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EBF3 EBF transcription factor 3 [ Homo sapiens (human) ]

Gene ID: 253738, updated on 13-Mar-2020

Summary

Official Symbol
EBF3provided by HGNC
Official Full Name
EBF transcription factor 3provided by HGNC
Primary source
HGNC:HGNC:19087
See related
Ensembl:ENSG00000108001 MIM:607407
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
COE3; OE-2; EBF-3; HADDS; O/E-2
Summary
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]
Expression
Biased expression in fat (RPKM 8.2), lymph node (RPKM 3.7) and 12 other tissues See more
Orthologs

Genomic context

See EBF3 in Genome Data Viewer
Location:
10q26.3
Exon count:
18
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 10 NC_000010.11 (129835233..129964274, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (131633496..131762546, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene O-6-methylguanine-DNA methyltransferase Neighboring gene uncharacterized LOC105378560 Neighboring gene long intergenic non-protein coding RNA 2666 Neighboring gene uncharacterized LOC107984281 Neighboring gene uncharacterized LOC105378558 Neighboring gene microRNA 4297 Neighboring gene VISTA enhancer hs232 Neighboring gene chromosome 10 open reading frame 143 Neighboring gene uncharacterized LOC102724883 Neighboring gene uncharacterized LOC105378561 Neighboring gene CTAGE family member 7, pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Hypotonia, ataxia, and delayed development syndrome
MedGen: C4310618 OMIM: 617330 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
A genome-wide association study of sleep habits and insomnia.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
transcription factor COE3
Names
early B cell factor 3
olf-1/EBF-like 2

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_030038.1 RefSeqGene

    Range
    4554..133595
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001005463.3NP_001005463.1  transcription factor COE3 isoform 6

    See identical proteins and their annotated locations for NP_001005463.1

    Status: REVIEWED

    Source sequence(s)
    AA330620, AK055710, AK097335, AK098025, AL354950, AL713797, BC130479
    Consensus CDS
    CCDS31314.1
    UniProtKB/Swiss-Prot
    Q9H4W6
    Related
    ENSP00000357637.3, ENST00000368648.7
    Conserved Domains (3) summary
    cd01175
    Location:254338
    IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...
    pfam16422
    Location:21247
    COE1_DBD; Transcription factor COE1 DNA-binding domain
    pfam16423
    Location:339382
    COE1_HLH; Transcription factor COE1 helix-loop-helix domain
  2. NM_001375379.1NP_001362308.1  transcription factor COE3 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AL354950
    Related
    ENSP00000347463.4, ENST00000355311.9
  3. NM_001375380.1NP_001362309.1  transcription factor COE3 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL354950
  4. NM_001375389.1NP_001362318.1  transcription factor COE3 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL354950
  5. NM_001375390.1NP_001362319.1  transcription factor COE3 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL354950
  6. NM_001375391.1NP_001362320.1  transcription factor COE3 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AL354950
  7. NM_001375392.1NP_001362321.1  transcription factor COE3 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AL354950

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p13 Primary Assembly

    Range
    129835233..129964274 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011539574.2XP_011537876.1  transcription factor COE3 isoform X9

    Conserved Domains (2) summary
    pfam16422
    Location:21247
    COE1_DBD; Transcription factor COE1 DNA-binding domain
    pfam16423
    Location:253296
    COE1_HLH; Transcription factor COE1 helix-loop-helix domain
  2. XM_005252669.3XP_005252726.1  transcription factor COE3 isoform X7

    See identical proteins and their annotated locations for XP_005252726.1

    Conserved Domains (3) summary
    cd01175
    Location:254338
    IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...
    pfam16422
    Location:21247
    COE1_DBD; Transcription factor COE1 DNA-binding domain
    pfam16423
    Location:339382
    COE1_HLH; Transcription factor COE1 helix-loop-helix domain
  3. XM_005252667.3XP_005252724.1  transcription factor COE3 isoform X3

    Conserved Domains (3) summary
    cd01175
    Location:254338
    IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...
    pfam16422
    Location:21247
    COE1_DBD; Transcription factor COE1 DNA-binding domain
    pfam16423
    Location:339382
    COE1_HLH; Transcription factor COE1 helix-loop-helix domain
  4. XM_017016027.1XP_016871516.1  transcription factor COE3 isoform X11

  5. XM_006717744.3XP_006717807.1  transcription factor COE3 isoform X10

    See identical proteins and their annotated locations for XP_006717807.1

    Conserved Domains (3) summary
    cd01175
    Location:263347
    IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...
    pfam16422
    Location:21247
    COE1_DBD; Transcription factor COE1 DNA-binding domain
    pfam16423
    Location:348391
    COE1_HLH; Transcription factor COE1 helix-loop-helix domain
  6. XM_006717740.3XP_006717803.1  transcription factor COE3 isoform X2

    See identical proteins and their annotated locations for XP_006717803.1

    Conserved Domains (3) summary
    cd01175
    Location:263347
    IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...
    pfam16422
    Location:21247
    COE1_DBD; Transcription factor COE1 DNA-binding domain
    pfam16423
    Location:348391
    COE1_HLH; Transcription factor COE1 helix-loop-helix domain
  7. XM_011539575.2XP_011537877.1  transcription factor COE3 isoform X12

    Conserved Domains (3) summary
    cd01175
    Location:91175
    IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...
    pfam16423
    Location:176219
    COE1_HLH; Transcription factor COE1 helix-loop-helix domain
    cl17007
    Location:1475
    COE_DBD; Colier/Olf/Early B-cell factor (EBF) DNA Binding Domain
  8. XM_006717741.3XP_006717804.1  transcription factor COE3 isoform X5

    Conserved Domains (3) summary
    cd01175
    Location:263347
    IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...
    pfam16422
    Location:21247
    COE1_DBD; Transcription factor COE1 DNA-binding domain
    pfam16423
    Location:348391
    COE1_HLH; Transcription factor COE1 helix-loop-helix domain

RNA

  1. XR_001747076.1 RNA Sequence

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