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    Rfx1 regulatory factor X1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 288906, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Rfx1provided by RGD
    Official Full Name
    regulatory factor X1provided by RGD
    Primary source
    RGD:1306574
    See related
    EnsemblRapid:ENSRNOG00000006049 AllianceGenome:RGD:1306574
    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 regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Orthologous to human RFX1 (regulatory factor X1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 46.9), Spleen (RPKM 38.2) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Rfx1 in Genome Data Viewer
    Location:
    19q11
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 19 NC_086037.1 (40966102..40996809, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 19 NC_051354.1 (24061336..24092044, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 19 NC_005118.4 (25181564..25212410)

    Chromosome 19 - NC_086037.1Genomic Context describing neighboring genes Neighboring gene podocan-like 1 Neighboring gene DDB1 and CUL4 associated factor 15 Neighboring gene microRNA mir-709 Neighboring gene uncharacterized LOC102555451 Neighboring gene interleukin 27 receptor subunit alpha Neighboring gene relaxin 3

    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. The transcription factor regulatory factor X1 increases the expression of neuronal glutamate transporter type 3. Ma K, et al. J Biol Chem, 2006 Jul 28. PMID 16723357
    2. Transcription factor RFX1 helps control the promoter of the mouse ribosomal protein-encoding gene rpL30 by binding to its alpha element. Sáfrány G, et al. Gene, 1993 Oct 15. PMID 8224874
    3. 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

    What's a GeneRIF?
    1. RFX1 enhances the activity of EAAT3 promoter to increase the expression of EAAT3 proteins
      Title: The transcription factor regulatory factor X1 increases the expression of neuronal glutamate transporter type 3.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding 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 double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    MHC class II regulatory factor RFX1
    Names
    regulatory factor X, 1 (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_001105944.2 → NP_001099414.1  MHC class II regulatory factor RFX1 isoform 1

      See identical proteins and their annotated locations for NP_001099414.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000019
      UniProtKB/TrEMBL
      A0A8I5XWQ1, A6IYB2, D3ZQ82
      Related
      ENSRNOP00000078002.1, ENSRNOT00000108714.2
      Conserved Domains (2) summary
      pfam02257
      Location:421 → 497
      RFX_DNA_binding; RFX DNA-binding domain
      pfam04589
      Location:216 → 357
      RFX1_trans_act; RFX1 transcription activation region

    2. NM_001433980.1 → NP_001420909.1  MHC class II regulatory factor RFX1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000019
      UniProtKB/TrEMBL
      A0A8I5XWQ1, A0A8I5ZPW7

    3. NM_001433981.1 → NP_001420910.1  MHC class II regulatory factor RFX1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000019
      UniProtKB/TrEMBL
      A0A8I5XWQ1

    4. NM_001433982.1 → NP_001420911.1  MHC class II regulatory factor RFX1 isoform 4

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000019
      UniProtKB/TrEMBL
      A0A8I5XWQ1

    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_086037.1 Reference GRCr8

      Range
      40966102..40996809 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017601192.3 → XP_017456681.1  MHC class II regulatory factor RFX1 isoform X4

      UniProtKB/TrEMBL
      A0A8I5XWQ1

    2. XM_039097530.2 → XP_038953458.1  MHC class II regulatory factor RFX1 isoform X2

      Conserved Domains (3) summary
      pfam02257
      Location:523 → 598
      RFX_DNA_binding; RFX DNA-binding domain
      pfam03154
      Location:90 → 456
      Atrophin-1; Atrophin-1 family
      pfam04589
      Location:209 → 458
      RFX1_trans_act; RFX1 transcription activation region

    3. XM_006255229.5 → XP_006255291.1  MHC class II regulatory factor RFX1 isoform X1

      Related
      ENSRNOP00000080081.1, ENSRNOT00000097141.2
      Conserved Domains (2) summary
      pfam02257
      Location:531 → 607
      RFX_DNA_binding; RFX DNA-binding domain
      pfam04589
      Location:216 → 467
      RFX1_trans_act; RFX1 transcription activation region

    4. XM_006255231.5 → XP_006255293.1  MHC class II regulatory factor RFX1 isoform X3

      UniProtKB/TrEMBL
      A0A8I5XWQ1
      Conserved Domains (2) summary
      pfam02257
      Location:531 → 607
      RFX_DNA_binding; RFX DNA-binding domain
      pfam04589
      Location:216 → 467
      RFX1_trans_act; RFX1 transcription activation region
    Nucleotide Protein Strain
    Heading Accession and Version

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