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

Gene ID: 53970, updated on 2-Nov-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, Nov 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

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