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Aliases for EBF3 Gene

Aliases for EBF3 Gene

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

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

UniProtKB/Swiss-Prot for EBF3 Gene

  • Transcriptional activator which recognizes variations of the palindromic sequence 5-ATTCCCNNGGGAATT-3.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for EBF3 Gene

Genomics for EBF3 Gene

Regulatory Elements for EBF3 Gene

Enhancers for EBF3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH10G129020 2.9 VISTA Ensembl ENCODE dbSUPER 11.8 +936.7 936693 14.6 HDAC1 TBP ZNF2 RAD21 KAT2B TCF12 GATA2 FOS ZNF263 ZNF654 EBF3 GC10P129032 ENSG00000232985
GH10G129888 2.2 FANTOM5 Ensembl ENCODE 6.9 +74.8 74815 1.9 CTCF ZFHX2 GABPB1 SMC3 MNT FOXP2 RAD21 EZH2 EBF3 GC10P129907 LOC105378558
GH10G129949 2.7 FANTOM5 Ensembl ENCODE dbSUPER 2.9 +6.8 6848 16.2 PKNOX1 FOXA2 YBX1 FOS ZNF263 ZNF202 SP5 REST NFIL3 CBX8 EBF3 GC10P129955
GH10G129845 1.3 FANTOM5 3.7 +118.4 118428 0.2 EBF3 ENSG00000275005 GC10P129853
GH10G129933 0.4 dbSUPER 11.8 +29.8 29772 1.8 MNT EBF3 GC10P129955 GC10P129908
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around EBF3 on UCSC Golden Path with GeneCards custom track

Promoters for EBF3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000035270 381 1401 SUZ12 MAX ZIC2 POLR2A PATZ1 ZNF600 PRDM10 ZNF391 KLF8 ZBTB20

Genomic Location for EBF3 Gene

Chromosome:
10
Start:
129,835,232 bp from pter
End:
129,964,281 bp from pter
Size:
129,050 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

Suggested Antigen Peptide Sequences for EBF3 Gene

GenScript: Design optimal peptide antigens:

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

No data available for Gene Families for EBF3 Gene

Function for EBF3 Gene

Molecular function for EBF3 Gene

UniProtKB/Swiss-Prot Function:
Transcriptional activator which recognizes variations of the palindromic sequence 5-ATTCCCNNGGGAATT-3.

Gene Ontology (GO) - Molecular Function for EBF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding IEA --
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding IEA --
GO:0003677 DNA binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with EBF3: view
genes like me logo Genes that share phenotypes with EBF3: view

Animal Models for EBF3 Gene

MGI Knock Outs for EBF3:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , 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 2

Gene Ontology (GO) - Cellular Components for EBF3 Gene

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

Pathways & Interactions 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

Gene Ontology (GO) - Biological Process for EBF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription from RNA polymerase II promoter IEA --
GO:0007275 multicellular organism development IEA --
GO:0045893 positive regulation of transcription, DNA-templated IEA,IMP 28017370
genes like me logo Genes that share ontologies with EBF3: view

No data available for SIGNOR curated interactions for EBF3 Gene

Drugs & Compounds for EBF3 Gene

No Compound Related Data Available

Transcripts for EBF3 Gene

Unigene Clusters for EBF3 Gene

Early B-cell factor 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

No ASD Table

Relevant External Links for EBF3 Gene

GeneLoc Exon Structure for
EBF3
ECgene alternative splicing isoforms for
EBF3

Expression for EBF3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for EBF3 Gene



Protein tissue co-expression partners for EBF3 Gene

NURSA nuclear receptor signaling pathways regulating expression of EBF3 Gene:

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.
genes like me logo Genes that share expression patterns with EBF3: view

Primer Products

No data available for Evidence on tissue expression from TISSUES and 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 34 35
  • 99.7 (n)
mouse
(Mus musculus)
Mammalia Ebf3 34 16 35
  • 94.25 (n)
rat
(Rattus norvegicus)
Mammalia Ebf3 34
  • 93.89 (n)
dog
(Canis familiaris)
Mammalia EBF3 35
  • 91 (a)
OneToOne
cow
(Bos Taurus)
Mammalia EBF3 35
  • 90 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia EBF3 35
  • 79 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia EBF3 35
  • 59 (a)
OneToOne
chicken
(Gallus gallus)
Aves EBF3 35
  • 84 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia EBF3 35
  • 95 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ebf3 34
  • 83.55 (n)
MGC75916 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.632 34
zebrafish
(Danio rerio)
Actinopterygii ebf3 34 35
  • 81.6 (n)
fruit fly
(Drosophila melanogaster)
Insecta kn 34 35
  • 68.43 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011437 34
  • 67.67 (n)
worm
(Caenorhabditis elegans)
Secernentea unc-3 35
  • 55 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 52 (a)
OneToMany
Species where no ortholog for EBF3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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)

Paralogs for EBF3 Gene

Paralogs for EBF3 Gene

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

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

Variants for EBF3 Gene

Sequence variations from dbSNP and Humsavar for EBF3 Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type
VAR_078033 Hypotonia, ataxia, and delayed development syndrome (HADDS) [MIM:617330]
VAR_078034 Hypotonia, ataxia, and delayed development syndrome (HADDS) [MIM:617330]
VAR_078036 Hypotonia, ataxia, and delayed development syndrome (HADDS) [MIM:617330]
VAR_078037 Hypotonia, ataxia, and delayed development syndrome (HADDS) [MIM:617330]
VAR_078038 Hypotonia, ataxia, and delayed development syndrome (HADDS) [MIM:617330]

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)

Relevant External Links for EBF3 Gene

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

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

Disorders for EBF3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for EBF3 Gene - From: ClinVar, Swiss-Prot, and GeneCards

Disorder Aliases PubMed IDs
hypotonia, ataxia, and delayed development syndrome
  • hadds
- elite association - COSMIC cancer census association via MalaCards
Search EBF3 in MalaCards View complete list of genes associated with diseases

Relevant External Links for EBF3

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

No data available for UniProtKB/Swiss-Prot and Genatlas for EBF3 Gene

Publications for EBF3 Gene

  1. Integrated genomic and epigenomic analyses pinpoint biallelic gene inactivation in tumors. (PMID: 12355068) Zardo G. … Costello J.F. (Nat. Genet. 2002) 2 3 4 64
  2. Frequently methylated tumor suppressor genes in head and neck squamous cell carcinoma. (PMID: 18559491) Bennett K.L. … Plass C. (Cancer Res. 2008) 3 22 64
  3. The DNA sequence and comparative analysis of human chromosome 10. (PMID: 15164054) Deloukas P. … Rogers J. (Nature 2004) 3 4 64
  4. Mutations in EBF3 Disturb Transcriptional Profiles and Cause Intellectual Disability, Ataxia, and Facial Dysmorphism. (PMID: 28017373) Harms F.L. … Kutsche K. (Am. J. Hum. Genet. 2017) 3 64
  5. A Syndromic Neurodevelopmental Disorder Caused by De Novo Variants in EBF3. (PMID: 28017372) Chao H.T. … Malicdan M.C. (Am. J. Hum. Genet. 2017) 3 64

Products for EBF3 Gene

Sources for EBF3 Gene

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