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    Rfx3 regulatory factor X3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 361746, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Rfx3provided by RGD
    Official Full Name
    regulatory factor X3provided by RGD
    Primary source
    RGD:1307779
    See related
    EnsemblRapid:ENSRNOG00000014486 AllianceGenome:RGD:1307779
    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 factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including epithelial cilium movement involved in determination of left/right asymmetry; positive regulation of type B pancreatic cell development; and regulation of DNA-templated transcription. Predicted to act upstream of or within determination of left/right symmetry. Predicted to be located in chromatin. Predicted to be part of transcription regulator complex. Orthologous to human RFX3 (regulatory factor X3). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Brain (RPKM 78.1), Lung (RPKM 52.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Rfx3 in Genome Data Viewer
    Location:
    1q52
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (234863462..235122989, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (225449872..225709622, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (245853332..246110648, complement)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102555989 Neighboring gene uncharacterized LOC134485216 Neighboring gene eukaryotic translation initiation factor 4E, pseudogene 2 Neighboring gene U6atac minor spliceosomal RNA Neighboring gene small nucleolar RNA SNORA51 Neighboring gene THO complex 3, pseudogene 1 Neighboring gene peptidylprolyl isomerase D, pseudogene 2 Neighboring gene RNA, U6 small nuclear 613

    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. Novel function of the ciliogenic transcription factor RFX3 in development of the endocrine pancreas. Ait-Lounis A, et al. Diabetes, 2007 Apr. PMID 17229940
    2. RFX3 governs growth and beating efficiency of motile cilia in mouse and controls the expression of genes involved in human ciliopathies. El Zein L, et al. J Cell Sci, 2009 Sep 1. PMID 19671664
    3. Role for RFX transcription factors in non-neuronal cell-specific inactivation of the microtubule-associated protein MAP1A promoter. Nakayama A, et al. J Biol Chem, 2003 Jan 3. PMID 12411430
    4. Evolutionarily dynamic alternative splicing of GPR56 regulates regional cerebral cortical patterning. Bae BI, et al. Science, 2014 Feb 14. PMID 24531968, Free PMC Article
    5. The transcription factor RFX3 directs nodal cilium development and left-right asymmetry specification. Bonnafe E, et al. Mol Cell Biol, 2004 May. PMID 15121860, Free PMC Article

    See all (9) citations in PubMed

    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 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 sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables sequence-specific double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription cis-regulatory region binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cell maturation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cilium assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cilium-dependent cell motility ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within determination of left/right symmetry ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endocrine pancreas development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in epithelial cilium movement involved in determination of left/right asymmetry ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative 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 positive regulation of type B pancreatic cell development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of insulin secretion 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
    		  
    involved_in type B pancreatic cell maturation ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of transcription regulator complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    transcription factor RFX3
    Names
    regulatory factor X, 3 (influences HLA class II expression)

    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_001395594.1 → NP_001382523.1  transcription factor RFX3

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/TrEMBL
      A0A8I5Y6Y1, A6I0T9
      Conserved Domains (2) summary
      pfam02257
      Location:184 → 256
      RFX_DNA_binding; RFX DNA-binding domain
      pfam04589
      Location:51 → 134
      RFX1_trans_act; RFX1 transcription activation region

    RNA

    1. NR_172644.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001

    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
      234863462..235122989 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063268579.1 → XP_063124649.1  transcription factor RFX3 isoform X6

      UniProtKB/TrEMBL
      A0A0G2JYT9, A0A8I5Y6Y1

    2. XM_063268574.1 → XP_063124644.1  transcription factor RFX3 isoform X6

      UniProtKB/TrEMBL
      A0A0G2JYT9, A0A8I5Y6Y1

    3. XM_017589448.3 → XP_017444937.1  transcription factor RFX3 isoform X2

      UniProtKB/TrEMBL
      A0A8I5Y6Y1
      Related
      ENSRNOP00000091275.2, ENSRNOT00000096629.2
      Conserved Domains (2) summary
      pfam02257
      Location:210 → 282
      RFX_DNA_binding; RFX DNA-binding domain
      pfam04589
      Location:77 → 160
      RFX1_trans_act; RFX1 transcription activation region

    4. XM_006231235.5 → XP_006231297.1  transcription factor RFX3 isoform X5

      See identical proteins and their annotated locations for XP_006231297.1

      UniProtKB/TrEMBL
      A0A8I5Y6Y1, A6I0T9
      Conserved Domains (2) summary
      pfam02257
      Location:184 → 256
      RFX_DNA_binding; RFX DNA-binding domain
      pfam04589
      Location:51 → 134
      RFX1_trans_act; RFX1 transcription activation region

    5. XM_039084350.2 → XP_038940278.1  transcription factor RFX3 isoform X3

      UniProtKB/TrEMBL
      A0A8I5Y6Y1, A0A8I6AF97
      Related
      ENSRNOP00000105449.1, ENSRNOT00000136770.1

    6. XM_039084355.2 → XP_038940283.1  transcription factor RFX3 isoform X4

      UniProtKB/TrEMBL
      A0A8I5Y6Y1
      Related
      ENSRNOP00000070787.3, ENSRNOT00000077544.3
      Conserved Domains (2) summary
      pfam02257
      Location:187 → 262
      RFX_DNA_binding; RFX DNA-binding domain
      pfam04589
      Location:82 → 165
      RFX1_trans_act; RFX1 transcription activation region

    7. XM_039084334.2 → XP_038940262.1  transcription factor RFX3 isoform X1

      UniProtKB/TrEMBL
      A0A8I5Y6Y1, A0A8I6GK32
      Related
      ENSRNOP00000093035.1, ENSRNOT00000095133.2

    8. XM_017589450.3 → XP_017444939.1  transcription factor RFX3 isoform X5

      UniProtKB/TrEMBL
      A0A8I5Y6Y1, A6I0T9
      Related
      ENSRNOP00000076688.2, ENSRNOT00000104467.2
      Conserved Domains (2) summary
      pfam02257
      Location:184 → 256
      RFX_DNA_binding; RFX DNA-binding domain
      pfam04589
      Location:51 → 134
      RFX1_trans_act; RFX1 transcription activation region

    9. XM_063268582.1 → XP_063124652.1  transcription factor RFX3 isoform X7

      UniProtKB/TrEMBL
      Q5U2M9
      Related
      ENSRNOP00000023762.5, ENSRNOT00000023762.9

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001012172.1: Suppressed sequence

      Description
      NM_001012172.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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