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Aliases for RFX5 Gene

Aliases for RFX5 Gene

  • Regulatory Factor X, 5 (Influences HLA Class II Expression) 2 3
  • 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 X, 5 (Influences HLA Class II Expression)) is a Protein Coding gene. Diseases associated with RFX5 include bare lymphocyte syndrome, type ii, complementation group c and mhc class ii deficiency. Among its related pathways are Tuberculosis and Allograft rejection. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity.

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

Genomic Location for RFX5 Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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

Antibody Products

No data available for DME Specific Peptides for RFX5 Gene

Domains for RFX5 Gene

Protein Domains for RFX5 Gene

Graphical View of Domain Structure for InterPro Entry

P48382

UniProtKB/Swiss-Prot:

RFX5_HUMAN :
  • P48382
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

No data available for Gene Families for RFX5 Gene

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:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding IBA --
GO:0003677 DNA binding TAS 9806546
GO:0003700 sequence-specific DNA binding transcription factor activity IBA --
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

Animal Models for RFX5 Gene

MGI Knock Outs for RFX5:

Animal Model Products

CRISPR Products

miRNA for RFX5 Gene

miRTarBase miRNAs that target RFX5
Targeting motifs for RFX5 Gene
HOMER Transcription Factor Regulatory Elements motif RFX5
  • Consensus sequence: SCCTAGCAACAG Submotif: canonical Cell Type: GM12878 GeoId: GSE31477

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for RFX5

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) and Transcription Factor Targeting 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
plasma membrane 2

Gene Ontology (GO) - Cellular Components for RFX5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with RFX5: view

Pathways 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:0000122 negative regulation of transcription from RNA polymerase II promoter IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated --
GO:0006357 regulation of transcription from RNA polymerase II promoter IBA --
genes like me logo Genes that share ontologies with RFX5: view

Transcripts for RFX5 Gene

Unigene Clusters for RFX5 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for RFX5

Primer Products

Flow Cytometry Products

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression 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 expressions with RFX5: view

In Situ Assay Products

No data available for 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
chimpanzee
(Pan troglodytes)
Mammalia RFX5 35
  • 99.68 (n)
  • 99.51 (a)
RFX5 36
  • 98 (a)
OneToOne
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
mouse
(Mus musculus)
Mammalia Rfx5 16
Rfx5 36
  • 71 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RFX5 36
  • 58 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rfx5 35
  • 83.22 (n)
  • 82.3 (a)
chicken
(Gallus gallus)
Aves RFX5 36
  • 61 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RFX5 36
  • 61 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.13493 35
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC395025 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

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

No data available for Paralogs for RFX5 Gene

Variants for RFX5 Gene

Sequence variations from dbSNP and Humsavar for RFX5 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs1057805 -- 151,342,007(-) TTCAG(A/C)TTGAT utr-variant-3-prime
rs1752386 -- 151,343,685(-) GGGCT(C/T)GCTGG reference, synonymous-codon
rs1752387 -- 151,341,903(-) TGAAT(A/G)TATAG utr-variant-3-prime
rs2233849 -- 151,344,933(-) AATTT(A/G)GTCCA intron-variant
rs2233850 -- 151,344,670(-) CTCAC(A/C)CATGA intron-variant

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

Relevant External Links for RFX5 Gene

HapMap Linkage Disequilibrium report
RFX5
Human Gene Mutation Database (HGMD)
RFX5
Locus Specific Mutation Databases (LSDB)
RFX5

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

Disorders for RFX5 Gene

(1) OMIM Diseases for RFX5 Gene (601863)

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.

(1) University of Copenhagen DISEASES for RFX5 Gene

(3) Novoseek inferred disease relationships for RFX5 Gene

Disease -log(P) Hits PubMed IDs
bare lymphocyte syndrome 96 5
immunodeficiency 53.3 4
severe combined immunodeficiency 41.7 1

Relevant External Links for RFX5

Genetic Association Database (GAD)
RFX5
Human Genome Epidemiology (HuGE) Navigator
RFX5
genes like me logo Genes that share disorders with RFX5: view

Publications for RFX5 Gene

  1. A novel DNA-binding regulatory factor is mutated in primary MHC class II deficiency (bare lymphocyte syndrome). (PMID: 7744245) Steimle V. … Reith W. (Genes Dev. 1995) 3 4 23
  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. 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
  4. Mutations in the bare lymphocyte syndrome define critical steps in the assembly of the regulatory factor X complex. (PMID: 10825209) Nekrep N. … Peterlin B.M. (Mol. Cell. Biol. 2000) 3 4 23
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4

Products for RFX5 Gene

Sources for RFX5 Gene

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