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Aliases for RFX5 Gene

Aliases for RFX5 Gene

  • Regulatory Factor X5 2 3 5
  • Regulatory Factor X, 5 (Influences HLA Class II Expression) 2
  • Regulatory Factor X 5 4

External Ids for RFX5 Gene

Previous GeneCards Identifiers for RFX5 Gene

  • GC01M149155
  • GC01M147060
  • GC01M148088
  • GC01M148529
  • GC01M148126
  • GC01M149579
  • GC01M122691

Summaries for RFX5 Gene

Entrez Gene Summary for RFX5 Gene

  • A lack of MHC-II expression results in a severe immunodeficiency syndrome called MHC-II deficiency, or the bare lymphocyte syndrome (BLS; MIM 209920). At least 4 complementation groups have been identified in B-cell lines established from patients with BLS. The molecular defects in complementation groups B, C, and D all lead to a deficiency in RFX, a nuclear protein complex that binds to the X box of MHC-II promoters. The lack of RFX binding activity in complementation group C results from mutations in the RFX5 gene encoding the 75-kD subunit of RFX (Steimle et al., 1995). RFX5 is the fifth member of the growing family of DNA-binding proteins sharing a novel and highly characteristic DNA-binding domain called the RFX motif. Multiple alternatively spliced transcript variants have been found but the full-length natures of only two have been determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for RFX5 Gene

RFX5 (Regulatory Factor X5) is a Protein Coding gene. Diseases associated with RFX5 include bare lymphocyte syndrome, type ii, complementation group c and immunodeficiency by defective expression of hla class 2. Among its related pathways are Primary immunodeficiency and Tuberculosis. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and RNA polymerase II core promoter proximal region sequence-specific DNA binding. An important paralog of this gene is RFX3.

UniProtKB/Swiss-Prot for RFX5 Gene

  • Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding between RFX and NF-Y. RFX binds the X1 box of MHC-II promoters.

Gene Wiki entry for RFX5 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RFX5 Gene

Genomics for RFX5 Gene

Regulatory Elements for RFX5 Gene

Promoters for RFX5 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around RFX5 on UCSC Golden Path with GeneCards custom track

Genomic Location for RFX5 Gene

Chromosome:
1
Start:
151,340,640 bp from pter
End:
151,347,357 bp from pter
Size:
6,718 bases
Orientation:
Minus strand

Genomic View for RFX5 Gene

Genes around RFX5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RFX5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RFX5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RFX5 Gene

Proteins for RFX5 Gene

  • Protein details for RFX5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P48382-RFX5_HUMAN
    Recommended name:
    DNA-binding protein RFX5
    Protein Accession:
    P48382
    Secondary Accessions:
    • B7Z848
    • D3DV19
    • E9PFU4
    • Q5VWC3

    Protein attributes for RFX5 Gene

    Size:
    616 amino acids
    Molecular mass:
    65323 Da
    Quaternary structure:
    • Homodimer. The RFX heterotetrameric complex consists of 2 molecules of RFX5 and one each of RFXAP and RFX-B/RFXANK; with each subunit representing a separate complementation group. RFX forms cooperative DNA binding complexes with X2BP and CBF/NF-Y. RFX associates with CIITA to form an active transcriptional complex.

    Three dimensional structures from OCA and Proteopedia for RFX5 Gene

    Alternative splice isoforms for RFX5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RFX5 Gene

Proteomics data for RFX5 Gene at MOPED

Post-translational modifications for RFX5 Gene

No data available for DME Specific Peptides for RFX5 Gene

Domains & Families for RFX5 Gene

Gene Families for RFX5 Gene

Protein Domains for RFX5 Gene

Graphical View of Domain Structure for InterPro Entry

P48382

UniProtKB/Swiss-Prot:

RFX5_HUMAN :
  • The N-terminus is required for dimer formation, association with RFXANK and RFXAP, assembly of the RFX complex, and for binding of this complex to its X box target site in the MHC-II promoter. The C-terminus mediates cooperative binding between the RFX complex and NF-Y.
  • Belongs to the RFX family.
Domain:
  • The N-terminus is required for dimer formation, association with RFXANK and RFXAP, assembly of the RFX complex, and for binding of this complex to its X box target site in the MHC-II promoter. The C-terminus mediates cooperative binding between the RFX complex and NF-Y.
  • Contains 1 RFX-type winged-helix DNA-binding domain.
Family:
  • Belongs to the RFX family.
genes like me logo Genes that share domains with RFX5: view

Function for RFX5 Gene

Molecular function for RFX5 Gene

GENATLAS Biochemistry:
transactivating DNA binding regulatory factor 5,75kDa,involved in MHC class II expression,binding the MHC promotor box X
UniProtKB/Swiss-Prot Function:
Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding between RFX and NF-Y. RFX binds the X1 box of MHC-II promoters.

Gene Ontology (GO) - Molecular Function for RFX5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16464847
genes like me logo Genes that share ontologies with RFX5: view
genes like me logo Genes that share phenotypes with RFX5: view

Human Phenotype Ontology for RFX5 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for RFX5 Gene

Targeted motifs for RFX5 Gene
HOMER Transcription Factor Regulatory Elements motif RFX5
  • Consensus sequence: SCCTAGCAACAG Submotif: canonical Cell Type: GM12878 GEO ID: GSE31477

No data available for Enzyme Numbers (IUBMB) , Animal Models and Transcription Factor Targets for RFX5 Gene

Localization for RFX5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RFX5 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for RFX5 Gene COMPARTMENTS Subcellular localization image for RFX5 gene
Compartment Confidence
nucleus 5
cytosol 2

No data available for Gene Ontology (GO) - Cellular Components for RFX5 Gene

Pathways & Interactions for RFX5 Gene

genes like me logo Genes that share pathways with RFX5: view

Pathways by source for RFX5 Gene

Gene Ontology (GO) - Biological Process for RFX5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with RFX5: view

No data available for SIGNOR curated interactions for RFX5 Gene

Drugs & Compounds for RFX5 Gene

No Compound Related Data Available

Transcripts for RFX5 Gene

Unigene Clusters for RFX5 Gene

Regulatory factor X, 5 (influences HLA class II expression):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for RFX5 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8a · 8b · 8c · 8d ^ 9 ^ 10 ^ 11 ^ 12 ^ 13
SP1: -
SP2: - - - -
SP3: - -
SP4: - -
SP5: - -
SP6: -

Relevant External Links for RFX5 Gene

GeneLoc Exon Structure for
RFX5
ECgene alternative splicing isoforms for
RFX5

Expression for RFX5 Gene

mRNA expression in normal human tissues for RFX5 Gene

Protein differential expression in normal tissues from HIPED for RFX5 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (17.7), Blymphocyte (12.8), CD8 Tcells (10.9), Heart (7.4), NK cells (6.7), and Adrenal (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for RFX5 Gene



SOURCE GeneReport for Unigene cluster for RFX5 Gene Hs.632472

mRNA Expression by UniProt/SwissProt for RFX5 Gene

P48382-RFX5_HUMAN
Tissue specificity: Ubiquitous.
genes like me logo Genes that share expression patterns with RFX5: view

Protein tissue co-expression partners for RFX5 Gene

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for RFX5 Gene

Orthologs for RFX5 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for RFX5 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia RFX5 35
  • 88.56 (n)
  • 87.64 (a)
RFX5 36
  • 86 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RFX5 35
  • 88.62 (n)
  • 85.69 (a)
RFX5 36
  • 84 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia RFX5 35
  • 99.68 (n)
  • 99.51 (a)
RFX5 36
  • 98 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rfx5 35
  • 83.22 (n)
  • 82.3 (a)
oppossum
(Monodelphis domestica)
Mammalia RFX5 36
  • 58 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rfx5 36
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves RFX5 36
  • 61 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RFX5 36
  • 61 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC395025 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.13493 35
zebrafish
(Danio rerio)
Actinopterygii rfx5 36
  • 31 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG9727 36
  • 7 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RFX1 36
  • 5 (a)
OneToMany
Species with no ortholog for RFX5:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for RFX5 Gene

ENSEMBL:
Gene Tree for RFX5 (if available)
TreeFam:
Gene Tree for RFX5 (if available)

Paralogs for RFX5 Gene

Paralogs for RFX5 Gene

genes like me logo Genes that share paralogs with RFX5: view

Variants for RFX5 Gene

Sequence variations from dbSNP and Humsavar for RFX5 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
VAR_015550 Bare lymphocyte syndrome 2 (BLS2)
rs2233851 - 151,343,848(-) ACCTC(A/G)AGATG reference, missense
rs2233854 - 151,342,811(-) TCAGC(C/G)CCGGG reference, missense
rs2233855 - 151,342,542(-) GGTTA(C/T)CATGG reference, missense
rs1057805 -- 151,342,007(-) TTCAG(A/C)TTGAT utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for RFX5 Gene

Variant ID Type Subtype PubMed ID
nsv522840 CNV Gain 19592680
esv34461 CNV Gain 17911159
nsv831581 CNV Loss 17160897
nsv438026 CNV Loss 16468122

Variation tolerance for RFX5 Gene

Residual Variation Intolerance Score: 17.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.54; 64.85% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RFX5 Gene

HapMap Linkage Disequilibrium report
RFX5
Human Gene Mutation Database (HGMD)
RFX5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RFX5 Gene

Disorders for RFX5 Gene

MalaCards: The human disease database

(7) MalaCards diseases for RFX5 Gene - From: OMIM, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
bare lymphocyte syndrome, type ii, complementation group c
  • bare lymphocyte syndrome, type ii, complementation group e
immunodeficiency by defective expression of hla class 2
  • bare lymphocyte syndrome 2
mhc class ii deficiency
  • severe combined immunodeficiency
mhc class i deficiency
  • bare lymphocyte syndrome, type i
severe combined immunodeficiency
  • adenosine deaminase deficiency
- elite association - COSMIC cancer census association via MalaCards
Search RFX5 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

RFX5_HUMAN
  • Bare lymphocyte syndrome 2 (BLS2) [MIM:209920]: A severe combined immunodeficiency disease with early onset. It is characterized by a profound defect in constitutive and interferon-gamma induced MHC II expression, absence of cellular and humoral T-cell response to antigen challenge, hypogammaglobulinemia and impaired antibody production. The consequence include extreme susceptibility to viral, bacterial and fungal infections. {ECO:0000269 PubMed:10825209}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for RFX5

Genetic Association Database (GAD)
RFX5
Human Genome Epidemiology (HuGE) Navigator
RFX5
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RFX5
genes like me logo Genes that share disorders with RFX5: view

No data available for Genatlas for RFX5 Gene

Publications for RFX5 Gene

  1. A functionally essential domain of RFX5 mediates activation of major histocompatibility complex class II promoters by promoting cooperative binding between RFX and NF-Y. (PMID: 10779326) Villard J. … Reith W. (Mol. Cell. Biol. 2000) 3 4 23 67
  2. Analysis of mutations and chromosomal localisation of the gene encoding RFX5, a novel transcription factor affected in major histocompatibility complex class II deficiency. (PMID: 9401005) Villard J. … Mach B. (Hum. Mutat. 1997) 2 3 23
  3. HDAC2 deacetylates class II transactivator and suppresses its activity in macrophages and smooth muscle cells. (PMID: 19041327) Kong X. … Xu Y. (J. Mol. Cell. Cardiol. 2009) 3 23
  4. Regulatory factor for X-box family proteins differentially interact with histone deacetylases to repress collagen alpha2(I) gene (COL1A2) expression. (PMID: 16464847) Xu Y. … Smith B.D. (J. Biol. Chem. 2006) 3 23
  5. Histone deacetylase 1/mSin3A disrupts gamma interferon-induced CIITA function and major histocompatibility complex class II enhanceosome formation. (PMID: 12697811) Zika E. … Ting J.P. (Mol. Cell. Biol. 2003) 3 23

Products for RFX5 Gene

Sources for RFX5 Gene

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