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    Ebf4 EBF family member 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 680751, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Ebf4provided by RGD
    Official Full Name
    EBF family member 4provided by RGD
    Primary source
    RGD:1588215
    See related
    EnsemblRapid:ENSRNOG00000007408 AllianceGenome:RGD:1588215
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; DNA-binding transcription factor binding activity; and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in T cell apoptotic process and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of DNA-templated transcription. Predicted to be located in chromatin. Orthologous to human EBF4 (EBF family member 4). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Uterus (RPKM 27.5), Brain (RPKM 14.8) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Ebf4 in Genome Data Viewer
    Location:
    3q36
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (137951310..138019682)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (117498186..117566566)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (122836468..122890663)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene ribosomal protein S12-like 12 Neighboring gene ribosomal protein L31-like 6 Neighboring gene carboxypeptidase X (M14 family), member 1 Neighboring gene uncharacterized LOC129351010 Neighboring gene PC-esterase domain containing 1A

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. 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
    2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    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
    early B-cell factor 4
    early B-cell factor 4-like

    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_001191076.2 → NP_001178005.1  transcription factor COE4 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC130173, JAXUCZ010000003
      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_001415850.1 → NP_001402779.1  transcription factor COE4 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003
      UniProtKB/TrEMBL
      D3ZW79
      Related
      ENSRNOP00000028816.7, ENSRNOT00000028816.8

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      137951310..138019682
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039105845.2 → XP_038961773.1  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_039105846.2 → XP_038961774.1  transcription factor COE4 isoform X2

      Related
      ENSRNOP00000111404.1, ENSRNOT00000157960.1
      Conserved Domains (3) summary
      cd01175
      Location:353 → 437
      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:438 → 481
      COE1_HLH; Transcription factor COE1 helix-loop-helix domain

    3. XM_039105847.1 → XP_038961775.1  transcription factor COE4 isoform X3

      Conserved Domains (4) summary
      PHA03247
      Location:534 → 697
      PHA03247; large tegument protein UL36; Provisional
      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

    4. XM_063284541.1 → XP_063140611.1  transcription factor COE4 isoform X4

    5. XM_039105849.2 → XP_038961777.1  transcription factor COE4 isoform X5

      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

    6. XM_039105853.2 → XP_038961781.1  transcription factor COE4 isoform X7

      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

    7. XM_039105850.2 → XP_038961778.1  transcription factor COE4 isoform X6

      Conserved Domains (3) summary
      cd11606
      Location:6 → 207
      COE_DBD; Colier/Olf/Early B-cell factor (EBF) DNA Binding Domain
      cd01175
      Location:243 → 327
      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:328 → 371
      COE1_HLH; Transcription factor COE1 helix-loop-helix domain

    RNA

    1. XR_005501982.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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