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

Gene ID: 3148, updated on 12-Oct-2019

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
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

Genomic context

See HMGB2 in Genome Data Viewer
Location:
4q34.1
Exon count:
5
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (173331376..173334358, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (174252527..174255595, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101930370 Neighboring gene RNA, 7SL, cytoplasmic 253, pseudogene Neighboring gene polypeptide N-acetylgalactosaminyltransferase 7 Neighboring gene microRNA 548t Neighboring gene uncharacterized LOC105377541 Neighboring gene SAP30 divergent transcript

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 BioSystems

  • Activation of DNA fragmentation factor, organism-specific biosystem (from REACTOME)
    Activation of DNA fragmentation factor, organism-specific biosystemDNA fragmentation in response to apoptotic signals is achieved, in part, through the activity of apoptotic nucleases, termed DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) (reviewed ...
  • Apoptosis, organism-specific biosystem (from REACTOME)
    Apoptosis, organism-specific biosystemApoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and ...
  • Apoptosis induced DNA fragmentation, organism-specific biosystem (from REACTOME)
    Apoptosis induced DNA fragmentation, organism-specific biosystemDNA fragmentation in response to apoptotic signals is achieved through the activity of two apoptotic nucleases, termed DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) and endonuclease...
  • Apoptotic execution phase, organism-specific biosystem (from REACTOME)
    Apoptotic execution phase, organism-specific biosystemIn the execution phase of apoptosis, effector caspases cleave vital cellular proteins leading to the morphological changes that characterize apoptosis. These changes include destruction of the nucle...
  • Ectoderm Differentiation, organism-specific biosystem (from WikiPathways)
    Ectoderm Differentiation, organism-specific biosystemModel depicting ectoderm specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell lin...
  • Programmed Cell Death, organism-specific biosystem (from REACTOME)
    Programmed Cell Death, organism-specific biosystemCell death is a fundamental cellular response that has a crucial role in shaping our bodies during development and in regulating tissue homeostasis by eliminating unwanted cells. There are a number o...
  • Retinoblastoma (RB) in Cancer, organism-specific biosystem (from WikiPathways)
    Retinoblastoma (RB) in Cancer, organism-specific biosystemDescribes the role of retinoblastoma (RB) gene in cancer.

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
DNA binding, bending IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA binding, bending IDA
Inferred from Direct Assay
more info
PubMed 
RAGE receptor binding IGI
Inferred from Genetic Interaction
more info
PubMed 
RNA binding HDA PubMed 
chemoattractant activity IDA
Inferred from Direct Assay
more info
PubMed 
damaged DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
double-stranded DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
drug binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enhancer sequence-specific 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
 
non-sequence-specific DNA binding, bending ISS
Inferred from Sequence or Structural Similarity
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific binding IEA
Inferred from Electronic Annotation
more info
 
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 ISS
Inferred from Sequence or Structural Similarity
more info
 
transcription regulatory region 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 topological change ISS
Inferred from Sequence or Structural Similarity
more info
 
V(D)J recombination ISS
Inferred from Sequence or Structural Similarity
more info
 
apoptotic DNA fragmentation TAS
Traceable Author Statement
more info
 
cell chemotaxis IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to lipopolysaccharide IEP
Inferred from Expression Pattern
more info
PubMed 
chromatin organization NAS
Non-traceable Author Statement
more info
PubMed 
defense response to Gram-negative bacterium IDA
Inferred from Direct Assay
more info
PubMed 
defense response to Gram-positive bacterium IDA
Inferred from Direct Assay
more info
PubMed 
inflammatory response to antigenic stimulus ISS
Inferred from Sequence or Structural Similarity
more info
 
innate immune response IEA
Inferred from Electronic Annotation
more info
 
male gonad development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of extrinsic apoptotic signaling pathway via death domain receptors IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
nucleosome assembly NAS
Non-traceable Author Statement
more info
PubMed 
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 endothelial cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of erythrocyte 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-beta production IEA
Inferred from Electronic Annotation
more info
 
positive regulation of megakaryocyte differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of nuclease activity IDA
Inferred from Direct Assay
more info
PubMed 
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 transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
regulation of neurogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of stem cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
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 
response to drug ISS
Inferred from Sequence or Structural Similarity
more info
 
response to lipopolysaccharide ISS
Inferred from Sequence or Structural Similarity
more info
 
response to steroid hormone IEA
Inferred from Electronic Annotation
more info
 
spermatid nucleus differentiation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cell 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 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
nuclear chromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear chromatin ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
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)

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
    P26583
    Related
    ENSP00000393448.2, ENST00000446922.6
    Conserved Domains (2) summary
    pfam00505
    Location:95162
    HMG_box; HMG (high mobility group) box
    cl00082
    Location:1078
    HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...
  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
    P26583
    Related
    ENSP00000404912.2, ENST00000438704.6
    Conserved Domains (2) summary
    pfam00505
    Location:95162
    HMG_box; HMG (high mobility group) box
    cl00082
    Location:1078
    HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...
  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
    P26583
    Related
    ENSP00000296503.5, ENST00000296503.10
    Conserved Domains (2) summary
    pfam00505
    Location:95162
    HMG_box; HMG (high mobility group) box
    cl00082
    Location:1078
    HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

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