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

    Gene ID: 19724, updated on 27-Nov-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. Located in nucleus. 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, Nov 2024]
    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. 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
    2. 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
    3. Regulatory factor X1 induces macrophage M1 polarization by promoting DNA demethylation in autoimmune inflammation. Yang S, et al. JCI Insight, 2023 Oct 23. PMID 37733446, Free PMC Article
    4. RFX1 regulates foam cell formation and atherosclerosis by mediating CD36 expression. Yang S, et al. Int Immunopharmacol, 2024 Mar 30. PMID 38402833
    5. 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

    See all (52) 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)
    • Endonuclease-mediated (2) 
    • Gene trapped (1) 
    • Targeted (3)  1 citation

    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 IEA
    Inferred from Electronic Annotation
    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 IEA
    Inferred from Electronic Annotation
    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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