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    EBF4 EBF family member 4 [ Homo sapiens (human) ]

    Gene ID: 57593, updated on 2-Nov-2024

    Summary

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    Official Symbol
    EBF4provided by HGNC
    Official Full Name
    EBF family member 4provided by HGNC
    Primary source
    HGNC:HGNC:29278
    See related
    Ensembl:ENSG00000088881 MIM:609935; AllianceGenome:HGNC:29278
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    COE4; OE-4; O/E-4
    Summary
    EBF4 belongs to the conserved Olf/EBF family of helix-loop-helix transcription factors, members of which play important roles in neural development and B-cell maturation (Wang et al., 2002 [PubMed 12139918]).[supplied by OMIM, Mar 2008]
    Expression
    Broad expression in prostate (RPKM 9.6), endometrium (RPKM 8.9) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See EBF4 in Genome Data Viewer
    Location:
    20p13
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (2692780..2760108)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (2723172..2790570)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (2673426..2740754)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2645500-2646285 Neighboring gene uncharacterized LOC105372507 Neighboring gene IDH3B divergent transcript Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2674597-2675581 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:2678055-2678598 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:2681405-2682133 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr20:2682134-2682861 Neighboring gene VISTA enhancer hs632 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12605 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:2731029-2731709 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:2731778-2732289 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12606 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2739980-2740630 Neighboring gene Sharpr-MPRA regulatory region 9456 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17471 Neighboring gene ribosomal protein L19 pseudogene 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2778855-2779842 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2779843-2780830 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2780831-2781816 Neighboring gene carboxypeptidase X, M14 family member 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. Early B cell factor 4 modulates FAS-mediated apoptosis and promotes cytotoxic function in human immune cells. Kubo S, et al. Proc Natl Acad Sci U S A, 2022 Aug 16. PMID 35939714, Free PMC Article
    2. Cloning of a novel Olf-1/EBF-like gene, O/E-4, by degenerate oligo-based direct selection. Wang SS, et al. Mol Cell Neurosci, 2002 Jul. PMID 12139918
    3. Biochemical and computational analysis of LNX1 interacting proteins. Wolting CD, et al. PLoS One, 2011. PMID 22087225, Free PMC Article
    4. A systematic screen for CDK4/6 substrates links FOXM1 phosphorylation to senescence suppression in cancer cells. Anders L, et al. Cancer Cell, 2011 Nov 15. PMID 22094256, Free PMC Article
    5. Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 2000 Feb 28. PMID 10718198

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Early B cell factor 4 modulates FAS-mediated apoptosis and promotes cytotoxic function in human immune cells.
      Title: Early B cell factor 4 modulates FAS-mediated apoptosis and promotes cytotoxic function in human immune cells.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1442

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
    		  
    enables DNA-binding transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in T cell apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    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
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    transcription factor COE4
    Names
    early B cell factor 4
    olf-1/EBF-like 4

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_001110514.2 → NP_001103984.2  transcription factor COE4 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AL035460
      Consensus CDS
      CCDS46573.1
      Related
      ENSP00000370022.4, ENST00000380648.9

    2. NM_001395167.1 → NP_001382096.1  transcription factor COE4 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL035460
      Consensus CDS
      CCDS93003.1
      UniProtKB/Swiss-Prot
      Q1MTP7, Q5JY53, Q9BQW3, Q9NUB6, Q9P2A6
      UniProtKB/TrEMBL
      E9PEI2
      Related
      ENSP00000477023.1, ENST00000609451.6
      Conserved Domains (4) summary
      PHA03247
      Location:411 → 573
      PHA03247; large tegument protein UL36; Provisional
      cd01175
      Location:256 → 340
      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:22 → 248
      COE1_DBD; Transcription factor COE1 DNA-binding domain
      pfam16423
      Location:341 → 384
      COE1_HLH; Transcription factor COE1 helix-loop-helix domain

    3. NM_001395168.1 → NP_001382097.1  transcription factor COE4 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL035460
      UniProtKB/TrEMBL
      E9PEI2
      Conserved Domains (3) summary
      PHA03247
      Location:334 → 496
      PHA03247; large tegument protein UL36; Provisional
      cd01175
      Location:179 → 263
      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 ...
      cl17007
      Location:86 → 171
      COE_DBD; Colier/Olf/Early B-cell factor (EBF) DNA Binding Domain

    RNA

    1. NR_138537.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AB037863, AI859365, AL035460, BC037555
      Related
      ENST00000449079.7

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      2692780..2760108
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006723600.2 → XP_006723663.2  transcription factor COE4 isoform X2

    2. XM_017027984.2 → XP_016883473.1  transcription factor COE4 isoform X1

      UniProtKB/TrEMBL
      E9PEI2

    3. XM_047440335.1 → XP_047296291.1  transcription factor COE4 isoform X4

    4. XM_017027985.1 → XP_016883474.1  transcription factor COE4 isoform X3

      Conserved Domains (2) summary
      pfam16423
      Location:108 → 151
      COE1_HLH; Transcription factor COE1 helix-loop-helix domain
      cl15674
      Location:23 → 107
      IPT; Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor ...

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      2723172..2790570
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054323774.1 → XP_054179749.1  transcription factor COE4 isoform X2

    2. XM_054323773.1 → XP_054179748.1  transcription factor COE4 isoform X1

    3. XM_054323776.1 → XP_054179751.1  transcription factor COE4 isoform X4

    4. XM_054323775.1 → XP_054179750.1  transcription factor COE4 isoform X3

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_020833.2: Suppressed sequence

      Description
      NM_020833.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BQW3.2 GenPept UniProtKB/Swiss-Prot:Q9BQW3

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    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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