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Aliases for RFXAP Gene

Aliases for RFXAP Gene

  • Regulatory Factor X-Associated Protein 2 3
  • RFX DNA-Binding Complex 36 KDa Subunit 4
  • RFX-Associated Protein 4

External Ids for RFXAP Gene

Previous GeneCards Identifiers for RFXAP Gene

  • GC13P035379
  • GC13P031379
  • GC13P036329
  • GC13P035191
  • GC13P036291
  • GC13P037393
  • GC13P018207

Summaries for RFXAP Gene

Entrez Gene Summary for RFXAP Gene

  • Major histocompatibility (MHC) class II molecules are transmembrane proteins that have a central role in development and control of the immune system. The protein encoded by this gene, along with regulatory factor X-associated ankyrin-containing protein and regulatory factor-5, forms a complex that binds to the X box motif of certain MHC class II gene promoters and activates their transcription. Once bound to the promoter, this complex associates with the non-DNA-binding factor MHC class II transactivator, which controls the cell type specificity and inducibility of MHC class II gene expression. Mutations in this gene have been linked to bare lymphocyte syndrome type II, complementation group D. Transcript variants utilizing different polyA signals have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for RFXAP Gene

RFXAP (Regulatory Factor X-Associated Protein) is a Protein Coding gene. Diseases associated with RFXAP 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 and transcription coactivator activity.

UniProtKB/Swiss-Prot for RFXAP Gene

  • Part of the RFX complex that binds to the X-box of MHC II promoters

Gene Wiki entry for RFXAP Gene

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

Genomics for RFXAP Gene

Regulatory Elements for RFXAP Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for RFXAP Gene

36,819,202 bp from pter
36,829,603 bp from pter
10,402 bases
Plus strand

Genomic View for RFXAP Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for RFXAP Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RFXAP Gene

Proteins for RFXAP Gene

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

    Protein Symbol:
    Recommended name:
    Regulatory factor X-associated protein
    Protein Accession:
    Secondary Accessions:
    • B2R9T8
    • Q5VZM6
    • Q8TC40

    Protein attributes for RFXAP Gene

    272 amino acids
    Molecular mass:
    28232 Da
    Quaternary structure:
    • 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 RFXAP Gene

neXtProt entry for RFXAP Gene

Proteomics data for RFXAP Gene at MOPED

Post-translational modifications for RFXAP Gene

Other Protein References for RFXAP Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for RFXAP Gene

Domains for RFXAP Gene

Protein Domains for RFXAP Gene


Suggested Antigen Peptide Sequences for RFXAP Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • The C-terminal domain is necessary for the RFX complex formation.
  • The C-terminal domain is necessary for the RFX complex formation.
genes like me logo Genes that share domains with RFXAP: view

No data available for Gene Families for RFXAP Gene

Function for RFXAP Gene

Molecular function for RFXAP Gene

GENATLAS Biochemistry:
transactivating DNA binding regulatory factor,component AP,36kDa,involved in MHC class II expression,subunit of the RFX complex,interacting with RFX5
UniProtKB/Swiss-Prot Function:
Part of the RFX complex that binds to the X-box of MHC II promoters

Gene Ontology (GO) - Molecular Function for RFXAP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003700 sequence-specific DNA binding transcription factor activity NAS 9118943
GO:0003713 transcription coactivator activity TAS 9118943
genes like me logo Genes that share ontologies with RFXAP: view

Phenotypes for RFXAP Gene

GenomeRNAi human phenotypes for RFXAP:
genes like me logo Genes that share phenotypes with RFXAP: view

Animal Model Products

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

Localization for RFXAP Gene

Subcellular locations from UniProtKB/Swiss-Prot for RFXAP Gene

Subcellular locations from

Jensen Localization Image for RFXAP Gene COMPARTMENTS Subcellular localization image for RFXAP gene
Compartment Confidence
nucleus 5
plasma membrane 2
cytosol 1

Gene Ontology (GO) - Cellular Components for RFXAP Gene

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

Pathways for RFXAP Gene

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

Pathways by source for RFXAP Gene

Gene Ontology (GO) - Biological Process for RFXAP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0045893 positive regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with RFXAP: view

Transcripts for RFXAP Gene

mRNA/cDNA for RFXAP Gene

(1) REFSEQ mRNAs :
(2) Additional mRNA sequences :
(46) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for RFXAP Gene

Regulatory factor X-associated protein:
Representative Sequences:

Inhibitory RNA Products

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

Flow Cytometry Products

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

No ASD Table

Relevant External Links for RFXAP Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for RFXAP Gene

mRNA expression in normal human tissues for RFXAP Gene

Protein differential expression in normal tissues for RFXAP Gene

This gene is overexpressed in Blymphocyte (23.3), Peripheral blood mononuclear cells (8.8), CD8 Tcells (7.8), and Thyroid (7.1).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for RFXAP Gene

SOURCE GeneReport for Unigene cluster for RFXAP Gene Hs.24422

mRNA Expression by UniProt/SwissProt for RFXAP Gene

Tissue specificity: Ubiquitous
genes like me logo Genes that share expressions with RFXAP: view

Expression partners for RFXAP Gene

* - Elite partner

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 RFXAP Gene

Orthologs for RFXAP Gene

This gene was present in the common ancestor of chordates.

Orthologs for RFXAP Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia RFXAP 35
  • 87.58 (n)
  • 87.45 (a)
  • 82 (a)
(Canis familiaris)
Mammalia RFXAP 35
  • 88.74 (n)
  • 87.45 (a)
  • 84 (a)
(Mus musculus)
Mammalia Rfxap 35
  • 78.22 (n)
  • 76.24 (a)
Rfxap 16
Rfxap 36
  • 77 (a)
(Pan troglodytes)
Mammalia RFXAP 35
  • 99.14 (n)
  • 98.9 (a)
  • 99 (a)
(Rattus norvegicus)
Mammalia Rfxap 35
  • 83.73 (n)
  • 86.75 (a)
(Monodelphis domestica)
Mammalia RFXAP 36
  • 67 (a)
(Gallus gallus)
Aves RFXAP 36
  • 48 (a)
(Anolis carolinensis)
Reptilia RFXAP 36
  • 75 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.20047 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.30365 35
(Danio rerio)
Actinopterygii Dr.12444 35
rfxap 36
  • 50 (a)
Species with no ortholog for RFXAP:
  • 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)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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 RFXAP Gene

Gene Tree for RFXAP (if available)
Gene Tree for RFXAP (if available)

Paralogs for RFXAP Gene

No data available for Paralogs for RFXAP Gene

Variants for RFXAP Gene

Sequence variations from dbSNP and Humsavar for RFXAP Gene

SNP ID Clin Chr 13 pos Sequence Context AA Info Type MAF
rs10976 -- 36,829,006(-) AAAAA(C/T)GTTCT utr-variant-3-prime
rs1980881 -- 36,821,956(-) ATCCC(C/T)GTAAT intron-variant
rs2323115 -- 36,822,506(-) GAGAC(G/T)CTAAT intron-variant
rs2323116 -- 36,822,357(-) TCACC(C/T)GTAAT intron-variant
rs3814802 -- 36,818,717(-) ACTTT(G/T)TTTTT upstream-variant-2KB

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

Variant ID Type Subtype PubMed ID
nsv899993 CNV Gain 21882294
nsv522336 CNV Gain 19592680

Relevant External Links for RFXAP Gene

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

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

Disorders for RFXAP Gene

(1) OMIM Diseases for RFXAP Gene (601861)


  • 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:10072068, ECO:0000269 PubMed:9118943}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(1) University of Copenhagen DISEASES for RFXAP Gene

(3) Novoseek inferred disease relationships for RFXAP Gene

Disease -log(P) Hits PubMed IDs
bare lymphocyte syndrome 94.8 3
immunodeficiency 54.8 5
severe combined immunodeficiency 46.9 1

Relevant External Links for RFXAP

Genetic Association Database (GAD)
genes like me logo Genes that share disorders with RFXAP: view

No data available for Genatlas for RFXAP Gene

Publications for RFXAP Gene

  1. RFXAP, a novel subunit of the RFX DNA binding complex is mutated in MHC class II deficiency. (PMID: 9118943) Durand B. … Reith W. (EMBO J. 1997) 2 3 4 23
  2. Mutation of RFXAP, a regulator of MHC class II genes, in primary MHC class II deficiency. (PMID: 9287230) Villard J. … Mach B. (N. Engl. J. Med. 1997) 3 23
  3. The bare lymphocyte syndrome and the regulation of MHC expression. (PMID: 11244040) Reith W. … Mach B. (Annu. Rev. Immunol. 2001) 3 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 23
  5. Conserved residues of the bare lymphocyte syndrome transcription factor RFXAP determine coordinate MHC class II expression. (PMID: 16337482) Long A.B. … Boss J.M. (Mol. Immunol. 2006) 3 23

Products for RFXAP Gene

Sources for RFXAP Gene

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