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Aliases for HMGB2 Gene

Aliases for HMGB2 Gene

  • High Mobility Group Box 2 2 3 5
  • High-Mobility Group (Nonhistone Chromosomal) Protein 2 2 3
  • High Mobility Group Protein 2 3 4
  • HMG-2 3 4
  • HMG2 3 4
  • High Mobility Group Protein B2 3
  • High-Mobility Group Box 2 2

External Ids for HMGB2 Gene

Previous HGNC Symbols for HMGB2 Gene

  • HMG2

Previous GeneCards Identifiers for HMGB2 Gene

  • GC04M175172
  • GC04M174790
  • GC04M174948
  • GC04M174627
  • GC04M174489
  • GC04M174252
  • GC04M170000

Summaries for HMGB2 Gene

Entrez Gene Summary for HMGB2 Gene

  • 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]

GeneCards Summary for HMGB2 Gene

HMGB2 (High Mobility Group Box 2) is a Protein Coding gene. Among its related pathways are Apoptotic cleavage of cellular proteins and Apoptosis induced DNA fragmentation. Gene Ontology (GO) annotations related to this gene include chromatin binding. An important paralog of this gene is HMGB1.

UniProtKB/Swiss-Prot for HMGB2 Gene

  • Multifunctional protein with various roles in different cellular compartments. May act in a redox sensitive manner. In the nucleus is an abundant chromatin-associated non-histone protein involved in transcription, chromatin remodeling and V(D)J recombination and probably other processes. Binds DNA with a preference to non-canonical DNA structures such as single-stranded DNA. Can bent DNA and enhance DNA flexibility by looping thus providing a mechanism to promote activities on various gene promoters by enhancing transcription factor binding and/or bringing distant regulatory sequences into close proximity (PubMed:7797075, PubMed:11909973, PubMed:19522541, PubMed:18413230, PubMed:19965638, PubMed:20123072). Involved in V(D)J recombination by acting as a cofactor of the RAG complex: acts by stimulating cleavage and RAG protein binding at the 23 bp spacer of conserved recombination signal sequences (RSS) (By similarity). Proposed to be involved in the innate immune response to nucleic acids by acting as a promiscuous immunogenic DNA/RNA sensor which cooperates with subsequent discriminative sensing by specific pattern recognition receptors (By similarity). In the extracellular compartment acts as a chemokine. Promotes proliferation and migration of endothelial cells implicating AGER/RAGE (PubMed:19811285). Has antimicrobial activity in gastrointestinal epithelial tissues (PubMed:23877675). Involved in inflammatory response to antigenic stimulus coupled with proinflammatory activity (By similarity). Involved in modulation of neurogenesis probably by regulation of neural stem proliferation (By similarity). Involved in articular cartilage surface maintenance implicating LEF1 and the Wnt/beta-catenin pathway (By similarity).

Gene Wiki entry for HMGB2 Gene

Additional gene information for HMGB2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HMGB2 Gene

Genomics for HMGB2 Gene

GeneHancer (GH) Regulatory Elements for HMGB2 Gene

Promoters and enhancers for HMGB2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04J173369 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 663.1 -36.0 -35976 4.2 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 HMGB2 LOC105377540 SAP30 CEP44 ENSG00000248774 SCRG1 FBXO8 LOC101928383 GC04M173250
GH04J173331 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 +0.8 775 4.9 HDGF PKNOX1 CLOCK FOXA2 SMAD1 ARNT ZFP64 ARID4B NEUROD1 SIN3A GC04P173336 HMGB2 LOC105377541 SAP30 CEP44 SCRG1 RPL5P11 ENSG00000248774 GC04M173250
GH04J173414 Promoter/Enhancer 2 EPDnew FANTOM5 Ensembl ENCODE 24.7 -81.1 -81075 2.8 HDGF PKNOX1 SMAD1 ARNT NEUROD1 YBX1 ZNF2 TCF12 ARID2 E2F8 SCRG1 CEP44 HMGB2 ENSG00000261646 HAND2-AS1 SAP30 RPL5P11 LOC101928383 GC04M173250
GH04J174120 Promoter/Enhancer 1.6 Ensembl ENCODE dbSUPER 11.2 -785.3 -785276 0.8 HDAC1 ATF1 ARNT ZSCAN4 ZNF2 ZNF48 RAD21 ARID2 EGR1 ZNF366 LINC02268 CEP44 HMGB2 ENSG00000261646 HAND2-AS1 GC04P174110 ENSG00000250957
GH04J173366 Enhancer 0.9 Ensembl ENCODE 13.6 -32.5 -32541 1.6 JUN BATF IRF4 CHAMP1 FOSL1 SCRT2 RUNX3 CREM CBFA2T3 JUNB HMGB2 ENSG00000248774 SCRG1 RNU6-1096P CEP44 FBXO8 LOC105377540 SAP30 GC04P173358 GC04M173250
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HMGB2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HMGB2 gene promoter:
  • FOXI1
  • HFH-3
  • E2F
  • E2F-1

Genomic Locations for HMGB2 Gene

Genomic Locations for HMGB2 Gene
chr4:173,331,376-173,335,125
(GRCh38/hg38)
Size:
3,750 bases
Orientation:
Minus strand
chr4:174,252,527-174,256,276
(GRCh37/hg19)
Size:
3,750 bases
Orientation:
Minus strand

Genomic View for HMGB2 Gene

Genes around HMGB2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HMGB2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HMGB2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HMGB2 Gene

Proteins for HMGB2 Gene

  • Protein details for HMGB2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P26583-HMGB2_HUMAN
    Recommended name:
    High mobility group protein B2
    Protein Accession:
    P26583
    Secondary Accessions:
    • B2R4K8
    • D3DP37
    • Q5U072

    Protein attributes for HMGB2 Gene

    Size:
    209 amino acids
    Molecular mass:
    24034 Da
    Quaternary structure:
    • Interacts with POU2F2, POU2F1 and POU3F1 (By similarity). Component of the RAG complex composed of core components RAG1 and RAG2, and associated component HMGB1 or HMGB2 (By similarity). Component of the SET complex, composed of at least ANP32A, APEX1, HMGB2, NME1, SET and TREX1. Directly interacts with SET (PubMed:11909973). Interacts with LEF1 (By similarity).

neXtProt entry for HMGB2 Gene

Post-translational modifications for HMGB2 Gene

  • Reduction/oxidation of cysteine residues Cys-23, Cys-45 and Cys-106 and a possible intramolecular disulfide bond involving Cys-23 and Cys-45 give rise to different redox forms with specific functional activities in various cellular compartments: 1- fully reduced HMGB2 (HMGB2C23hC45hC106h), 2- disulfide HMGB2 (HMGB2C23-C45C106h) and 3- sulfonyl HMGB2 (HMGB2C23soC45soC106so).
  • Acetylation enhances nucleosome binding and chromation remodeling activity.
  • Ubiquitination at Lys147
  • Modification sites at PhosphoSitePlus

Other Protein References for HMGB2 Gene

No data available for DME Specific Peptides for HMGB2 Gene

Domains & Families for HMGB2 Gene

Gene Families for HMGB2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for HMGB2 Gene

Suggested Antigen Peptide Sequences for HMGB2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P26583

UniProtKB/Swiss-Prot:

HMGB2_HUMAN :
  • Both, HMG box 1 and HMG box 2, show antimicrobial activity.
  • Belongs to the HMGB family.
Domain:
  • Both, HMG box 1 and HMG box 2, show antimicrobial activity.
Family:
  • Belongs to the HMGB family.
genes like me logo Genes that share domains with HMGB2: view

Function for HMGB2 Gene

Molecular function for HMGB2 Gene

UniProtKB/Swiss-Prot Function:
Multifunctional protein with various roles in different cellular compartments. May act in a redox sensitive manner. In the nucleus is an abundant chromatin-associated non-histone protein involved in transcription, chromatin remodeling and V(D)J recombination and probably other processes. Binds DNA with a preference to non-canonical DNA structures such as single-stranded DNA. Can bent DNA and enhance DNA flexibility by looping thus providing a mechanism to promote activities on various gene promoters by enhancing transcription factor binding and/or bringing distant regulatory sequences into close proximity (PubMed:7797075, PubMed:11909973, PubMed:19522541, PubMed:18413230, PubMed:19965638, PubMed:20123072). Involved in V(D)J recombination by acting as a cofactor of the RAG complex: acts by stimulating cleavage and RAG protein binding at the 23 bp spacer of conserved recombination signal sequences (RSS) (By similarity). Proposed to be involved in the innate immune response to nucleic acids by acting as a promiscuous immunogenic DNA/RNA sensor which cooperates with subsequent discriminative sensing by specific pattern recognition receptors (By similarity). In the extracellular compartment acts as a chemokine. Promotes proliferation and migration of endothelial cells implicating AGER/RAGE (PubMed:19811285). Has antimicrobial activity in gastrointestinal epithelial tissues (PubMed:23877675). Involved in inflammatory response to antigenic stimulus coupled with proinflammatory activity (By similarity). Involved in modulation of neurogenesis probably by regulation of neural stem proliferation (By similarity). Involved in articular cartilage surface maintenance implicating LEF1 and the Wnt/beta-catenin pathway (By similarity).

Gene Ontology (GO) - Molecular Function for HMGB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000400 four-way junction DNA binding ISS --
GO:0001158 enhancer sequence-specific DNA binding ISS --
GO:0003677 DNA binding IMP,IEA 11909973
GO:0003682 chromatin binding IBA --
GO:0003684 damaged DNA binding IDA 8226934
genes like me logo Genes that share ontologies with HMGB2: view
genes like me logo Genes that share phenotypes with HMGB2: view

Animal Models for HMGB2 Gene

MGI Knock Outs for HMGB2:

Animal Model Products

miRNA for HMGB2 Gene

miRTarBase miRNAs that target HMGB2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HMGB2 Gene

Localization for HMGB2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HMGB2 Gene

Nucleus. Chromosome. Cytoplasm. Secreted. Note=In basal state predominantly nuclear. {ECO:0000305}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HMGB2 gene
Compartment Confidence
extracellular 5
nucleus 5
endoplasmic reticulum 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleus (3)
  • Nucleoli (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HMGB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin ISS --
GO:0000793 condensed chromosome IDA 12925773
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IDA 19811285
GO:0005623 cell IDA 15496585
genes like me logo Genes that share ontologies with HMGB2: view

Pathways & Interactions for HMGB2 Gene

genes like me logo Genes that share pathways with HMGB2: view

Pathways by source for HMGB2 Gene

2 Qiagen pathways for HMGB2 Gene
1 Cell Signaling Technology pathway for HMGB2 Gene

Gene Ontology (GO) - Biological Process for HMGB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001938 positive regulation of endothelial cell proliferation IDA 19811285
GO:0002376 immune system process IEA --
GO:0002437 inflammatory response to antigenic stimulus ISS --
GO:0006265 DNA topological change ISS --
GO:0006309 apoptotic DNA fragmentation TAS --
genes like me logo Genes that share ontologies with HMGB2: view

No data available for SIGNOR curated interactions for HMGB2 Gene

Drugs & Compounds for HMGB2 Gene

(3) Drugs for HMGB2 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with HMGB2: view

Transcripts for HMGB2 Gene

mRNA/cDNA for HMGB2 Gene

Unigene Clusters for HMGB2 Gene

High mobility group box 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HMGB2 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f ^ 2a · 2b ^ 3a · 3b · 3c · 3d · 3e ^ 4a · 4b ^ 5a · 5b · 5c ^ 6a · 6b · 6c
SP1: - - - -
SP2: - - - - - - -
SP3: - - -
SP4: - - - - -
SP5: - - - -
SP6: - - - - -
SP7: -
SP8: - - -
SP9:
SP10: - - - -

Relevant External Links for HMGB2 Gene

GeneLoc Exon Structure for
HMGB2
ECgene alternative splicing isoforms for
HMGB2

Expression for HMGB2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HMGB2 Gene

mRNA differential expression in normal tissues according to GTEx for HMGB2 Gene

This gene is overexpressed in Whole Blood (x6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HMGB2 Gene



Protein tissue co-expression partners for HMGB2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HMGB2 Gene:

HMGB2

SOURCE GeneReport for Unigene cluster for HMGB2 Gene:

Hs.434953

mRNA Expression by UniProt/SwissProt for HMGB2 Gene:

P26583-HMGB2_HUMAN
Tissue specificity: Expressed in gastric and intestinal tissues (at protein level).

Evidence on tissue expression from TISSUES for HMGB2 Gene

  • Liver(4.6)
  • Skin(4.3)
  • Nervous system(4.3)
  • Bone marrow(2.8)
  • Blood(2.4)
  • Eye(2.4)
  • Lymph node(2.3)
  • Bone(2.2)
  • Lung(2.2)
  • Spleen(2.1)
  • Intestine(2)
genes like me logo Genes that share expression patterns with HMGB2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for HMGB2 Gene

Orthologs for HMGB2 Gene

This gene was present in the common ancestor of animals.

Orthologs for HMGB2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HMGB2 34 33
  • 99.84 (n)
OneToOne
cow
(Bos Taurus)
Mammalia -- 34
  • 95 (a)
OneToMany
HMGB2 34 33
  • 91.07 (n)
OneToMany
dog
(Canis familiaris)
Mammalia HMGB2 34 33
  • 94.65 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia HMGB2 34
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Hmgb2 16 34 33
  • 90.55 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia HMGB2 34
  • 52 (a)
OneToOne
chicken
(Gallus gallus)
Aves HMGB2 34 33
  • 83.96 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia HMGB2 34
  • 88 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii hmgb2a 34 33
  • 76.06 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000005 33
  • 59.24 (n)
fruit fly
(Drosophila melanogaster)
Insecta Dsp1 33
  • 58.54 (n)
worm
(Caenorhabditis elegans)
Secernentea hmg-1.2 33
  • 51.1 (n)
Species where no ortholog for HMGB2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for HMGB2 Gene

ENSEMBL:
Gene Tree for HMGB2 (if available)
TreeFam:
Gene Tree for HMGB2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HMGB2: view image

Paralogs for HMGB2 Gene

Variants for HMGB2 Gene

Sequence variations from dbSNP and Humsavar for HMGB2 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs1000939790 -- 173,333,755(-) T/C 5_prime_UTR_variant, intron_variant
rs1002221210 -- 173,333,246(-) G/A intron_variant
rs1002310680 -- 173,331,972(-) G/A 3_prime_UTR_variant
rs1002492482 -- 173,333,443(-) C/T intron_variant
rs1002897949 -- 173,334,437(-) A/G 5_prime_UTR_variant, genic_upstream_transcript_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for HMGB2 Gene

Variant ID Type Subtype PubMed ID
nsv4610 CNV deletion 18451855

Variation tolerance for HMGB2 Gene

Residual Variation Intolerance Score: 44.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.92; 19.01% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HMGB2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HMGB2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HMGB2 Gene

Disorders for HMGB2 Gene

Additional Disease Information for HMGB2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for HMGB2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HMGB2 Gene

Publications for HMGB2 Gene

  1. Sequence of human HMG2 cDNA. (PMID: 1754403) Majumdar A … Seidman MM (Nucleic acids research 1991) 2 3 4 58
  2. Antimicrobial activity of high-mobility-group box 2: a new function to a well-known protein. (PMID: 23877675) Küchler R … Wehkamp J (Antimicrobial agents and chemotherapy 2013) 3 4 58
  3. High-mobility group protein HMGB2 regulates human erythroid differentiation through trans-activation of GFI1B transcription. (PMID: 19965638) Laurent B … Duménil D (Blood 2010) 3 4 58
  4. High mobility group B2 is secreted by myeloid cells and has mitogenic and chemoattractant activities similar to high mobility group B1. (PMID: 19811285) Pusterla T … Bianchi ME (Autoimmunity 2009) 3 4 58
  5. HMGB1 and HMGB2 proteins up-regulate cellular expression of human topoisomerase IIalpha. (PMID: 19223331) Stros M … Pospísilová S (Nucleic acids research 2009) 3 22 58

Products for HMGB2 Gene

Sources for HMGB2 Gene

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