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    HMGB2 high mobility group box 2 [ Homo sapiens (human) ]

    Gene ID: 3148, updated on 9-Dec-2024

    Summary

    Official Symbol
    HMGB2provided by HGNC
    Official Full Name
    high mobility group box 2provided by HGNC
    Primary source
    HGNC:HGNC:5000
    See related
    Ensembl:ENSG00000164104 MIM:163906; AllianceGenome:HGNC:5000
    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
    HMG2
    Summary
    This gene encodes a member of the non-histone chromosomal high mobility group protein family. The proteins of this family are chromatin-associated and ubiquitously distributed in the nucleus of higher eukaryotic cells. In vitro studies have demonstrated that this protein is able to efficiently bend DNA and form DNA circles. These studies suggest a role in facilitating cooperative interactions between cis-acting proteins by promoting DNA flexibility. This protein was also reported to be involved in the final ligation step in DNA end-joining processes of DNA double-strand breaks repair and V(D)J recombination. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in bone marrow (RPKM 603.0), lymph node (RPKM 141.8) and 10 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See HMGB2 in Genome Data Viewer
    Location:
    4q34.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (173331376..173334358, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (176670801..176673783, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (174252527..174255509, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene GALNT7 divergent transcript Neighboring gene RNA, 7SL, cytoplasmic 253, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22154 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22155 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15803 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15804 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15805 Neighboring gene polypeptide N-acetylgalactosaminyltransferase 7 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:174147305-174147821 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:174147822-174148337 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15806 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15807 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22156 Neighboring gene uncharacterized LOC124900812 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:174196465-174196667 Neighboring gene microRNA 548t Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:174227831-174228613 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:174228614-174229395 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15808 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15809 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:174255709-174256444 Neighboring gene SAP30 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22157 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22158 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15812 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:174292649-174293212 Neighboring gene Sin3A associated protein 30

    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?

    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 DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables DNA binding, bending IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables DNA binding, bending IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables RAGE receptor binding IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    enables RNA binding HDA PubMed 
    enables chemoattractant activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables cis-regulatory region sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables damaged DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables double-stranded DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables four-way junction DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables non-sequence-specific DNA binding, bending ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein domain specific binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables single-stranded DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables supercoiled DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables transcription cis-regulatory region binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription coactivator activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription factor binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    involved_in DNA geometric change ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in DNA topological change ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in V(D)J recombination ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell chemotaxis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cellular response to lipopolysaccharide IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in chromatin organization NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in defense response to Gram-negative bacterium IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in defense response to Gram-positive bacterium IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in double-strand break repair via nonhomologous end joining ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in extrinsic apoptotic signaling pathway via death domain receptors IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in inflammatory response to antigenic stimulus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in innate immune response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in male gonad development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of extrinsic apoptotic signaling pathway via death domain receptors IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in nucleosome assembly NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in positive chemotaxis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of endothelial cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of erythrocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of innate immune response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of interferon-beta production IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of megakaryocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of neurogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of stem cell proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to lipopolysaccharide ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in response to steroid hormone IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in spermatid nucleus differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in chromatin ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in condensed chromosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular space IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    high mobility group protein B2
    Names
    HMG-2
    high mobility group protein 2
    high-mobility group (nonhistone chromosomal) protein 2

    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_001130688.1NP_001124160.1  high mobility group protein B2

      See identical proteins and their annotated locations for NP_001124160.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1.
      Source sequence(s)
      AA576809, AK311864, BM727941
      Consensus CDS
      CCDS3816.1
      UniProtKB/Swiss-Prot
      B2R4K8, D3DP37, P26583, Q5U072
      Related
      ENSP00000393448.2, ENST00000446922.6
      Conserved Domains (2) summary
      pfam00505
      Location:95162
      HMG_box; HMG (high mobility group) box
      pfam09011
      Location:678
      HMG_box_2; HMG-box domain
    2. NM_001130689.1NP_001124161.1  high mobility group protein B2

      See identical proteins and their annotated locations for NP_001124161.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1.
      Source sequence(s)
      AA576809, AC097534, BM727941, BM781845
      Consensus CDS
      CCDS3816.1
      UniProtKB/Swiss-Prot
      B2R4K8, D3DP37, P26583, Q5U072
      Related
      ENSP00000404912.2, ENST00000438704.6
      Conserved Domains (2) summary
      pfam00505
      Location:95162
      HMG_box; HMG (high mobility group) box
      pfam09011
      Location:678
      HMG_box_2; HMG-box domain
    3. NM_002129.4NP_002120.1  high mobility group protein B2

      See identical proteins and their annotated locations for NP_002120.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript.
      Source sequence(s)
      AA576809, AC097534, BM727941
      Consensus CDS
      CCDS3816.1
      UniProtKB/Swiss-Prot
      B2R4K8, D3DP37, P26583, Q5U072
      Related
      ENSP00000296503.5, ENST00000296503.10
      Conserved Domains (2) summary
      pfam00505
      Location:95162
      HMG_box; HMG (high mobility group) box
      pfam09011
      Location:678
      HMG_box_2; HMG-box domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      173331376..173334358 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      176670801..176673783 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)