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Rfx1 regulatory factor X, 1 (influences HLA class II expression) [ Mus musculus (house mouse) ]

Gene ID: 19724, updated on 31-Mar-2024

Summary

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Official Symbol
Rfx1provided by MGI
Official Full Name
regulatory factor X, 1 (influences HLA class II expression)provided by MGI
Primary source
MGI:MGI:105982
See related
Ensembl:ENSMUSG00000031706 AllianceGenome:MGI:105982
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Summary
Enables DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Is expressed in several structures, including central nervous system; dorsal root ganglion; early conceptus; eye; and genitourinary system. Orthologous to human RFX1 (regulatory factor X1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis adult (RPKM 37.0), thymus adult (RPKM 23.2) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Rfx1 in Genome Data Viewer
Location:
8 C2; 8 40.28 cM
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (84789787..84823630)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (84063564..84097001)

Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene paralemmin 3 Neighboring gene interleukin 27 receptor, alpha Neighboring gene STARR-seq mESC enhancer starr_22106 Neighboring gene relaxin 3 Neighboring gene STARR-positive B cell enhancer ABC_E73 Neighboring gene STARR-positive B cell enhancer ABC_E5024 Neighboring gene predicted gene 10643 Neighboring gene microRNA 709 Neighboring gene STARR-positive B cell enhancer mm9_chr8:86628640-86628941 Neighboring gene predicted gene, 39210 Neighboring gene DDB1 and CUL4 associated factor 15 Neighboring gene CapStarr-seq enhancer MGSCv37_chr8:86650788-86650941 Neighboring gene CapStarr-seq enhancer MGSCv37_chr8:86651237-86651346 Neighboring gene podocan-like 1 Neighboring gene coiled-coil and C2 domain containing 1A

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Expression of the transcription factor regulatory factor X1 in the mouse brain. Feng C, et al. Folia Histochem Cytobiol, 2011. PMID 21744337, Free PMC Article
  2. Knockout of the regulatory factor X1 gene leads to early embryonic lethality. Feng C, et al. Biochem Biophys Res Commun, 2009 Sep 4. PMID 19559676, Free PMC Article
  3. Regulatory factor X1 depresses ApoE-dependent Aβ uptake by miRNA-124 in microglial response to oxidative stress. Feng CZ, et al. Neuroscience, 2017 Mar 6. PMID 28003160
  4. Regulatory factor X transcription factors control Musashi1 transcription in mouse neural stem/progenitor cells. Kawase S, et al. Stem Cells Dev, 2014 Sep 15. PMID 25058468, Free PMC Article
  5. Spermatogenesis associated 4 promotes Sertoli cell proliferation modulated negatively by regulatory factor X1. Jiang J, et al. PLoS One, 2013. PMID 24146794, Free PMC Article

See all (50) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RFX1 regulates foam cell formation and atherosclerosis by mediating CD36 expression.
    Title: RFX1 regulates foam cell formation and atherosclerosis by mediating CD36 expression.
  2. Regulatory factor X1 induces macrophage M1 polarization by promoting DNA demethylation in autoimmune inflammation.
    Title: Regulatory factor X1 induces macrophage M1 polarization by promoting DNA demethylation in autoimmune inflammation.
  3. Interplay of RFX transcription factors 1, 2 and 3 in motile ciliogenesis.
    Title: Interplay of RFX transcription factors 1, 2 and 3 in motile ciliogenesis.
  4. RFX1 transcriptionally targets Itga6 in Sertoli cells, thereby, helping maintain the integrity of the basal lamina during testis cord development.
    Title: RFX1 maintains testis cord integrity by regulating the expression of Itga6 in male mouse embryos.
  5. Results show that reduced miRNA-124 improved microglia activation and up-regulated its downstream target RFX1, indicating that RFX1, as one of the target transcripts, facilitates microglial activation by miR-124 regulation; identified the binding site through which RFX1 directly regulates ApoE, may explain the missing link between decreased miRNA-124 and ineffective Abeta uptaking during aging.
    Title: Regulatory factor X1 depresses ApoE-dependent Aβ uptake by miRNA-124 in microglial response to oxidative stress.
  6. This study suggests that ciliogenic Rfx transcription factors regulate Msi1 expression in neural stem/progenitor cells.
    Title: Regulatory factor X transcription factors control Musashi1 transcription in mouse neural stem/progenitor cells.
  7. regulatory factor 1 directly regulates CD44 expression in glioblastoma
    Title: Regulatory factor X1 is a new tumor suppressive transcription factor that acts via direct downregulation of CD44 in glioblastoma.
  8. RFX1 may have negative effect on cell proliferation of Sertoli cells via modulating Spata4 expression levels by binding the conserved 14-bp cis-elements of Spata4 promoter.
    Title: Spermatogenesis associated 4 promotes Sertoli cell proliferation modulated negatively by regulatory factor X1.
  9. Rfx1 could be an indicator of progression from Barrett's esophagus to adenocarcinoma.
    Title: Study of FoxA pioneer factor at silent genes reveals Rfx-repressed enhancer at Cdx2 and a potential indicator of esophageal adenocarcinoma development.
  10. These results suggest a significant expression of RFX1 proteins in the mammalian brain.
    Title: Expression of the transcription factor regulatory factor X1 in the mouse brain.
Submit: New GeneRIF Correction See all GeneRIFs (14)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Gene trapped (1) 
  • Targeted (3)  1 citation
  • Endonuclease-mediated (2) 

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
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 DNA-templated transcription IEA
Inferred from Electronic Annotation
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 intracellular membrane-bounded organelle ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
MHC class II regulatory factor RFX1
Names
regulatory factor X 1
transcription factor RFX1
vregulatory 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_009055.4 → NP_033081.3  MHC class II regulatory factor RFX1

    See identical proteins and their annotated locations for NP_033081.3

    Status: VALIDATED

    Source sequence(s)
    BB642620, BC057018, CF623008
    Consensus CDS
    CCDS22468.1
    UniProtKB/Swiss-Prot
    P48377, Q6PGH8
    UniProtKB/TrEMBL
    Q8BJK3
    Related
    ENSMUSP00000005600.6, ENSMUST00000005600.6
    Conserved Domains (2) summary
    pfam02257
    Location:421 → 496
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:209 → 357
    RFX1_trans_act; RFX1 transcription activation region

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000074.7 Reference GRCm39 C57BL/6J

    Range
    84789787..84823630
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036153839.1 → XP_036009732.1  MHC class II regulatory factor RFX1 isoform X1

    UniProtKB/TrEMBL
    Q8BJK3
    Conserved Domains (2) summary
    pfam02257
    Location:531 → 606
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:209 → 467
    RFX1_trans_act; RFX1 transcription activation region

  2. XM_006530779.5 → XP_006530842.1  MHC class II regulatory factor RFX1 isoform X3

    UniProtKB/TrEMBL
    A0A1B0GRV3
    Conserved Domains (2) summary
    pfam02257
    Location:531 → 606
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:209 → 467
    RFX1_trans_act; RFX1 transcription activation region

  3. XM_011248329.4 → XP_011246631.1  MHC class II regulatory factor RFX1 isoform X1

    UniProtKB/TrEMBL
    Q8BJK3
    Conserved Domains (2) summary
    pfam02257
    Location:531 → 606
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:209 → 467
    RFX1_trans_act; RFX1 transcription activation region

  4. XM_006530778.5 → XP_006530841.1  MHC class II regulatory factor RFX1 isoform X2

    UniProtKB/TrEMBL
    Q8BJK3
    Conserved Domains (2) summary
    pfam02257
    Location:522 → 597
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:209 → 458
    RFX1_trans_act; RFX1 transcription activation region

  5. XM_030243361.2 → XP_030099221.1  MHC class II regulatory factor RFX1 isoform X5

    UniProtKB/Swiss-Prot
    P48377, Q6PGH8
    UniProtKB/TrEMBL
    Q8BJK3
    Conserved Domains (2) summary
    pfam02257
    Location:421 → 496
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:209 → 357
    RFX1_trans_act; RFX1 transcription activation region

  6. XM_006530780.5 → XP_006530843.1  MHC class II regulatory factor RFX1 isoform X4

    UniProtKB/TrEMBL
    Q8BJK3
    Conserved Domains (2) summary
    pfam02257
    Location:429 → 504
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:107 → 365
    RFX1_trans_act; RFX1 transcription activation region

  7. XM_030243363.2 → XP_030099223.1  MHC class II regulatory factor RFX1 isoform X7

    UniProtKB/TrEMBL
    Q8BJK3
    Conserved Domains (2) summary
    pfam02257
    Location:319 → 394
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:107 → 255
    RFX1_trans_act; RFX1 transcription activation region

  8. XM_030243362.2 → XP_030099222.1  MHC class II regulatory factor RFX1 isoform X6

    UniProtKB/TrEMBL
    A0A1B0GRV3
    Conserved Domains (2) summary
    pfam02257
    Location:531 → 606
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:209 → 467
    RFX1_trans_act; RFX1 transcription activation region

RNA

  1. XR_003947247.2 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P48377.2 GenPept UniProtKB/Swiss-Prot:P48377

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