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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

RFXAP Gene

protein-coding   GIFtS: 53
GCID: GC13P037393

regulatory factor X-associated protein

 Explore 10 diseases affiliated with
RFXAP via our new
 Human Malady Compendium 
Biological research products
for RFXAP
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

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, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for RFXAP:
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)

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


(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000013.10  NC_018924.1  NT_024524.14  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for RFXAP

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

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
Subcellular location: Nucleus
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

Post-translational modifications:

  • Phosphorylated1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_O00287

  • RFXAP Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_000529.1  
    ENSEMBL proteins: 
     ENSP00000255476  

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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for RFXAP

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

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


    RFXAP for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: 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

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    Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    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


    RFXAP for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for RFXAP:
     Increased G1 DNA content 


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Tuberculosis
    Tuberculosis1.00
    2Primary immunodeficiency
    Primary immunodeficiency1.00
    3Allograft rejection
    Antigen processing and presentation0.25

    Pathway sources
    See GeneCards unified pathways
    Show all pathways



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


    RFXAP for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for RFXAP

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

    5/9 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): 2 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006355regulation of transcription, DNA-dependent ----
    GO:0045893positive regulation of transcription, DNA-dependent IEA--


    RFXAP for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for RFXAP
    Search CenterWatch for drugs/clinical trials and news about RFXAP 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    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

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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 cDNA sequence: 

    AK313912.1 BC026088.1 

    3 DOTS entries:

    DT.442706  DT.444375  DT.120779631 

    24/46 AceView cDNA sequences (see all 46):

    AW628164 AI360517 CA441149 AI360510 BM856211 BI823132 BF590889 CK825179 
    W00532 NM_000538 BC026088 BG722888 BM769875 AL079864 BU754029 BG701333 
    AA253207 AI742868 BE671897 BF059183 BF111841 BX113684 BI560026 H89304 

    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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    RFXAP expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GCTGTTCTAA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See RFXAP Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RFXAP

    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)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for RFXAP gene from 5/12 species (see all 12)    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 79.97(n)1
    80.7(a)1
      3 (25.69 cM)5
    1707671  NM_133231.21  NP_573494.11 
     548031165 
    chicken
    (Gallus gallus)
    Aves RFXAP1 regulatory factor X-associated protein 67.62(n)
    62.6(a)
      418899  XM_417095.3  XP_417095.3 
    lizard
    (Anolis carolinensis)
    Reptilia RFXAP6
    --
    76(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)
    About This Section
      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/177 NCBI SNPs in RFXAP are shown (see all 177    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 13 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs124281571,2
    C,H--18204038(+) agcagA/Tgttta 1 -- us2k1 tfbs30--------
    rs73183021,2
    C,--18204723(+) CCTCTA/GCCTTC 1 -- us2k10--------
    rs362311371,2
    C,F,--18204926(+) ATAGGA/TTCAGG 1 -- us2k15Minor allele frequency- T:0.18NA WA 126
    rs115391821,2
    C,F,H--18205290(+) CGCAGG/AGTGTA 2 /S /G mis16Minor allele frequency- A:0.01NS NA 782
    rs1128039421,2
    C,F--18205736(+) CAGGTG/AGCCAA 2 /V syn12Minor allele frequency- A:0.00CSA NA 3808
    rs412922211,2
    --18205964(+) CCTCCC/TCACTT 1 -- int10--------
    rs1140918721,2
    C,--18206310(+) TTTGTA/CATACT 1 -- int10--------
    rs782381721,2
    C,F,--18206571(+) GTACCC/TCTGAG 1 -- int11Minor allele frequency- T:0.03WA 118
    rs759487691,2
    C,--18207193(+) TCCTAG/AGATGT 1 -- int12Minor allele frequency- A:0.10WA 120
    rs764153811,2
    F,--18207234(+) GCTGAA/GCTTGA 1 -- int11Minor allele frequency- G:0.02WA 118

    HapMap Linkage Disequilibrium report for RFXAP (37393339 - 37403740 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for RFXAP: --
    Human Gene Mutation Database (HGMD): RFXAP

    Locus Specific Mutation Databases (LSDB): RFXAP

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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.)
    About This Section

    RFXAP for disorders           About GeneDecksing

    OMIM gene information: 601861   
    OMIM disorders: 209920  
    UniProtKB/Swiss-Prot: RFXAP_HUMAN, O00287
  • Defects in RFXAP are a cause of bare lymphocyte syndrome type 2 (BLS2) [MIM:209920]; also known as hereditary
  • MHC class II deficiency or HLA class II-deficient combined immunodeficiency. BLS2 is 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

    10 diseases for RFXAP:    About MalaCards
    bare lymphocyte syndrome, type ii, complementation group d    bare lymphocyte syndrome    mhc class ii deficiency    severe combined immunodeficiency
    graft versus host disease    combined immunodeficiency    b-cell lymphomas    immunodeficiency
    tuberculosis    acute graft versus host disease

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

    3 Novoseek 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)


    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)
    About This Section

    PubMed articles for RFXAP gene, integrated from 9 sources (see all 43):
    (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. (1997)
    2. Solution structure of the heterotrimeric complex betw een the interaction domains of RFX5 and RFXAP from the RFX gene regulatory comp lex. (PubMed id 20732328)1, 2 Laird K.M....Garvie C.W. (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. (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. (2006)
    5. Coordinate loss of MHC class II expression in the dif fuse 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. (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. (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. (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. (2008)
    9. Multiple interactions between BRG1 and MHC class II promoter binding proteins. (PubMed id 15781111)1, 9 Mudhasani R. and Fontes J.D. (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. (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)
    About This Section
    Entrez Gene: 5994 HGNC: 9988 AceView: RFXAP Ensembl:ENSG00000133111 euGenes: HUgn5994
    ECgene: RFXAP Kegg: 5994 H-InvDB: RFXAP

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

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for RFXAP gene:
    Search GeneIP for patents involving RFXAP

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