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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 and Bare Lymphocyte Syndrome, Type I. Among its related pathways are Allograft rejection and Primary immunodeficiency. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and RNA polymerase II proximal promoter sequence-specific DNA binding. An important paralog of this gene is RFX7.

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

Additional gene information for RFX5 Gene

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

Genomics for RFX5 Gene

GeneHancer (GH) Regulatory Elements for RFX5 Gene

Promoters and enhancers for RFX5 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I151345 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 550.8 +0.3 273 2.9 PKNOX1 CLOCK SMAD1 ARNT ARID4B SIN3A YBX1 DMAP1 ZNF2 ZBTB7B GBAT2 RFX5 ARNT SETDB1 PI4KB GOLPH3L UBE2D3P3 CTSK RPS10P6 ZNF687
GH01I151308 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 13.3 +35.4 35421 6.1 PKNOX1 SMAD1 FOXA2 ARNT ARID4B NEUROD1 SIN3A YY1 ZNF766 E2F8 PIP5K1A PRPF3 GABPB2 PI4KB MRPL9 ZNF687 RFX5 LOC100507670 SETDB1 POGZ
GH01I151068 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 9.8 +276.9 276871 3.3 CLOCK FEZF1 IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 ZNF548 SP3 GABPB2 CDC42SE1 PRPF3 SETDB1 PI4KB PIP5K1A MRPL9 UBE2D3P3 ARNT CTSK
GH01I150557 Promoter/Enhancer 2.6 EPDnew Ensembl ENCODE dbSUPER 4.8 +778.1 778053 23.1 CLOCK MLX DMAP1 IRF4 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC RN7SL600P MCL1 GOLPH3L SETDB1 HORMAD1 PRPF3 PIP5K1A PI4KB SF3B4 ARNT
GH01I151818 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 9.1 -472.8 -472772 2.7 RFX1 RXRA NFIB MAX CEBPB YY1 JUND NFIC ATF3 ELK1 GC01P151821 TDRKH TDRKH-AS1 ENSG00000201134 C2CD4D THEM5 ENSG00000232937 MRPL9 OAZ3 RPS10P6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RFX5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RFX5 gene promoter:

Genomic Locations for RFX5 Gene

Genomic Locations for RFX5 Gene
chr1:151,340,640-151,347,357
(GRCh38/hg38)
Size:
6,718 bases
Orientation:
Minus strand
chr1:151,313,116-151,319,833
(GRCh37/hg19)

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. Interacts (via PxLPxI/L motif) with RFXANK (via ankyrin repeats); the interaction is direct. 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

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

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

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.
  • The PxLPxI/L motif mediates interaction with ankyrin repeats of RFXANK.
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.

Phenotypes From GWAS Catalog for RFX5 Gene

Gene Ontology (GO) - Molecular Function for RFX5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IBA --
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IC --
GO:0003677 DNA binding TAS,IEA 9806546
GO:0003700 DNA binding transcription factor activity NAS,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

Human Phenotype Ontology for RFX5 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

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

Clone Products

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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RFX5 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for RFX5 Gene

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

No data available for Subcellular locations from the Human Protein Atlas (HPA) 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:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA,IEA --
GO:0006366 transcription by RNA polymerase II 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:

Clone 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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for RFX5 Gene



Protein tissue co-expression partners for RFX5 Gene

NURSA nuclear receptor signaling pathways regulating expression of RFX5 Gene:

RFX5

SOURCE GeneReport for Unigene cluster for RFX5 Gene:

Hs.632472

mRNA Expression by UniProt/SwissProt for RFX5 Gene:

P48382-RFX5_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for RFX5 Gene

  • Blood(4.5)
  • Nervous system(4.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for RFX5 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • immune
  • integumentary
  • nervous
  • respiratory
  • urinary
Regions:
Head and neck:
  • brain
  • head
  • larynx
  • meninges
  • neck
  • pharynx
Thorax:
  • bronchus
  • lung
  • trachea
Abdomen:
  • biliary tract
  • gallbladder
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
Pelvis:
  • ureter
  • urethra
  • urinary bladder
Limb:
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • nail
  • toe
  • upper limb
General:
  • blood
  • skin
  • white blood cell
genes like me logo Genes that share expression patterns with RFX5: view

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
chimpanzee
(Pan troglodytes)
Mammalia RFX5 33 34
  • 99.68 (n)
dog
(Canis familiaris)
Mammalia RFX5 33 34
  • 88.62 (n)
cow
(Bos Taurus)
Mammalia RFX5 33 34
  • 88.56 (n)
rat
(Rattus norvegicus)
Mammalia Rfx5 33
  • 83.22 (n)
mouse
(Mus musculus)
Mammalia Rfx5 34
  • 71 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RFX5 34
  • 58 (a)
OneToOne
chicken
(Gallus gallus)
Aves RFX5 34
  • 61 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RFX5 34
  • 61 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC395025 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.13493 33
zebrafish
(Danio rerio)
Actinopterygii rfx5 34
  • 31 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG9727 34
  • 7 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RFX1 34
  • 5 (a)
OneToMany
Species where no ortholog for RFX5 was found in the sources mined by GeneCards:
  • 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 Variation AA Info Type
rs116826799 uncertain-significance, Bare lymphocyte syndrome 2 151,341,102(-) T/G 3_prime_UTR_variant
rs137853099 pathogenic, Bare lymphocyte syndrome type 2, complementation group E, Bare lymphocyte syndrome 2 (BLS2) [MIM:209920] 151,344,444(-) C/T 5_prime_UTR_variant, coding_sequence_variant, missense_variant
rs138110902 uncertain-significance, Bare lymphocyte syndrome 2 151,346,542(-) A/C 5_prime_UTR_variant
rs140885618 uncertain-significance, Bare lymphocyte syndrome 2 151,343,099(-) G/A/C coding_sequence_variant, missense_variant
rs143245407 uncertain-significance, Bare lymphocyte syndrome 2 151,346,281(-) C/A/T 5_prime_UTR_variant, coding_sequence_variant, missense_variant

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

Variant ID Type Subtype PubMed ID
esv34461 CNV gain 17911159
nsv438026 CNV loss 16468122
nsv522840 CNV gain 19592680
nsv831581 CNV loss 17160897

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)

Additional Variant Information for RFX5 Gene

Human Gene Mutation Database (HGMD)
RFX5
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RFX5

SNP Genotyping and Copy Number Assay Products

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

Disorders for RFX5 Gene

MalaCards: The human disease database

(6) MalaCards diseases for RFX5 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
bare lymphocyte syndrome, type ii
  • bls, type ii
bare lymphocyte syndrome, type i
  • bls, type i
severe combined immunodeficiency
  • combined t and b cell inborn immunodeficiency
three m syndrome 1
  • 3m1
combined immunodeficiency, x-linked
  • cidx
- 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.

Additional Disease Information for RFX5

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 (Molecular and cellular biology 2000) 3 4 22 58
  2. Mutations in the bare lymphocyte syndrome define critical steps in the assembly of the regulatory factor X complex. (PMID: 10825209) Nekrep N … Peterlin BM (Molecular and cellular biology 2000) 3 4 22 58
  3. 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 (Human mutation 1997) 2 3 22 58
  4. A novel DNA-binding regulatory factor is mutated in primary MHC class II deficiency (bare lymphocyte syndrome). (PMID: 7744245) Steimle V … Reith W (Genes & development 1995) 3 4 22 58
  5. Sequence-specific recognition of a PxLPxI/L motif by an ankyrin repeat tumbler lock. (PMID: 22649097) Xu C … Min J (Science signaling 2012) 3 4 58

Products for RFX5 Gene

Sources for RFX5 Gene

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