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RFXAP Gene

protein-coding   GIFtS: 55
GCID: GC13P037393

Regulatory Factor X-Associated Protein

  See RFXAP-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Regulatory Factor X-Associated Protein1 2
RFX DNA-Binding Complex 36 KDa Subunit2 3
RFX-Associated Protein2 3

External Ids:    HGNC: 99881   Entrez Gene: 59942   Ensembl: ENSG000001331117   OMIM: 6018615   UniProtKB: O002873   

Export aliases for RFXAP gene to outside databases

Previous GC identifers: GC13P035379 GC13P031379 GC13P036329 GC13P035191 GC13P036291 GC13P018207


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 d, and bare lymphocyte syndrome, type ii, complementation group c. GO annotations related to this gene include transcription coactivator activity and sequence-specific DNA binding transcription factor activity.

UniProtKB/Swiss-Prot: RFXAP_HUMAN, O00287
Function: Part of the RFX complex that binds to the X-box of MHC II promoters

Gene Wiki entry for RFXAP Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000013.10  NC_018924.2  NT_024524.15  
Regulatory elements:
   Regulatory transcription factor binding sites in the RFXAP gene promoter:
         USF1   ISGF-3   MyoD   Tal-1beta   HNF-1A   E47   Nkx6-1   HNF-1   FOXO1a   FOXO1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRFXAP promoter sequence
   Search Chromatin IP Primers for RFXAP

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RFXAP


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 13q14   Ensembl cytogenetic band:  13q13.3   HGNC cytogenetic band: 13q14

RFXAP Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RFXAP gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13P037393:  view genomic region     (about GC identifiers)

Start:
37,393,339 bp from pter      End:
37,403,740 bp from pter
Size:
10,402 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: RFXAP_HUMAN, O00287 (See protein sequence)
Recommended Name: Regulatory factor X-associated protein  
Size: 272 amino acids; 28232 Da
Subunit: 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
1 PDB 3D structure from and Proteopedia for RFXAP:
2KW3 (3D)    
Secondary accessions: B2R9T8 Q5VZM6 Q8TC40

Explore the universe of human proteins at neXtProt for RFXAP: NX_O00287

Explore proteomics data for RFXAP at MOPED

Post-translational modifications: 

  • Phosphorylated1
  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See RFXAP Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_000529.1  
    ENSEMBL proteins: 
     ENSP00000255476  

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    antibodies-online proteins for RFXAP (5 products) 

     
    antibodies-online peptides for RFXAP

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    ProtoNet protein and cluster: O00287

    UniProtKB/Swiss-Prot: RFXAP_HUMAN, O00287
    Domain: The C-terminal domain is necessary for the RFX complex formation


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RFXAP_HUMAN, O00287
    Function: Part of the RFX complex that binds to the X-box of MHC II promoters

         Genatlas biochemistry entry for RFXAP:
    transactivating DNA binding regulatory factor,component AP,36kDa,involved in MHC class II expression,subunit of
    the RFX complex,interacting with RFX5

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0003700sequence-specific DNA binding transcription factor activity NAS9118943
    GO:0003713transcription coactivator activity TAS9118943
         
    Find genes that share ontologies with RFXAP           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for RFXAP:
     Increased G1 DNA content 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for RFXAP

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    hsa-miR-548j hsa-miR-548i hsa-miR-3692 hsa-miR-105 hsa-miR-654-5p hsa-miR-548a-5p hsa-miR-548d-5p hsa-miR-589
    SwitchGear 3'UTR luciferase reporter plasmidRFXAP 3' UTR sequence
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    RFXAP_HUMAN, O00287: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    plasma membrane2
    cytosol1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--

    Find genes that share ontologies with RFXAP           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for RFXAP About    
    See pathways by source

    SuperPathContained pathways About
    1Allograft rejection
    Antigen processing and presentation0.36
    2Tuberculosis
    Tuberculosis
    3Primary immunodeficiency
    Primary immunodeficiency


    Find genes that share SuperPaths with RFXAP           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways



    3 Kegg Pathways  (Kegg details for RFXAP):
        Antigen processing and presentation
    Tuberculosis
    Primary immunodeficiency

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RFXAP
    Interactions:

        GeneGlobe Interaction Network for RFXAP

    STRING Interaction Network Preview (showing 5 interactants - click image to see 7)

    Selected Interacting proteins for RFXAP (O002873 ENSP000002554764) via UniProtKB, MINT, STRING, and/or I2D (see all 9)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RFX5P483823, ENSP000002905244I2D: score=2 STRING: ENSP00000290524
    RFXANKO145933, ENSP000003050714I2D: score=2 STRING: ENSP00000305071
    HDAC4P565243, ENSP000002646064I2D: score=1 STRING: ENSP00000264606
    MLLT1Q031113, ENSP000002526744I2D: score=1 STRING: ENSP00000252674
    EWSR1Q018443I2D: score=1 
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0045893positive regulation of transcription, DNA-templated IEA--

    Find genes that share ontologies with RFXAP           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for RFXAP



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for RFXAP gene: 
    NM_000538.3  

    Unigene Cluster for RFXAP:

    Regulatory factor X-associated protein
    Hs.24422  [show with all ESTs]
    Unigene Representative Sequence: NM_000538
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000255476(uc001uvu.1) ENST00000472888
    miRNA
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    hsa-miR-548j hsa-miR-548i hsa-miR-3692 hsa-miR-105 hsa-miR-654-5p hsa-miR-548a-5p hsa-miR-548d-5p hsa-miR-589
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    Additional mRNA sequence: 

    AK313912.1 BC026088.1 

    3 DOTS entries:

    DT.442706  DT.444375  DT.120779631 

    Selected AceView cDNA sequences (see all 46):

    CK825179 CA441149 BF590889 AI360517 AI360510 AW628164 BM856211 BI823132 
    BI818483 BM769875 NM_000538 W00532 BU754029 AI742868 BI560026 BF059183 
    AA253207 BE671897 AL079864 CK825178 BX113684 BG722888 H89304 BC026088 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    RFXAP expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCTGTTCTAA
    RFXAP Expression
    About this image

    RFXAP Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RFXAP Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.24422

    UniProtKB/Swiss-Prot: RFXAP_HUMAN, O00287
    Tissue specificity: Ubiquitous

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for RFXAP gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rfxap1 , 5 regulatory factor X-associated protein1, 5 78.22(n)1
    76.24(a)1
      3 (25.69 cM)5
    1707671  NM_133231.21  NP_573494.11 
     548031155 
    chicken
    (Gallus gallus)
    Aves RFXAP6
    regulatory factor X-associated protein
    48(a)
    1 ↔ 1
    1(171711512-171717479)
    lizard
    (Anolis carolinensis)
    Reptilia RFXAP6
    regulatory factor X-associated protein
    75(a)
    1 ↔ 1
    3(181462708-181464178)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.303652 Xenopus laevis transcribed sequence with weak similarity more 77.73(n)    BJ625098.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.124442 Transcribed sequence with weak similarity to protein more 78.44(n)    CD760266.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for RFXAP (see all 223)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 13 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs112851051,2
    C--18213697(+) CATGG-/TTTTTT 1 -- ut313Minor allele frequency- T:0.17NA CSA 6
    rs2003859481,2
    C--18213697(+) CATGGG/TTNNNN 1 -- ut310--------
    rs1863238711,2
    --18336187(+) GATGTG/TATGTA 1 -- us2k10--------
    rs1921994171,2
    --18336236(+) ACTGAA/TAGAAT 1 -- us2k10--------
    rs1818611601,2
    --18336297(+) GAATAA/CATTTT 1 -- us2k10--------
    rs1869345821,2
    --18336439(+) TCAGCC/TTCCTG 1 -- us2k10--------
    rs1913758001,2
    --18336788(+) GAAAAA/TGTGCA 1 -- us2k10--------
    rs95319851,2
    C,F,A,H--18336933(+) atataT/Atctta 1 -- us2k110Minor allele frequency- A:0.29NA WA CSA EA 370
    rs124281571,2
    C,H--18336976(+) agcagA/Tgttta 1 -- us2k1 tfbs30--------
    rs1823692831,2
    C--18337119(+) CACACA/GGGAAG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for RFXAP (37393339 - 37403740 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for RFXAP:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv522336CNV Gain19592680
    nsv899993CNV Gain21882294

    Human Gene Mutation Database (HGMD): RFXAP
    Locus Specific Mutation Databases (LSDB): RFXAP

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 601861   
    OMIM disorders: 209920  
    UniProtKB/Swiss-Prot: RFXAP_HUMAN, O00287
  • 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. Note=The
    disease is caused by mutations affecting the gene represented in this entry

  • 4 diseases for RFXAP:    
    About MalaCards
    bare lymphocyte syndrome, type ii, complementation group d    bare lymphocyte syndrome, type ii, complementation group c    bare lymphocyte syndrome    mhc class ii deficiency

    1 disease from the University of Copenhagen DISEASES database for RFXAP:
    Severe combined immunodeficiency

    Find genes that share disorders with RFXAP           About GenesLikeMe

    3 Novoseek inferred disease relationships for RFXAP gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    bare lymphocyte syndrome 94.8 3 10938133 (1), 15655668 (1), 16337482 (1)
    immunodeficiency 54.8 5 15655668 (1), 16337482 (1), 12618906 (1), 12498778 (1) (see all 5)
    severe combined immunodeficiency 46.9 1 10938133 (1)

    Genetic Association Database (GAD): RFXAP

    Export disorders for RFXAP gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for RFXAP gene, integrated from 10 sources (see all 45):
    (articles sorted by number of sources associating them with RFXAP)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. RFXAP, a novel subunit of the RFX DNA binding complex is mutated in MHC class II deficiency. (PubMed id 9118943)1, 2, 3, 9 Durand B....Reith W. (EMBO J. 1997)
    2. Solution structure of the heterotrimeric complex between the interaction domains of RFX5 and RFXAP from the RFX gene regulatory complex. (PubMed id 20732328)1, 2 Laird K.M.... Garvie C.W. (J. Mol. Biol. 2010)
    3. RFX-B is the gene responsible for the most common cause of the bare lymphocyte syndrome, an MHC class II immunodeficiency. (PubMed id 10072068)1, 2 Nagarajan U.M....Boss J.M. (Immunity 1999)
    4. Conserved residues of the bare lymphocyte syndrome transcription factor RFXAP determine coordinate MHC class II expression. (PubMed id 16337482)1, 9 Long A.B....Boss J.M. (Mol. Immunol. 2006)
    5. Coordinate loss of MHC class II expression in the diffuse large B cell lymphoma cell line OCI-Ly2 is due to a novel mutation in RFX-AP. (PubMed id 20024540)1, 9 Bushway M....Murphy S.P. (Immunogenetics 2010)
    6. Formation of the RFX gene regulatory complex induces folding of the interaction domain of RFXAP. (PubMed id 19274739)1, 9 Briggs L....Garvie C.W. (Proteins 2009)
    7. Assembly of the RFX complex on the MHCII promoter: role of RFXAP and RFXB in relieving autoinhibition of RFX5. (PubMed id 18723135)1, 9 Garvie C.W. and Boss J.M. (Biochim. Biophys. Acta 2008)
    8. Transcriptional silencing of RFXAP in MHC class II-deficiency. (PubMed id 18336911)1, 9 van Eggermond M.C....van den Elsen P.J. (Mol. Immunol. 2008)
    9. Multiple interactions between BRG1 and MHC class II promoter binding proteins. (PubMed id 15781111)1, 9 Mudhasani R. and Fontes J.D. (Mol. Immunol. 2005)
    10. Mutation of RFXAP, a regulator of MHC class II genes, in primary MHC class II deficiency. (PubMed id 9287230)1, 9 Villard J....Mach B. (N. Engl. J. Med. 1997)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 5994 HGNC: 9988 AceView: RFXAP Ensembl:ENSG00000133111 euGenes: HUgn5994
    ECgene: RFXAP Kegg: 5994 H-InvDB: RFXAP

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for RFXAP Pharmacogenomics, SNPs, Pathways
    RFXAPbasehttp://bioinf.uta.fi/RFXAPbase/

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