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

Gene ID: 3120, updated on 6-Aug-2018

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; Vega:OTTHUMG00000031125
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
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

Genomic context

See HLA-DQB2 in Genome Data Viewer
Location:
6p21.32
Exon count:
6
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (32756094..32763553, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (32723837..32731330, 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 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

  • Adaptive Immune System, organism-specific biosystem (from REACTOME)
    Adaptive Immune System, organism-specific biosystemAdaptive immunity refers to antigen-specific immune response efficiently involved in clearing the pathogens. The adaptive immune system is comprised of B and T lymphocytes that express receptors with...
  • Costimulation by the CD28 family, organism-specific biosystem (from REACTOME)
    Costimulation by the CD28 family, organism-specific biosystemOptimal activation of T-lymphocytes requires at least two signals. A primary one is delivered by the T-cell receptor (TCR) complex after antigen recognition and additional costimulatory signals are d...
  • Cytokine Signaling in Immune system, organism-specific biosystem (from REACTOME)
    Cytokine Signaling in Immune system, organism-specific biosystemCytokines are small proteins that regulate and mediate immunity, inflammation, and hematopoiesis. They are secreted in response to immune stimuli, and usually act briefly, locally, at very low concen...
  • Downstream TCR signaling, organism-specific biosystem (from REACTOME)
    Downstream TCR signaling, organism-specific biosystemChanges in gene expression are required for the T cell to gain full proliferative competence and to produce effector cytokines. Three transcription factors in particular have been found to play a key...
  • Generation of second messenger molecules, organism-specific biosystem (from REACTOME)
    Generation of second messenger molecules, organism-specific biosystemIn addition to serving as a scaffold via auto-phosphorylation, ZAP-70 also phosphorylates a restricted set of substrates following TCR stimulation - including LAT and SLP-76. These substrates have be...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Interferon Signaling, organism-specific biosystem (from REACTOME)
    Interferon Signaling, organism-specific biosystemInterferons (IFNs) are cytokines that play a central role in initiating immune responses, especially antiviral and antitumor effects. There are three types of IFNs:Type I (IFN-alpha, -beta and others...
  • Interferon gamma signaling, organism-specific biosystem (from REACTOME)
    Interferon gamma signaling, organism-specific biosystemInterferon-gamma (IFN-gamma) belongs to the type II interferon family and is secreted by activated immune cells-primarily T and NK cells, but also B-cells and APC. INFG exerts its effect on cells by ...
  • MHC class II antigen presentation, organism-specific biosystem (from REACTOME)
    MHC class II antigen presentation, organism-specific biosystemAntigen presenting cells (APCs) such as B cells, dendritic cells (DCs) and monocytes/macrophages express major histocompatibility complex class II molecules (MHC II) at their surface and present exog...
  • PD-1 signaling, organism-specific biosystem (from REACTOME)
    PD-1 signaling, organism-specific biosystemThe Programmed cell death protein 1 (PD-1) is one of the negative regulators of TCR signaling. PD-1 may exert its effects on cell differentiation and survival directly by inhibiting early activation ...
  • Phosphorylation of CD3 and TCR zeta chains, organism-specific biosystem (from REACTOME)
    Phosphorylation of CD3 and TCR zeta chains, organism-specific biosystemPrior to T cell receptor (TCR) stimulation, CD4/CD8 associated Lck remains seperated from the TCR and is maintained in an inactive state by the action of Csk. Csk phosphorylates the negative regulato...
  • TCR signaling, organism-specific biosystem (from REACTOME)
    TCR signaling, organism-specific biosystemThe TCR is a multisubunit complex that consists of clonotypic alpha/beta chains noncovalently associated with the invariant CD3 delta/epsilon/gamma and TCR zeta chains. T cell activation by antigen p...
  • Translocation of ZAP-70 to Immunological synapse, organism-specific biosystem (from REACTOME)
    Translocation of ZAP-70 to Immunological synapse, organism-specific biosystemThe dual phosphorylated ITAMs recruit Syk kinase ZAP-70 via their tandem SH2 domains (step 4). ZAP-70 subsequently undergoes phosphorylation on multiple tyrosine residues for further activation. ZAP-...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
MHC class II receptor activity NAS
Non-traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
T cell receptor signaling pathway TAS
Traceable Author Statement
more info
 
antigen processing and presentation of exogenous peptide antigen via MHC class II TAS
Traceable Author Statement
more info
 
immune response NAS
Non-traceable Author Statement
more info
PubMed 
interferon-gamma-mediated signaling pathway TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
ER to Golgi transport vesicle membrane TAS
Traceable Author Statement
more info
 
Golgi membrane TAS
Traceable Author Statement
more info
 
MHC class II protein complex NAS
Non-traceable Author Statement
more info
PubMed 
clathrin-coated endocytic vesicle membrane TAS
Traceable Author Statement
more info
 
endocytic vesicle membrane TAS
Traceable Author Statement
more info
 
endosome membrane IEA
Inferred from Electronic Annotation
more info
 
integral component of lumenal side of endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
lysosomal membrane TAS
Traceable Author Statement
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 
trans-Golgi network membrane TAS
Traceable Author Statement
more info
 
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)

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_001198858.1NP_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/Swiss-Prot
    P05538
    Related
    ENSP00000390431.1, OTTHUMP00000178596, ENST00000411527.5, OTTHUMT00000276174
    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_001300790.1NP_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/TrEMBL
    Q5SR05
    Related
    ENSP00000396330.2, OTTHUMP00000029168, ENST00000437316.6, OTTHUMT00000076216
    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: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p12 Primary Assembly

    Range
    32756094..32763553 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011514560.2XP_011512862.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X2

    See identical proteins and their annotated locations for XP_011512862.1

    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. XM_011514561.3XP_011512863.1  HLA class II histocompatibility antigen, DQ beta 2 chain isoform X3

    See identical proteins and their annotated locations for XP_011512863.1

    Related
    ENSP00000415997.1, OTTHUMP00000029169, 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
  3. XM_005249051.4XP_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/TrEMBL
    A2ADX3
    Related
    ENSP00000410512.2, OTTHUMP00000178595, ENST00000435145.6, OTTHUMT00000276173
    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.p12 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p12 ALT_REF_LOCI_1

    Range
    4062237..4069693 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p12 ALT_REF_LOCI_2

    Range
    4169671..4177127 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p12 ALT_REF_LOCI_3

    Range
    4000854..4008312 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p12 ALT_REF_LOCI_4

    Range
    4175450..4182908 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p12 ALT_REF_LOCI_5

    Range
    4055473..4062931 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p12 ALT_REF_LOCI_6

    Range
    3950399..3957857 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p12 ALT_REF_LOCI_7

    Range
    4156243..4163698 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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.
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