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    HMGB1 high mobility group box 1 [ Homo sapiens (human) ]

    Gene ID: 3146, updated on 25-Nov-2021

    Summary

    Official Symbol
    HMGB1provided by HGNC
    Official Full Name
    high mobility group box 1provided by HGNC
    Primary source
    HGNC:HGNC:4983
    See related
    Ensembl:ENSG00000189403 MIM:163905
    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
    HMG1; HMG3; HMG-1; SBP-1
    Summary
    This gene encodes a protein that belongs to the High Mobility Group-box superfamily. The encoded non-histone, nuclear DNA-binding protein regulates transcription, and is involved in organization of DNA. This protein plays a role in several cellular processes, including inflammation, cell differentiation and tumor cell migration. Multiple pseudogenes of this gene have been identified. Alternative splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Sep 2015]
    Expression
    Ubiquitous expression in bone marrow (RPKM 98.7), lymph node (RPKM 87.4) and 25 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See HMGB1 in Genome Data Viewer
    Location:
    13q12.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    109.20211119 current GRCh38.p13 (GCF_000001405.39) 13 NC_000013.11 (30456704..30617597, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (31030841..31191734, complement)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene ubiquitin conjugating enzyme E2 L5 Neighboring gene uncharacterized LOC107984577 Neighboring gene RNA binding motif protein 22 pseudogene 2 Neighboring gene microfibril associated protein 1 pseudogene 1 Neighboring gene PTPN2 pseudogene 2 Neighboring gene ubiquitin specific peptidase like 1 Neighboring gene tRNA-Asn (anticodon GTT) 2-4

    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
    Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease.
    GeneReviews: Not available

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of high mobility group box 1 (HMGB1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 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

    Homology

    Clone Names

    • DKFZp686A04236

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables C-X-C chemokine binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA binding, bending IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables DNA binding, bending IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables DNA binding, bending ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables DNA polymerase binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables RAGE receptor binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables RNA binding HDA PubMed 
    enables RNA polymerase II-specific DNA-binding transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables bubble DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables chemoattractant activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables cytokine activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables damaged DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables damaged DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    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 integrin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables lipopolysaccharide binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables lyase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables phosphatidylserine binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    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 corepressor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in DNA geometric change ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in DNA recombination 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 T-helper 1 cell activation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in T-helper 1 cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in V(D)J recombination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in activation of innate immune response IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in apoptotic cell clearance IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in autophagy IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to lipopolysaccharide ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in dendritic cell chemotaxis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in double-strand break repair via nonhomologous end joining ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in inflammatory response IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in inflammatory response to antigenic stimulus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in innate immune response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in myeloid dendritic cell activation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of CD4-positive, alpha-beta T cell differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of RNA polymerase II transcription preinitiation complex assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of apoptotic cell clearance IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of blood vessel endothelial cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of interferon-gamma production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in neuron projection development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in neutrophil clearance IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive chemotaxis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of DNA ligation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of ERK1 and ERK2 cascade IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of JNK cascade IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of MAPK cascade IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of activated T cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of autophagy IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of blood vessel endothelial cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of chemokine (C-X-C motif) ligand 2 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cysteine-type endopeptidase activity involved in apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cytosolic calcium ion concentration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of dendritic cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of interleukin-1 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of interleukin-10 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of interleukin-12 production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of interleukin-6 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of interleukin-8 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of mismatch repair IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of monocyte chemotaxis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of toll-like receptor 9 signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of tumor necrosis factor production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of vascular endothelial cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of T cell mediated immune response to tumor cell ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of restriction endodeoxyribonuclease activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of tolerance induction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of alphav-beta3 integrin-HMGB1 complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cell surface IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in condensed chromosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endoplasmic reticulum-Golgi intermediate compartment IEA
    Inferred from Electronic Annotation
    more info
     
    located_in endosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    located_in extracellular space IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular space ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in ficolin-1-rich granule lumen TAS
    Traceable Author Statement
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in secretory granule lumen TAS
    Traceable Author Statement
    more info
     
    part_of transcription repressor complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    high mobility group protein B1
    Names
    Amphoterin
    Sulfoglucuronyl carbohydrate binding protein
    high-mobility group (nonhistone chromosomal) protein 1

    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_001313892.2NP_001300821.1  high mobility group protein B1 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AL353648
      Consensus CDS
      CCDS9335.1
      UniProtKB/Swiss-Prot
      P09429
      UniProtKB/TrEMBL
      A0A024RDR0
      Related
      ENSP00000343040.4, ENST00000339872.8
      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_001313893.1NP_001300822.1  high mobility group protein B1 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AK122825, AL353648
      Consensus CDS
      CCDS9335.1
      UniProtKB/Swiss-Prot
      P09429
      UniProtKB/TrEMBL
      A0A024RDR0
      Related
      ENSP00000384678.1, ENST00000405805.5
      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_001363661.2NP_001350590.1  high mobility group protein B1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AL353648
      Consensus CDS
      CCDS86347.1
      Related
      ENSP00000382412.1, ENST00000399489.5
      Conserved Domains (2) summary
      pfam00505
      Location:95157
      HMG_box; HMG (high mobility group) box
      pfam09011
      Location:678
      HMG_box_2; HMG-box domain
    4. NM_001370339.1NP_001357268.1  high mobility group protein B1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AL353648
      Related
      ENSP00000369904.1, ENST00000326004.4
      Conserved Domains (2) summary
      pfam00505
      Location:95157
      HMG_box; HMG (high mobility group) box
      pfam09011
      Location:678
      HMG_box_2; HMG-box domain
    5. NM_001370340.1NP_001357269.1  high mobility group protein B1 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AL138681, AL353648
      Conserved Domains (2) summary
      pfam00505
      Location:95162
      HMG_box; HMG (high mobility group) box
      pfam09011
      Location:678
      HMG_box_2; HMG-box domain
    6. NM_001370341.1NP_001357270.1  high mobility group protein B1 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AL353648
      Related
      ENSP00000382417.1, ENST00000399494.5
      Conserved Domains (2) summary
      pfam00505
      Location:95162
      HMG_box; HMG (high mobility group) box
      pfam09011
      Location:678
      HMG_box_2; HMG-box domain
    7. NM_002128.7NP_002119.1  high mobility group protein B1 isoform 1

      See identical proteins and their annotated locations for NP_002119.1

      Status: REVIEWED

      Source sequence(s)
      AL353648
      Consensus CDS
      CCDS9335.1
      UniProtKB/Swiss-Prot
      P09429
      UniProtKB/TrEMBL
      A0A024RDR0
      Related
      ENSP00000345347.5, ENST00000341423.10
      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: Homo sapiens Updated Annotation Release 109.20211119

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000013.11 Reference GRCh38.p13 Primary Assembly

      Range
      30456704..30617597 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024449341.1XP_024305109.1  high mobility group protein B1 isoform X1

      Conserved Domains (2) summary
      pfam00505
      Location:95162
      HMG_box; HMG (high mobility group) box
      pfam09011
      Location:678
      HMG_box_2; HMG-box domain
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