This gene encodes a member of the early B-cell factor (EBF) family of DNA binding transcription factors. EBF proteins are involved in B-cell differentiation, bone development and neurogenesis, and may also function as tumor suppressors. The encoded protein inhibits cell survival through the regulation of genes involved in cell cycle arrest and apoptosis, and aberrant methylatio... See more...

Aliases for EBF3 Gene

Aliases for EBF3 Gene

  • EBF Transcription Factor 3 2 3 5
  • Transcription Factor COE3 2 3 4
  • COE3 2 3 4
  • Early B Cell Factor 3 2 3
  • Olf-1/EBF-Like 2 3 4
  • EBF-3 3 4
  • O/E-2 3 4
  • OE-2 3 4
  • Early B-Cell Factor 3 4
  • DKFZp667B0210 2
  • HADDS 3
  • EBF3 5

External Ids for EBF3 Gene

Previous GeneCards Identifiers for EBF3 Gene

  • GC00U908396
  • GC10M131109
  • GC20P002669
  • GC10M131524
  • GC10M131633
  • GC10M125212

Summaries for EBF3 Gene

Entrez Gene Summary for EBF3 Gene

  • This gene encodes a member of the early B-cell factor (EBF) family of DNA binding transcription factors. EBF proteins are involved in B-cell differentiation, bone development and neurogenesis, and may also function as tumor suppressors. The encoded protein inhibits cell survival through the regulation of genes involved in cell cycle arrest and apoptosis, and aberrant methylation or deletion of this gene may play a role in multiple malignancies including glioblastoma multiforme and gastric carcinoma. [provided by RefSeq, Sep 2011]

GeneCards Summary for EBF3 Gene

EBF3 (EBF Transcription Factor 3) is a Protein Coding gene. Diseases associated with EBF3 include Hypotonia, Ataxia, And Delayed Development Syndrome and Neurogenic Bladder. Among its related pathways are Differentiation of white and brown adipocyte. Gene Ontology (GO) annotations related to this gene include protein dimerization activity. An important paralog of this gene is EBF1.

UniProtKB/Swiss-Prot Summary for EBF3 Gene

  • Transcriptional activator (PubMed:28017373, PubMed:28017372, PubMed:28017370). Recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for EBF3 Gene

Genomics for EBF3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for EBF3 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
GH10J129973 Promoter/Enhancer 1.2 ENCODE CraniofacialAtlas dbSUPER 600.7 +1.5 1516 1.2 PRDM10 CTCF ZIC2 PATZ1 EZH2 ZNF600 ZNF341 ZNF561 ZBTB20 SP2 EBF3 lnc-MGMT-7 lnc-EBF3-8 MGMT
GH10J129020 Enhancer 2 VISTA UCNEbase Ensembl ENCODE CraniofacialAtlas dbSUPER 11.8 +945.5 945464 14.6 CTCF ZIC2 POLR2A REST RAD21 DPF2 HDAC1 SOX6 TCF12 ZNF561 EBF3 lnc-EBF3-6 lnc-EBF3-7 MGMT MKI67
GH10J129888 Enhancer 1.4 UCNEbase FANTOM5 Ensembl ENCODE CraniofacialAtlas 6.9 +83.6 83587 1.9 CTCF SMC3 ZFHX2 GABPB1 RAD21 ZNF143 XRCC5 TBP TRIM22 EBF3 lnc-MGMT-4 ENSG00000287997 MGMT
GH10J129863 Enhancer 0.9 UCNEbase Ensembl CraniofacialAtlas 11 +109.5 109484 1.3 USF1 CTCF SMARCA4 EBF3 ENSG00000287997 LOC105378558 lnc-MGMT-4 MGMT
GH10J129949 Promoter/Enhancer 2.3 UCNEbase FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 2.9 +15.4 15388 16.7 PRDM10 ZNF629 ZNF692 FOXA1 ZIC2 POLR2A PATZ1 EZH2 ZNF600 ZNF341 CTAGE7P EBF3 lnc-MGMT-7 lnc-EBF3-8 MGMT
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around EBF3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for EBF3

Top Transcription factor binding sites by QIAGEN in the EBF3 gene promoter:
  • E2F
  • E2F-2
  • E2F-3a
  • E2F-4
  • FOXO4

Genomic Locations for EBF3 Gene

Genomic Locations for EBF3 Gene
chr10:129,835,233-129,973,053
(GRCh38/hg38)
Size:
137,821 bases
Orientation:
Minus strand
chr10:131,633,547-131,762,105
(GRCh37/hg19)
Size:
128,559 bases
Orientation:
Minus strand

Genomic View for EBF3 Gene

Genes around EBF3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EBF3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EBF3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for EBF3 Gene

Proteins for EBF3 Gene

  • Protein details for EBF3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H4W6-COE3_HUMAN
    Recommended name:
    Transcription factor COE3
    Protein Accession:
    Q9H4W6
    Secondary Accessions:
    • A0AUY1
    • Q5T6H9
    • Q9H4W5

    Protein attributes for EBF3 Gene

    Size:
    596 amino acids
    Molecular mass:
    64864 Da
    Quaternary structure:
    • Forms either a homodimer or a heterodimer with a related family member.

    Three dimensional structures from OCA and Proteopedia for EBF3 Gene

    Alternative splice isoforms for EBF3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for EBF3 Gene

Post-translational modifications for EBF3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for EBF3 Gene

Domains & Families for EBF3 Gene

Gene Families for EBF3 Gene

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

Protein Domains for EBF3 Gene

InterPro:
Blocks:
  • Cell surface receptor IPT/TIG
  • Basic helix-loop-helix dimerization domain bHLH
  • Transcription factor COE
ProtoNet:

Suggested Antigen Peptide Sequences for EBF3 Gene

GenScript: Design optimal peptide antigens:
  • Olf-1/EBF-like 2 (COE3_HUMAN)
  • Early B-cell factor 3 (Q5T6H8_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9H4W6

UniProtKB/Swiss-Prot:

COE3_HUMAN :
  • Belongs to the COE family.
Family:
  • Belongs to the COE family.
genes like me logo Genes that share domains with EBF3: view

Function for EBF3 Gene

Molecular function for EBF3 Gene

UniProtKB/Swiss-Prot Function:
Transcriptional activator (PubMed:28017373, PubMed:28017372, PubMed:28017370). Recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity).

Phenotypes From GWAS Catalog for EBF3 Gene

Gene Ontology (GO) - Molecular Function for EBF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISM 19274049
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IBA 21873635
GO:0003677 DNA binding IEA --
GO:0003700 DNA-binding transcription factor activity IEA --
genes like me logo Genes that share ontologies with EBF3: view
genes like me logo Genes that share phenotypes with EBF3: view

Human Phenotype Ontology for EBF3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for EBF3 Gene

MGI Knock Outs for EBF3:
  • Ebf3 Ebf3<tm1Reed>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for EBF3

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for EBF3 Gene

Localization for EBF3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for EBF3 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 EBF3 gene
Compartment Confidence
nucleus 5
cytosol 3
plasma membrane 2
extracellular 2
cytoskeleton 2
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for EBF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin ISA --
GO:0005634 nucleus IEA,IDA 28017373
genes like me logo Genes that share ontologies with EBF3: view

Pathways & Interactions for EBF3 Gene

PathCards logo

SuperPathways for EBF3 Gene

genes like me logo Genes that share pathways with EBF3: view

Pathways by source for EBF3 Gene

1 BioSystems pathway for EBF3 Gene

SIGNOR curated interactions for EBF3 Gene

Is inactivated by:

Gene Ontology (GO) - Biological Process for EBF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007275 multicellular organism development IEA --
GO:0045893 positive regulation of transcription, DNA-templated IMP 28017370
GO:0045944 positive regulation of transcription by RNA polymerase II IBA 21873635
genes like me logo Genes that share ontologies with EBF3: view

Drugs & Compounds for EBF3 Gene

No Compound Related Data Available

Transcripts for EBF3 Gene

mRNA/cDNA for EBF3 Gene

7 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
3 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 EBF3

Alternative Splicing Database (ASD) splice patterns (SP) for EBF3 Gene

No ASD Table

Relevant External Links for EBF3 Gene

GeneLoc Exon Structure for
EBF3

Expression for EBF3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for EBF3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for EBF3 Gene

This gene is overexpressed in Adipose - Subcutaneous (x6.6) and Adipose - Visceral (Omentum) (x4.9).

Protein differential expression in normal tissues from HIPED for EBF3 Gene

This gene is overexpressed in Fetal Brain (55.7) and Peripheral blood mononuclear cells (13.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for EBF3 Gene



Protein tissue co-expression partners for EBF3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for EBF3

SOURCE GeneReport for Unigene cluster for EBF3 Gene:

Hs.591374

mRNA Expression by UniProt/SwissProt for EBF3 Gene:

Q9H4W6-COE3_HUMAN
Tissue specificity: Expressed in brain.

Evidence on tissue expression from TISSUES for EBF3 Gene

  • Blood(2.2)
  • Skin(2.2)
  • Nervous system(2.1)
genes like me logo Genes that share expression patterns with EBF3: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for EBF3 Gene

Orthologs for EBF3 Gene

This gene was present in the common ancestor of animals.

Orthologs for EBF3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia EBF3 30 31
  • 99.7 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Ebf3 30 17 31
  • 94.25 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ebf3 30
  • 93.89 (n)
Dog
(Canis familiaris)
Mammalia EBF3 31
  • 91 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia EBF3 31
  • 90 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia EBF3 31
  • 79 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia EBF3 31
  • 59 (a)
OneToOne
Chicken
(Gallus gallus)
Aves EBF3 31
  • 84 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia EBF3 31
  • 95 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia ebf3 30
  • 83.55 (n)
MGC75916 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.632 30
Zebrafish
(Danio rerio)
Actinopterygii ebf3 30 31
  • 81.6 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta kn 30 31
  • 68.43 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011437 30
  • 67.67 (n)
Worm
(Caenorhabditis elegans)
Secernentea unc-3 31
  • 55 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 52 (a)
OneToMany
Species where no ortholog for EBF3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)

Evolution for EBF3 Gene

ENSEMBL:
Gene Tree for EBF3 (if available)
TreeFam:
Gene Tree for EBF3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for EBF3: view image

Paralogs for EBF3 Gene

Paralogs for EBF3 Gene

(4) SIMAP similar genes for EBF3 Gene using alignment to 2 proteins:

  • COE3_HUMAN
  • H0Y3W9_HUMAN
genes like me logo Genes that share paralogs with EBF3: view

Variants for EBF3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for EBF3 Gene

SNP ID Clinical significance and condition Chr 10 pos Variation AA Info Type
684472 Not Provided: Hypotonia, ataxia, and delayed development syndrome 129,867,860(-) AC/A FRAMESHIFT_VARIANT
692039 Pathogenic: Hypotonia, ataxia, and delayed development syndrome 129,963,495(-) C/A NONSENSE
715911 Likely Benign: not provided 129,867,854(-) G/A SYNONYMOUS_VARIANT
716312 Benign: not provided 129,963,672(-) T/C MISSENSE_VARIANT
716964 Benign: not provided 129,958,987(-) C/T SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for EBF3 Gene

Structural Variations from Database of Genomic Variants (DGV) for EBF3 Gene

Variant ID Type Subtype PubMed ID
dgv181n67 CNV gain 20364138
esv1978602 CNV deletion 18987734
esv3577850 CNV gain 25503493
nsv1048253 CNV gain 25217958
nsv1069522 CNV deletion 25765185
nsv1145903 CNV deletion 26484159
nsv552315 CNV loss 21841781
nsv552316 CNV loss 21841781
nsv7618 CNV insertion 18451855
nsv825621 CNV gain 20364138
nsv825626 CNV loss 20364138
nsv832023 CNV gain+loss 17160897
nsv832024 CNV loss 17160897

Variation tolerance for EBF3 Gene

Residual Variation Intolerance Score: 6.78% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.98; 20.14% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for EBF3 Gene

Human Gene Mutation Database (HGMD)
EBF3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
EBF3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for EBF3 Gene

Disorders for EBF3 Gene

MalaCards: The human disease database

(17) MalaCards diseases for EBF3 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
hypotonia, ataxia, and delayed development syndrome
  • hadds
neurogenic bladder
  • neurogenic dysfunction of the urinary bladder
vesicoureteral reflux 1
  • vur1
urinary tract infections, recurrent
  • urinary tract infections, recurrent, susceptibility to
isolated pierre robin sequence
  • pierre robin syndrome
- elite association - COSMIC cancer census association via MalaCards
Search EBF3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

COE3_HUMAN
  • Hypotonia, ataxia, and delayed development syndrome (HADDS) [MIM:617330]: An autosomal dominant neurodevelopmental syndrome characterized by global developmental delay, moderate to severe intellectual disability, cerebellar ataxia, hypotonia, speech delay, variable dysmorphic features, and genitourinary abnormalities including vesicoureteric reflux. {ECO:0000269 PubMed:28017370, ECO:0000269 PubMed:28017372, ECO:0000269 PubMed:28017373}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for EBF3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with EBF3: view

No data available for Genatlas for EBF3 Gene

Publications for EBF3 Gene

  1. A Syndromic Neurodevelopmental Disorder Caused by De Novo Variants in EBF3. (PMID: 28017372) Chao HT … Malicdan MCV (American journal of human genetics 2017) 2 3 4
  2. Mutations in EBF3 Disturb Transcriptional Profiles and Cause Intellectual Disability, Ataxia, and Facial Dysmorphism. (PMID: 28017373) Harms FL … Kutsche K (American journal of human genetics 2017) 2 3 4
  3. De Novo Mutations in EBF3 Cause a Neurodevelopmental Syndrome. (PMID: 28017370) Sleven H … Németh AH (American journal of human genetics 2017) 2 3 4
  4. Integrated genomic and epigenomic analyses pinpoint biallelic gene inactivation in tumors. (PMID: 12355068) Zardo G … Costello JF (Nature genetics 2002) 2 3 4
  5. Frequently methylated tumor suppressor genes in head and neck squamous cell carcinoma. (PMID: 18559491) Bennett KL … Plass C (Cancer research 2008) 3 23

Products for EBF3 Gene

Sources for EBF3 Gene