Hi Ateeq, The reason why you are seeing different sequences for those splice variants is because you are looking that 5' end which is what differs between the two splice variants. These two splice variants are transcribed from the "-" strand. If you take a look at the 3' end you will see that that the sequences are the same. The other examples you gave are transcribed from the "+" strand.
I hope that clarifies things for you. If you have further questions, please email the list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Ateeq Muhammed Khaliq <[email protected]> Date: Tue, May 8, 2012 at 3:42 AM Subject: Re: [Genome] discrepancy in gene co-ordinates To: "[email protected]" <[email protected]>, "[email protected]" <[email protected]>, Pauline Fujita <[email protected]> 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: Ateeq Muhammed Khaliq Sent: 08 May 2012 PM 04:12 To: '[email protected]'; '[email protected]' Subject: RE: discrepancy in gene co-ordinates 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&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&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 The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. 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