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

Gene ID: 680751, updated on 2-Nov-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, Nov 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 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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