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

    Gene ID: 361668, updated on 2-Nov-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 DNA-templated transcription. Predicted to be located in nucleus. Human ortholog(s) of this gene implicated in hypotonia, ataxia, and delayed development syndrome. Orthologous to human EBF3 (EBF transcription factor 3). [provided by Alliance of Genome Resources, Nov 2024]
    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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    See Ebf3 in Genome Data Viewer
    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
      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

    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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