chi-like sequence 5'-GCTGGTGG-3' at intron 2 of CYP21 genes

CYP21A2_Intron2_282nt
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。

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

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.

Paper at a galance

http://eurheartj.oxfordjournals.org/content/31/24/3017.full.pdf+html

Sequence Analysis of CYP21A1P in Germany

http://www.clinchem.org/cgi/reprint/clinchem.2010.156893v1

Finding CYP21A1P gene sequence

1. go to UCSC and type CYP21A1P

http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr6:31973413-31976228&hgsid=176822215&wgEncodeGencode=pack&hgFind.matches=CYP21A1P,

2. click either (pink or yellow), you can see the next page containing link to Enseml,

http://www.ensembl.org/Homo_sapiens/Gene/Sequence?db=core;g=ENSG00000204338;r=6:31973413-31976228;t=ENST00000354927

At Enseml, you can see the defined and validated genomic sequence of the gene. No matter you click which transcript, the genomic sequence will be the same. Here we go! I can add this reference information to the manuscript.

Things to Do

Explore the HapMap Browser...

http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/hapmap28_B36/