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. 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 scanned for viruses and dangerous content by Mail Scanner, and is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. www.jubl.com _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
