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

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: mouse all
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Genomic context

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_000004.12 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
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?

HMGB2-induced calreticulin translocation required for immunogenic cell death and ferroptosis of cancer cells are controlled by the nuclear exporter XPO1.
Title: HMGB2-induced calreticulin translocation required for immunogenic cell death and ferroptosis of cancer cells are controlled by the nuclear exporter XPO1.
LncRNA SNHG16 accelerates atherosclerosis and promotes ox-LDL-induced VSMC growth via the miRNA-22-3p/HMGB2 axis.
Title: LncRNA SNHG16 accelerates atherosclerosis and promotes ox-LDL-induced VSMC growth via the miRNA-22-3p/HMGB2 axis.
The transcription factor HMGB2 indirectly regulates APRIL expression and Gd-IgA1 production in patients with IgA nephropathy.
Title: The transcription factor HMGB2 indirectly regulates APRIL expression and Gd-IgA1 production in patients with IgA nephropathy.
The Effect of HMGB1 and HMGB2 on Transcriptional Regulation Differs in Neuroendocrine and Adenocarcinoma Models of Prostate Cancer.
Title: The Effect of HMGB1 and HMGB2 on Transcriptional Regulation Differs in Neuroendocrine and Adenocarcinoma Models of Prostate Cancer.
Correlation of serum HMGB1 and HMGB2 levels with clinical symptoms in allergic rhinitis children.
Title: Correlation of serum HMGB1 and HMGB2 levels with clinical symptoms in allergic rhinitis children.
Clinical and Experimental Study of High Mobility Group Box-2 and Valvular Calcification in Elderly Patients with Degenerative Heart Valve Disease.
Title: Clinical and Experimental Study of High Mobility Group Box-2 and Valvular Calcification in Elderly Patients with Degenerative Heart Valve Disease.
Structure and Functions of HMGB2 Protein.
Title: Structure and Functions of HMGB2 Protein.
Circular RNA SLTM as a miR-421-competing endogenous RNA to mediate HMGB2 expression stimulates apoptosis and inflammation in arthritic chondrocytes.
Title: Circular RNA SLTM as a miR-421-competing endogenous RNA to mediate HMGB2 expression stimulates apoptosis and inflammation in arthritic chondrocytes.
Long non-coding RNA NR2F2-AS1 regulates human osteosarcoma growth and metastasis through miR-425-5p-mediated HMGB2.
Title: Long non-coding RNA NR2F2-AS1 regulates human osteosarcoma growth and metastasis through miR-425-5p-mediated HMGB2.
[microRNA let-7g-3p regulates proliferation, migration, invasion and apoptosis of bladder cancer cells by targeting HMGB2].
Title: [microRNA let-7g-3p regulates proliferation, migration, invasion and apoptosis of bladder cancer cells by targeting HMGB2].

Submit: New GeneRIF Correction See all GeneRIFs (61)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-12669 (e-PCR)
- UniSTS:73475

PMC170950P6 (e-PCR)
- UniSTS:271624

HMGB2 (e-PCR)
- UniSTS:503325

SHGC-67901 (e-PCR)
- UniSTS:49708

HMGB2_3099 (e-PCR)
- UniSTS:462899

SHGC-60210 (e-PCR)
- UniSTS:68948

RH126943 (e-PCR)
- UniSTS:209768

RH101915 (e-PCR)
- UniSTS:96250

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 more info	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

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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)

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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_001130688.1 → NP_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:95 → 162

HMG_box; HMG (high mobility group) box

pfam09011
Location:6 → 78

HMG_box_2; HMG-box domain
NM_001130689.1 → NP_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:95 → 162

HMG_box; HMG (high mobility group) box

pfam09011
Location:6 → 78

HMG_box_2; HMG-box domain
NM_002129.4 → NP_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:95 → 162

HMG_box; HMG (high mobility group) box

pfam09011
Location:6 → 78

HMG_box_2; HMG-box domain