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HLA-DRA Gene

protein-coding   GIFtS: 64
GCID: GC06P032412

Major Histocompatibility Complex, Class II, DR Alpha


(Previous symbol: HLA-DRA1)
  See HLA-DRA-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Major Histocompatibility Complex, Class II, DR Alpha1 2     Histocompatibility Antigen HLA-DR Alpha2
HLA-DRA11 2 3     HLA Class II Histocompatibility Antigen, DR Alpha Chain2
MHC Class II Antigen DRA2 3     MHC Cell Surface Glycoprotein2
MLRW2     

External Ids:    HGNC: 49471   Entrez Gene: 31222   Ensembl: ENSG000002042877   OMIM: 1428605   UniProtKB: P019033   

Export aliases for HLA-DRA gene to outside databases

Previous GC identifers: GC06P032434 GC06Pd32422 GC06P032178


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for HLA-DRA Gene:
HLA-DRA is one of the HLA class II alpha chain paralogues. This class II molecule is a heterodimer consisting of
an alpha and a beta chain, both anchored in the membrane. It plays a central role in the immune system by
presenting peptides derived from extracellular proteins. Class II molecules are expressed in antigen presenting
cells (APC: B lymphocytes, dendritic cells, macrophages). The alpha chain is approximately 33-35 kDa and its gene
contains 5 exons. Exon 1 encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, and exon
4 encodes the transmembrane domain and the cytoplasmic tail. DRA does not have polymorphisms in the peptide
binding part and acts as the sole alpha chain for DRB1, DRB3, DRB4 and DRB5. (provided by RefSeq, Jul 2008)

GeneCards Summary for HLA-DRA Gene:
HLA-DRA (major histocompatibility complex, class II, DR alpha) is a protein-coding gene. Diseases associated with HLA-DRA include graham little-piccardi-lassueur syndrome, and allergic encephalomyelitis. GO annotations related to this gene include MHC class II receptor activity. An important paralog of this gene is HLA-DRB5.

UniProtKB/Swiss-Prot: DRA_HUMAN, P01903
Function: Binds peptides derived from antigens that access the endocytic route of antigen presenting cells (APC)
and presents them on the cell surface for recognition by the CD4 T-cells. The peptide binding cleft accommodates
peptides of 10-30 residues. The peptides presented by MHC class II molecules are generated mostly by degradation
of proteins that access the endocytic route, where they are processed by lysosomal proteases and other
hydrolases. Exogenous antigens that have been endocytosed by the APC are thus readily available for presentation
via MHC II molecules, and for this reason this antigen presentation pathway is usually referred to as exogenous.
As membrane proteins on their way to degradation in lysosomes as part of their normal turn-over are also
contained in the endosomal/lysosomal compartments, exogenous antigens must compete with those derived from
endogenous components. Autophagy is also a source of endogenous peptides, autophagosomes constitutively fuse with
MHC class II loading compartments. In addition to APCs, other cells of the gastrointestinal tract, such as
epithelial cells, express MHC class II molecules and CD74 and act as APCs, which is an unusual trait of the GI
tract. To produce a MHC class II molecule that presents an antigen, three MHC class II molecules (heterodimers of
an alpha and a beta chain) associate with a CD74 trimer in the ER to form a heterononamer. Soon after the entry
of this complex into the endosomal/lysosomal system where antigen processing occurs, CD74 undergoes a sequential
degradation by various proteases, including CTSS and CTSL, leaving a small fragment termed CLIP
(class-II-associated invariant chain peptide). The removal of CLIP is facilitated by HLA-DM via direct binding to
the alpha-beta-CLIP complex so that CLIP is released. HLA-DM stabilizes MHC class II molecules until primary high
affinity antigenic peptides are bound. The MHC II molecule bound to a peptide is then transported to the cell
membrane surface. In B-cells, the interaction between HLA-DM and MHC class II molecules is regulated by HLA-DO.
Primary dendritic cells (DCs) also to express HLA-DO. Lysosomal microenvironment has been implicated in the
regulation of antigen loading into MHC II molecules, increased acidification produces increased proteolysis and
efficient peptide loading

Gene Wiki entry for HLA-DRA Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000006.11  NC_018917.2  NT_007592.16  NT_113891.3  NT_167245.2  NT_167246.2  NT_167247.2  NT_167248.2  
NT_167249.2  NT_187692.1  
Regulatory elements:
   Regulatory transcription factor binding sites in the HLA-DRA gene promoter:
         Pax-5   AML1a   GCNF   CUTL1   Arnt   AREB6   IRF-2   GCNF-1   Pax-4a   GCNF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidHLA-DRA promoter sequence
   Search Chromatin IP Primers for HLA-DRA

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HLA-DRA


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

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

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

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P032412:  view genomic region     (about GC identifiers)

Start:
32,407,619 bp from pter      End:
32,412,823 bp from pter
Size:
5,205 bases      Orientation:
plus strand

6 alternative locations:
Chr6+,NT_167248 3,668,487-3,673,697      Chr6+,NT_167247 3,786,393-3,791,603      Chr6+,NT_167245 3,685,732-3,690,942     
Chr6+,NT_167246 3,749,679-3,754,890      Chr6+,NT_167249 3,754,283-3,759,493      Chr6+,NT_113891.2 3,878,074-3,883,241     

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: DRA_HUMAN, P01903 (See protein sequence)
Recommended Name: HLA class II histocompatibility antigen, DR alpha chain precursor  
Size: 254 amino acids; 28607 Da
Subunit: Heterodimer of an alpha and a beta subunit; also referred as MHC class II molecule. In the endoplasmic
reticulum (ER) it forms a heterononamer; 3 MHC class II molecules bind to a CD74 homotrimer (also known as
invariant chain or HLA class II histocompatibility antigen gamma chain). In the endosomal/lysosomal system; CD74
undergoes sequential degradation by various proteases; leaving a small fragment termed CLIP on each MHC class II
molecule. MHC class II molecule interacts with HLA_DM, and HLA_DO in B-cells, in order to release CLIP and
facilitate the binding of antigenic peptides
Sequence caution: Sequence=CAA25076.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Selected PDB 3D structures from and Proteopedia for HLA-DRA (see all 69):
1A6A (3D)        1AQD (3D)        1BX2 (3D)        1D5M (3D)        1D5X (3D)        1D5Z (3D)    
Secondary accessions: A2BET4 Q30160 Q6IAZ1 Q861I2 Q9TP70

Explore the universe of human proteins at neXtProt for HLA-DRA: NX_P01903

Explore proteomics data for HLA-DRA at MOPED

Post-translational modifications: 

  • Ubiquitinated by MARCH1 or MARCH8 at Lys-244 leading to down-regulation of MHC class II. When associated with
    ubiquitination of the beta subunit of HLA-DR: HLA-DRB4 'Lys-254', the down-regulation of MHC class II may be
    highly effective1
  • Ubiquitination2 at Lys244
  • Glycosylation2 at Asn143
  • Modification sites at PhosphoSitePlus

  • See HLA-DRA Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_061984.2  
    ENSEMBL proteins: 
     ENSP00000378786   ENSP00000364121  
    Reactome Protein details: P01903

    HLA-DRA Human Recombinant Protein Products:

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    Novus Biologicals HLA-DRA Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp.

     
    Search eBioscience for Proteins for HLA-DRA 

    HLA-DRA Antibody Products:

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    HLA-DRA Assay Products:

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    Browse Enzo Life Sciences for kits & assays
    Browse ELISAs at Cloud-Clone Corp.
    Browse CLIAs at Cloud-Clone Corp.
    Search eBioscience for ELISAs for HLA-DRA 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    HLA: Histocompatibility complex
    C1SET: Immunoglobulin superfamily / C1-set domain containing

    Selected InterPro protein domains (see all 7):
     IPR001003 MHC_II_a_N
     IPR011162 MHC_I/II-like_Ag-recog
     IPR013783 Ig-like_fold
     IPR014745 MHC_II_a/b_N
     IPR003597 Ig_C1-set

    Graphical View of Domain Structure for InterPro Entry P01903

    ProtoNet protein and cluster: P01903

    2 Blocks protein domains:
    IPB001003 MHC Class II alpha chain
    IPB003597 Immunoglobulin C-type


    UniProtKB/Swiss-Prot: DRA_HUMAN, P01903
    Similarity: Belongs to the MHC class II family
    Similarity: Contains 1 Ig-like C1-type (immunoglobulin-like) domain


    Find genes that share domains with HLA-DRA           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: DRA_HUMAN, P01903
    Function: Binds peptides derived from antigens that access the endocytic route of antigen presenting cells (APC)
    and presents them on the cell surface for recognition by the CD4 T-cells. The peptide binding cleft accommodates
    peptides of 10-30 residues. The peptides presented by MHC class II molecules are generated mostly by degradation
    of proteins that access the endocytic route, where they are processed by lysosomal proteases and other
    hydrolases. Exogenous antigens that have been endocytosed by the APC are thus readily available for presentation
    via MHC II molecules, and for this reason this antigen presentation pathway is usually referred to as exogenous.
    As membrane proteins on their way to degradation in lysosomes as part of their normal turn-over are also
    contained in the endosomal/lysosomal compartments, exogenous antigens must compete with those derived from
    endogenous components. Autophagy is also a source of endogenous peptides, autophagosomes constitutively fuse with
    MHC class II loading compartments. In addition to APCs, other cells of the gastrointestinal tract, such as
    epithelial cells, express MHC class II molecules and CD74 and act as APCs, which is an unusual trait of the GI
    tract. To produce a MHC class II molecule that presents an antigen, three MHC class II molecules (heterodimers of
    an alpha and a beta chain) associate with a CD74 trimer in the ER to form a heterononamer. Soon after the entry
    of this complex into the endosomal/lysosomal system where antigen processing occurs, CD74 undergoes a sequential
    degradation by various proteases, including CTSS and CTSL, leaving a small fragment termed CLIP
    (class-II-associated invariant chain peptide). The removal of CLIP is facilitated by HLA-DM via direct binding to
    the alpha-beta-CLIP complex so that CLIP is released. HLA-DM stabilizes MHC class II molecules until primary high
    affinity antigenic peptides are bound. The MHC II molecule bound to a peptide is then transported to the cell
    membrane surface. In B-cells, the interaction between HLA-DM and MHC class II molecules is regulated by HLA-DO.
    Primary dendritic cells (DCs) also to express HLA-DO. Lysosomal microenvironment has been implicated in the
    regulation of antigen loading into MHC II molecules, increased acidification produces increased proteolysis and
    efficient peptide loading

         Genatlas biochemistry entry for HLA-DRA:
    HLA-DR,alpha chain

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
    GO:0023026MHC class II protein complex binding IDA--
    GO:0032395MHC class II receptor activity NAS6304715
         
    Find genes that share ontologies with HLA-DRA           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for HLA-DRA:
     Increased G1 DNA content  Synthetic lethal with imatinib 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for HLA-DRA
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for HLA-DRA

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for HLA-DRA
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for HLA-DRA

    miRNA
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    4 qRT-PCR Assays for microRNAs that regulate HLA-DRA:
    hsa-miR-942 hsa-miR-875-3p hsa-miR-525-5p hsa-miR-520a-5p
    SwitchGear 3'UTR luciferase reporter plasmidHLA-DRA 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for HLA-DRA
    Predesigned siRNA for gene silencing in human, mouse, rat HLA-DRA

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for HLA-DRA

    Clone
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    OriGene clones in human, mouse for HLA-DRA (see all 7)
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: HLA-DRA (NM_019111)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for HLA-DRA
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    Addgene plasmids for HLA-DRA 

    Cell Line
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    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HLA-DRA


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    DRA_HUMAN, P01903: Cell membrane; Single-pass type I membrane protein. Endoplasmic reticulum membrane;
    Single-pass type I membrane protein. Golgi apparatus, trans-Golgi network membrane; Single-pass type I membrane
    protein. Endosome membrane; Single-pass type I membrane protein. Lysosome membrane; Single-pass type I membrane
    protein. Late endosome membrane; Single-pass type I membrane protein. Note=The MHC class II complex transits
    through a number of intracellular compartments in the endocytic pathway until it reaches the cell membrane for
    antigen presentation
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    endoplasmic reticulum5
    endosome5
    lysosome5
    plasma membrane5
    vacuole5
    golgi apparatus4
    extracellular3

    Gene Ontology (GO): Selected cellular component terms (see all 16):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000139Golgi membrane TAS--
    GO:0005764lysosome IDA8890155
    GO:0005765lysosomal membrane TAS--
    GO:0005886plasma membrane TAS--
    GO:0005887integral component of plasma membrane NAS6304715

    Find genes that share ontologies with HLA-DRA           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for HLA-DRA About   (see all 32)  
    See pathways by source

    SuperPathSelected contained pathways About (see all per SuperPath)
    1Allograft rejection
    Allograft rejection0.86
    Intestinal immune network for IgA production0.41
    Allograft Rejection0.86
    Viral myocarditis0.40
    Type I diabetes mellitus0.69
    CTL Mediated Apoptosis0.38
    Graft-versus-host disease0.65
    THC Differentiation Pathway0.38
    2CD28 co-stimulation
    Costimulation by the CD28 family0.44
    CTLA4 Signaling0.30
    3Translocation of ZAP-70 to Immunological synapse
    Translocation of ZAP-70 to Immunological synapse0.83
    PD-1 signaling0.72
    Phosphorylation of CD3 and TCR zeta chains0.83
    Generation of second messenger molecules0.62
    4Immune response Antigen presentation by MHC class II
    Immune response Antigen presentation by MHC class II0.46
    Immune response IL 22 signaling pathway0.31
    G protein signaling N RAS regulation pathway0.46
    5ICos-ICosL Pathway in T-Helper Cell
    ICos-ICosL Pathway in T-Helper Cell0.66
    Calcium Mediated T-Cell Apoptosis0.31
    CD28 Signaling in T-Helper Cell0.66


    Find genes that share SuperPaths with HLA-DRA           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    3 R&D Systems Pathways for HLA-DRA
        IL-21 Signaling and its Primary Biological Effects in Different Immune Cell Types
    Th1 Differentiation
    Th17 Differentiation

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for HLA-DRA (see all 12)
        THC Differentiation Pathway
    Calcium Mediated T-Cell Apoptosis
    IL-4 Pathway
    ICos-ICosL Pathway in T-Helper Cell
    CDC42 Pathway

    Selected GeneGo (Thomson Reuters) Pathways for HLA-DRA (see all 6)
        Immune response Antigen presentation by MHC class II
    Immune response ICOS pathway in T-helper cell
    Immune response T cell receptor signaling pathway
    Immune response IL-22 signaling pathway
    G-protein signaling N-RAS regulation pathway

    Selected BioSystems Pathways for HLA-DRA (see all 6)
        Cytokines and Inflammatory Response
    Allograft Rejection
    IL12-mediated signaling events
    TCR signaling in naive CD4+ T cells
    IL12 signaling mediated by STAT4

    Selected Reactome Pathways for HLA-DRA (see all 7)
        Translocation of ZAP-70 to Immunological synapse
    Interferon gamma signaling
    Downstream TCR signaling
    PD-1 signaling
    MHC class II antigen presentation


    Selected Kegg Pathways  (Kegg details for HLA-DRA) (see all 22):
        Phagosome
    Cell adhesion molecules (CAMs)
    Antigen processing and presentation
    Hematopoietic cell lineage
    Intestinal immune network for IgA production

        Pathway & Disease-focused RT2 Profiler PCR Array including HLA-DRA: 
              Cell Surface Markers in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for HLA-DRA

    STRING Interaction Network Preview (showing 5 interactants - click image to see 11)

    Selected Interacting proteins for HLA-DRA (P019032, 3 ENSP000003787864) via UniProtKB, MINT, STRING, and/or I2D (see all 40)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HLA-DRB1P019122, 3, ENSP000003530994I2D: score=1 I2D: score=1 MINT-24881 I2D: score=2 MINT-24910 I2D: score=1 I2D: score=1 STRING: ENSP00000353099
    ENSG00000206240P019122, 3MINT-24910 I2D: score=1 
    ENSG00000206306P019122, 3MINT-24910 I2D: score=1 
    CD74P042332, 3, ENSP000000095304MINT-72789 I2D: score=2 STRING: ENSP00000009530
    ENSG00000242092P280683, ENSP000003787234I2D: score=2 STRING: ENSP00000378723
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0002504antigen processing and presentation of peptide or polysaccharide antigen via MHC class II ----
    GO:0006955immune response NAS6304715
    GO:0019221cytokine-mediated signaling pathway TAS--
    GO:0019882antigen processing and presentation ----
    GO:0019886antigen processing and presentation of exogenous peptide antigen via MHC class II TAS--

    Find genes that share ontologies with HLA-DRA           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
    About This Section

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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for HLA-DRA (DRA)

    1 Novoseek inferred chemical compound relationship for HLA-DRA gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    chloramphenicol 10.9 1 1454841 (1)



    Find genes that share compounds with HLA-DRA           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
    About This Section

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    REFSEQ mRNAs for HLA-DRA gene: 
    NM_019111.4  

    Unigene Cluster for HLA-DRA:

    Major histocompatibility complex, class II, DR alpha
    Hs.520048  [show with all ESTs]
    Unigene Representative Sequence: BQ057851
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000395388(uc003obh.3 uc003obi.3) ENST00000374982
    miRNA
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    SwitchGear 3'UTR luciferase reporter plasmidHLA-DRA 3' UTR sequence
    Inhib. RNA
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    DNA2.0 Custom Codon Optimized Gene Synthesis Service for HLA-DRA
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HLA-DRA
    Addgene plasmids for HLA-DRA 
    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat HLA-DRA
      QuantiFast Probe-based Assays in human, mouse, rat HLA-DRA

    Additional mRNA sequence: 

    AK297032.1 AK301134.1 AK301354.1 AK304429.1 AK310161.1 AK313123.1 BC032350.1 BC071659.1 
    CR457013.1 J00194.1 J00195.1 J00197.1 K01171.1 M35979.1 M60333.1 M60334.1 
    V00523.1 V00528.1 

    Selected DOTS entries (see all 49):

    DT.85105175  DT.456002  DT.95158848  DT.121341027  DT.91983131  DT.100684470  DT.100059742  DT.100857584 
    DT.91882867  DT.121340976  DT.91982743  DT.121340896  DT.121340984  DT.86847432  DT.121340956  DT.121341004 
    DT.95158819  DT.100684466  DT.100857051  DT.100857583  DT.91695661  DT.95089770  DT.121341006  DT.121341029 

    17 AceView cDNA sequences:

    CR622870 CR613451 CR596644 CR594558 CR590143 J00197 J00195 BC071659 
    BV183551 V00523 CR457013 V00528 K01171 M35979 BV204329 J00194 
    AF522250 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    HLA-DRA expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGGCATCTCT
    HLA-DRA Expression
    About this image


    HLA-DRA expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 11) fully expand
     
     Blood (Cardiovascular System)    fully expand to see all 4 entries
             Plasmacytoid Dendritic cells Peripheral Blood
             Facilitating cells
     
     Umbilical Cord (Extraembryonic Tissues)    fully expand to see all 4 entries
             Umbilical Veins
             Umbilical tissue-derived cells (CNTO2476)
     
     Epithelial Cells
             Adult Retinal Pigmented Epithelium Cells Retinal Pigmented Epithelium
     
     Thymus (Hematopoietic System)
             T Helper Cells Thymus
     
     Neural Tube (Nervous System)
             Floor plate-like cells
    HLA-DRA Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    HLA-DRA Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.520048
        Pathway & Disease-focused RT2 Profiler PCR Array including HLA-DRA: 
              Cell Surface Markers in human mouse rat

    Primer
    Products:
    OriGene qPCR primer pairs and template standards for HLA-DRA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HLA-DRA

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for HLA-DRA gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia H2-Ea-ps1 , 5 histocompatibility 2, class II antigen E alpha, pseudogene1, 5 76.75(n)1
    73.11(a)1
      17 (17.98 cM)5
    1005044041  XM_003688950.11  XP_003688998.11 
     343429335 
    chicken
    (Gallus gallus)
    Aves BLA1 Major histocompatibility complex class II alpha chain more 57.82(n)
    50.44(a)
      430189  NM_001245061.1  NP_001231990.1 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    Uncharacterized protein
    55(a)
    53(a)
    many ↔ many
    many ↔ many
    GL343775.1(20845-38928)
    GL343809.1(2435-3996)
    zebrafish
    (Danio rerio)
    Actinopterygii zgc:1231076
    zgc:123107
    30(a)
    many ↔ many
    4(61887203-61893205) ENSDARG00000020286


    ENSEMBL Gene Tree for HLA-DRA (if available)
    TreeFam Gene Tree for HLA-DRA (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for HLA-DRA gene
    HLA-DRB52  HLA-DQA12  HLA-DPA12  HLA-DQB12  HLA-DRB12  HLA-DOB2  HLA-DMA2  HLA-DQB22  
    HLA-DOA2  ENSG000002489932  HLA-DMB2  HLA-DQA22  HLA-DPB12  
    9 SIMAP similar genes for HLA-DRA using alignment to 6 protein entries:     DRA_HUMAN (see all proteins):
    HLA-DRA1    HLA-DQA1/DRA    HLA-DQA2    HLA-DQA1    HLA-DPA1    DQA1-0103
    DQ-A1    HLA-DOA    HLA-DRB4

    Find genes that share paralogs with HLA-DRA           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Polymorphic Variants from UniProtKB/Swiss-Prot
    DRA_HUMAN, P01903: The following alleles of DRA are known: DRA*01:01 and DRA*01:02. The sequence shown is that of
    DRA*01:01
    DRA_HUMAN, P01903: Genetic variations in HLA-DRA influence susceptibility to hepatitis B virus (HBV) infection
    [MIM:610424]


    Selected SNPs for HLA-DRA (see all 255)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs31298691,2
    C,F,A,H--32405671(+) CTTTAC/ACTTTC 1 -- us2k115Minor allele frequency- A:0.38NS EA NA WA 1178
    rs38348571,2
    C--32405693(+) TCCTG-/AAAAAT 1 -- us2k10--------
    rs1895567531,2
    --32405733(+) TCTAGC/TGATCT 1 -- us2k10--------
    rs92686271,2
    C,F,A--32405821(+) TAACTT/CGTGAG 1 -- us2k17Minor allele frequency- C:0.16NA WA EA 502
    rs69397871,2
    C,F,H--32405835(+) GGCTGC/TATGGC 1 -- us2k15Minor allele frequency- T:0.02NS EA WA 528
    rs92686281,2
    C,F,A,H--32405865(+) ACAGTA/CTGGAA 1 -- us2k1 tfbs320Minor allele frequency- C:0.21NS EA NA WA 1694
    rs1144743271,2
    C,F--32405894(+) ATGTCA/TTGACT 1 -- us2k11Minor allele frequency- T:0.03NA 120
    rs92686291,2
    C--32406085(+) TGGCCG/TGGCAT 1 -- us2k11Minor allele frequency- T:0.00NA 2
    rs31298701,2
    C,F,H--32406100(+) GCGGGC/TGCCTG 1 -- us2k12Minor allele frequency- T:0.50NA 4
    rs287322141,2
    C--32406122(+) ACTCGA/GGAGGC 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for HLA-DRA (32407619 - 32412823 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 8 variations for HLA-DRA:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv830630CNV Loss17160897
    nsv830631CNV Gain17160897
    esv33476CNV Gain+Loss17666407
    esv21985CNV Gain+Loss19812545
    nsv428142CNV Gain+Loss18775914
    dgv1932e1CNV Complex17122850
    dgv1931e1CNV Complex17122850
    dgv1930e1CNV Complex17122850

    Human Gene Mutation Database (HGMD): HLA-DRA
    Locus Specific Mutation Databases (LSDB): HLA-DRA

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing HLA-DRA
    DNA2.0 Custom Variant and Variant Library Synthesis for HLA-DRA

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

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    OMIM gene information: 142860    OMIM disorders: --

    4 diseases for HLA-DRA:    
    About MalaCards
    graham little-piccardi-lassueur syndrome    allergic encephalomyelitis    mhc class ii deficiency    diffuse panbronchiolitis


    Find genes that share disorders with HLA-DRA           About GenesLikeMe

    6 Novoseek inferred disease relationships for HLA-DRA gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    carcinoma non-small cell lung 45.7 1 16360016 (1)
    retinoblastoma 45.5 2 9396821 (1), 11533238 (1)
    necrosis 0 2 1454841 (1)
    tumors 0 7 11533238 (3), 1454841 (1), 15688398 (1)
    lymphoma 0 1 9352360 (1)
    cancer 0 2 8170082 (1)

    Genetic Association Database (GAD): HLA-DRA
    Human Genome Epidemiology (HuGE) Navigator: HLA-DRA (53 documents)

    Export disorders for HLA-DRA gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

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    PubMed articles for HLA-DRA gene, integrated from 10 sources (see all 313):
    (articles sorted by number of sources associating them with HLA-DRA)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The HLA-DRA*0102 allele: correct nucleotide sequence and associated HLA haplotypes. (PubMed id 12445311)1, 2, 9 Kralovicova J....Vorechovsky I. (Tissue Antigens 2002)
    2. A genome-wide association study reveals that variants within the HLA region are associated with risk for nonobstructive azoospermia. (PubMed id 22541561)1, 4 Zhao H....Chen Z.J. (Am. J. Hum. Genet. 2012)
    3. Genome-wide association study identifies three new susceptibility loci for adult asthma in the Japanese population. (PubMed id 21804548)1, 4 Hirota T....Tamari M. (Nat. Genet. 2011)
    4. Identification of novel genetic markers associated with clinical phenotypes of systemic sclerosis through a genome-wide association strategy. (PubMed id 21779181)1, 4 Gorlova O....Martin J. (PLoS Genet. 2011)
    5. Biological, clinical and population relevance of 95 loci for blood lipids. (PubMed id 20686565)1, 4 Teslovich T.M....Kathiresan S. (Nature 2010)
    6. Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL). (PubMed id 20228798)1, 4 Franke A....Schreiber S. (Nat. Genet. 2010)
    7. Genetic analysis in a Dutch study sample identifies more ulcerative colitis susceptibility loci and shows their additive role in disease risk. (PubMed id 19861958)1, 4 Festen E.A....Weersma R.K. (Am. J. Gastroenterol. 2010)
    8. Common genetic variation in the HLA region is associated with late-onset sporadic Parkinson's disease. (PubMed id 20711177)1, 4 Hamza T.H....Payami H. (Nat. Genet. 2010)
    9. Robust replication of genotype-phenotype associations across multiple diseases in an electronic medical record. (PubMed id 20362271)1, 4 Ritchie M.D....Roden D.M. (Am. J. Hum. Genet. 2010)
    10. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (Diabetes Care 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    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, Kegg, and/or H-InvDB)
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    Entrez Gene: 3122 HGNC: 4947 AceView: HLA-DRA.1 Ensembl:ENSG00000204287 euGenes: HUgn3122
    ECgene: HLA-DRA Kegg: 3122 H-InvDB: HLA-DRA

    (According to HUGE)
    About This Section

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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for HLA-DRA Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

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    Patent Information for HLA-DRA gene:
    Search GeneIP for patents involving HLA-DRA

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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