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    Ebf1 EBF transcription factor 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 116543, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Ebf1provided by RGD
    Official Full Name
    EBF transcription factor 1provided by RGD
    Primary source
    RGD:620953
    See related
    EnsemblRapid:ENSRNOG00000028845 AllianceGenome:RGD:620953
    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
    Also known as
    Ebf; Olf1
    Summary
    Enables C2H2 zinc finger domain binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of DNA-templated transcription. Predicted to be located in nucleus. Orthologous to human EBF1 (EBF transcription factor 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Spleen (RPKM 50.7), Heart (RPKM 38.6) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Ebf1 in Genome Data Viewer
    Location:
    10q21
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (29597221..29990571)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (29095858..29489142)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (23654849..24051627)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120095078 Neighboring gene uncharacterized LOC120095081 Neighboring gene uncharacterized LOC134480679 Neighboring gene uncharacterized LOC120095079 Neighboring gene uncharacterized LOC134480680 Neighboring gene uncharacterized LOC134480681

    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. Identification of DNA recognition sequences and protein interaction domains of the multiple-Zn-finger protein Roaz. Tsai RY, et al. Mol Cell Biol, 1998 Nov. PMID 9774661, Free PMC Article
    2. Molecular cloning of the olfactory neuronal transcription factor Olf-1 by genetic selection in yeast. Wang MM, et al. Nature, 1993 Jul 8. PMID 8321284
    3. Early B-cell factor, E2A, and Pax-5 cooperate to activate the early B cell-specific mb-1 promoter. Sigvardsson M, et al. Mol Cell Biol, 2002 Dec. PMID 12446773, Free PMC Article
    4. Promoter architecture of mouse olfactory receptor genes. Plessy C, et al. Genome Res, 2012 Mar. PMID 22194471, Free PMC Article
    5. Cloning and functional characterization of Roaz, a zinc finger protein that interacts with O/E-1 to regulate gene expression: implications for olfactory neuronal development. Tsai RY, et al. J Neurosci, 1997 Jun 1. PMID 9151733, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    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 RGD

    Function Evidence Code Pubs
    enables C2H2 zinc finger domain binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription factor activity 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 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 metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    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 nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    transcription factor COE1
    Names
    OE-1
    early B-cell factor (olfactory neuronal transcription factor 1)
    early B-cell factor 1
    o/E-1
    olf-1
    olfactory neuronal transcription factor

    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_053820.2 → NP_446272.2  transcription factor COE1

      See identical proteins and their annotated locations for NP_446272.2

      Status: VALIDATED

      Source sequence(s)
      FQ175272, FQ177833, FQ232013, L24051
      UniProtKB/Swiss-Prot
      Q63398
      UniProtKB/TrEMBL
      A6HDP7
      Conserved Domains (3) summary
      cd01175
      Location:255 → 339
      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:21 → 247
      COE1_DBD; Transcription factor COE1 DNA-binding domain
      pfam16423
      Location:340 → 383
      COE1_HLH; Transcription factor COE1 helix-loop-helix domain

    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_086028.1 Reference GRCr8

      Range
      29597221..29990571
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006246120.5 → XP_006246182.1  transcription factor COE1 isoform X8

      See identical proteins and their annotated locations for XP_006246182.1

      UniProtKB/TrEMBL
      A0A8I5ZU01
      Conserved Domains (3) summary
      cd01175
      Location:249 → 333
      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:7 → 233
      COE1_DBD; Transcription factor COE1 DNA-binding domain
      pfam16423
      Location:334 → 377
      COE1_HLH; Transcription factor COE1 helix-loop-helix domain

    2. XM_006246117.5 → XP_006246179.1  transcription factor COE1 isoform X1

      See identical proteins and their annotated locations for XP_006246179.1

      UniProtKB/TrEMBL
      A0A8L2QZ79
      Related
      ENSRNOP00000105851.1, ENSRNOT00000128797.1
      Conserved Domains (3) summary
      cd01175
      Location:263 → 347
      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:21 → 247
      COE1_DBD; Transcription factor COE1 DNA-binding domain
      pfam16423
      Location:348 → 391
      COE1_HLH; Transcription factor COE1 helix-loop-helix domain

    3. XM_017596958.3 → XP_017452447.1  transcription factor COE1 isoform X3

      Conserved Domains (3) summary
      cd01175
      Location:254 → 338
      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:21 → 247
      COE1_DBD; Transcription factor COE1 DNA-binding domain
      pfam16423
      Location:339 → 382
      COE1_HLH; Transcription factor COE1 helix-loop-helix domain

    4. XM_006246118.4 → XP_006246180.1  transcription factor COE1 isoform X2

      See identical proteins and their annotated locations for XP_006246180.1

      Conserved Domains (3) summary
      cd01175
      Location:262 → 346
      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:21 → 247
      COE1_DBD; Transcription factor COE1 DNA-binding domain
      pfam16423
      Location:347 → 390
      COE1_HLH; Transcription factor COE1 helix-loop-helix domain

    5. XM_063268302.1 → XP_063124372.1  transcription factor COE1 isoform X6

    6. XM_039085048.2 → XP_038940976.1  transcription factor COE1 isoform X4

      UniProtKB/TrEMBL
      A0A8I5ZU01
      Related
      ENSRNOP00000068319.3, ENSRNOT00000076664.4
      Conserved Domains (3) summary
      cd11606
      Location:10 → 215
      COE_DBD; Colier/Olf/Early B-cell factor (EBF) DNA Binding Domain
      cd01175
      Location:231 → 315
      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:316 → 359
      COE1_HLH; Transcription factor COE1 helix-loop-helix domain

    7. XM_039085049.2 → XP_038940977.1  transcription factor COE1 isoform X5

      UniProtKB/TrEMBL
      A0A8I5ZU01
      Conserved Domains (3) summary
      cd11606
      Location:10 → 215
      COE_DBD; Colier/Olf/Early B-cell factor (EBF) DNA Binding Domain
      cd01175
      Location:230 → 314
      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:315 → 358
      COE1_HLH; Transcription factor COE1 helix-loop-helix domain

    8. XM_063268303.1 → XP_063124373.1  transcription factor COE1 isoform X7

    9. XM_017596960.3 → XP_017452449.1  transcription factor COE1 isoform X10

      UniProtKB/TrEMBL
      A0A8I5ZU01

    10. XM_017596962.3 → XP_017452451.1  transcription factor COE1 isoform X9

      Conserved Domains (3) summary
      cd01175
      Location:130 → 214
      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:215 → 258
      COE1_HLH; Transcription factor COE1 helix-loop-helix domain
      cl17007
      Location:1 → 114
      COE_DBD; Colier/Olf/Early B-cell factor (EBF) DNA Binding Domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q63398.2 GenPept UniProtKB/Swiss-Prot:Q63398

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