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

    Gene ID: 53970, updated on 9-Dec-2024

    Summary

    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, Dec 2024]
    Expression
    Ubiquitous expression in limb E14.5 (RPKM 5.9), spleen adult (RPKM 5.5) and 28 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • 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

    Variation

    Alleles

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    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

    Preferred Names
    DNA-binding protein Rfx5
    Names
    regulatory factor X 5

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

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

      Status: VALIDATED

      Source sequence(s)
      AC087062
      UniProtKB/TrEMBL
      Q0P5W9
    2. NM_001355705.2NP_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:89165
      RFX_DNA_binding; RFX DNA-binding domain
      pfam14621
      Location:442656
      RFX5_DNA_bdg; RFX5 DNA-binding domain
      pfam18326
      Location:2785
      RFX5_N; RFX5 N-terminal domain
    3. NM_001355706.2NP_001342635.1  DNA-binding protein Rfx5 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC087062
      Conserved Domains (3) summary
      pfam02257
      Location:64140
      RFX_DNA_binding; RFX DNA-binding domain
      pfam14621
      Location:417631
      RFX5_DNA_bdg; RFX5 DNA-binding domain
      pfam18326
      Location:2560
      RFX5_N; RFX5 N-terminal domain
    4. NM_001355707.2NP_001342636.1  DNA-binding protein Rfx5 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC087062
      UniProtKB/TrEMBL
      Q0P5W9
      Conserved Domains (2) summary
      pfam02257
      Location:177
      RFX_DNA_binding; RFX DNA-binding domain
      pfam14621
      Location:354568
      RFX5_DNA_bdg; RFX5 DNA-binding domain
    5. NM_001410649.1NP_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_001410650.1NP_001397579.1  DNA-binding protein Rfx5 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC087062
      UniProtKB/Swiss-Prot
      D3Z1N0, G3X9S6, Q3U180, Q9JL61
    7. NM_001410651.1NP_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_001410652.1NP_001397581.1  DNA-binding protein Rfx5 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC087062
    9. NM_001410653.1NP_001397582.1  DNA-binding protein Rfx5 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC087062
    10. NM_001410654.1NP_001397583.1  DNA-binding protein Rfx5 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC087062
      UniProtKB/TrEMBL
      Q0P5W9
    11. NM_001410655.1NP_001397584.1  DNA-binding protein Rfx5 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC087062
      UniProtKB/TrEMBL
      Q0P5W9
    12. NM_001410656.1NP_001397585.1  DNA-binding protein Rfx5 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC087062
      UniProtKB/TrEMBL
      Q0P5W9
    13. NM_017395.4NP_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:89165
      RFX_DNA_binding; RFX DNA-binding domain
      pfam14621
      Location:442656
      RFX5_DNA_bdg; RFX5 DNA-binding domain
      pfam18326
      Location:2785
      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_030252687.2XP_030108547.1  DNA-binding protein Rfx5 isoform X4

      UniProtKB/TrEMBL
      Q6DI69
      Related
      ENSMUSP00000102874.2, ENSMUST00000107253.8
      Conserved Domains (2) summary
      pfam02257
      Location:89165
      RFX_DNA_binding; RFX DNA-binding domain
      pfam18326
      Location:2785
      RFX5_N; RFX5 N-terminal domain
    2. XM_030252686.2XP_030108546.1  DNA-binding protein Rfx5 isoform X3

      UniProtKB/TrEMBL
      Q0P5W9
      Conserved Domains (2) summary
      pfam02257
      Location:177
      RFX_DNA_binding; RFX DNA-binding domain
      pfam14621
      Location:354568
      RFX5_DNA_bdg; RFX5 DNA-binding domain
    3. XM_011240164.4XP_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:89165
      RFX_DNA_binding; RFX DNA-binding domain
      pfam14621
      Location:442656
      RFX5_DNA_bdg; RFX5 DNA-binding domain
      pfam18326
      Location:2785
      RFX5_N; RFX5 N-terminal domain
    4. XM_006501698.4XP_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:64140
      RFX_DNA_binding; RFX DNA-binding domain
      pfam14621
      Location:417631
      RFX5_DNA_bdg; RFX5 DNA-binding domain
      pfam18326
      Location:2560
      RFX5_N; RFX5 N-terminal domain