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H-Invitational ID: HIT000193129 Accession number: L34084 Created date: 26-Mar-2013 Last modified: 26-Mar-2013
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 ENST00000343139ENST00000374949ENST00000395363ENST00000395364ENST00000422863ENST00000460633ENST00000482745ENST00000486548ENST00000495840ENST00000496318
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 Q30065Q30066
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 8929711ALL
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 7
Interaction partner(s) HIP000034894HIP000053465HIP000058916HIP000063225HIP000070464HIP000104285HIP000104882
BIND 157823; 
DIP NA
MINT NA
HPRD 00102;  00825;  02557;  04927;  05054;  05125;  17975; 
IntAct NA
Database links RefSeq NM_002122
Ensembl ENST00000343139ENST00000374949ENST00000395363ENST00000395364ENST00000422863ENST00000460633ENST00000482745ENST00000486548ENST00000495840ENST00000496318
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:26-Mar-2013
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:26-Mar-2013
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:  122550143400604519608545610294611724612558
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 ViewerLEGENDALEGENDA

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