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

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; AllianceGenome:HGNC:4983
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: mouse all
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Genomic context

Location:: 13q12.3

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (30456704..30617597, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (29679118..29839654, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (31030841..31191734, complement)

Chromosome 13 - NC_000013.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

IFN-gamma induces acute graft-versus-host disease by promoting HMGB1-mediated nuclear-to-cytoplasm translocation and autophagic degradation of p53.
Title: IFN-γ induces acute graft-versus-host disease by promoting HMGB1-mediated nuclear-to-cytoplasm translocation and autophagic degradation of p53.
Elevated levels of damage-associated molecular patterns HMGB1 and S100A8/A9 coupled with toll-like receptor-triggered monocyte activation are associated with inflammation in patients with myelofibrosis.
Title: Elevated levels of damage-associated molecular patterns HMGB1 and S100A8/A9 coupled with toll-like receptor-triggered monocyte activation are associated with inflammation in patients with myelofibrosis.
LncRNA ILF3-AS1 mediates oxidative stress and inflammation through miR-504-3p/HMGB1 axis in a cellular model of temporal lobe epilepsy.
Title: LncRNA ILF3-AS1 mediates oxidative stress and inflammation through miR-504-3p/HMGB1 axis in a cellular model of temporal lobe epilepsy.
S100A9 and HMGB1 orchestrate MDSC-mediated immunosuppression in melanoma through TLR4 signaling.
Title: S100A9 and HMGB1 orchestrate MDSC-mediated immunosuppression in melanoma through TLR4 signaling.
HMGB1 released from pyroptotic vascular endothelial cells promotes immune disorders in exertional heatstroke.
Title: HMGB1 released from pyroptotic vascular endothelial cells promotes immune disorders in exertional heatstroke.
Intestinal Epithelia and Myeloid Immune Cells Shape Colitis Severity and Colorectal Carcinogenesis via High-mobility Group Box Protein 1.
Title: Intestinal Epithelia and Myeloid Immune Cells Shape Colitis Severity and Colorectal Carcinogenesis via High-mobility Group Box Protein 1.
HMGB1-Mediated Cell Death-A Crucial Element in Post-Hepatectomy Liver Failure.
Title: HMGB1-Mediated Cell Death-A Crucial Element in Post-Hepatectomy Liver Failure.
Effects of High-Mobility Group Box-1 on Mucosal Immunity and Epithelial Differentiation in Colitic Carcinoma.
Title: Effects of High-Mobility Group Box-1 on Mucosal Immunity and Epithelial Differentiation in Colitic Carcinoma.
The Association of HMGB1 and RAGE Gene Polymorphisms with IgA Vasculitis.
Title: The Association of HMGB1 and RAGE Gene Polymorphisms with IgA Vasculitis.
CircUBE2D2 regulates HMGB1 through miR-885-5p to promote ovarian cancer malignancy.
Title: CircUBE2D2 regulates HMGB1 through miR-885-5p to promote ovarian cancer malignancy.

Submit: New GeneRIF Correction See all GeneRIFs (1281)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

HMGB1_1600 (e-PCR)
- UniSTS:277311

RH91371 (e-PCR)
- UniSTS:85878

STS-N92507 (e-PCR)
- UniSTS:933

SHGC-142889 (e-PCR)
- UniSTS:171727

GDB:554977 (e-PCR)
- UniSTS:157665

MARC_26602-26603:1033757772:1 (e-PCR)
- UniSTS:269038

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
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 more info	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 receptor ligand activity	IDA Inferred from Direct Assay 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 heterochromatin formation	IGI Inferred from Genetic Interaction more info	PubMed
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 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 negative regulation of type II interferon production	IDA Inferred from Direct Assay 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 positive regulation of viral entry into host cell	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
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	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
is_active_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
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

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Preferred Names: high mobility group protein B1

Names: Amphoterin; Sulfoglucuronyl carbohydrate binding protein; high-mobility group (nonhistone chromosomal) protein 1

NCBI Reference Sequences (RefSeq)

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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)

NM_001313892.2 → NP_001300821.1 high mobility group protein B1 isoform 1

Status: REVIEWED

Source sequence(s)

AL353648

Consensus CDS

CCDS9335.1

UniProtKB/Swiss-Prot

A5D8W9, P09429, Q14321, Q5T7C3, Q6IBE1

Related

ENSP00000343040.4, ENST00000339872.8

Conserved Domains (2) summary

pfam00505
Location:95 → 162

HMG_box; HMG (high mobility group) box

pfam09011
Location:6 → 78

HMG_box_2; HMG-box domain
NM_001313893.1 → NP_001300822.1 high mobility group protein B1 isoform 1

Status: REVIEWED

Source sequence(s)

AK122825, AL353648

Consensus CDS

CCDS9335.1

UniProtKB/Swiss-Prot

A5D8W9, P09429, Q14321, Q5T7C3, Q6IBE1

Related

ENSP00000384678.1, ENST00000405805.5

Conserved Domains (2) summary

pfam00505
Location:95 → 162

HMG_box; HMG (high mobility group) box

pfam09011
Location:6 → 78

HMG_box_2; HMG-box domain
NM_001363661.2 → NP_001350590.1 high mobility group protein B1 isoform 2

Status: REVIEWED

Source sequence(s)

AL353648

Consensus CDS

CCDS86347.1

UniProtKB/TrEMBL

Q59GW1, Q5T7C4

Related

ENSP00000382412.1, ENST00000399489.5

Conserved Domains (2) summary

pfam00505
Location:95 → 157

HMG_box; HMG (high mobility group) box

pfam09011
Location:6 → 78

HMG_box_2; HMG-box domain
NM_001370339.1 → NP_001357268.1 high mobility group protein B1 isoform 2

Status: REVIEWED

Source sequence(s)

AL353648

Consensus CDS

CCDS86347.1

UniProtKB/TrEMBL

Q59GW1, Q5T7C4

Related

ENSP00000369904.1, ENST00000326004.4

Conserved Domains (2) summary

pfam00505
Location:95 → 157

HMG_box; HMG (high mobility group) box

pfam09011
Location:6 → 78

HMG_box_2; HMG-box domain
NM_001370340.1 → NP_001357269.1 high mobility group protein B1 isoform 1

Status: REVIEWED

Source sequence(s)

AL138681, AL353648

Consensus CDS

CCDS9335.1

UniProtKB/Swiss-Prot

A5D8W9, P09429, Q14321, Q5T7C3, Q6IBE1

Conserved Domains (2) summary

pfam00505
Location:95 → 162

HMG_box; HMG (high mobility group) box

pfam09011
Location:6 → 78

HMG_box_2; HMG-box domain
NM_001370341.1 → NP_001357270.1 high mobility group protein B1 isoform 1

Status: REVIEWED

Source sequence(s)

AL353648

Consensus CDS

CCDS9335.1

UniProtKB/Swiss-Prot

A5D8W9, P09429, Q14321, Q5T7C3, Q6IBE1

Related

ENSP00000382417.1, ENST00000399494.5

Conserved Domains (2) summary

pfam00505
Location:95 → 162

HMG_box; HMG (high mobility group) box

pfam09011
Location:6 → 78

HMG_box_2; HMG-box domain
NM_002128.7 → NP_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

A5D8W9, P09429, Q14321, Q5T7C3, Q6IBE1

Related

ENSP00000345347.5, ENST00000341423.10

Conserved Domains (2) summary

pfam00505
Location:95 → 162

HMG_box; HMG (high mobility group) box

pfam09011
Location:6 → 78

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

NC_000013.11 Reference GRCh38.p14 Primary Assembly

Range

30456704..30617597 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_024449341.2 → XP_024305109.1 high mobility group protein B1 isoform X1

UniProtKB/Swiss-Prot

A5D8W9, P09429, Q14321, Q5T7C3, Q6IBE1

Conserved Domains (2) summary

pfam00505
Location:95 → 162

HMG_box; HMG (high mobility group) box

pfam09011
Location:6 → 78

HMG_box_2; HMG-box domain
XM_047430285.1 → XP_047286241.1 high mobility group protein B1 isoform X2

UniProtKB/TrEMBL

Q5T7C4
XM_047430284.1 → XP_047286240.1 high mobility group protein B1 isoform X3

UniProtKB/TrEMBL

B7Z965

Alternate T2T-CHM13v2.0

Genomic

NC_060937.1 Alternate T2T-CHM13v2.0

Range

29679118..29839654 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054374485.1 → XP_054230460.1 high mobility group protein B1 isoform X1

UniProtKB/Swiss-Prot

A5D8W9, P09429, Q14321, Q5T7C3, Q6IBE1
XM_054374486.1 → XP_054230461.1 high mobility group protein B1 isoform X2

UniProtKB/TrEMBL

Q5T7C4