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

Gene ID: 116543, updated on 11-Apr-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
Ensembl: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 transcription, DNA-templated. Predicted to be located in nucleus. Orthologous to human EBF1 (EBF transcription factor 1). [provided by Alliance of Genome Resources, Apr 2022]
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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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
  • 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 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 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
    ENSRNOP00000068319.2
    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

    Related
    ENSRNOP00000067433.3
    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
    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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