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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 B3 3
  • 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. Gene Ontology (GO) annotations related to this gene include 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

Additional gene information for HMGB3 Gene

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

Genomics for HMGB3 Gene

GeneHancer (GH) Regulatory Elements for HMGB3 Gene

Promoters and enhancers for HMGB3 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
GH0XI150982 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 550.8 +3.5 3461 2.9 HDGF PKNOX1 ARID4B SIN3A BRCA1 RFX5 YY1 ZNF335 FOS EGR2 HMGB3 XRCC6P2 RPL19P21
GH0XI150980 Promoter 0.7 EPDnew 550.8 +0.0 18 0.1 CREB1 ATF2 HMGB3 RPL19P21
GH0XI150846 Enhancer 1.4 FANTOM5 Ensembl ENCODE 11.7 -130.7 -130679 5.9 FOXA2 ARID4B NEUROD1 SIN3A YY1 TCF12 FOS RXRA REST ZNF592 CD99L2 MTMR1 HMGB3 PPIAP91
GH0XI150766 Enhancer 0.8 Ensembl ENCODE 12.4 -213.1 -213148 2.1 CTCF BHLHE40 CEBPB MAX CBFA2T3 MNT DPF2 FOSL1 NFIC NFE2 MTMR1 HMGB3 CD99L2 PIR43679 PPIAP91
GH0XI151082 Enhancer 0.8 Ensembl 12 +102.0 101993 0.6 ATF1 RB1 SIN3A RAD21 ARID2 ZNF143 RUNX3 EGR2 ZNF654 CBFB HMGB3 GC0XP151077 MIR4330
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around HMGB3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HMGB3 gene promoter:

Genomic Locations for HMGB3 Gene

Genomic Locations for HMGB3 Gene
chrX:150,980,508-150,990,775
(GRCh38/hg38)
Size:
10,268 bases
Orientation:
Plus strand
chrX:150,148,982-150,159,248
(GRCh37/hg19)

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

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 posLast=112112

No data available for DME Specific Peptides for HMGB3 Gene

Domains & Families for HMGB3 Gene

Gene Families for HMGB3 Gene

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

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 :
  • Belongs to the HMGB family.
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:0000400 four-way junction DNA binding ISS --
GO:0003677 DNA binding IEA --
GO:0003690 double-stranded DNA binding ISS --
GO:0003723 RNA binding HDA,IDA 22681889
GO:0005515 protein binding IPI 21044950
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

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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
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 HMGB3 gene
Compartment Confidence
nucleus 5
cytoskeleton 2

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for HMGB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005694 chromosome IEA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with HMGB3: view

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:0002376 immune system process IEA --
GO:0006310 DNA recombination ISS --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007275 multicellular organism development TAS 9598312
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:

CRISPR Products

Inhibitory RNA Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for HMGB3 Gene



Protein tissue co-expression partners for HMGB3 Gene

NURSA nuclear receptor signaling pathways regulating expression of HMGB3 Gene:

HMGB3

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.

Evidence on tissue expression from TISSUES for HMGB3 Gene

  • Eye(4.2)
  • Liver(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for HMGB3 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • outer ear
  • skull
General:
  • peripheral nervous system
  • skin
genes like me logo Genes that share expression patterns with HMGB3: view

Primer 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
chimpanzee
(Pan troglodytes)
Mammalia HMGB3 33 34
  • 99.83 (n)
mouse
(Mus musculus)
Mammalia Hmgb3 34
  • 98 (a)
OneToMany
Gm6104 34
  • 97 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia HMGB3 34
  • 94 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia HMGB3 34
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia HMGB3 33 34
  • 91.67 (n)
cow
(Bos Taurus)
Mammalia HMGB3 33 34
  • 90.67 (n)
rat
(Rattus norvegicus)
Mammalia LOC688583 33
  • 87.9 (n)
chicken
(Gallus gallus)
Aves HMGB3 33 34
  • 84.33 (n)
lizard
(Anolis carolinensis)
Reptilia HMGB3 34
  • 83 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia hmgb3 33
  • 80.24 (n)
Str.2163 33
African clawed frog
(Xenopus laevis)
Amphibia hmgb3-prov 33
zebrafish
(Danio rerio)
Actinopterygii hmgb3a 34
  • 65 (a)
OneToMany
hmgb3b 34
  • 65 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Dsp1 34
  • 24 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea hmg-1.1 34
  • 51 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NHP6A 34
  • 46 (a)
ManyToMany
NHP6B 34
  • 42 (a)
ManyToMany
IXR1 36
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3845 34
  • 15 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.2712 33
Species where no ortholog for HMGB3 was found in the sources mined by GeneCards:
  • 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 Variation AA Info Type
rs431825172 not-provided, pathogenic, not provided, Microphthalmia, syndromic 13 150,987,789(+) TATA/TATATA coding_sequence_variant, frameshift
rs1064793149 uncertain-significance, not specified 150,985,687(+) AAAAA/AAAA coding_sequence_variant, frameshift
rs1000038319 -- 150,989,146(+) A/G 3_prime_UTR_variant
rs1001262740 -- 150,989,703(+) C/G 3_prime_UTR_variant
rs1003740428 -- 150,981,385(+) T/A genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for HMGB3 Gene

Variant ID Type Subtype PubMed ID
nsv1077247 CNV deletion 25765185
dgv4318n106 CNV deletion 24896259

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)

Additional Variant Information for HMGB3 Gene

Human Gene Mutation Database (HGMD)
HMGB3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HMGB3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HMGB3 Gene

Disorders for HMGB3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for HMGB3 Gene - From: HGMD, OMIM, ClinVar, GTR, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
microphthalmia, syndromic 13
  • mcops13
colobomatous microphthalmia
  • microphthalmia with colobomatous cyst
terminal osseous dysplasia
  • tod
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.

Additional Disease Information for 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 AF … Jabs EW (JAMA ophthalmology 2014) 3 4 58
  2. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross MT … Bentley DR (Nature 2005) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Hmg4, a new member of the Hmg1/2 gene family. (PMID: 9598312) Vaccari T … Bianchi ME (Genomics 1998) 2 3 58
  5. Isolation of human and mouse HMG2a cDNAs: evidence for an HMG2a-specific 3' untranslated region. (PMID: 9370291) Wilke K … Poustka A (Gene 1997) 3 4 58

Products for HMGB3 Gene

Sources for HMGB3 Gene

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