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

    Gene ID: 253738, updated on 17-Jun-2024

    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; AllianceGenome:HGNC:19087
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See EBF3 in Genome Data Viewer
    Location:
    10q26.3
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (129835233..129964274, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (130762552..130891466, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (131633497..131762538, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902531 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:131318758-131319273 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:131320305-131320819 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:131329433-131330277 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:131330278-131331122 Neighboring gene O-6-methylguanine-DNA methyltransferase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:131344545-131345044 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4203 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:131378975-131379951 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:131389051-131389616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:131391090-131391764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4204 Neighboring gene VISTA enhancer hs656 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2939 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2940 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:131474191-131474764 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:131483209-131483710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:131483711-131484210 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:131489399-131490266 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:131491009-131491509 Neighboring gene uncharacterized LOC105378560 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:131509515-131510230 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:131516429-131517628 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:131542389-131542890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:131542891-131543390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:131560022-131560594 Neighboring gene uncharacterized LOC107984281 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:131571913-131572610 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:131664970-131665634 Neighboring gene microRNA 4297 Neighboring gene VISTA enhancer hs232 Neighboring gene EBF3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:131692870-131693478 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:131694193-131695097 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:131695098-131696001 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:131725181-131725712 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:131747356-131748190 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:131756502-131757174 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:131758519-131759190 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:131762665-131763636 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:131764672-131765292 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:131766535-131767154 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:131769017-131769636 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:131771163-131772046 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:131770277-131771162 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:131811814-131812654 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:131842637-131843136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:131847250-131848134 Neighboring gene chromosome 10 open reading frame 143 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:131903776-131904291 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4206 Neighboring gene uncharacterized LOC102724883 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2941 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4207 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4209 Neighboring gene uncharacterized LOC124902560 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:131919446-131919946 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:131919947-131920447 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

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2023-12-06)

    ClinGen Genome Curation PagePubMed
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2023-12-06)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    A genome-wide association study of sleep habits and insomnia.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in positive regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in 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)

    NEW Try the new Transcript table

    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/TrEMBL
      Q658Y5
      Related
      ENSP00000357637.3, ENST00000368648.8
      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
      Consensus CDS
      CCDS91376.1
      UniProtKB/Swiss-Prot
      A0AUY1, Q5T6H9, Q9H4W5, Q9H4W6
      UniProtKB/TrEMBL
      Q658Y5
      Related
      ENSP00000347463.4, ENST00000355311.10
      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
    3. NM_001375380.1NP_001362309.1  transcription factor COE3 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AL354950
      Consensus CDS
      CCDS91377.1
      UniProtKB/TrEMBL
      H0Y3W9, Q658Y5
      Related
      ENSP00000387543.2, ENST00000440978.2
      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
    4. NM_001375389.1NP_001362318.1  transcription factor COE3 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AL354950
      UniProtKB/TrEMBL
      Q658Y5
      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
    5. NM_001375390.1NP_001362319.1  transcription factor COE3 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL354950
      UniProtKB/TrEMBL
      Q658Y5
      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
    6. NM_001375391.1NP_001362320.1  transcription factor COE3 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AL354950
      UniProtKB/TrEMBL
      Q658Y5
      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. NM_001375392.1NP_001362321.1  transcription factor COE3 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AL354950
      UniProtKB/TrEMBL
      Q658Y5
      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

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p14 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 X5

      UniProtKB/TrEMBL
      Q658Y5
      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_047424961.1XP_047280917.1  transcription factor COE3 isoform X8

      UniProtKB/TrEMBL
      Q658Y5
    3. XM_005252669.3XP_005252726.1  transcription factor COE3 isoform X4

      See identical proteins and their annotated locations for XP_005252726.1

      UniProtKB/TrEMBL
      Q658Y5
      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_005252667.3XP_005252724.1  transcription factor COE3 isoform X2

      UniProtKB/TrEMBL
      Q658Y5
      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
    5. XM_017016027.1XP_016871516.1  transcription factor COE3 isoform X7

      UniProtKB/TrEMBL
      Q658Y5
    6. XM_006717744.3XP_006717807.1  transcription factor COE3 isoform X6

      See identical proteins and their annotated locations for XP_006717807.1

      UniProtKB/TrEMBL
      Q658Y5
      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_006717740.3XP_006717803.1  transcription factor COE3 isoform X1

      See identical proteins and their annotated locations for XP_006717803.1

      UniProtKB/TrEMBL
      Q658Y5
      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
    8. XM_011539575.3XP_011537877.1  transcription factor COE3 isoform X9

      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
    9. XM_006717741.4XP_006717804.1  transcription factor COE3 isoform X3

      UniProtKB/TrEMBL
      Q658Y5
      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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      130762552..130891466 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054365411.1XP_054221386.1  transcription factor COE3 isoform X5

      UniProtKB/TrEMBL
      Q658Y5
    2. XM_054365414.1XP_054221389.1  transcription factor COE3 isoform X8

      UniProtKB/TrEMBL
      Q658Y5
    3. XM_054365410.1XP_054221385.1  transcription factor COE3 isoform X4

      UniProtKB/TrEMBL
      Q658Y5
    4. XM_054365408.1XP_054221383.1  transcription factor COE3 isoform X2

      UniProtKB/TrEMBL
      Q658Y5
    5. XM_054365413.1XP_054221388.1  transcription factor COE3 isoform X7

      UniProtKB/TrEMBL
      Q658Y5
    6. XM_054365412.1XP_054221387.1  transcription factor COE3 isoform X6

      UniProtKB/TrEMBL
      Q658Y5
    7. XM_054365407.1XP_054221382.1  transcription factor COE3 isoform X1

      UniProtKB/TrEMBL
      Q658Y5
    8. XM_054365415.1XP_054221390.1  transcription factor COE3 isoform X9

    9. XM_054365409.1XP_054221384.1  transcription factor COE3 isoform X3

      UniProtKB/TrEMBL
      Q658Y5