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    Rfx5 regulatory factor X, 5 (influences HLA class II expression) [ Mus musculus (house mouse) ]

    Gene ID: 53970, updated on 28-Oct-2024

    Summary

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    Official Symbol
    Rfx5provided by MGI
    Official Full Name
    regulatory factor X, 5 (influences HLA class II expression)provided by MGI
    Primary source
    MGI:MGI:1858421
    See related
    Ensembl:ENSMUSG00000005774 AllianceGenome:MGI:1858421
    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
    Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Predicted to be part of RNA polymerase II transcription regulator complex. Is expressed in several structures, including branchial arch; eye; genitourinary system; heart; and nervous system. Human ortholog(s) of this gene implicated in severe combined immunodeficiency. Orthologous to human RFX5 (regulatory factor X5). [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in limb E14.5 (RPKM 5.9), spleen adult (RPKM 5.5) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Rfx5 in Genome Data Viewer
    Location:
    3 F2.1; 3 40.74 cM
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (94861355..94868685)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (94950689..94961561)

    Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 36237 Neighboring gene predicted gene, 26279 Neighboring gene selenium binding protein 1 Neighboring gene STARR-positive B cell enhancer ABC_E231 Neighboring gene RIKEN cDNA B230398E01 gene Neighboring gene STARR-seq mESC enhancer starr_08361 Neighboring gene STARR-positive B cell enhancer ABC_E652 Neighboring gene phosphatidylinositol 4-kinase beta Neighboring gene STARR-positive B cell enhancer ABC_E3449 Neighboring gene zinc finger protein 687 Neighboring gene microRNA 7013 Neighboring gene RIKEN cDNA 4930481B07 gene Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:94820548-94820749

    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 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. MHC class I and II deficiencies. Hanna S, et al. J Allergy Clin Immunol, 2014 Aug. PMID 25001848
    2. A functionally essential domain of RFX5 mediates activation of major histocompatibility complex class II promoters by promoting cooperative binding between RFX and NF-Y. Villard J, et al. Mol Cell Biol, 2000 May. PMID 10779326, Free PMC Article
    3. A novel DNA-binding regulatory factor is mutated in primary MHC class II deficiency (bare lymphocyte syndrome). Steimle V, et al. Genes Dev, 1995 May 1. PMID 7744245
    4. NLRC5 exclusively transactivates MHC class I and related genes through a distinctive SXY module. Ludigs K, et al. PLoS Genet, 2015 Mar. PMID 25811463, Free PMC Article
    5. Residual MHC class II expression on mature dendritic cells and activated B cells in RFX5-deficient mice. Clausen BE, et al. Immunity, 1998 Feb. PMID 9491996

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Targeted (2)  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 transcription activator activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription activator activity, RNA polymerase II-specific 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 RNA polymerase II transcription regulatory region sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    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
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II 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
    		  
    Component Evidence Code Pubs
    part_of RNA polymerase II transcription regulator complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of RNA polymerase II transcription regulator complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    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
    DNA-binding protein Rfx5
    Names
    regulatory factor X 5

    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_001025601.2 → NP_001020772.2  DNA-binding protein Rfx5 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC087062
      UniProtKB/TrEMBL
      Q0P5W9

    2. NM_001355705.2 → NP_001342634.1  DNA-binding protein Rfx5 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC087062
      Consensus CDS
      CCDS17598.1
      UniProtKB/Swiss-Prot
      D3Z1N0, G3X9S6, Q3U180, Q9JL61
      Conserved Domains (3) summary
      pfam02257
      Location:89 → 165
      RFX_DNA_binding; RFX DNA-binding domain
      pfam14621
      Location:442 → 656
      RFX5_DNA_bdg; RFX5 DNA-binding domain
      pfam18326
      Location:27 → 85
      RFX5_N; RFX5 N-terminal domain

    3. NM_001355706.2 → NP_001342635.1  DNA-binding protein Rfx5 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC087062
      Conserved Domains (3) summary
      pfam02257
      Location:64 → 140
      RFX_DNA_binding; RFX DNA-binding domain
      pfam14621
      Location:417 → 631
      RFX5_DNA_bdg; RFX5 DNA-binding domain
      pfam18326
      Location:25 → 60
      RFX5_N; RFX5 N-terminal domain

    4. NM_001355707.2 → NP_001342636.1  DNA-binding protein Rfx5 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC087062
      UniProtKB/TrEMBL
      Q0P5W9
      Conserved Domains (2) summary
      pfam02257
      Location:1 → 77
      RFX_DNA_binding; RFX DNA-binding domain
      pfam14621
      Location:354 → 568
      RFX5_DNA_bdg; RFX5 DNA-binding domain

    5. NM_001410649.1 → NP_001397578.1  DNA-binding protein Rfx5 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC087062
      UniProtKB/Swiss-Prot
      D3Z1N0, G3X9S6, Q3U180, Q9JL61
      Related
      ENSMUSP00000029772.3, ENSMUST00000029772.3

    6. NM_001410650.1 → NP_001397579.1  DNA-binding protein Rfx5 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC087062
      UniProtKB/Swiss-Prot
      D3Z1N0, G3X9S6, Q3U180, Q9JL61

    7. NM_001410651.1 → NP_001397580.1  DNA-binding protein Rfx5 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC087062
      UniProtKB/Swiss-Prot
      D3Z1N0, G3X9S6, Q3U180, Q9JL61
      Related
      ENSMUSP00000102881.3, ENSMUST00000107260.9

    8. NM_001410652.1 → NP_001397581.1  DNA-binding protein Rfx5 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC087062

    9. NM_001410653.1 → NP_001397582.1  DNA-binding protein Rfx5 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC087062

    10. NM_001410654.1 → NP_001397583.1  DNA-binding protein Rfx5 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC087062
      UniProtKB/TrEMBL
      Q0P5W9

    11. NM_001410655.1 → NP_001397584.1  DNA-binding protein Rfx5 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC087062
      UniProtKB/TrEMBL
      Q0P5W9

    12. NM_001410656.1 → NP_001397585.1  DNA-binding protein Rfx5 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC087062
      UniProtKB/TrEMBL
      Q0P5W9

    13. NM_017395.4 → NP_059091.2  DNA-binding protein Rfx5 isoform 1

      See identical proteins and their annotated locations for NP_059091.2

      Status: VALIDATED

      Source sequence(s)
      AC087062
      Consensus CDS
      CCDS17598.1
      UniProtKB/Swiss-Prot
      D3Z1N0, G3X9S6, Q3U180, Q9JL61
      Related
      ENSMUSP00000117963.2, ENSMUST00000137088.8
      Conserved Domains (3) summary
      pfam02257
      Location:89 → 165
      RFX_DNA_binding; RFX DNA-binding domain
      pfam14621
      Location:442 → 656
      RFX5_DNA_bdg; RFX5 DNA-binding domain
      pfam18326
      Location:27 → 85
      RFX5_N; RFX5 N-terminal domain

    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_000069.7 Reference GRCm39 C57BL/6J

      Range
      94861355..94868685
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030252687.2 → XP_030108547.1  DNA-binding protein Rfx5 isoform X4

      UniProtKB/TrEMBL
      Q6DI69
      Related
      ENSMUSP00000102874.2, ENSMUST00000107253.8
      Conserved Domains (2) summary
      pfam02257
      Location:89 → 165
      RFX_DNA_binding; RFX DNA-binding domain
      pfam18326
      Location:27 → 85
      RFX5_N; RFX5 N-terminal domain

    2. XM_030252686.2 → XP_030108546.1  DNA-binding protein Rfx5 isoform X3

      UniProtKB/TrEMBL
      Q0P5W9
      Conserved Domains (2) summary
      pfam02257
      Location:1 → 77
      RFX_DNA_binding; RFX DNA-binding domain
      pfam14621
      Location:354 → 568
      RFX5_DNA_bdg; RFX5 DNA-binding domain

    3. XM_011240164.4 → XP_011238466.1  DNA-binding protein Rfx5 isoform X1

      See identical proteins and their annotated locations for XP_011238466.1

      UniProtKB/Swiss-Prot
      D3Z1N0, G3X9S6, Q3U180, Q9JL61
      Related
      ENSMUSP00000102876.2, ENSMUST00000107255.8
      Conserved Domains (3) summary
      pfam02257
      Location:89 → 165
      RFX_DNA_binding; RFX DNA-binding domain
      pfam14621
      Location:442 → 656
      RFX5_DNA_bdg; RFX5 DNA-binding domain
      pfam18326
      Location:27 → 85
      RFX5_N; RFX5 N-terminal domain

    4. XM_006501698.4 → XP_006501761.1  DNA-binding protein Rfx5 isoform X2

      See identical proteins and their annotated locations for XP_006501761.1

      Conserved Domains (3) summary
      pfam02257
      Location:64 → 140
      RFX_DNA_binding; RFX DNA-binding domain
      pfam14621
      Location:417 → 631
      RFX5_DNA_bdg; RFX5 DNA-binding domain
      pfam18326
      Location:25 → 60
      RFX5_N; RFX5 N-terminal domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9JL61.2 GenPept UniProtKB/Swiss-Prot:Q9JL61

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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