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Ebf1 early B-cell factor 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 116543, updated on 8-Jul-2018
Official Symbol
Ebf1provided by RGD
Official Full Name
early B-cell factor 1provided by RGD
Primary source
RGD:620953
See related
Ensembl:ENSRNOG00000028845 Vega:OTTRNOG00000000878
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
transcription factor that may regulate several olfactory-specific genes [RGD, Feb 2006]
Expression
Biased expression in Spleen (RPKM 50.7), Heart (RPKM 38.6) and 8 other tissues See more
Orthologs
See Ebf1 in Genome Data Viewer
Location:
10q12
Exon count:
20
Annotation release Status Assembly Chr Location
106 current Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (23654849..24051627)
104 previous assembly Rnor_5.0 (GCF_000001895.4) 10 NC_005109.3 (23518314..23912932)

Chromosome 10 - NC_005109.4Genomic Context describing neighboring genes Neighboring gene similar to thyroid hormone receptor associated protein 3 Neighboring gene uncharacterized LOC108352072 Neighboring gene uncharacterized LOC102547424 Neighboring gene uncharacterized LOC108352073 Neighboring gene similar to GC-rich promoter binding protein 1-like 1

  • 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
  • Adipogenesis, organism-specific biosystem (from WikiPathways)
    Adipogenesis, organism-specific biosystemThe different classess of factors involved in adipogenesis are shown. Adipogenesis is the process by which fat cells differentiate from predadipocytes to adipocytes (fat cells). Adipose tissue, compo...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
C2H2 zinc finger domain binding IPI
Inferred from Physical Interaction
more info
PubMed 
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA binding ISO
Inferred from Sequence Orthology
more info
 
DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
RNA polymerase II proximal promoter sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein dimerization activity IEA
Inferred from Electronic Annotation
more info
 
transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
positive regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IEA
Inferred from Electronic Annotation
more info
 
nucleus ISO
Inferred from Sequence Orthology
more info
 
Preferred Names
transcription factor COE1
Names
OE-1
early B-cell factor (olfactory neuronal transcription factor 1)
o/E-1
olf-1
olfactory neuronal transcription factor

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_053820.2NP_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
    Related
    ENSRNOP00000068319.1, OTTRNOP00000000701, ENSRNOT00000076664.2, OTTRNOT00000001324
    Conserved Domains (3) summary
    cd01175
    Location:255339
    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:21247
    COE1_DBD; Transcription factor COE1 DNA-binding domain
    pfam16423
    Location:340383
    COE1_HLH; Transcription factor COE1 helix-loop-helix domain

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

Reference Rnor_6.0 Primary Assembly

Genomic

  1. NC_005109.4 Reference Rnor_6.0 Primary Assembly

    Range
    23654849..24051627
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006246120.3XP_006246182.1  transcription factor COE1 isoform X4

    See identical proteins and their annotated locations for XP_006246182.1

    Conserved Domains (3) summary
    cd01175
    Location:249333
    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:7233
    COE1_DBD; Transcription factor COE1 DNA-binding domain
    pfam16423
    Location:334377
    COE1_HLH; Transcription factor COE1 helix-loop-helix domain
  2. XM_006246117.3XP_006246179.1  transcription factor COE1 isoform X1

    See identical proteins and their annotated locations for XP_006246179.1

    Conserved Domains (3) summary
    cd01175
    Location:263347
    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:21247
    COE1_DBD; Transcription factor COE1 DNA-binding domain
    pfam16423
    Location:348391
    COE1_HLH; Transcription factor COE1 helix-loop-helix domain
  3. XM_017596958.1XP_017452447.1  transcription factor COE1 isoform X3

    Conserved Domains (3) summary
    cd01175
    Location:254338
    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:21247
    COE1_DBD; Transcription factor COE1 DNA-binding domain
    pfam16423
    Location:339382
    COE1_HLH; Transcription factor COE1 helix-loop-helix domain
  4. XM_017596959.1XP_017452448.1  transcription factor COE1 isoform X4

  5. XM_006246118.2XP_006246180.1  transcription factor COE1 isoform X2

    See identical proteins and their annotated locations for XP_006246180.1

    Conserved Domains (3) summary
    cd01175
    Location:262346
    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:21247
    COE1_DBD; Transcription factor COE1 DNA-binding domain
    pfam16423
    Location:347390
    COE1_HLH; Transcription factor COE1 helix-loop-helix domain
  6. XM_017596960.1XP_017452449.1  transcription factor COE1 isoform X5

  7. XM_017596961.1XP_017452450.1  transcription factor COE1 isoform X6

  8. XM_017596962.1XP_017452451.1  transcription factor COE1 isoform X7

    Related
    ENSRNOP00000067433.2, ENSRNOT00000071435.2
    Conserved Domains (3) summary
    cd01175
    Location:130214
    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:1114
    COE_DBD; Colier/Olf/Early B-cell factor (EBF) DNA Binding Domain
    pfam16423
    Location:215258
    COE1_HLH; Transcription factor COE1 helix-loop-helix domain

Alternate Rn_Celera

Genomic

  1. AC_000078.1 Alternate Rn_Celera

    Range
    28580160..28966044
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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