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

Gene ID: 3120, updated on 2-Aug-2021

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
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
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Genomic context

See HLA-DQB2 in Genome Data Viewer
Location:
6p21.32
Exon count:
6
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (32756094..32763553, complement)
105.20201022 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 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

Associated conditions

Description Tests
A genome-wide association study identified new variants associated with the risk of chronic hepatitis B.
GeneReviews: Not available
A genome-wide association study identifies three new risk loci for Kawasaki disease.
GeneReviews: Not available
A genome-wide association study of chronic hepatitis B identified novel risk locus in a Japanese population.
GeneReviews: Not available
A genome-wide association study on chronic HBV infection and its clinical progression in male Han-Taiwanese.
GeneReviews: Not available
Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production.
GeneReviews: Not available
Genome-wide pathway analysis of genome-wide association studies on systemic lupus erythematosus and rheumatoid arthritis.
GeneReviews: Not available
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
GeneReviews: Not available
New loci associated with chronic hepatitis B virus infection in Han Chinese.
GeneReviews: Not available
Susceptibility loci associated with specific and shared subtypes of lymphoid malignancies.
GeneReviews: Not available

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

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
PubMed 
enables MHC class II receptor activity NAS
Non-traceable Author Statement
more info
PubMed 
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
PubMed 
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
 
located_in endosome membrane IEA
Inferred from Electronic Annotation
more info
 
located_in integral component of lumenal side of endoplasmic reticulum membrane TAS
Traceable Author Statement
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/Swiss-Prot
    P05538
    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/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: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 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, 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, 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.p13 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p13 ALT_REF_LOCI_1

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

Reference GRCh38.p13 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p13 ALT_REF_LOCI_2

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

Reference GRCh38.p13 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p13 ALT_REF_LOCI_3

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

Reference GRCh38.p13 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p13 ALT_REF_LOCI_4

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

Reference GRCh38.p13 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p13 ALT_REF_LOCI_5

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

Reference GRCh38.p13 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p13 ALT_REF_LOCI_6

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

Reference GRCh38.p13 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p13 ALT_REF_LOCI_7

    Range
    4156243..4163677 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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