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H-InvDB_8.3 released on March 26, 2013.
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H-Invitational ID: HIT000193129 Accession number: L34084 Created date: 26-Mar-2013 Last modified: 20-Apr-2012
Definition: MHC class II HLA-DQ-alpha chain; Fragment;
 
 

Transcript original information
Accession number L34084.1
CAGE tag ID NA
EST ID NA
Clone Number NA
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (HLA-DQA1) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (HLA-DQA1);
Sequence data provider NA
Annotation project NA
Length of cDNA 681[bp] (No. of exon:3)[A:148 T:179 G:177 C:177]
Devision HUM
Molecular type mRNA
Library origin Cell type B lymphoblastoid
Tissue type NA
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature N/C-truncated
Kozak sequence NA
PolyA NA
Vector/adapter sequence NA
Frame shift NA
Remaining intron NA
Splice site acceptor (NAGNAG) NA
Transcript quality feature Truncation; 
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0027959
Genomic location  G-integra Help Chromosome 6
Location 6p21.32
Position 32609086- 32610523
Strand +
Possible duplicated location(s) NA
Gene structure 3 exon(s)
Database links RefSeq NM_002122; 
Ensembl ENST00000343139;  ENST00000374949;  ENST00000395363;  ENST00000395364;  ENST00000422863;  ENST00000460633;  ENST00000482745;  ENST00000486548;  ENST00000495840;  ENST00000496318; 
Entrez Gene Entrez Gene ID:3117; 
KEGG GENES KEGG GENES(3117); 
GeneCard GeneCardHLA-DQA1;  *GeneCards is provided free to academic non-profit institutions.
Related H-InvDB links H-DBASH-DBAS;  G-integraG-integra;  cDNA-genome alignmentcDNA-genome alignment; 

Predicted CDS information
HIP ID HIP000005957
Predicted CDS 1..681;  227[aa];  Orientation:+1; 
Codon Adaptation Index (CAI). 0.83
Database links RefSeq NA
UniProt Q30065;  Q30066; 
CCDS NA

Motif information
ORF

length(227),orf(1:681) EDIVADHVASCGVNLYQFYGPSGQYTHEFDGDEQFYVDLERKETAWRWPE FSKFGGFDPQGALRNMAVAKHNLNIMIKRYNSTAATNEVPEVTVFSKSPV TLGQPNTLICLVDNIFPPVVNITWLSNGQSVTEGVSETSFLSKSDHSFFK ISYLTFLPSADEIYDCKVEHWGLDQPLLKHWEPEIPAPMSELTETVVCAL GLSVGLMGIVVGTVFIIQGLRSVGASR 		a.a.
length		 InterPro Name
length(84), motif(4:87) 84 IPR011162 MHC classes I/II-like antigen recognition protein [Domain]
length(78), motif(6:83) 78 IPR014745 MHC class II, alpha/beta chain, N-terminal [Domain]
length(82), motif(6:87) 82 IPR001003 MHC class II, alpha chain, N-terminal [Domain]
length(81), motif(7:87) 81 IPR001003 MHC class II, alpha chain, N-terminal [Domain]
length(117), motif(84:200) 117 IPR013783 Immunoglobulin-like fold [Domain]
length(81), motif(90:170) 81 IPR007110 Immunoglobulin-like [Domain]
length(81), motif(97:177) 81 IPR003597 Immunoglobulin C1-set [Domain]
length(72), motif(105:176) 72 IPR003597 Immunoglobulin C1-set [Domain]
length(7), motif(164:170) 7 IPR003006 Immunoglobulin/major histocompatibility complex, conserved site [Conserved_site]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000193129
H-Inv cluster ID Locus viewHIX0027959
Accession number L34084.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO; 
Coding potential  Help Protein coding; 
Definition MHC class II HLA-DQ-alpha chain; Fragment;
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (Q30066)  [Identity/coverage = 100.0%/100.0%] to Homo sapiens (Human). protein.
Experimental evidence Protein evidence
PubMed ID 8929711;  ALL; 
Gene family/group Gene family H-Inv gene family/group ID HIF0000002
Gene family/group name Major histocompatibility complex (MHC).
Evidence motif (InterPro) ID NA
Gene symbol/name HGNC symbol HLA-DQA1
HGNC aliases NA
HGNC name major histocompatibility complex, class II, DQ alpha 1
DDBJ HLA-DQA1
UniProt HLA-DQA1
EC number NA
GGDB
(GlycoGene Database)
 Gene symbol NA
Familly NA
Designation NA
Expression NA
KEGG metabolic pathway NA
Protein-protein interaction (PPI) PPI viewer H-Inv protein ID HIP000005957
No. of interaction 15
Interaction partner(s) HIP000014859;  HIP000021531;  HIP000024661;  HIP000024900;  HIP000026110;  HIP000026993;  HIP000031224;  HIP000031586;  HIP000033044;  HIP000037880;  HIP000042120;  HIP000059885;  HIP000079212;  HIP000094011;  HIP000101663; 
BIND 119538;  173257; 
DIP 66678E;  9950E; 
MINT MINT-1894801;  MINT-1894829; 
HPRD 00082;  00549;  02198;  02552;  03011;  04472;  05699;  09869;  10373;  11641;  16325; 
IntAct EBI-1538670;  EBI-1538625;  EBI-1034394; 
Database links RefSeq NM_002122; 
Ensembl ENST00000343139;  ENST00000374949;  ENST00000395363;  ENST00000395364;  ENST00000422863;  ENST00000460633;  ENST00000482745;  ENST00000486548;  ENST00000495840;  ENST00000496318; 
Entrez Gene Entrez Gene ID:3117; 
KEGG GENES KEGG GENES(3117); 
GeneCard GeneCardHLA-DQA1;  *GeneCards is provided free to academic non-profit institutions.
etc H-GOLDHuman-Gene diversity Of Life-style related Diseases; 
Curation status Auto-annotated
Notes NA
Related H-InvDB links Gene family;  Similarity Search ToolSimilarity Search Tool;  TACTTACT; 
fRNAdb (The functional RNA database) : overlapping fRNAdb entries with H-InvDB transcripts based on the location of the genome. 
NA

Gene ontology information
Biological process antigen processing and presentation (GO:0019882);  immune response (GO:0006955); 
Cellular component membrane (GO:0016020);  MHC class II protein complex (GO:0042613); 

Subcellular localization information  Last modified:20-Apr-2012
WoLF PSORT cytosol;  mitochondria;  peroxisome;  plasma membrane;  Other; 
Target P Other
SOSUI membrane protein
TMHMM membrane protein
PTS1 Twilight zone
Related H-InvDB links LIFEdb LIFEdb; 
JRE-1.4.0 or later is required. Download JRE at Sun's web site.

Disease/pathology information  DiseaseInfo Viewer LEGENDA Last modified:20-Apr-2012
Disease relation Disease name: {Celiac disease, susceptibility to} (212750); 
Related information in OMIM OMIM ID:  146880;  Title: MAJOR HISTOCOMPATIBILITY COMPLEX, CLASS II, DQ ALPHA-1
Co-localized orphan diseases OMIM ID:  122550;  143400;  604519;  608545;  610294;  611724;  612558; 
Disease related mutation MutationView:  146880; 
JRE-1.4.0 or later is required.Download JRE at Sun's web site.
Literature-Extracted GENe-Disease Associations (LEGENDA) LEGENDA Gene name Entrez Gene ID:(3117)
Disease Entrez Gene ID:(3117)
Substance Entrez Gene ID:(3117)
Related H-InvDB links DiseaseInfo ViewerDiseaseInfo Viewer;  LEGENDALEGENDA; 

Polymorphism (SNP, indel), microsatellite (Short Tandem Repeat, STR) and repeat information  VaryGene Repeat mask viewer
 Single Nucleotide Polymorphism (SNP) and indel  VaryGene
Location Variation dbSNP ID Strand CDS/UTR Translation
21 .. 21 C/T rs12722043 + CDS Synonymous[His7His]
21 .. 21 C/T rs1129737 + CDS Synonymous[His7His]
24 .. 24 T/C rs9272688 + CDS Synonymous[Val8Val]
24 .. 24 T/C rs79808132 + CDS Synonymous[Val8Val]
24 .. 24 T/C rs1129738 + CDS Synonymous[Val8Val]
32 .. 32 G/A rs1129740 + CDS Nonsynonymous[Cys11Tyr]
32 .. 32 G/A rs76832557 + CDS Nonsynonymous[Cys11Tyr]
32 .. 32 G/A rs78025123 + CDS Nonsynonymous[Cys11Tyr]
33 .. 33 T/C rs3205916 + CDS Synonymous[Cys11Cys]
39 .. 39 A/G rs1129742 + CDS Synonymous[Val13Val]
45 .. 45 G/C rs1129744 + CDS Nonsynonymous[Leu15Phe]
53 .. 53 T/C rs1071630 + CDS Nonsynonymous[Phe18Ser]
53 .. 53 T/C rs80027061 + CDS Nonsynonymous[Phe18Ser]
57 .. 57 C/T rs1129753 + CDS Synonymous[Tyr19Tyr]
62 .. 62 C/T rs41549715 + CDS Nonsynonymous[Pro21Leu]
69 .. 69 C/G rs12722050 + CDS Synonymous[Gly23Gly]
69 .. 69 C/G rs1129759 + CDS Synonymous[Gly23Gly]
74 .. 74 A/T rs12722051 + CDS Nonsynonymous[Tyr25Phe]
74 .. 74 A/T rs77275271 + CDS Nonsynonymous[Tyr25Phe]
77 .. 77 C/G rs3188011 + CDS Nonsynonymous[Thr26Ser]
77 .. 77 C/G rs1048023 + CDS Nonsynonymous[Thr26Ser]
92 .. 92 G/A rs112029808 - CDS Nonsynonymous[Gly31Glu]
96 .. 96 T/C rs1048027 + CDS Synonymous[Asp32Asp]
100 .. 100 C/G rs10093 + CDS Nonsynonymous[Gln34Glu]
108 .. 108 C/A/G/T rs1129765 + CDS
119 .. 119 A/G rs1142323 + CDS Nonsynonymous[Glu40Gly]
122 .. 122 G/A rs36219699 - CDS Nonsynonymous[Arg41Lys]
130 .. 130 A/G rs41543221 + CDS Nonsynonymous[Thr44Ala]
134 .. 134 C/T rs1142324 + CDS Nonsynonymous[Ala45Val]
139 .. 139 C/A/T rs1142326 + CDS
140 .. 140 G/A rs3207983 + CDS Nonsynonymous[Arg47Gln]
141 .. 141 G/T rs3207984 + CDS Synonymous[Arg47Arg]
143 .. 143 G/T rs1142328 + CDS Nonsynonymous[Trp48Leu]
148 .. 148 G/C rs12722061 + CDS Nonsynonymous[Glu50Gln]
149 .. 149 A/T rs3208105 + CDS Nonsynonymous[Glu50Val]
150 .. 150 G/T rs9272697 + CDS Nonsynonymous[Glu50Asp]
151 .. 151 T/C rs9272698 + CDS Nonsynonymous[Phe51Leu]
155 .. 155 G/A rs28383449 + CDS Nonsynonymous[Ser52Asn]
156 .. 156 C/A rs9272699 + CDS Nonsynonymous[Ser52Arg]
157 .. 157 A/C/G/T rs1048052 + CDS
158 .. 158 A/G rs12722069 + CDS Nonsynonymous[Lys53Arg]
160 .. 160 T/C rs3188043 + CDS Nonsynonymous[Phe54Leu]
163 .. 163 G/-/A/AGA rs4193 + CDS
166 .. 166 G/-/A rs12722072 + CDS
167 .. 167 G/- rs41556812 + CDS
168 .. 168 T/-/A rs12722074 + CDS
176 .. 176 C/G rs41541412 + CDS Nonsynonymous[Pro59Arg]
180 .. 180 G/A rs9272702 + CDS Synonymous[Gln60Gln]
181 .. 181 G/T rs1142331 + CDS Nonsynonymous[Gly61Cys]
182 .. 182 G/T rs1142332 + CDS Nonsynonymous[Gly61Val]
191 .. 191 G/C rs1142333 + CDS Nonsynonymous[Arg64Thr]
198 .. 198 G/C rs1142334 + CDS Nonsynonymous[Met66Ile]
201 .. 201 T/C/G rs1048491 + CDS
204 .. 204 G/C rs3188501 + CDS Synonymous[Val68Val]
205 .. 205 G/A/C rs1142335 + CDS
206 .. 206 C/T rs9272709 + CDS Nonsynonymous[Ala69Val]
213 .. 213 C/T rs1048087 + CDS Synonymous[His71His]
223 ^ 224 -/G rs9282026 + CDS
224 .. 224 T/-/A/G rs9279910 + CDS
225 .. 225 C/T rs36219014 - CDS Synonymous[Ile75Ile]
226 .. 226 A/C/G rs1064944 + CDS
235 .. 235 C/T rs41542116 + CDS Nonsynonymous[Arg79Cys]
239 .. 239 A/C rs1129808 + CDS Nonsynonymous[Tyr80Ser]
249 .. 249 C/T rs1142338 + CDS Synonymous[Thr83Thr]
293 .. 293 C/T rs1048122 + CDS Nonsynonymous[Ser98Phe]
297 .. 297 C/T rs1048124 + CDS Synonymous[Pro99Pro]
303 .. 303 A/G rs1048134 + CDS Synonymous[Thr101Thr]
304 .. 304 C/G rs41555012 + CDS Nonsynonymous[Leu102Val]
320 .. 320 C/T rs707952 + CDS Nonsynonymous[Thr107Ile]
320 .. 320 C/T rs75269270 - CDS Nonsynonymous[Thr107Ile]
327 .. 327 C/T rs707951 + CDS Synonymous[Ile109Ile]
327 .. 327 C/T rs75904915 + CDS Synonymous[Ile109Ile]
369 .. 369 A/C rs1048173 + CDS Synonymous[Thr123Thr]
387 .. 387 G/C rs707950 + CDS Nonsynonymous[Gln129His]
387 .. 387 G/C rs74438353 + CDS Nonsynonymous[Gln129His]
387 .. 387 G/C rs113584233 + CDS Nonsynonymous[Gln129His]
387 .. 387 G/C rs75794836 + CDS Nonsynonymous[Gln129His]
388 .. 388 T/G rs41547417 + CDS Nonsynonymous[Ser130Ala]
388 .. 388 T/G rs74646061 + CDS Nonsynonymous[Ser130Ala]
388 .. 388 T/G rs34078100 - CDS Nonsynonymous[Ser130Ala]
413 .. 413 C/T rs41545514 + CDS Nonsynonymous[Thr138Ile]
415 .. 415 A/C rs41552014 + CDS Nonsynonymous[Ser139Arg]
416 .. 416 G/T rs41544114 + CDS Nonsynonymous[Ser139Ile]
457 .. 457 T/C rs41550317 + CDS Nonsynonymous[Tyr153His]
466 .. 466 T/C rs707949 + CDS Nonsynonymous[Phe156Leu]
466 .. 466 T/C rs34847266 - CDS Nonsynonymous[Phe156Leu]
478 .. 478 G/T rs41561312 + CDS Nonsynonymous[Ala160Ser]
479 .. 479 C/A rs7990 + CDS Nonsynonymous[Ala160Asp]
479 .. 479 C/A rs79809169 + CDS Nonsynonymous[Ala160Asp]
483 .. 483 T/G rs707963 + CDS Nonsynonymous[Asp161Glu]
483 .. 483 T/G rs35999171 - CDS Nonsynonymous[Asp161Glu]
488 .. 488 T/G rs707962 + CDS Nonsynonymous[Ile163Ser]
488 .. 488 T/G rs34517295 - CDS Nonsynonymous[Ile163Ser]
516 .. 516 C/A rs2308889 + CDS Synonymous[Gly172Gly]
522 .. 522 C/T rs2308890 + CDS Synonymous[Asp174Asp]
522 .. 522 C/T rs17415959 + CDS Synonymous[Asp174Asp]
523 .. 523 C/A/G rs2308891 + CDS
523 .. 523 C/A/G rs1129957 + CDS
523 .. 523 C/A rs75833253 + CDS Nonsynonymous[Gln175Lys]
559 .. 559 G/A rs9272785 + CDS Nonsynonymous[Ala187Thr]
561 .. 561 C/A rs80031910 + CDS Synonymous[Ala187Ala]
561 .. 561 C/A rs3188543 + CDS Synonymous[Ala187Ala]
586 .. 586 G/T rs1048363 + CDS Nonsynonymous[Val196Leu]
594 .. 594 T/C rs1048372 + CDS Synonymous[Cys198Cys]
594 .. 594 T/C rs75214833 + CDS Synonymous[Cys198Cys]
594 .. 594 T/C rs79795281 + CDS Synonymous[Cys198Cys]
595 .. 595 G/A rs35087390 - CDS Nonsynonymous[Ala199Thr]
603 .. 603 G/A rs1048381 + CDS Synonymous[Gly201Gly]
619 .. 619 A/G rs9260 + CDS Nonsynonymous[Met207Val]
619 .. 619 A/G rs79227448 + CDS Nonsynonymous[Met207Val]
619 .. 619 A/G rs80176586 + CDS Nonsynonymous[Met207Val]
619 .. 619 A/G rs35029979 - CDS Nonsynonymous[Met207Val]
622 .. 622 G/T rs41545416 + CDS Nonsynonymous[Gly208Cys]
636 .. 636 C/G rs1048414 + CDS Synonymous[Gly212Gly]
639 .. 639 T/C rs1048419 + CDS Synonymous[Thr213Thr]
645 .. 645 C/G rs1048430 + CDS Nonsynonymous[Phe215Leu]
645 .. 645 C/G rs34494013 - CDS Nonsynonymous[Phe215Leu]
653 .. 653 A/G rs9272793 + CDS Nonsynonymous[Gln218Arg]
653 .. 653 A/G rs77143934 + CDS Nonsynonymous[Gln218Arg]
 Microsatellite (Short Tandem Repeat, STR)
No data available
 Microsatellite: Human-Gene diversity Of Life-style related Diseases (H-GOLD)
No data available
 Repeat  Repeat mask viewer
No data available
Database links H-GOLDHuman-Gene diversity Of Life-style related Diseases(H-GOLD); 
Related H-InvDB links VaryGeneVaryGene;  Repeat mask viewerRepeat Mask Viewer;