homo sapiens
programmed cell death 10 (PDCD10), transcript variant 1, mRNA.
Thanks and Regards,
Ateeq M Khaliq
Bioinformatics Division,
Jubilant Biosys Pvt Ltd,
#96, Industrial Suburb, 2nd Stage
Yeshwantpur, Bangalore 560 022
Ph No : +91-80-66628798
From: Pauline Fujita [mailto:[email protected]]
Sent: 05 May 2012 AM 05:14
To: Ateeq Muhammed Khaliq
Cc: [email protected]; [email protected]
Subject: Re: [Genome] discrepancy in gene co-ordinates
Hello Ateeq,
BCL2 has several splice variants of which you are seeing two. If you input
"BCL2" into the 'position or search term' box for human assembly hg19 it should
return a list of matching results - the top four of which are:
BCL2 (uc021ulf.1) at
chr18:60985282-60985899<http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr18:60985282-60985899&hgsid=263576055&knownGene=pack&hgFind.matches=uc021ulf.1,>
- Homo sapiens B-cell CLL/lymphoma 2 (BCL2), nuclear gene encoding
mitochondrial protein, transcript variant beta, mRNA.
BCL2 (uc002liv.1) at
chr18:60985187-60986613<http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr18:60985187-60986613&hgsid=263576055&knownGene=pack&hgFind.matches=uc002liv.1,>
- Homo sapiens B-cell CLL/lymphoma 2 (BCL2), nuclear gene encoding
mitochondrial protein, transcript variant beta, mRNA.
BCL2 (uc002liu.1) at
chr18:60790579-60986657<http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr18:60790579-60986657&hgsid=263576055&knownGene=pack&hgFind.matches=uc002liu.1,>
- Homo sapiens B-cell CLL/lymphoma 2 (BCL2), nuclear gene encoding
mitochondrial protein, transcript variant alpha, mRNA.
BCL2 (uc002lit.1) at
chr18:60790579-60986613<http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr18:60790579-60986613&hgsid=263576055&knownGene=pack&hgFind.matches=uc002lit.1,>
- Homo sapiens B-cell CLL/lymphoma 2 (BCL2), nuclear gene encoding
mitochondrial protein, transcript variant alpha, mRNA.
Notice that the UCSC ids for these include "uc002lit.1" and "uc002liu.1" which
correspond to the examples you give below (you can see these IDs with the urls
you have included). Within the main browser display if you click on each of the
BCL2 variants it should take you to a description page listing the relevant
information for that variant and help you to differentiate between the two.
Hopefully this information was helpful and answers your question. If you have
further questions or require clarification feel free to contact the mailing
list at [email protected]<mailto:[email protected]>.
Regards,
Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
On 5/2/12 4:42 AM, Ateeq Muhammed Khaliq wrote:
Hello all,
This is Ateeq, Sr research Associate, from Jubilant Biosys Ltd, Bangalore
India. I have a doubt regarding amplicon design. While designing an amplicon
for certain gene co-ordinate region, I have noticed a discrepancy, which is as
follows
http://genome.ucsc.edu/cgi-bin/hgTracks?hgHubConnect.destUrl=..%2Fcgi-bin%2FhgTracks&clade=mammal&org=Human&db=hg19&position=chr18%3A60790579-60986613&hgt.suggest=BCL2&hgt.suggestTrack=knownGene&Submit=submit&hgsid=262656015&knownGene=pack
Ø For BCL2 gene I got two different nucleotide sequences for the same start
position in UCSC
· For chr18:60790579-60986657 the start sequence obtained was-->
CTCGAGCTCTTGAGATCTCCGGTTGGGATTCCTGCGGATTGACATTTCTG
TGAAGCAGAAGTCTGGGAATCGATCTGGAAATCCTCCTAATTTTTACTCC
http://genome.ucsc.edu/cgi-bin/hgc?hgsid=262656015&g=htcDnaNearGene&i=uc002lit.1&c=chr18&l=60790578&r=60986613&o=knownGene&boolshad.hgSeq.promoter=0&hgSeq.promoterSize=1000&hgSeq.utrExon5=on&boolshad.hgSeq.utrExon5=0&hgSeq.cdsExon=on&a<http://genome.ucsc.edu/cgi-bin/hgc?hgsid=262656015&g=htcDnaNearGene&i=uc002lit.1&c=chr18&l=60790578&r=60986613&o=knownGene&boolshad.hgSeq.promoter=0&hgSeq.promoterSize=1000&hgSeq.utrExon5=on&boolshad.hgSeq.utrExon5=0&hgSeq.cdsExon=on&boolshad.hgSeq.cdsExon=0&hgSeq.utrExon3=on&boolshad.hgSeq.utrExon3=0&hgSeq.intron=on&boolshad.hgSeq.intron=0&boolshad.hgSeq.downstream=0&hgSeq.downstreamSize=1000&hgSeq.granularity=gene&hgSeq.padding5=0&hgSeq.padding3=0&boolshad.hgSeq.splitCDSUTR=0&hgSeq.casing=exon&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&submit=submit>
mp;boolsh<http://genome.ucsc.edu/cgi-bin/hgc?hgsid=262656015&g=htcDnaNearGene&i=uc002lit.1&c=chr18&l=60790578&r=60986613&o=knownGene&boolshad.hgSeq.promoter=0&hgSeq.promoterSize=1000&hgSeq.utrExon5=on&boolshad.hgSeq.utrExon5=0&hgSeq.cdsExon=on&boolshad.hgSeq.cdsExon=0&hgSeq.utrExon3=on&boolshad.hgSeq.utrExon3=0&hgSeq.intron=on&boolshad.hgSeq.intron=0&boolshad.hgSeq.downstream=0&hgSeq.downstreamSize=1000&hgSeq.granularity=gene&hgSeq.padding5=0&hgSeq.padding3=0&boolshad.hgSeq.splitCDSUTR=0&hgSeq.casing=exon&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&submit=submit>
ad.hgSeq.cdsExon=0&hgSeq.utrExon3=on&boolshad.hgSeq.utrExon3=0&hgSeq.intron=on&boolshad.hgSeq.intron=0&boolshad.hgSeq.downstream=0&hgSeq.downstreamSize=1000&hgSeq.granularity=gene&hgSeq.padding5=0&hgSeq.padding3=0&boolshad.hgSeq.splitCDSUTR=0&hgSeq.casing=exon&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&submit=submit<http://genome.ucsc.edu/cgi-bin/hgc?hgsid=262656015&g=htcDnaNearGene&i=uc002lit.1&c=chr18&l=60790578&r=60986613&o=knownGene&boolshad.hgSeq.promoter=0&hgSeq.promoterSize=1000&hgSeq.utrExon5=on&boolshad.hgSeq.utrExon5=0&hgSeq.cdsExon=on&boolshad.hgSeq.cdsExon=0&hgSeq.utrExon3=on&boolshad.hgSeq.utrExon3=0&hgSeq.intron=on&boolshad.hgSeq.intron=0&boolshad.hgSeq.downstream=0&hgSeq.downstreamSize=1000&hgSeq.granularity=gene&hgSeq.padding5=0&hgSeq.padding3=0&boolshad.hgSeq.splitCDSUTR=0&hgSeq.casing=exon&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&submit=submit>
And
· For chr18:60790579-60986613 the start sequence obtained was
TTTCTGTGAAGCAGAAGTCTGGGAATCGATCTGGAAATCCTCCTAATTTT
TACTCCCTCTCCCCGCGACTCCTGATTCATTGGGAAGTTTCAAATCAGCT
http://genome.ucsc.edu/cgi-bin/hgc?hgsid=262656015&g=htcDnaNearGene&i=uc002liu.1&c=chr18&l=60790578&r=60986657&o=knownGene&boolshad.hgSeq.promoter=0&hgSeq.promoterSize=1000&hgSeq.utrExon5=on&boolshad.hgSeq.utrExon5=0&hgSeq.cdsExon=on&a<http://genome.ucsc.edu/cgi-bin/hgc?hgsid=262656015&g=htcDnaNearGene&i=uc002liu.1&c=chr18&l=60790578&r=60986657&o=knownGene&boolshad.hgSeq.promoter=0&hgSeq.promoterSize=1000&hgSeq.utrExon5=on&boolshad.hgSeq.utrExon5=0&hgSeq.cdsExon=on&boolshad.hgSeq.cdsExon=0&hgSeq.utrExon3=on&boolshad.hgSeq.utrExon3=0&hgSeq.intron=on&boolshad.hgSeq.intron=0&boolshad.hgSeq.downstream=0&hgSeq.downstreamSize=1000&hgSeq.granularity=gene&hgSeq.padding5=0&hgSeq.padding3=0&boolshad.hgSeq.splitCDSUTR=0&hgSeq.casing=exon&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&submit=submit>
mp;boolsh<http://genome.ucsc.edu/cgi-bin/hgc?hgsid=262656015&g=htcDnaNearGene&i=uc002liu.1&c=chr18&l=60790578&r=60986657&o=knownGene&boolshad.hgSeq.promoter=0&hgSeq.promoterSize=1000&hgSeq.utrExon5=on&boolshad.hgSeq.utrExon5=0&hgSeq.cdsExon=on&boolshad.hgSeq.cdsExon=0&hgSeq.utrExon3=on&boolshad.hgSeq.utrExon3=0&hgSeq.intron=on&boolshad.hgSeq.intron=0&boolshad.hgSeq.downstream=0&hgSeq.downstreamSize=1000&hgSeq.granularity=gene&hgSeq.padding5=0&hgSeq.padding3=0&boolshad.hgSeq.splitCDSUTR=0&hgSeq.casing=exon&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&submit=submit>
ad.hgSeq.cdsExon=0&hgSeq.utrExon3=on&boolshad.hgSeq.utrExon3=0&hgSeq.intron=on&boolshad.hgSeq.intron=0&boolshad.hgSeq.downstream=0&hgSeq.downstreamSize=1000&hgSeq.granularity=gene&hgSeq.padding5=0&hgSeq.padding3=0&boolshad.hgSeq.splitCDSUTR=0&hgSeq.casing=exon&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&submit=submit<http://genome.ucsc.edu/cgi-bin/hgc?hgsid=262656015&g=htcDnaNearGene&i=uc002liu.1&c=chr18&l=60790578&r=60986657&o=knownGene&boolshad.hgSeq.promoter=0&hgSeq.promoterSize=1000&hgSeq.utrExon5=on&boolshad.hgSeq.utrExon5=0&hgSeq.cdsExon=on&boolshad.hgSeq.cdsExon=0&hgSeq.utrExon3=on&boolshad.hgSeq.utrExon3=0&hgSeq.intron=on&boolshad.hgSeq.intron=0&boolshad.hgSeq.downstream=0&hgSeq.downstreamSize=1000&hgSeq.granularity=gene&hgSeq.padding5=0&hgSeq.padding3=0&boolshad.hgSeq.splitCDSUTR=0&hgSeq.casing=exon&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&submit=submit>
Can you please explain the reason for the same? Is it an error or I am I
interpreting in other ways? Kindly let me know about this.
Thanks and Regards,
Ateeq M Khaliq
Bioinformatics Division,
Jubilant Biosys Pvt Ltd,
#96, Industrial Suburb, 2nd Stage
Yeshwantpur, Bangalore 560 022
Ph No : +91-80-66628798
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transmission or the information contained in it is strictly prohibited. Please
note that any views or opinions presented in this email are solely those of the
author and may not represent those of the Company or bind the Company. Any
commitments made over e-mail are not financially binding on the company unless
accompanied or followed by a valid purchase order. This message has been
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transmitted by this email.
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