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    HLA-DQB2 major histocompatibility complex, class II, DQ beta 2 [ Homo sapiens (human) ]

    Gene ID: 3120, updated on 3-Apr-2024

    Summary

    Official Symbol
    HLA-DQB2provided by HGNC
    Official Full Name
    major histocompatibility complex, class II, DQ beta 2provided by HGNC
    Primary source
    HGNC:HGNC:4945
    See related
    Ensembl:ENSG00000232629 MIM:615161; AllianceGenome:HGNC:4945
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    DQB2; HLA-DXB; HLA-DQB1
    Summary
    HLA-DQB2 belongs to the family of HLA class II beta chain paralogs. Class II molecules are heterodimers consisting of an alpha (DQA) and a beta chain (DQB), both anchored in the membrane. They play 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). Polymorphisms in the alpha and beta chains specify the peptide binding specificity, and typing for these polymorphisms is routinely done for bone marrow transplantation. However this gene, HLA-DQB2, is not routinely typed, as it is not thought to have an effect on transplantation. There is conflicting evidence in the literature and public sequence databases for the protein-coding capacity of HLA-DQB2. Because there is evidence of transcription and an intact ORF, HLA-DQB2 is represented in Entrez Gene and in RefSeq as a protein-coding locus. [provided by RefSeq, Oct 2010]
    Expression
    Biased expression in skin (RPKM 22.8), lung (RPKM 10.9) and 4 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Location:
    6p21.32
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (32756098..32763532, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (32578824..32586261, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (32723875..32731309, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene major histocompatibility complex, class II, DQ alpha 2 Neighboring gene microRNA 3135b Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32746394 Neighboring gene melanoma risk locus-associated MPRA allelic enhancers 6:32747727 and 6:32747786 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32748021 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32748137 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32749836 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32750346 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32751751 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32752130 Neighboring gene melanoma risk locus-associated MPRA allelic enhancers 6:32752436, 6:32752477 and 6:32752546 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32752973 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32753654 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32754294 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32754458 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32754921 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32755087 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32756916 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32762528 Neighboring gene major histocompatibility complex, class II, DO beta Neighboring gene transporter 2, ATP binding cassette subfamily B member Neighboring gene meiotic recombination hotspot TAP2

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    A genome-wide association study identified new variants associated with the risk of chronic hepatitis B.
    EBI GWAS Catalog
    A genome-wide association study identifies three new risk loci for Kawasaki disease.
    EBI GWAS Catalog
    A genome-wide association study of chronic hepatitis B identified novel risk locus in a Japanese population.
    EBI GWAS Catalog
    A genome-wide association study on chronic HBV infection and its clinical progression in male Han-Taiwanese.
    EBI GWAS Catalog
    Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production.
    EBI GWAS Catalog
    Genome-wide pathway analysis of genome-wide association studies on systemic lupus erythematosus and rheumatoid arthritis.
    EBI GWAS Catalog
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    EBI GWAS Catalog
    New loci associated with chronic hepatitis B virus infection in Han Chinese.
    EBI GWAS Catalog
    Susceptibility loci associated with specific and shared subtypes of lymphoid malignancies.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV envelope protein gp120 can specifically inhibit CD4-dependent class II MHC-restricted T cell response to Ag PubMed
    env Amino acid residues 42-49 in the V1 region of CD4 are involved in the interaction between HIV-1 gp120 and class II major histocompatibility complex molecules PubMed
    Envelope surface glycoprotein gp160, precursor env Processing of HIV-1 gp160 to gp120 and gp41 is necessary for the association of HIV-1 envelope glycoproteins with class II MHC PubMed
    Envelope transmembrane glycoprotein gp41 env A 43-amino-acid sequence between amino acids 708 and 750 in the HIV-1 gp41(TM) cytoplasmic tail is required for efficient incorporation of HLA class II proteins into virions PubMed
    env Soluble HIV-1 gp41 can selectively enhance MHC class I and II expression on human B cells, but does not increase expression of other cell surface antigens such as CD21 and CD54 (ICAM-1) PubMed
    env Soluble HIV-1 gp41 enhancement effects on MHC class I and II antigen expression can be inhibited by soluble gp41-binding proteins of 45, 49 and 62 kD from human B cells PubMed
    Nef nef Expression of patient-derived HIV-1 nef alleles downregulates MHC-II cell surface expression in activated CD4+ T cells PubMed
    nef HIV-1 group N and group O Nef alleles only weakly downregulate CD4, CD28, and class I and II MHC molecules PubMed
    nef HIV-1 Nef expression inhibits MHC II presentation of viral antigens in infected antigen-presenting cells PubMed
    nef Nef-triggered MHCII endocytosis requires Rab5 activity and lyst function, whereas lysosomal trafficking of internalized MHCII molecules requires Rab7 activity PubMed
    Pr55(Gag) gag HIV-1 Gag virus-like particles efficiently activate human monocyte-derived dendritic cells (MDDC) and induce MDDC maturation with an associated increase in the surface expression of CD80, CD86 and MHC classes I and II PubMed
    gag Two peptides of the CA domain of HIV-1 Gag, VDRFYKTLRAEQASQ and DRFYKLTRAEQASQ, are presented on MHC II molecules of dendritic cells and have similar sensitivity for antigen-specific T cells PubMed
    gag HIV-1 Gag virus-like particle-induced monocyte activation is shown by upregulation of molecules involved in antigen presentation (MHC II, CD80, CD86) and cell adhesion (CD54) PubMed
    Tat tat HIV-1 Tat downregulates expression of MHC class II genes in antigen-presenting cells (APC) by inhibiting the transactivator of MHC class II genes, CIITA PubMed
    Vpu vpu HIV-1 Vpu interacts with CD74 and modulates MHC II in HIV-1-infected cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables MHC class II protein complex binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables MHC class II receptor activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables peptide antigen binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Process Evidence Code Pubs
    involved_in adaptive immune response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in antigen processing and presentation of exogenous peptide antigen via MHC class II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in immune response NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in peptide antigen assembly with MHC class II protein complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of T cell activation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in ER to Golgi transport vesicle membrane TAS
    Traceable Author Statement
    more info
     
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
     
    part_of MHC class II protein complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of MHC class II protein complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in clathrin-coated endocytic vesicle membrane TAS
    Traceable Author Statement
    more info
     
    located_in endocytic vesicle membrane TAS
    Traceable Author Statement
    more info
     
    is_active_in late endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in lumenal side of endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
     
    is_active_in lysosomal membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in lysosomal membrane TAS
    Traceable Author Statement
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    located_in trans-Golgi network membrane TAS
    Traceable Author Statement
    more info
     
    located_in transport vesicle membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    HLA class II histocompatibility antigen, DQ beta 2 chain
    Names
    DV19.1 (major histocompatibility complex, class II, DQ beta 2 (HLA-DXB))
    HLA class II histocompatibility antigen, DX beta chain
    MHC class II antigen DQB2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001198858.2NP_001185787.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the 3' coding region, compared to variant 1. It encodes a shorter isoform (2), compared to isoform 1.
      Source sequence(s)
      AL672104
      Consensus CDS
      CCDS56419.1
      UniProtKB/TrEMBL
      Q5SQ91, Q8MGQ8
      Related
      ENSP00000390431.1, ENST00000411527.5
      Conserved Domains (3) summary
      cd05766
      Location:124217
      IgC_MHC_II_beta; Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain
      smart00410
      Location:142214
      IG_like; Immunoglobulin like
      pfam00969
      Location:41111
      MHC_II_beta; Class II histocompatibility antigen, beta domain
    2. NM_001300790.2NP_001287719.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL672104
      Consensus CDS
      CCDS78128.1
      UniProtKB/Swiss-Prot
      A6NIA5, P05538, Q29826, Q29870, Q29871, Q29872, Q29873, Q5SR06
      UniProtKB/TrEMBL
      Q5SR05
      Related
      ENSP00000396330.2, ENST00000437316.7
      Conserved Domains (3) summary
      cd05766
      Location:124217
      IgC_MHC_II_beta; Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain
      smart00410
      Location:142214
      IG_like; Immunoglobulin like
      pfam00969
      Location:41111
      MHC_II_beta; Class II histocompatibility antigen, beta domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      32756098..32763532 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011514561.4XP_011512863.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X3

      See identical proteins and their annotated locations for XP_011512863.1

      UniProtKB/TrEMBL
      A0A2H4Z4R5, A0A2H4Z4T8, A0A3B1EVN7
      Related
      ENSP00000415997.1, ENST00000427449.1
      Conserved Domains (2) summary
      cd05766
      Location:124216
      IgC_MHC_II_beta; Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain
      pfam00969
      Location:41111
      MHC_II_beta; Class II histocompatibility antigen, beta domain
    2. XM_011514560.3XP_011512862.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X2

      See identical proteins and their annotated locations for XP_011512862.1

      UniProtKB/Swiss-Prot
      A6NIA5, P05538, Q29826, Q29870, Q29871, Q29872, Q29873, Q5SR06
      Conserved Domains (3) summary
      cd05766
      Location:124217
      IgC_MHC_II_beta; Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain
      smart00410
      Location:142214
      IG_like; Immunoglobulin like
      pfam00969
      Location:41111
      MHC_II_beta; Class II histocompatibility antigen, beta domain
    3. XM_005249051.5XP_005249108.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X1

      See identical proteins and their annotated locations for XP_005249108.1

      UniProtKB/Swiss-Prot
      A6NIA5, P05538, Q29826, Q29870, Q29871, Q29872, Q29873, Q5SR06
      UniProtKB/TrEMBL
      A2ADX3
      Related
      ENSP00000410512.2, ENST00000435145.6
      Conserved Domains (3) summary
      cd05766
      Location:124217
      IgC_MHC_II_beta; Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain
      smart00410
      Location:142214
      IG_like; Immunoglobulin like
      pfam00969
      Location:41111
      MHC_II_beta; Class II histocompatibility antigen, beta domain

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      4062237..4069672 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054328498.1XP_054184473.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X3

      UniProtKB/TrEMBL
      A0A2H4Z4R5
    2. XM_054328497.1XP_054184472.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X2

    3. XM_054328496.1XP_054184471.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X1

      UniProtKB/TrEMBL
      A2ADX3

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      4169671..4177106 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054329805.1XP_054185780.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X3

      UniProtKB/TrEMBL
      A0A2H4Z4R5
    2. XM_054329804.1XP_054185779.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X2

    3. XM_054329803.1XP_054185778.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X1

      UniProtKB/TrEMBL
      A2ADX3

    Reference GRCh38.p14 ALT_REF_LOCI_3

    Genomic

    1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

      Range
      4000854..4008291 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330293.1XP_054186268.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X7

    2. XM_054330292.1XP_054186267.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X6

    3. XM_054330290.1XP_054186265.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X4

      UniProtKB/TrEMBL
      A0A0G2JH31
    4. XM_054330291.1XP_054186266.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X5

    Reference GRCh38.p14 ALT_REF_LOCI_4

    Genomic

    1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

      Range
      4175450..4182887 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330584.1XP_054186559.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X11

    2. XM_054330583.1XP_054186558.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X10

    3. XM_054330581.1XP_054186556.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X8

      UniProtKB/TrEMBL
      A0A0G2JH31
    4. XM_054330582.1XP_054186557.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X9

    Reference GRCh38.p14 ALT_REF_LOCI_5

    Genomic

    1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

      Range
      4055473..4062910 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330812.1XP_054186787.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X15

    2. XM_054330811.1XP_054186786.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X14

    3. XM_054330809.1XP_054186784.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X12

      UniProtKB/TrEMBL
      A0A0G2JH31
    4. XM_054330810.1XP_054186785.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X13

    Reference GRCh38.p14 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

      Range
      3950399..3957836 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331060.1XP_054187035.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X19

    2. XM_054331059.1XP_054187034.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X18

    3. XM_054331057.1XP_054187032.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X16

      UniProtKB/TrEMBL
      A0A0G2JH31
    4. XM_054331058.1XP_054187033.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X17

    Reference GRCh38.p14 ALT_REF_LOCI_7

    Genomic

    1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

      Range
      4156243..4163677 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331324.1XP_054187299.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X3

      UniProtKB/TrEMBL
      A0A2H4Z4R5
    2. XM_054331323.1XP_054187298.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X2

    3. XM_054331322.1XP_054187297.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X1

      UniProtKB/TrEMBL
      A2ADX3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      32578824..32586261 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355297.1XP_054211272.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X23

    2. XM_054355296.1XP_054211271.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X22

    3. XM_054355294.1XP_054211269.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X20

      UniProtKB/TrEMBL
      A0A0G2JH31
    4. XM_054355295.1XP_054211270.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X21

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_182549.1: Suppressed sequence

      Description
      NM_182549.1: This RefSeq was permanently suppressed because it is now thought that this gene is a pseudogene.
    2. NR_003937.1: Suppressed sequence

      Description
      NR_003937.1: This RefSeq was permanently suppressed because it is now thought that this gene does encode a protein.