Aliases for HMGB4 Gene

Aliases for HMGB4 Gene

  • High Mobility Group Box 4 2 3 5
  • High Mobility Group Protein B4 3 4
  • High-Mobility Group Box 4 2
  • DJ1007G16.5 3
  • HMG2 Like 3
  • FLJ40388 2
  • HMGB4 5

External Ids for HMGB4 Gene

Previous GeneCards Identifiers for HMGB4 Gene

  • GC01P033996
  • GC01P034098
  • GC01P034326
  • GC01P032442

Summaries for HMGB4 Gene

GeneCards Summary for HMGB4 Gene

HMGB4 (High Mobility Group Box 4) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include chromatin binding. An important paralog of this gene is HMGB2.

Gene Wiki entry for HMGB4 Gene

Additional gene information for HMGB4 Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HMGB4 Gene

Genomics for HMGB4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for HMGB4 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
GH01J033864 Promoter 0.4 EPDnew 600.7 +3.6 3585 0.1 ATF2 HMGB4 lnc-C1orf94-2 CSMD2-AS1 CSMD2
GH01J033903 Enhancer 0.9 FANTOM5 Ensembl 21.9 +42.7 42725 1.2 SP1 PKNOX1 TCF12 EP300 ZNF766 NFE2 ZNF316 ATF3 YY1 JUND HMGB4 CSMD2-AS1 piR-48209-029 piR-31508-001 CSMD2
GH01J033898 Enhancer 0.3 Ensembl 11.1 +38.2 38226 0.2 ZNF395 CSMD2-AS1 HMGB4 piR-48209-029 piR-31508-001 CSMD2
GH01J033996 Enhancer 0.2 FANTOM5 2.6 +136.6 136564 0.4 CSMD2 HMGB4 HSALNG0002416 HSALNG0002417
GH01J033876 Enhancer 0.4 Ensembl ENCODE 0.4 +16.7 16748 1.2 SCRT2 CSMD2 CSMD2-AS1 piR-48209-029 HMGB4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HMGB4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HMGB4

Top Transcription factor binding sites by QIAGEN in the HMGB4 gene promoter:
  • Cdc5
  • NF-AT
  • NF-AT1
  • NF-AT2
  • NF-kappaB1

Genomic Locations for HMGB4 Gene

Genomic Locations for HMGB4 Gene
chr1:33,860,475-33,864,791
(GRCh38/hg38)
Size:
4,317 bases
Orientation:
Plus strand
chr1:34,326,076-34,330,392
(GRCh37/hg19)
Size:
4,317 bases
Orientation:
Plus strand

Genomic View for HMGB4 Gene

Genes around HMGB4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HMGB4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HMGB4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HMGB4 Gene

Proteins for HMGB4 Gene

  • Protein details for HMGB4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8WW32-HMGB4_HUMAN
    Recommended name:
    High mobility group protein B4
    Protein Accession:
    Q8WW32
    Secondary Accessions:
    • B2R4X7
    • Q0QWA4

    Protein attributes for HMGB4 Gene

    Size:
    186 amino acids
    Molecular mass:
    22490 Da
    Quaternary structure:
    No Data Available

neXtProt entry for HMGB4 Gene

Post-translational modifications for HMGB4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HMGB4 Gene

No data available for DME Specific Peptides for HMGB4 Gene

Domains & Families for HMGB4 Gene

Gene Families for HMGB4 Gene

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

Protein Domains for HMGB4 Gene

InterPro:
Blocks:
  • High mobility group proteins HMG1 and HMG2
ProtoNet:

Suggested Antigen Peptide Sequences for HMGB4 Gene

GenScript: Design optimal peptide antigens:
  • cDNA, FLJ92258, highly similar to Homo sapiens HMG2 like (LOC127540), mRNA (B2R4X7_HUMAN)
  • High mobility group protein B4 (HMGB4_HUMAN)
  • High-mobility group box 4 (Q0QWA4_HUMAN)
  • High-mobility group box 4 (Q6NSH1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8WW32

UniProtKB/Swiss-Prot:

HMGB4_HUMAN :
  • Belongs to the HMGB family.
Family:
  • Belongs to the HMGB family.
genes like me logo Genes that share domains with HMGB4: view

Function for HMGB4 Gene

Phenotypes From GWAS Catalog for HMGB4 Gene

Gene Ontology (GO) - Molecular Function for HMGB4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding IBA 21873635
GO:0005515 protein binding IPI 25416956
GO:0008134 transcription factor binding IBA 21873635
GO:0008301 DNA binding, bending IBA 21873635
genes like me logo Genes that share ontologies with HMGB4: view
genes like me logo Genes that share phenotypes with HMGB4: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HMGB4

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for HMGB4 Gene

Localization for HMGB4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HMGB4 Gene

Nucleus. Chromosome.

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 HMGB4 gene
Compartment Confidence
nucleus 4
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
cytosol 1

Gene Ontology (GO) - Cellular Components for HMGB4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin IBA 21873635
GO:0005634 nucleus IEA,HDA 21630459
GO:0005694 chromosome IEA --
GO:0005737 cytoplasm IBA 21873635
genes like me logo Genes that share ontologies with HMGB4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HMGB4 Gene

Pathways & Interactions for HMGB4 Gene

PathCards logo

SuperPathways for HMGB4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for HMGB4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002218 activation of innate immune response IBA --
GO:0006310 DNA recombination IBA 21873635
GO:0006338 chromatin remodeling IBA 21873635
GO:0006355 regulation of transcription, DNA-templated IBA 21873635
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
genes like me logo Genes that share ontologies with HMGB4: view

No data available for Pathways by source and SIGNOR curated interactions for HMGB4 Gene

Drugs & Compounds for HMGB4 Gene

No Compound Related Data Available

Transcripts for HMGB4 Gene

mRNA/cDNA for HMGB4 Gene

3 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HMGB4

Alternative Splicing Database (ASD) splice patterns (SP) for HMGB4 Gene

No ASD Table

Relevant External Links for HMGB4 Gene

GeneLoc Exon Structure for
HMGB4

Expression for HMGB4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HMGB4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Testis (Reproductive System)

mRNA differential expression in normal tissues according to GTEx for HMGB4 Gene

This gene is overexpressed in Testis (x52.6).

Protein differential expression in normal tissues from HIPED for HMGB4 Gene

This gene is overexpressed in Testis (50.9) and Ovary (18.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for HMGB4 Gene



Protein tissue co-expression partners for HMGB4 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HMGB4

SOURCE GeneReport for Unigene cluster for HMGB4 Gene:

Hs.568628
genes like me logo Genes that share expression patterns with HMGB4: view

No data available for mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for HMGB4 Gene

Orthologs for HMGB4 Gene

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

Orthologs for HMGB4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia HMGB4 30
  • 98.75 (n)
Cow
(Bos Taurus)
Mammalia HMGB4 30 31
  • 86.96 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia HMGB4 30 31
  • 82.87 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Hmgb4 30 17 31
  • 78.97 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Hmgb4 30
  • 77.44 (n)
Oppossum
(Monodelphis domestica)
Mammalia HMGB4 31
  • 54 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 21 (a)
ManyToMany
Zebrafish
(Danio rerio)
Actinopterygii hmgb2b 31
  • 31 (a)
ManyToMany
Fruit Fly
(Drosophila melanogaster)
Insecta Dsp1 31
  • 15 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea hmg-1.1 31
  • 32 (a)
OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NHP6A 31
  • 33 (a)
ManyToMany
NHP6B 31
  • 32 (a)
ManyToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.3845 31
  • 12 (a)
OneToMany
Species where no ortholog for HMGB4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • Chicken (Gallus gallus)
  • 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)
  • Lizard (Anolis carolinensis)
  • 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 Vase (Ciona intestinalis)
  • 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 HMGB4 Gene

ENSEMBL:
Gene Tree for HMGB4 (if available)
TreeFam:
Gene Tree for HMGB4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HMGB4: view image

Paralogs for HMGB4 Gene

(9) SIMAP similar genes for HMGB4 Gene using alignment to 2 proteins:

  • HMGB4_HUMAN
  • Q6NSH1_HUMAN
genes like me logo Genes that share paralogs with HMGB4: view

Variants for HMGB4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HMGB4 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs10379 - p.Glu92Ala
rs11542686 - p.Lys59Arg
rs57068937 - p.Tyr170His

Additional dbSNP identifiers (rs#s) for HMGB4 Gene

Structural Variations from Database of Genomic Variants (DGV) for HMGB4 Gene

Variant ID Type Subtype PubMed ID
esv34112 CNV loss 18971310
esv3585686 CNV gain 21293372
nsv834624 CNV loss 17160897

Variation tolerance for HMGB4 Gene

Residual Variation Intolerance Score: 78.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.07; 37.86% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HMGB4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HMGB4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HMGB4 Gene

Disorders for HMGB4 Gene

Additional Disease Information for HMGB4

No disorders were found for HMGB4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HMGB4 Gene

Publications for HMGB4 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  2. 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
  3. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  4. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T … Vidal M (Cell 2014) 3
  5. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PMID: 21832049) Oláh J … Ovádi J (The Journal of biological chemistry 2011) 3

Products for HMGB4 Gene

Sources for HMGB4 Gene