High mobility group (HMG) proteins are nonhistone chromosomal proteins. See HMG2 (MIM 163906) for additional information on HMG proteins.[supplied by OMIM, Nov 2010] See more...

Aliases for HMGXB4 Gene

Aliases for HMGXB4 Gene

  • HMG-Box Containing 4 2 3 5
  • High Mobility Group Protein 2-Like 1 3 4
  • HMG Domain-Containing Protein 4 3 4
  • HMG Box-Containing Protein 4 3 4
  • HMG Box Domain Containing 4 2 3
  • THC211630 2 3
  • HMG2L1 3 4
  • HMGBCG 3 4
  • High-Mobility Group Protein 2-Like 1 2
  • Protein HMGBCG 4
  • HMGXB4 5

External Ids for HMGXB4 Gene

Previous HGNC Symbols for HMGXB4 Gene

  • HMG2L1

Previous GeneCards Identifiers for HMGXB4 Gene

  • GC22P033983
  • GC22P035653
  • GC22P018614
  • GC22P035257
  • GC22P035241

Summaries for HMGXB4 Gene

Entrez Gene Summary for HMGXB4 Gene

  • High mobility group (HMG) proteins are nonhistone chromosomal proteins. See HMG2 (MIM 163906) for additional information on HMG proteins.[supplied by OMIM, Nov 2010]

GeneCards Summary for HMGXB4 Gene

HMGXB4 (HMG-Box Containing 4) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include chromatin binding. An important paralog of this gene is TOX4.

UniProtKB/Swiss-Prot Summary for HMGXB4 Gene

Additional gene information for HMGXB4 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HMGXB4 Gene

Genomics for HMGXB4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for HMGXB4 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
GH22J035256 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 634.9 +1.2 1204 2.6 GATAD2A ZNF629 NFKBIZ ZNF692 NFRKB POLR2A ZHX2 JUND LARP7 PRDM1 HMGXB4 LOC105373017 LINC01399 lnc-TOM1-3 TOM1
GH22J035253 Promoter 0.6 EPDnew 600.7 -3.1 -3120 0.1 USF1 ZBTB33 RAD51 HMGXB4 LINC01399 lnc-HMGXB4-1 LOC105373017 ISX
GH22J035298 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 42.3 +44.3 44310 4.8 SP1 HNRNPL CREB1 GATAD2A ATF7 PRDM10 REST ZNF629 TFE3 IKZF1 TOM1 ENSG00000273176 HMGXB4 RBFOX2 MCM5 MIR3909 HMOX1
GH22J035371 Promoter/Enhancer 1.8 FANTOM5 Ensembl ENCODE CraniofacialAtlas 51.4 +115.7 115745 2.1 SP1 CREB1 GATAD2A PRDM10 ZNF629 TFE3 LEF1 SOX13 IKZF1 NFKBIZ ENSG00000282602 HMGXB4 TOM1 HMOX1 MCM5 RBFOX2 APOL6 ENSG00000282041
GH22J035376 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 37.2 +122.9 122944 7.1 SP1 HNRNPL CREB1 GATAD2A TEAD4 PRDM10 ZNF629 TFE3 LEF1 SOX13 HMOX1 NONHSAG033802.2 HMGXB4 MCM5 TOM1 RBFOX2 APOL6 ENSG00000282041
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HMGXB4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HMGXB4

Top Transcription factor binding sites by QIAGEN in the HMGXB4 gene promoter:
  • AML1a
  • AP-1
  • c-Fos
  • COMP1
  • GR
  • Ik-2
  • p300
  • POU6F1 (c2)
  • RREB-1

Genomic Locations for HMGXB4 Gene

Genomic Locations for HMGXB4 Gene
chr22:35,256,697-35,295,807
(GRCh38/hg38)
Size:
39,111 bases
Orientation:
Plus strand
chr22:35,653,445-35,691,800
(GRCh37/hg19)
Size:
38,356 bases
Orientation:
Plus strand

Genomic View for HMGXB4 Gene

Genes around HMGXB4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HMGXB4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HMGXB4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HMGXB4 Gene

Proteins for HMGXB4 Gene

  • Protein details for HMGXB4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UGU5-HMGX4_HUMAN
    Recommended name:
    HMG domain-containing protein 4
    Protein Accession:
    Q9UGU5
    Secondary Accessions:
    • O75672
    • O75673
    • Q9UMT5

    Protein attributes for HMGXB4 Gene

    Size:
    601 amino acids
    Molecular mass:
    65712 Da
    Quaternary structure:
    No Data Available

neXtProt entry for HMGXB4 Gene

Post-translational modifications for HMGXB4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HMGXB4 Gene

No data available for DME Specific Peptides for HMGXB4 Gene

Domains & Families for HMGXB4 Gene

Gene Families for HMGXB4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for HMGXB4 Gene

Suggested Antigen Peptide Sequences for HMGXB4 Gene

GenScript: Design optimal peptide antigens:
  • Protein HMGBCG (HMGX4_HUMAN)
  • High-mobility group protein 2-like 1, isoform CRA_a (Q2M3X1_HUMAN)
  • HMGXB4 protein (Q2T9L2_HUMAN)
  • HMGXB4 protein (Q6P681_HUMAN)
  • HMGXB4 protein (Q6PJ09_HUMAN)
genes like me logo Genes that share domains with HMGXB4: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for HMGXB4 Gene

Function for HMGXB4 Gene

Molecular function for HMGXB4 Gene

UniProtKB/Swiss-Prot Function:
Negatively regulates Wnt/beta-catenin signaling during development.

Phenotypes From GWAS Catalog for HMGXB4 Gene

Gene Ontology (GO) - Molecular Function for HMGXB4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
genes like me logo Genes that share ontologies with HMGXB4: view
genes like me logo Genes that share phenotypes with HMGXB4: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HMGXB4

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HMGXB4 Gene

Localization for HMGXB4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HMGXB4 Gene

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 HMGXB4 gene
Compartment Confidence
nucleus 5
extracellular 1
cytoskeleton 1
mitochondrion 1
peroxisome 1
cytosol 1
plasma membrane 0

Gene Ontology (GO) - Cellular Components for HMGXB4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0016589 NURF complex IDA 20850016
genes like me logo Genes that share ontologies with HMGXB4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HMGXB4 Gene

Pathways & Interactions for HMGXB4 Gene

PathCards logo

SuperPathways for HMGXB4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for HMGXB4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008333 endosome to lysosome transport NAS 10329004
GO:0016055 Wnt signaling pathway IEA --
GO:0030178 negative regulation of Wnt signaling pathway ISS --
genes like me logo Genes that share ontologies with HMGXB4: view

No data available for Pathways by source and SIGNOR curated interactions for HMGXB4 Gene

Drugs & Compounds for HMGXB4 Gene

No Compound Related Data Available

Transcripts for HMGXB4 Gene

mRNA/cDNA for HMGXB4 Gene

4 REFSEQ mRNAs :
20 NCBI additional mRNA sequence :
8 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 HMGXB4

Alternative Splicing Database (ASD) splice patterns (SP) for HMGXB4 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14
SP1: -
SP2: - - -
SP3: - - - -
SP4: - - - -
SP5: - - - - -
SP6:
SP7: -
SP8:
SP9:

Relevant External Links for HMGXB4 Gene

GeneLoc Exon Structure for
HMGXB4

Expression for HMGXB4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HMGXB4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for HMGXB4 Gene

This gene is overexpressed in Platelet (26.1), Placenta (22.0), and Fetal ovary (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HMGXB4 Gene



Protein tissue co-expression partners for HMGXB4 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HMGXB4

SOURCE GeneReport for Unigene cluster for HMGXB4 Gene:

Hs.588815

Evidence on tissue expression from TISSUES for HMGXB4 Gene

  • Liver(4.4)
  • Nervous system(2.3)
genes like me logo Genes that share expression patterns with HMGXB4: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HMGXB4 Gene

Orthologs for HMGXB4 Gene

This gene was present in the common ancestor of animals.

Orthologs for HMGXB4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia HMGXB4 30 31
  • 99.61 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia HMGXB4 30 31
  • 91.22 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia HMGXB4 30 31
  • 89.02 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Hmgxb4 30 17 31
  • 85.35 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Hmgxb4 30
  • 83.28 (n)
Oppossum
(Monodelphis domestica)
Mammalia HMGXB4 31
  • 77 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia HMGXB4 31
  • 69 (a)
OneToOne
Chicken
(Gallus gallus)
Aves HMGXB4 30 31
  • 72.94 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia HMGXB4 31
  • 72 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia hmgxb4 30
  • 63.21 (n)
Str.822 30
African clawed frog
(Xenopus laevis)
Amphibia HMG2L1 30
Zebrafish
(Danio rerio)
Actinopterygii hmgxb4a 31
  • 52 (a)
OneToMany
hmgxb4b 31
  • 34 (a)
OneToMany
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6678 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG4617 31
  • 26 (a)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.702 31
  • 29 (a)
OneToOne
Species where no ortholog for HMGXB4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • 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)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for HMGXB4 Gene

ENSEMBL:
Gene Tree for HMGXB4 (if available)
TreeFam:
Gene Tree for HMGXB4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HMGXB4: view image

Paralogs for HMGXB4 Gene

genes like me logo Genes that share paralogs with HMGXB4: view

Variants for HMGXB4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HMGXB4 Gene

SNP ID Clinical significance and condition Chr 22 pos Variation AA Info Type
rs1053593 - p.Gly165Val

Additional dbSNP identifiers (rs#s) for HMGXB4 Gene

Structural Variations from Database of Genomic Variants (DGV) for HMGXB4 Gene

Variant ID Type Subtype PubMed ID
esv2170801 CNV deletion 18987734
nsv1136672 CNV deletion 24896259
nsv588948 CNV loss 21841781

Variation tolerance for HMGXB4 Gene

Residual Variation Intolerance Score: 12.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.13; 84.63% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HMGXB4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HMGXB4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HMGXB4 Gene

Disorders for HMGXB4 Gene

Additional Disease Information for HMGXB4

No disorders were found for HMGXB4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HMGXB4 Gene

Publications for HMGXB4 Gene

  1. The DNA sequence of human chromosome 22. (PMID: 10591208) Dunham I … O'Brien KP (Nature 1999) 2 3 4
  2. TOM1 genes map to human chromosome 22q13.1 and mouse chromosome 8C1 and encode proteins similar to the endosomal proteins HGS and STAM. (PMID: 10329004) Seroussi E … Dumanski JP (Genomics 1999) 2 3 4
  3. Repression of smooth muscle differentiation by a novel high mobility group box-containing protein, HMG2L1. (PMID: 20511232) Zhou J … Wang X (The Journal of biological chemistry 2010) 2 3
  4. A genome annotation-driven approach to cloning the human ORFeome. (PMID: 15461802) Collins JE … Dunham I (Genome biology 2004) 3 4
  5. Reevaluating human gene annotation: a second-generation analysis of chromosome 22. (PMID: 12529303) Collins JE … Dunham I (Genome research 2003) 3 4

Products for HMGXB4 Gene

Sources for HMGXB4 Gene