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Ebf3 EBF transcription factor 3 [ Rattus norvegicus (Norway rat) ]

Gene ID: 361668, updated on 17-Aug-2024

Summary

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Official Symbol
Ebf3provided by RGD
Official Full Name
EBF transcription factor 3provided by RGD
Primary source
RGD:1304956
See related
EnsemblRapid:ENSRNOG00000016102 AllianceGenome:RGD:1304956
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 and RNA polymerase II cis-regulatory region sequence-specific DNA 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 EBF3 (EBF transcription factor 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Muscle (RPKM 34.8), Heart (RPKM 33.5) and 8 other tissues See more
Orthologs
human mouse all
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Genomic context

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Location:
1q41
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (201426446..201544444, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (191996726..192114593, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (209523153..209641143, complement)

Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene O-6-methylguanine-DNA methyltransferase Neighboring gene uncharacterized LOC102552565 Neighboring gene nucleolin, pseudogene 4 Neighboring gene nucleolin, pseudogene 6

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. Mutations in EBF3 Disturb Transcriptional Profiles and Cause Intellectual Disability, Ataxia, and Facial Dysmorphism. Harms FL, et al. Am J Hum Genet, 2017 Jan 5. PMID 28017373, Free PMC Article
  2. De Novo Mutations in EBF3 Cause a Neurodevelopmental Syndrome. Sleven H, et al. Am J Hum Genet, 2017 Jan 5. PMID 28017370, Free PMC Article
  3. A Syndromic Neurodevelopmental Disorder Caused by De Novo Variants in EBF3. Chao HT, et al. Am J Hum Genet, 2017 Jan 5. PMID 28017372, Free PMC Article
  4. 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
  5. 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 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 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 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 transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
transcription factor COE3
Names
early B-cell factor 3

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_001108506.3 → NP_001101976.1  transcription factor COE3 isoform 1

    See identical proteins and their annotated locations for NP_001101976.1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000001
    UniProtKB/TrEMBL
    A0A8I5ZU01, A6HX79, D4A274
    Related
    ENSRNOP00000021702.5, ENSRNOT00000021702.7
    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

  2. NM_001415982.1 → NP_001402911.1  transcription factor COE3 isoform 2

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000001
    UniProtKB/TrEMBL
    A0A8I5ZU01, A6HX78

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_086019.1 Reference GRCr8

    Range
    201426446..201544444 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039083383.2 → XP_038939311.1  transcription factor COE3 isoform X7

    UniProtKB/TrEMBL
    A0A8I5ZU01
    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

  2. XM_039083400.2 → XP_038939328.1  transcription factor COE3 isoform X10

    UniProtKB/TrEMBL
    A0A8I5ZU01
    Related
    ENSRNOP00000107429.1, ENSRNOT00000162603.1
    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_039083394.2 → XP_038939322.1  transcription factor COE3 isoform X9

    UniProtKB/TrEMBL
    A0A8I5ZU01
    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

  4. XM_039083357.2 → XP_038939285.1  transcription factor COE3 isoform X2

    UniProtKB/TrEMBL
    A0A8I5ZU01
    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

  5. XM_006230462.5 → XP_006230524.1  transcription factor COE3 isoform X1

    See identical proteins and their annotated locations for XP_006230524.1

    UniProtKB/TrEMBL
    A0A8I5ZU01
    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

  6. XM_039083406.2 → XP_038939334.1  transcription factor COE3 isoform X11

    UniProtKB/TrEMBL
    A0A8I5ZU01
    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

  7. XM_039083361.2 → XP_038939289.1  transcription factor COE3 isoform X3

    UniProtKB/TrEMBL
    A0A8I5ZU01, A0A8I6A4F0
    Related
    ENSRNOP00000085956.1, ENSRNOT00000115779.2
    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

  8. XM_039083413.2 → XP_038939341.1  transcription factor COE3 isoform X12

    UniProtKB/TrEMBL
    A0A8I5ZU01
    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 ...
    pfam16423
    Location:348 → 391
    COE1_HLH; Transcription factor COE1 helix-loop-helix domain
    pfam16422
    Location:21 → 247
    COE1_DBD; Transcription factor COE1 DNA-binding domain

  9. XM_039083366.2 → XP_038939294.1  transcription factor COE3 isoform X4

    UniProtKB/TrEMBL
    A0A8I5ZU01
    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

  10. XM_063267948.1 → XP_063124018.1  transcription factor COE3 isoform X13

    UniProtKB/TrEMBL
    A0A8I5ZU01

  11. XM_039083378.2 → XP_038939306.1  transcription factor COE3 isoform X6

    UniProtKB/TrEMBL
    A0A8I5ZU01
    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

  12. XM_006230464.5 → XP_006230526.1  transcription factor COE3 isoform X5

    See identical proteins and their annotated locations for XP_006230526.1

    UniProtKB/TrEMBL
    A0A8I5ZU01
    Related
    ENSRNOP00000082695.1, ENSRNOT00000107995.2
    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

  13. XM_039083384.2 → XP_038939312.1  transcription factor COE3 isoform X8

    UniProtKB/TrEMBL
    A0A8I5ZU01
    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
Nucleotide Protein Strain
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