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HLA-DQA2 Gene

protein-coding GIFtS: 50

GC06P032817

major histocompatibility complex, class II, DQ alpha 2
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: HLA-DXA)

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc , and/or ⁷Ensembl, ⁸miRBase)
About This Section

Aliases
HLA-DQA1 ^³
HLA-DXA ^², ³
OTTHUMP00000029144 ^²

Descriptions
DX alpha chain ^³
major histocompatibility complex, class II, DQ alpha 2 ^²

External Ids
HGNC: 4943¹
Entrez Gene: 3118²
UniProtKB: P01906³
Ensembl: ENSG00000204276⁷

Search outside databases for aliases for HLA-DQA2 gene

Previous GC identifers: GC06P032711 GC06P032479 GC06P032756

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Gene Wiki entry for HLA-DQA2

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:

UCSC Golden Path with GeneCards custom track

Transcription factor binding sites upstream to the HLA-DQA2 gene

Entrez Gene cytogenetic band: 6p21.3 Ensembl cytogenetic band: 6p21.32 HGNC cytogenetic band: 6p21.3

HLA-DQA2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 6 GeneLoc Exon Structure

GeneLoc location for GC06P032817: (about GC identifiers)

Start:	32,817,141 bp from pter
End:	32,823,199 bp from pter
Size:	6,059 bases
Orientation:	plus strand

2 alternative locations:

Chr6+,c6_COX 32,779,890-32,785,994

Chr6+,c6_QBL 32,780,702-32,786,784

RefSeq DNA sequence:

NC_000006.10 NT_007592.14 NT_113891.1 NT_113896.1

(According to ¹UniProtKB, and/or Ensembl, Phosphorylation sites according to ²Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: HA26_HUMAN, P01906 (See protein sequence)

Recommended Name: HLA class II histocompatibility antigen, DQ(6) alpha chain precursor

Size: 255 amino acids; 28033 Da

Subcellular location: Membrane; Single-pass type I membrane protein (Potential)

Secondary accessions: B0V0E7 O19789 Q5SQ94

REFSEQ proteins: NP_064440.1

ENSEMBL proteins:

ENSP00000364076

Human Recombinant Proteins

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	Recombinant Proteins from Abcam (HLA DQ)
	Browse Abnova for Human Recombinant Proteins

Browse Origene for full length recombinant human proteins expressed in human HEK293 cells

3 Gene Ontology (GO) cellular component terms (links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005886	plasma membrane	EXP	11048639 11827988 15489916 17652306
GO:0005887	integral to plasma membrane	NAS	3036828
GO:0042613	MHC class II protein complex	IEA	--

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Antibodies for HLA-DQA2:

	Browse Antibodies Central at Invitrogen
	Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
	Sigma-Aldrich Antibodies for HLA-DQA2
	Browse R&D Systems for Antibodies
	Antibodies from Abcam (HLA DQ), each with their Abpromise^SM
	Browse Abnova for Monoclonal and Polyclonal Antibodies
	Search Novus for antibodies for HLA-DQA2

Assays for HLA-DQA2:

	Browse Invitrogen for biochemical assays
	Browse Kits and Assays available from Millipore
	Browse R&D Systems for biochemical assays
	Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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Graphical View of Domain Structure for InterPro Entry P01906

ProtoNet protein and cluster: P01906

2 Blocks protein families:

IPB001003 MHC Class II alpha chain

IPB003597 Immunoglobulin C-type

UniProtKB/Swiss-Prot: HA26_HUMAN, P01906

Similarity: Belongs to the MHC class II family

Similarity: Contains 1 Ig-like C1-type (immunoglobulin-like) domain

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (HLA-DQA2)
		Browse for Gene Knock-down Tools from Millipore
		Abnova Chimera RNAi Products for Gene knock-down (HLA-DQA2)

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_020056

Applied Biosystems Silencer® siRNAs for HLA-DQA2

Sigma-Aldrich siRNA for HLA-DQA2

Sigma-Aldrich shRNA for HLA-DQA2

Explore Sigma-Aldrich super-pooled esiRNAs

Clones:		Browse Clone Ranger at Invitrogen for clones
		Browse Clones for the Expression of Recombinant Proteins Available from Millipore

OriGene GFP tagged cDNA clone in CMV expression vector: NM_020056
Myc/DDK tagged cDNA clone in CMV expression vector: NM_020056
untagged cDNA clone in CMV expression vector: NM_020056

Primers:

Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers

OriGene genome-wide validated SYBR primer pairs: NM_020056

Genatlas biochemistry entry for HLA-DQA2:

HLA-DQ,alpha chain-related,not known to be expressed

1 Gene Ontology (GO) molecular function term (links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0032395	MHC class II receptor activity	NAS	3036828

About this table

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to ¹UniProtKB, ²MINT, and/or ³STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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1 Sigma-Aldrich "Your Favorite Gene" Pathway for HLA-DQA2 (Your Favorite Gene powered by Ingenuity)

Antigen Presentation Pathway

GeneDecks HLA-DQA2 for the pathways selected above

About GeneDecksing

5/8 Interacting proteins for HLA-DQA2 (ENSP00000364076³) via UniProtKB, MINT, and/or STRING (see all 8 )

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
TOR1A	ENSP00000345719³	STRING (score=.828)
INS	ENSP00000370731³	STRING (score=.81)
TOR1B	ENSP00000352879³	STRING (score=.778)
PLEKHG5	ENSP00000366977³	STRING (score=.75)
LDLR	ENSP00000252444³	STRING (score=.728)

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2 Gene Ontology (GO) biological process terms (links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0002504	antigen processing and presentation of peptide or polysaccharide antigen via MHC class II	IEA	--
GO:0006955	immune response	NAS	3036828

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(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse drugs & compounds from Enzo Life Sciences

Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for HLA-DQA2

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (HLA-DQA2)
		Browse for Gene Knock-down Tools from Millipore
		Abnova Chimera RNAi Products for Gene knock-down (HLA-DQA2)

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_020056

Sigma-Aldrich siRNA for HLA-DQA2

Sigma-Aldrich shRNA for HLA-DQA2

Explore Sigma-Aldrich super-pooled esiRNAs

Applied Biosystems Silencer® siRNAs:

NM_020056

REFSEQ mRNAs for HLA-DQA2 gene:

NM_020056.3

Applied Biosystems TaqMan ® Gene Expression Assays:

NM_020056

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_020056
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_020056
                                 untagged cDNA clone in CMV expression vector: NM_020056

Additional cDNA sequence:

J00199.1 L34089.1 L34352.1 M11124.1 M95727.1 M95728.1

24 DOTS entries:

DT.317668 DT.121314709 DT.415581 DT.97855223 DT.121314540 DT.121314796 DT.91771262 DT.100031266

DT.97789469 DT.95134359 DT.121314538 DT.121314757 DT.91771249 DT.91837951 DT.91838397 DT.95269101

DT.100031261 DT.100031265 DT.100794757 DT.100794758 DT.121314551 DT.121314723 DT.121314760 DT.121314770

24/548 AceView cDNA sequences (see all 548 ):

AF533930 BV177713 BM694667 BG756170 NM_002122 BV177276 BV176870 BV177061

BV177914 BV176869 BV177637 BU680454 AW388115 CA309331 AW388107 BU617246

AU076978 CA306036 L34083 CK820437 L46875 AW388120 BV177094 BC051832

highest scoring ESTs for HLA-DQA2:

CA306089 CD366175 NM_020056 AA405114 AA862420 AI433246 BC125044 BE041211 BE718938 BF890947

Unigene Cluster for HLA-DQA2:

Major histocompatibility complex, class II, DQ alpha 2

Hs.591798 [show with all ESTs]

Unigene Representative Sequence: NM_020056

GeneLoc Exon Structure

1 Ensembl transcript including schematic representation:

ENST00000374940

(Experimental results according to ¹GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to ²GeneAnnot , ³GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
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HLA-DQA2 expression in normal and diseased human tissues

Applied Biosystems TaqMan ® Gene Expression Assays for HLA-DQA2

¹ / ² / ³

2 probe-sets matching HLA-DQA2 gene

Affymetrix probe-set	Array	# genes	Sensitivity	Specificity	Correlation	Length	Gb_Accession	Consensus	Uniqueness	Score	Rank
Affymetrix probe-set	Array	GeneAnnot data			GeneNote data		GeneTide data
212671_s_at²^{, 3}	U133-A	6	1.00	0.17	--	--	BG397856	0.20	0.25	0.23	2
212671_s_at²	U133Plus2	6	1.00	0.17	--	--	--	--	--	--	--

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Data from

(Publications) and GNF BioGPS
About these images
About these images

CGAP SAGE TAG: --

SOURCE GeneReport for Unigene cluster: Hs.591798

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD and/or ⁵MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
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Orthologs for HLA-DQA2 gene from 2 species

Organism	Gene	Locus	Description	Human Similarity	NCBI accessions
chimpanzee (Pan troglodytes)	PATR-DQA2¹	--	major histocompatibility complex, class II, DQ alpha more	98.95(n) 98.04(a)	471976 XM_527354.2 XP_527354.1
cow (Bos taurus)	BOLA-DQA5¹	--	major histocompatibility complex, class II, DQ alpha more	84.18(n) 77.65(a)	282494 NM_001012675.1 NP_001012693.1

About this table Species with no ortholog for HLA-DQA2

ENSEMBL Gene Tree for HLA-DQA2

(Paralogs according to ¹HomoloGene
and ²Ensembl, Pseudogenes according to ³Pseudogene.org)
About This Section

Paralogs for HLA-DQA2 gene

ENSG00000168384² ENSG00000196735² HLA-DRA²

(According to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section

10/259 NCBI SNPs in HLA-DQA2 are shown (see all 259 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay) (see all 187)

AB	SNP ID	Valid	Chr 6 pos	Sequence	Recs	AA Chg	Type	More	Recs	Pop	Total sample	More
AB	Genomic Data				Transcription Data				Allele Frequencies
				--	--	--		--	--			--
	rs2894287^1,2	A,C,F,H	32815260(+)	`aggtaA/Gttttg`	1	--	ng5¹		4	EU EA WA	420
--	rs5021448^1,2	A,C,F,H	32815684(+)	`caggaC/Tacttt`	1	--	ng5¹		8	EU EA WA NS	824
--	rs9276441^1,2	A,C,F,H	32822872(+)	`TGCCAC/GCCACC`	1	--	ut3¹		2	EA	162
--	rs9276377^1,2	A,C,F,H	32815614(+)	`CTGTGA/CACACC`	1	--	ng5¹		3	EA WA	300
--	rs5021450^1,2	A,C,F,H	32815865(+)	`GTGATG/TACTAC`	1	--	ng5¹		6	EA WA NA	430
	rs2071798^1,2	A,C,F,O	32822570(-)	`CTTACT/CCAGGC`	1	--	ut3¹ ese³		4	EA NA	1636
	rs9276447^1,2	A,C,F,H	32823547(+)	`ATAAGT/GGGGTA`	1	--	ng3¹		4	EU EA WA	420
	rs9276440^1,2	A,C,F,H	32822761(+)	`TTTCAA/TGTCCA`	1	--	ut3¹ ese³		16	EU EA WA NA	1474
--	rs2071799^1,2	A,C,F,H	32822153(-)	`GGATGA/GGATTC`	1	--	ut3¹ ese³		7	NA EU EA WA	554
	rs2395253^1,2	C,F,H,O	32823138(+)	`CTTGAG/AGAGAT`	1	--	ut3¹ ese³		11	EU EA WA NA	980

About this table

HapMap Linkage Disequilibrium images for HLA-DQA2 (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

Human Genome Epidemiology Navigator: HLA-DQA2 (2 documents)

(Possibly Related Articles in Doctor's Guide)
About This Section

(in PubMed. Associations of this gene to articles via ¹Novoseek, ²HGNC, ³Entrez Gene, ⁴UniProtKB/Swiss-Prot, ⁵UniProtKB/TrEMBL, ⁶GAD, and/or ⁷PharmGKB)
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10/39 PubMed articles for HLA-DQA2 gene (see all 39 ):

Limited polymorphism of the HLA-DQA2 promoter and identification of a variant octamer. (PubMed id 8026991)^{3, 4} Rudy G. and Lew A.M. (1994)
Ancient roots for polymorphism at the HLA-DQ alpha locus in primates. (PubMed id 2513578)^{3, 4} Gyllensten U.B. and Erlich H.A. (1989)
Structure and expression of HLA-DQ alpha and -DX alpha genes: interallelic alternate splicing of the HLA-DQ alpha gene and functional splicing of the HLA-DQ alpha gene using a retroviral vector. (PubMed id 3610256)^{3, 4} Auffray C.... Strominger J.L. (1987)
Class II genes of the human major histocompatibility complex. Comparisons of the DQ and DX alpha and beta genes. (PubMed id 3036828)^{3, 4} Jonsson A.-K.... Rask L. (1987)
Isotypic and allotypic variation of human class II histocompatibility antigen alpha-chain genes. (PubMed id 6584734)^{3, 4} Auffray C....Strominger J.L. (1984)
Genetic association of the major histocompatibility complex with rheumatoid arthritis implicates two non-DRB1 loci. (PubMed id 19116923)³ Vignal C....Wilson A.G. (2009)
The MHC type 1 diabetes susceptibility gene is centromeric to HLA-DQB1. (PubMed id 18065200)³ Husain Z....Alper C.A. (2008)
Genome-wide association study of rheumatoid arthritis in the Spanish population: KLF12 as a risk locus for rheumatoid arthritis susceptibility. (PubMed id 18668548)³ Julia A....Marsal S. (2008)
Keeping the (kinase) party going: SLP-76 and ITK dance to the beat. (PubMed id 17652306)³ Qi Q. and August A. (2007)
Function of the Src-family kinases, Lck and Fyn, in T-cell development and activation. (PubMed id 15489916)³ Palacios E.H. and Weiss A. (2004)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
About This Section

Entrez Gene: 3118	HGNC: 4943	AceView: HLA-DQA1andHLA-DQA2	Ensembl:ENSG00000204276	euGenes: HUgn3118
ECgene: HLA-DQA2	H-InvDB: HLA-DQA2

(According to HUGE)
About This Section

(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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Licensable Technologies for HLA-DQA2
(Available from WIS Yeda, Salk, Tufts)

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(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
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Products for HLA-DQA2:

TaqMan ® Gene Expression Assays

TaqMan ® Genotyping Assays

Free SNP selection tool

Invitrogen iPath Pathways	Invitrogen BLOCK-iT™ RNAi
Invitrogen Antibodies	Invitrogen Assays
Invitrogen Clones	Invitrogen Q-PCR Products
Invitrogen Human Recombinant Kinases	Invitrogen Custom Antibody and Peptide Service
Invitrogen Proteins / Assays / Screening Services	Search Invitrogen catalog for HLA-DQA2-related products

	Millipore Custom Antibody & Bulk Services
	Millipore Preclinical / Clinical Development Services
	Millipore Immunoassay Services
	Millipore Target Screening & Profiling Services

	Predesigned and custom siRNAs for HLA-DQA2		Antibodies for HLA-DQA2
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	Lentivirus-delivered shRNAs for HLA-DQA2		Browse small molecules at Sigma-Aldrich
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HLA-DQA2 Gene

protein-coding GIFtS: 50

Aliases &
Descriptions
for HLA-DQA2

Summaries
for HLA-DQA2

Genomic Location
for HLA-DQA2

Proteins
for HLA-DQA2

Protein Domains/
Families
for HLA-DQA2

Gene Function
for HLA-DQA2

Pathways & Interactions
for HLA-DQA2

Drugs & Compounds
for HLA-DQA2

Transcripts
for HLA-DQA2

Expression
for HLA-DQA2

Orthologs
for HLA-DQA2

Paralogs
for HLA-DQA2

SNPs/Variants
for HLA-DQA2

Disorders & Mutations
for HLA-DQA2

Medical News
for HLA-DQA2

Publications
for HLA-DQA2

Search for HLA-DQA2

Genome Databases showing HLA-DQA2

Other Databases showing HLA-DQA2

Specialized Databases showing HLA-DQA2

Licensable Technologies
for HLA-DQA2

Services
for HLA-DQA2

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

HLA-DQA2 Gene

protein-coding GIFtS: 50

Aliases & Descriptionsfor HLA-DQA2

Summariesfor HLA-DQA2

Genomic Locationfor HLA-DQA2

Proteinsfor HLA-DQA2

Protein Domains/Familiesfor HLA-DQA2

Gene Functionfor HLA-DQA2

Pathways & Interactionsfor HLA-DQA2

Drugs & Compoundsfor HLA-DQA2

Transcriptsfor HLA-DQA2

Expression for HLA-DQA2

Orthologsfor HLA-DQA2

Paralogsfor HLA-DQA2

SNPs/Variantsfor HLA-DQA2

Disorders & Mutationsfor HLA-DQA2

Medical Newsfor HLA-DQA2

Publicationsfor HLA-DQA2

Search for HLA-DQA2

Genome Databases showing HLA-DQA2

Other Databases showing HLA-DQA2

Specialized Databases showing HLA-DQA2

Licensable Technologiesfor HLA-DQA2

Servicesfor HLA-DQA2

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Aliases &
Descriptions
for HLA-DQA2

Summaries
for HLA-DQA2

Genomic Location
for HLA-DQA2

Proteins
for HLA-DQA2

Protein Domains/
Families
for HLA-DQA2

Gene Function
for HLA-DQA2

Pathways & Interactions
for HLA-DQA2

Drugs & Compounds
for HLA-DQA2

Transcripts
for HLA-DQA2

Expression
for HLA-DQA2

Orthologs
for HLA-DQA2

Paralogs
for HLA-DQA2

SNPs/Variants
for HLA-DQA2

Disorders & Mutations
for HLA-DQA2

Medical News
for HLA-DQA2

Publications
for HLA-DQA2

Licensable Technologies
for HLA-DQA2

Services
for HLA-DQA2