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]. 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&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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