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

Gene ID: 288906, updated on 5-Mar-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
Ensembl:ENSRNOG00000006049 AllianceGenome:RGD:1306574
Gene type
protein coding
RefSeq status
PROVISIONAL
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, Apr 2022]
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_001105944.1 → NP_001099414.1  MHC class II regulatory factor RFX1

    See identical proteins and their annotated locations for NP_001099414.1

    Status: PROVISIONAL

    Source sequence(s)
    CH473972
    UniProtKB/TrEMBL
    A0A8I5XWQ1, A6IYB2, D3ZQ82
    Related
    ENSRNOP00000008104.4, ENSRNOT00000008104.6
    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

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

    UniProtKB/TrEMBL
    A0A8I5XWQ1
    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

    UniProtKB/TrEMBL
    A0A8I5XWQ1, A0A8I5ZPW7
    Related
    ENSRNOP00000080081.1
    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
    Related
    ENSRNOP00000078002.1
    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

Gene LinkOut

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