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

Gene ID: 3146, updated on 1-Jun-2020

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

Genomic context

See HMGB1 in Genome Data Viewer
Location:
13q12.3
Exon count:
9
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 13 NC_000013.11 (30456704..30617597, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (31032877..31191942, 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

NHGRI GWAS Catalog

Description
Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease.
NHGRI GWA Catalog

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

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

    Status: REVIEWED

    Source sequence(s)
    AK122825, AL353648, AV763680, BC030981, CB051582
    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:1078
    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:1078
    HMG_box_2; HMG-box domain
  3. NM_001363661.1NP_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:1078
    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:1078
    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:1078
    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:1078
    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:1078
    HMG_box_2; HMG-box domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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:1078
    HMG_box_2; HMG-box domain
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