Article Figures & Data
Figures
- Fig. 2.
Polymorphisms in the sequence. Fig.2 Polymorphisms in the coding sequence from Fig.1 and Table 2. This region shows a Block aligned in the coding sequence. Two missense changes (number 1 and 5 in Table 2) in red and the other missense changes in black. Two missense changes (number 1 and 5) are colored red because the PSSM difference s∞re ¡s>10. The residues of the reference protein are colored to indicate how each position compares to the aligned Block. Those residues ∞lored green are most similar to the correspong¡ng column in the Block, while those colored red are most diverged.
- Fig. 1.
Overview of polymorphisms and Blocks in the HLA-DQA1 gene, (a) Genomic Sequence (b) Coding Sequence. Overview of polymorphisms and blocks in the HLA-DQA1 gene. The sequence and variants ∞me from GenBank NC_000006.9 and the homology model deπves from the Block IPB001003 families. In the ‘Genomic Sequence’ plot, the top region of the graphics shows the locations of the Blocks on the reference sequence. The green graphics correspond to blocks IPB001003A, IPB001003B and IPB001003C. The middle shows the locations of the exons, represented by boxes. The bottom region displays the locations of the polymorphisms, the first row displays missense changes in black and the se∞nd row shows silent changes in purple.
Tables
#SNP rs# SNP position Band Distance from previous SNP Alleles Gene(s) Role rs9272430 chr6:32713235 6p21.32 A/C HLA-DQAI Coding exon rs9469203 chr6:32713244 6p21.32 9 A/G HLA-DQAI Coding exon rs927243l chr6:327l3249 6p21.32 5 C/T HLA-DQAI Coding exon rs9272433 chr6:327l3273 6p21.32 24 C/T HLA-DQAI Coding exon rs9272688 chr6:3277075 6p21.32 3802 C/T HLA-DQA1 Coding exon rs9272689 chr6:327l7083 6p21.32 8 A/G HLA-DQA1 Coding exon rsl07l630 chr6:327l7l04 6p21.32 21 C/T HLA-DQA1 Coding exon rs6: 129753 chr6:327l7l08 6p21.32 4 C/T HLA-DQA1 Coding exon rs 1048027 chr6:327l7147 6p21.32 39 C/T HLA-DQA1 Coding exon rs927269l chr6:327l7l70 6p21.32 23 A/G HLA-DQA1 Coding exon rs9272692 chr6:327l7l85 6p21.32 15 C/T HLA-DQA1 Coding exon rs9272693 chr6:327l7l90 6p21.32 5 C/T HLA-DQA1 Coding exon rs 2722058 Chr6:327l7l9l 6p21.32 1 A/G HLA-DQA1 Coding exon rs9272694 chr6:327l7192 6p21.32 1 G/T HLA-DQA1 Coding exon rs9272695 Chr6:327l7l94 6p21.32 2 G/T HLA-DQA1 Coding exon rs9272696 chr6:327l7200 6p21.32 6 A/T HLA-DQA1 Coding exon rsl2722065 chr6:32717205 6p21.32 5 A/C/G HLA-DQA1 Coding exon rs9272699 chr6:327l7207 6p21.32 2 A/C HLA-DQA1 Coding exon rs048052 chr6:327l7209 6p21.32 2 A/C/G/T HLA-DQA1 Coding exon rsl2722070 chr6:327l72l1 6p21.32 2 C/T HLA-DQA1 Coding exon rsl2722076 chr6:327l7235 6p21.32 24 A/G/T HLA-DQA1 Coding exon rs9272706 chr6:327l7249 6p21.32 14 C/G HLA-DQA1 Coding exon rs 1048491 chr6:327l7256 6p21.32 7 C/G/T HLA-DQA1 Coding exon rs 2722081 chr6:32717259 6p21.32 3 A/C/G HLA-DQA1 Coding exon rs048087 chr6:32717264 6p21.32 5 C/T HLA-DQA1 Coding exon rs1048124 chr6:327l776l 6p21.32 497 C/T HLA-DQA1 Coding exon rs048134 chr6:32717767 6p21.32 6 A/G HLA-DQA1 Coding exon rs707952 chr6:327l7784 6p21.32 17 C/T HLA-DQA1 Coding exon rs9272745 chr6:327l7784 6p21.32 0 C/T HLA-DQAI Coding exon rs70795l Chr6:327l779l 6p21.32 7 C/T HLA-DQA1 Coding exon rs9272746 chr6:327l779l 6p21.32 0 C/T HLA-DQA1 Coding exon rs1048173 chr6:327l7833 6p21.32 42 A/C HLA-DQA1 Coding exon rs707950 chr6:327l785l 6p21.32 18 C/G HLA-DQA1 Coding exon rs2308883 chr6:32717852 6p21.32 1 G/T HLA-DQA1 Coding exon rs707949 chr6:327l7930 6p21.32 78 C/T HLA-DQA1 Coding exon rs2308885 chr6:32717942 6p21.32 12 G/T HLA-DQA1 Coding exon rs7990 chr6:32717943 6p21.32 1 A/C HLA-DQA1 Coding exon rs707963 chr6:327l7947 6p21.32 4 G/T HLA-DQA1 Coding exon rs707962 chr6:327l7952 6p21.32 5 G/T HLA-DQA1 Coding exon rs2308889 chr6:327l7980 6p21.32 28 A/C HLA-DQA1 Coding exon rs2308890 chr6:327l7986 6p21.32 6 C/T HLA-DQA1 Coding exon rs2308891 chr6:32717987 6p21.32 1 A/C/G HLA-DQA1 Coding exon rs9272785 chr6:32718379 6p21.32 392 A/G HLA-DQA1 Coding exon rs9272786 chr6:32718381 6p21.32 2 A/C HLA-DQA1 Coding exon rs9272787 chr6:327l84l4 6p21.32 33 C/T HLA-DQA1 Coding exon rsl04838l chr6:32718423 6p21.32 9. A/G HLA-DQA1 Coding exon rsl0484l4 chr6:32718456 6p21.32 33 C/G HLA-DQA1 Coding exon rs1048419 chr6:32718459 6p21.32 3 C/T HLA-DQA1 Coding exon rsl048430 chr6:327l8465 6p21.32 6 C/G HLA-DQAI Coding exon rs9272793 chr6:327l8473 6p21.32 8 A/G HLA-DQA1 Coding exon Variant No. Nucleotide Change Effect RE Gained in Variant RE Lost from Reference PSSM Difference SIFT Score Description Zygosity 1 C3977T R70W Acil 20 0.01 rs9272693 Homo 2 A3987T E73V BseMII, Ddel 8.1 0.2 rs9272696 Homo 3 G3988T E73D BseMII, Ddel 2.5 0.51 rs9272697 Homo 4 A3995C K76Q CviJI Apol -0.1 0.36 rs9272700 Homo 5 G4019T G84C BtsI,TspRI 15.1 0.12 rs9272703 Homo 6 G4020T G84V BspMI ApaLI, BseSI, HgiAI, MjaΓV, Sdul 9.3 0.4 rs9272704 Homo 7 C4044T A92V rs9272709 Homo 8 C4051T H94= rsl0480087 Homo 9 A4053C N95T rs1048089 Homo 10 A4058G N97D rsl048090 Homo 11 A4077C Y103S Mtnel 0 0.99 rs92727ll Homo 12 C4571T T130I FokI 5.7 0.28 rs9272745 Homo 13 A5226G M230V Bsil Nlal¤ rs9272789 Homo 14 A5300C P254= Apal, BseSI, Drall, HgiJII, NlalV, Sdul rs9272794 Homo Table of polymorphisms for the HLA-DQA1 gene shown in Table 2. The restriction enzyme names link to the entries in REBASE, describing commercial availability and ¡soschizomers. Descriptions are extracted from the dbSNP database. The last column shows the zygosity of the change, if a variant had been entered using an ambiguous nucleotide, this ∞lumn would read ‘hetero’.
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