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    Ebf4 early B cell factor 4 [ Mus musculus (house mouse) ]

    Gene ID: 228598, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Ebf4provided by MGI
    Official Full Name
    early B cell factor 4provided by MGI
    Primary source
    MGI:MGI:2385972
    See related
    Ensembl:ENSMUSG00000053552 AllianceGenome:MGI:2385972
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Ebf3; O/E-4; Olf-1
    Summary
    Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Acts upstream of or within regulation of DNA-templated transcription. Predicted to be located in chromatin. Is expressed in several structures, including diaphragm; genitourinary system; nervous system; retina; and skeletal muscle. Orthologous to human EBF4 (EBF family member 4). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in ovary adult (RPKM 14.4), limb E14.5 (RPKM 10.1) and 18 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Ebf4 in Genome Data Viewer
    Location:
    2 F1; 2 63.21 cM
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (130134832..130212402)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (130295126..130370482)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene NOP56 ribonucleoprotein Neighboring gene STARR-positive B cell enhancer ABC_E3405 Neighboring gene small nucleolar RNA, C/D box 57 Neighboring gene STARR-seq mESC enhancer starr_05691 Neighboring gene isocitrate dehydrogenase 3 (NAD+) beta Neighboring gene predicted gene, 39936 Neighboring gene ribosomal protein L27A pseudogene Neighboring gene carboxypeptidase X, M14 family member 1 Neighboring gene predicted gene, 54153

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Expression patterns of the coe/ebf transcription factor genes during chicken and mouse limb development. Mella S, et al. Gene Expr Patterns, 2004 Sep. PMID 15261831
    2. Ebf factors and MyoD cooperate to regulate muscle relaxation via Atp2a1. Jin S, et al. Nat Commun, 2014 May 2. PMID 24786561
    3. 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
    4. Transient and lineage-restricted requirement of Ebf3 for sternum ossification. Kuriki M, et al. Development, 2020 May 12. PMID 32398354, Free PMC Article
    5. An ancient role for collier/Olf/Ebf (COE)-type transcription factors in axial motor neuron development. Catela C, et al. Neural Dev, 2019 Jan 18. PMID 30658714, Free PMC Article

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in T cell apoptotic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of DNA-templated transcription 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 ISO
    Inferred from Sequence Orthology
    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
    EBF-4
    OE-4
    Olf-1/EBF-like 4
    early B-cell factor 3

    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_001110513.1 → NP_001103983.1  transcription factor COE4 isoform 2

      See identical proteins and their annotated locations for NP_001103983.1

      Status: VALIDATED

      Source sequence(s)
      AF387633, BE944141
      Consensus CDS
      CCDS50709.1
      UniProtKB/Swiss-Prot
      A2BI82, A2BI83, Q8K4J1, Q8K4J2, Q8K4J3, Q8K4J4, Q8K4J5
      UniProtKB/TrEMBL
      A2BI84, B2RQX3
      Related
      ENSMUSP00000105915.2, ENSMUST00000110286.8
      Conserved Domains (3) summary
      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

    2. NM_001415846.1 → NP_001402775.1  transcription factor COE4 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      BX890605, BX936285
      UniProtKB/TrEMBL
      A2BI80
      Related
      ENSMUSP00000105917.3, ENSMUST00000110288.9

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000068.8 Reference GRCm39 C57BL/6J

      Range
      130134832..130212402
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030250437.2 → XP_030106297.1  transcription factor COE4 isoform X1

      Conserved Domains (3) summary
      cd01175
      Location:381 → 465
      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:119 → 345
      COE1_DBD; Transcription factor COE1 DNA-binding domain
      pfam16423
      Location:466 → 509
      COE1_HLH; Transcription factor COE1 helix-loop-helix domain

    2. XM_030250430.2 → XP_030106290.1  transcription factor COE4 isoform X3

      Conserved Domains (3) summary
      cd01175
      Location:381 → 465
      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:119 → 345
      COE1_DBD; Transcription factor COE1 DNA-binding domain
      pfam16423
      Location:466 → 509
      COE1_HLH; Transcription factor COE1 helix-loop-helix domain

    3. XM_011239472.4 → XP_011237774.1  transcription factor COE4 isoform X5

      See identical proteins and their annotated locations for XP_011237774.1

      UniProtKB/TrEMBL
      A2BI84
      Conserved Domains (3) summary
      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

    4. XM_006499285.4 → XP_006499348.1  transcription factor COE4 isoform X4

      Conserved Domains (3) summary
      cd01175
      Location:48 → 132
      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:1 → 40
      COE_DBD; Colier/Olf/Early B-cell factor (EBF) DNA Binding Domain
      pfam16423
      Location:133 → 176
      COE1_HLH; Transcription factor COE1 helix-loop-helix domain

    RNA

    1. XR_004940010.1 RNA Sequence

    2. XR_004940016.1 RNA Sequence

    3. XR_003952508.2 RNA Sequence

    4. XR_004940027.1 RNA Sequence

    5. XR_004940028.1 RNA Sequence

    6. XR_374450.4 RNA Sequence

    7. XR_004940026.1 RNA Sequence

    8. XR_004940020.1 RNA Sequence

      Related
      ENSMUST00000126740.8

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_152993.1: Suppressed sequence

      Description
      NM_152993.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8K4J2.1 GenPept UniProtKB/Swiss-Prot:Q8K4J2

    Gene LinkOut

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

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