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Aliases for HMGB3 Gene

Aliases for HMGB3 Gene

  • High Mobility Group Box 3 2 3 5
  • High-Mobility Group (Nonhistone Chromosomal) Protein 4 2 3
  • High Mobility Group Protein 2a 3 4
  • HMG-2a 3 4
  • HMG-4 3 4
  • HMG2A 3 4
  • HMG4 3 4
  • Non-Histone Chromosomal Protein 2
  • High Mobility Group Protein 4 4
  • High-Mobility Group Box 3 2

External Ids for HMGB3 Gene

Previous HGNC Symbols for HMGB3 Gene

  • HMG4

Previous GeneCards Identifiers for HMGB3 Gene

  • GC0XP144450
  • GC0XP146834
  • GC0XP147919
  • GC0XP148792
  • GC0XP149822
  • GC0XP150148
  • GC0XP139013

Summaries for HMGB3 Gene

Entrez Gene Summary for HMGB3 Gene

  • This gene encodes a member of a family of proteins containing one or more high mobility group DNA-binding motifs. The encoded protein plays an important role in maintaining stem cell populations, and may be aberrantly expressed in tumor cells. A mutation in this gene was associated with microphthalmia, syndromic 13. There are numerous pseudogenes of this gene on multiple chromosomes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

GeneCards Summary for HMGB3 Gene

HMGB3 (High Mobility Group Box 3) is a Protein Coding gene. Diseases associated with HMGB3 include microphthalmia, syndromic 13 and colobomatous microphthalmia. GO annotations related to this gene include poly(A) RNA binding and double-stranded DNA binding. An important paralog of this gene is HMGB1.

UniProtKB/Swiss-Prot for HMGB3 Gene

  • Multifunctional protein with various roles in different cellular compartments. May act in a redox sensitive manner. Associates with chromatin and 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 similarity). Proposed to be involved in the innate immune response to nucleic acids by acting as a cytoplasmic promiscuous immunogenic DNA/RNA sensor (By similarity). Negatively regulates B-cell and myeloid cell differentiation. In hematopoietic stem cells may regulate the balance between self-renewal and differentiation. Involved in negative regulation of canonical Wnt signaling (By similarity).

Gene Wiki entry for HMGB3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HMGB3 Gene

Genomics for HMGB3 Gene

Regulatory Elements for HMGB3 Gene

Genomic Location for HMGB3 Gene

Chromosome:
X
Start:
150,980,508 bp from pter
End:
150,990,775 bp from pter
Size:
10,268 bases
Orientation:
Plus strand

Genomic View for HMGB3 Gene

Genes around HMGB3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HMGB3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HMGB3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HMGB3 Gene

Proteins for HMGB3 Gene

  • Protein details for HMGB3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O15347-HMGB3_HUMAN
    Recommended name:
    High mobility group protein B3
    Protein Accession:
    O15347
    Secondary Accessions:
    • O95556
    • Q6NS40

    Protein attributes for HMGB3 Gene

    Size:
    200 amino acids
    Molecular mass:
    22980 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for HMGB3 Gene

neXtProt entry for HMGB3 Gene

Proteomics data for HMGB3 Gene at MOPED

Post-translational modifications for HMGB3 Gene

  • Reduction/oxidation of cysteine residues Cys-23, Cys-45 and Cys-104 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 HMGB3 (HMGB3C23hC45hC104h), 2- disulfide HMGB3 (HMGB3C23-C45C104h) and 3- sulfonyl HMGB3 (HMGB3C23soC45soC104so).
  • Ubiquitination at Lys 112
  • Modification sites at PhosphoSitePlus

Antibody Products

No data available for DME Specific Peptides for HMGB3 Gene

Domains & Families for HMGB3 Gene

Gene Families for HMGB3 Gene

Protein Domains for HMGB3 Gene

Suggested Antigen Peptide Sequences for HMGB3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O15347

UniProtKB/Swiss-Prot:

HMGB3_HUMAN :
  • Contains 2 HMG box DNA-binding domains.
  • Belongs to the HMGB family.
Domain:
  • Contains 2 HMG box DNA-binding domains.
Family:
  • Belongs to the HMGB family.
genes like me logo Genes that share domains with HMGB3: view

Function for HMGB3 Gene

Molecular function for HMGB3 Gene

UniProtKB/Swiss-Prot Function:
Multifunctional protein with various roles in different cellular compartments. May act in a redox sensitive manner. Associates with chromatin and 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 similarity). Proposed to be involved in the innate immune response to nucleic acids by acting as a cytoplasmic promiscuous immunogenic DNA/RNA sensor (By similarity). Negatively regulates B-cell and myeloid cell differentiation. In hematopoietic stem cells may regulate the balance between self-renewal and differentiation. Involved in negative regulation of canonical Wnt signaling (By similarity).

Gene Ontology (GO) - Molecular Function for HMGB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003690 double-stranded DNA binding ISS --
genes like me logo Genes that share ontologies with HMGB3: view

Phenotypes for HMGB3 Gene

genes like me logo Genes that share phenotypes with HMGB3: view

Human Phenotype Ontology for HMGB3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for HMGB3

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for HMGB3 Gene

Localization for HMGB3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HMGB3 Gene

Nucleus. Chromosome. Cytoplasm.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for HMGB3 Gene COMPARTMENTS Subcellular localization image for HMGB3 gene
Compartment Confidence
nucleus 5
cytoskeleton 2

No data available for Gene Ontology (GO) - Cellular Components for HMGB3 Gene

Pathways & Interactions for HMGB3 Gene

SuperPathways for HMGB3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for HMGB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0032392 DNA geometric change ISS --
GO:0045596 negative regulation of cell differentiation IEA --
genes like me logo Genes that share ontologies with HMGB3: view

No data available for Pathways by source and SIGNOR curated interactions for HMGB3 Gene

Drugs & Compounds for HMGB3 Gene

No Compound Related Data Available

Transcripts for HMGB3 Gene

Unigene Clusters for HMGB3 Gene

High mobility group box 3:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for HMGB3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b
SP1:
SP2:

Relevant External Links for HMGB3 Gene

GeneLoc Exon Structure for
HMGB3
ECgene alternative splicing isoforms for
HMGB3

Expression for HMGB3 Gene

mRNA expression in normal human tissues for HMGB3 Gene

mRNA differential expression in normal tissues according to GTEx for HMGB3 Gene

This gene is overexpressed in Liver (x6.7).

Protein differential expression in normal tissues from HIPED for HMGB3 Gene

This gene is overexpressed in Lung (14.0), Placenta (9.6), and Lavage (8.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for HMGB3 Gene



SOURCE GeneReport for Unigene cluster for HMGB3 Gene Hs.19114

mRNA Expression by UniProt/SwissProt for HMGB3 Gene

O15347-HMGB3_HUMAN
Tissue specificity: Expressed predominantly in placenta.
genes like me logo Genes that share expression patterns with HMGB3: view

Protein tissue co-expression partners for HMGB3 Gene

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for HMGB3 Gene

Orthologs for HMGB3 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for HMGB3 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia HMGB3 35
  • 90.67 (n)
  • 97.62 (a)
HMGB3 36
  • 82 (a)
OneToOne
dog
(Canis familiaris)
Mammalia HMGB3 35
  • 91.67 (n)
  • 98.21 (a)
HMGB3 36
  • 89 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia HMGB3 35
  • 99.83 (n)
  • 100 (a)
HMGB3 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia LOC688583 35
  • 87.9 (n)
  • 92.26 (a)
oppossum
(Monodelphis domestica)
Mammalia HMGB3 36
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Gm6104 36
  • 97 (a)
OneToMany
Hmgb3 36
  • 98 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia HMGB3 36
  • 94 (a)
OneToOne
chicken
(Gallus gallus)
Aves HMGB3 35
  • 84.33 (n)
  • 94.64 (a)
HMGB3 36
  • 87 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia HMGB3 36
  • 83 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia hmgb3 35
  • 80.24 (n)
  • 91.02 (a)
Str.2163 35
African clawed frog
(Xenopus laevis)
Amphibia hmgb3-prov 35
zebrafish
(Danio rerio)
Actinopterygii hmgb3a 36
  • 65 (a)
OneToMany
hmgb3b 36
  • 65 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Dsp1 36
  • 24 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea hmg-1.1 36
  • 51 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NHP6A 36
  • 46 (a)
ManyToMany
NHP6B 36
  • 42 (a)
ManyToMany
IXR1 38
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.2712 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3845 36
  • 15 (a)
OneToMany
Species with no ortholog for HMGB3:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • wheat (Triticum aestivum)

Evolution for HMGB3 Gene

ENSEMBL:
Gene Tree for HMGB3 (if available)
TreeFam:
Gene Tree for HMGB3 (if available)

Paralogs for HMGB3 Gene

Paralogs for HMGB3 Gene

(14) SIMAP similar genes for HMGB3 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with HMGB3: view

Variants for HMGB3 Gene

Sequence variations from dbSNP and Humsavar for HMGB3 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
rs16995792 - 150,986,051(+) TGCAG(A/G)CGATG reference, missense
VAR_064162 -
rs1324 -- 150,988,555(-) AAAAA(A/T)ATTCT utr-variant-3-prime
rs237377 -- 150,987,556(+) ATAGT(C/G)CTACT intron-variant
rs237401 -- 150,980,395(+) CCTCC(A/G)TTGGT upstream-variant-2KB

Variation tolerance for HMGB3 Gene

Residual Variation Intolerance Score: 29.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.10; 2.32% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HMGB3 Gene

HapMap Linkage Disequilibrium report
HMGB3
Human Gene Mutation Database (HGMD)
HMGB3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for HMGB3 Gene

Disorders for HMGB3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for HMGB3 Gene - From: OMIM, ClinVar, GeneTests, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
microphthalmia, syndromic 13
  • maine microphthalmos
colobomatous microphthalmia
  • mac
microphthalmia
  • microphthalmos
- elite association - COSMIC cancer census association via MalaCards
Search HMGB3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

HMGB3_HUMAN
  • Microphthalmia, syndromic, 13 (MCOPS13) [MIM:300915]: A form of microphthalmia, a disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues (anophthalmia). In many cases, microphthalmia/anophthalmia occurs in association with syndromes that include non-ocular abnormalities. MCOPS13 patients exhibit colobomatous microphthalmia with microcephaly, short stature, and psychomotor retardation. {ECO:0000269 PubMed:24993872}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for HMGB3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HMGB3
genes like me logo Genes that share disorders with HMGB3: view

No data available for Genatlas for HMGB3 Gene

Publications for HMGB3 Gene

  1. Identification of an HMGB3 Frameshift Mutation in a Family With an X-linked Colobomatous Microphthalmia Syndrome Using Whole-Genome and X-Exome Sequencing. (PMID: 24993872) Scott A.F. … Jabs E.W. (JAMA Ophthalmol 2014) 3 4 67
  2. Hmg4, a new member of the Hmg1/2 gene family. (PMID: 9598312) Vaccari T. … Bianchi M.E. (Genomics 1998) 2 3
  3. Panorama of ancient metazoan macromolecular complexes. (PMID: 26344197) Wan C. … Emili A. (Nature 2015) 3
  4. Upregulation of miR-513b inhibits cell proliferation, migration, and promotes apoptosis by targeting high mobility group-box 3 protein in gastric cancer. (PMID: 25095979) Chen X. … Song G. (Tumour Biol. 2014) 3
  5. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T. … Vidal M. (Cell 2014) 3

Products for HMGB3 Gene

Sources for HMGB3 Gene

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