Wednesday, January 12, 2011
Tuesday, December 28, 2010
chi-like sequence 5'-GCTGGTGG-3' at intron 2 of CYP21 genes
CYP21A2_Intron2_282nt
0 mismatch: no
1 mismatch: 1
CYP21A1P_Intron2_288nt
0 mismatch: no
1 mismatch: no
2 mismatch: 4
aLSO, THERE IS ONE SITE A LITTLE (22BP) UPSTREAM OF P30L MUTATION AT EXON 1 OF both 21A2 and 21a1p.
TGGAACTGGTGGAAGC
Chi-like sequence was summarized basing on an old version (1986) reference sequence of CYP21.
http://www.nature.com/jhg/journal/v49/n2/pdf/jhg200411a.pdf
0 mismatch: no
1 mismatch: 1
Catatctggtggggag
2 mismatch: 3
Aagggccgggggcatt
Ccaggctggtcttaaa
Ggaagctcttgggggg
CYP21A1P_Intron2_288nt
0 mismatch: no
1 mismatch: no
2 mismatch: 4
Aagggccgggggcatt
Ccaggctggtcttgaa
Ggaagctcttgggggg
agaagcaggtgttgag
aLSO, THERE IS ONE SITE A LITTLE (22BP) UPSTREAM OF P30L MUTATION AT EXON 1 OF both 21A2 and 21a1p.
TGGAACTGGTGGAAGC
Chi-like sequence was summarized basing on an old version (1986) reference sequence of CYP21.
http://www.nature.com/jhg/journal/v49/n2/pdf/jhg200411a.pdf
关于 CYP21A2 的序列
http://genome.ucsc.edu/cgi-bin/hgc?hgsid=180461787&g=htcDnaNearGene&i=NM_000500&c=chr6_qbl_hap2&l=3221082&r=3224420&o=refGene&hgSeq.promoter=on&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
http://genome.ucsc.edu/cgi-bin/hgc?hgsid=180461787&o=3221082&t=3224420&g=refGene&i=NM_000500
http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr6_qbl_hap2:3221083-3224420&hgsid=180461787&refGene=pack&hgFind.matches=NM_000500,
UCSC Genome Browser on Human Mar. 2006 (NCBI36/hg18) Assembly
注解： NCBI36的数据和Ensembl的数据ENSG00000206338完全吻合，但是和GRCh37的数据有较大差别，所以记住比对数据均来自NCBI36或者Ensembl ENSG00000206338 (1000 genomes)，intron 2的长度是282bp.
但是，1000genome 显示有6个不同的CYP21A2 protein链接，相对应有3个ENSG （ENSG00000206338, ENSG00000198457 and ENSG00000168482），SEQUENCHER显示它们之间有9个不匹配的位置，但是没有gap差异，也就是长度上没有不同。
http://genome.ucsc.edu/cgi-bin/hgc?hgsid=180461787&o=3221082&t=3224420&g=refGene&i=NM_000500
http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr6_qbl_hap2:3221083-3224420&hgsid=180461787&refGene=pack&hgFind.matches=NM_000500,
UCSC Genome Browser on Human Mar. 2006 (NCBI36/hg18) Assembly
注解： NCBI36的数据和Ensembl的数据ENSG00000206338完全吻合，但是和GRCh37的数据有较大差别，所以记住比对数据均来自NCBI36或者Ensembl ENSG00000206338 (1000 genomes)，intron 2的长度是282bp.
但是，1000genome 显示有6个不同的CYP21A2 protein链接，相对应有3个ENSG （ENSG00000206338, ENSG00000198457 and ENSG00000168482），SEQUENCHER显示它们之间有9个不匹配的位置，但是没有gap差异，也就是长度上没有不同。
Wednesday, December 22, 2010
CYP21 Papers
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B7RKV-51921F6-1&_user=1072900&_coverDate=10%2F21%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000048262&_version=1&_urlVersion=0&_userid=1072900&md5=cf82242b14b3c64de45dfc3d983aee6c&searchtype=a
http://www.nature.com/jhg/journal/v49/n2/pdf/jhg200411a.pdf
http://www.nature.com/jhg/journal/v49/n2/pdf/jhg200411a.pdf
Things to do: Uncommon Chimeric CYP21 Gene
1. 8.5kb digestion figure of #256/268.
done
2. Discuss chi-like sequence and make a figure.
figure is done.
Review German paper and H.H. Lee 2004 review paper: chi-like sequence in intron 2.
3. Change alignment method to be Vector NTI.
4. Add TA cloning-seq to method.
5. Endnote.
done
2. Discuss chi-like sequence and make a figure.
figure is done.
Review German paper and H.H. Lee 2004 review paper: chi-like sequence in intron 2.
3. Change alignment method to be Vector NTI.
4. Add TA cloning-seq to method.
5. Endnote.
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