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RFX5 Gene

protein-coding   GIFtS: 64
GCID: GC01M151313

Regulatory Factor X, 5 (Influences HLA Class II Expression)

  See 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, 5 (Influences HLA Class II Expression)1 2
Regulatory Factor X 52 3
DNA-Binding Protein RFX52

External Ids:    HGNC: 99861   Entrez Gene: 59932   Ensembl: ENSG000001433907   OMIM: 6018635   UniProtKB: P483823   

Export aliases for RFX5 gene to outside databases

Previous GC identifers: GC01M149155 GC01M147060 GC01M148088 GC01M148529 GC01M148126 GC01M149579 GC01M122691


(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 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, and bare lymphocyte syndrome, type ii, complementation group e. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity. An important paralog of this gene is RFX7.

UniProtKB/Swiss-Prot: RFX5_HUMAN, P48382
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 Wiki entry for RFX5 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:
NC_000001.11  NT_004487.20  NC_018912.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the RFX5 gene promoter:
         CREB   deltaCREB   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRFX5 promoter sequence
   Search Chromatin IP Primers for RFX5

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RFX5


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

Entrez Gene cytogenetic band: 1q21   Ensembl cytogenetic band:  1q21.3   HGNC cytogenetic band: 1q21

RFX5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RFX5 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M151313:  view genomic region     (about GC identifiers)

Start:
151,313,116 bp from pter      End:
151,319,833 bp from pter
Size:
6,718 bases      Orientation:
minus 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: RFX5_HUMAN, P48382 (See protein sequence)
Recommended Name: DNA-binding protein RFX5  
Size: 616 amino acids; 65323 Da
Subunit: 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
2 PDB 3D structures from and Proteopedia for RFX5:
2KW3 (3D)        3V30 (3D)    
Secondary accessions: D3DV19 Q5VWC3

Explore the universe of human proteins at neXtProt for RFX5: NX_P48382

Explore proteomics data for RFX5 at MOPED

Post-translational modifications: 

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

  • See RFX5 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_000440.1  NP_001020774.1  

    ENSEMBL proteins: 
     ENSP00000290524   ENSP00000357864   ENSP00000390769   ENSP00000389130   ENSP00000376502  
     ENSP00000399095   ENSP00000398666   ENSP00000409187   ENSP00000399372   ENSP00000387618  
     ENSP00000415012   ENSP00000396810   ENSP00000413153   ENSP00000390720   ENSP00000412900  
     ENSP00000405067   ENSP00000398388  

    RFX5 Human Recombinant Protein Products:

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    Novus Biologicals RFX5 Proteins
    Novus Biologicals RFX5 Lysates
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    Browse Sino Biological Cell Lysates
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    Cloud-Clone Corp. Proteins for RFX5

    RFX5 Antibody Products:

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    LSBio Antibodies in human, mouse, rat for RFX5

    RFX5 Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    Cloud-Clone Corp. ELISAs for RFX5
    Cloud-Clone Corp. CLIAs for RFX5


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR011991 WHTH_DNA-bd_dom
     IPR003150 DNA-bd_RFX

    Graphical View of Domain Structure for InterPro Entry P48382

    ProtoNet protein and cluster: P48382

    1 Blocks protein domain: IPB003150 DNA-binding RFX

    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
    Similarity: Belongs to the RFX family
    Similarity: Contains 1 RFX-type winged-helix DNA-binding domain


    RFX5 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, 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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RFX5_HUMAN, P48382
    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

         Genatlas biochemistry entry for RFX5:
    transactivating DNA binding regulatory factor 5,75kDa,involved in MHC class II expression,binding the MHC promotor
    box X

         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 NAS9806546
    GO:0005515protein binding IPI16464847
         
    RFX5 for ontologies           About GeneDecksing


    Phenotypes:
         4 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Rfx5):
     cardiovascular system  hematopoietic system  immune system  liver/biliary system 

    RFX5 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Rfx5tm1.1Ifo for RFX5

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for RFX5
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for RFX5

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for RFX5
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for RFX5

    Transcription Factor Targeting: 
    Targeting motifs: HOMER Transcription Factor Regulatory Elements motif viewer 
                                          Consensus sequence:  SCCTAGCAACAG 

    miRNA
    Products:
        
    miRTarBase miRNAs that target RFX5:
    hsa-let-7d-5p (MIRT032137), hsa-mir-484 (MIRT042366), hsa-mir-196a-5p (MIRT026061)

    Block miRNA regulation of human, mouse, rat RFX5 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate RFX5 (see all 27):
    hsa-miR-4307 hsa-miR-3938 hsa-miR-125a-5p hsa-miR-642a hsa-miR-4254 hsa-miR-3660 hsa-miR-519a hsa-miR-125b
    SwitchGear 3'UTR luciferase reporter plasmidRFX5 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for RFX5
    Predesigned siRNA for gene silencing in human, mouse, rat RFX5

    Gene Editing
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    DNA2.0 Custom Protein Engineering Service for RFX5

    Clone
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    OriGene clones in human, mouse for RFX5 (see all 13)
    OriGene ORF clones in mouse, rat for RFX5
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): RFX5 (NM_000449)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for RFX5
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RFX5

    Cell Line
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    GenScript Custom overexpressing Cell Line Services for RFX5
    Browse ESI BIO Cell Lines and PureStem Progenitors for RFX5 
    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RFX5


    (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
    RFX5_HUMAN, P48382: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2
    plasma membrane2

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

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

    RFX5 for ontologies           About GeneDecksing


    (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 RFX5 About    
    See pathways by source

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

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways



    3 Kegg Pathways  (Kegg details for RFX5):
        Antigen processing and presentation
    Tuberculosis
    Primary immunodeficiency


    RFX5 for pathways           About GeneDecksing

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RFX5
    Interactions:

        GeneGlobe Interaction Network for RFX5

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for RFX5 (P483821, 2, 3 ENSP000002905244) via UniProtKB, MINT, STRING, and/or I2D (see all 578)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HDAC2Q927691, 2, 3, ENSP000003813314EBI-923266,EBI-301821 MINT-7947479 I2D: score=3 STRING: ENSP00000381331
    RFXANKO145933, ENSP000003050714I2D: score=3 STRING: ENSP00000305071
    RFXAPO002873, ENSP000002554764I2D: score=2 STRING: ENSP00000255476
    SIN3BO751823, ENSP000003691314I2D: score=2 STRING: ENSP00000369131
    HDAC4P565243, ENSP000002646064I2D: score=1 STRING: ENSP00000264606
    About this table

    Gene Ontology (GO): 3 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IEA--
    GO:0006351transcription, DNA-templated IEA--
    GO:0006355regulation of transcription, DNA-templated ----

    RFX5 for ontologies           About GeneDecksing



    (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 RFX5



    (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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for RFX5 gene (2 alternative transcripts): 
    NM_000449.3  NM_001025603.1  

    Unigene Cluster for RFX5:

    Regulatory factor X, 5 (influences HLA class II expression)
    Hs.632472  [show with all ESTs]
    Unigene Representative Sequence: NM_000449
    Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 22):
    ENST00000290524(uc001exv.1 uc001exw.1 uc010pcx.1) ENST00000368870
    ENST00000436637 ENST00000452671 ENST00000392746 ENST00000475144 ENST00000422595
    ENST00000450506 ENST00000458484 ENST00000469513 ENST00000421986 ENST00000430227
    ENST00000435314 ENST00000478564 ENST00000412774 ENST00000437327 ENST00000436271
    ENST00000494217
    miRNA
    Products:
         
    Block miRNA regulation of human, mouse, rat RFX5 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate RFX5 (see all 27):
    hsa-miR-4307 hsa-miR-3938 hsa-miR-125a-5p hsa-miR-642a hsa-miR-4254 hsa-miR-3660 hsa-miR-519a hsa-miR-125b
    SwitchGear 3'UTR luciferase reporter plasmidRFX5 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for RFX5
    Predesigned siRNA for gene silencing in human, mouse, rat RFX5
    Clone
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    OriGene clones in human, mouse for RFX5 (see all 13)
    OriGene ORF clones in mouse, rat for RFX5
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): RFX5 (NM_000449)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for RFX5
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RFX5
    Primer
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    OriGene qPCR primer pairs and template standards for RFX5
    OriGene qSTAR qPCR primer pairs in human, mouse for RFX5
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat RFX5
      QuantiTect SYBR Green Assays in human, mouse, rat RFX5
      QuantiFast Probe-based Assays in human, mouse, rat RFX5

    Additional mRNA sequence: 

    AK223526.1 AK302891.1 AK309072.1 AK311525.1 AK312289.1 AL050135.1 BC017471.1 X85786.1 

    14 DOTS entries:

    DT.214919  DT.95167462  DT.70104550  DT.100814795  DT.100028565  DT.121384205  DT.95167445  DT.95167446 
    DT.95283447  DT.121384173  DT.121384204  DT.75103417  DT.91806607  DT.95167448 

    Selected AceView cDNA sequences (see all 218):

    AI613136 CA389047 BQ686723 BU166686 AA418216 BM459237 H96664 CA394760 
    AW137021 BG250872 BX280988 BM470233 BQ643090 AI167924 BM453709 BP364412 
    AI620121 CB146819 BF055492 BG574203 BU165341 BM905177 AI127781 BX415732 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for RFX5 (see all 6)    About this scheme

    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:                          -     -                                                                                             


    ECgene alternative splicing isoforms for RFX5

    (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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    RFX5 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGTTCATTTA
    RFX5 Expression
    About this image


    RFX5 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 10) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Ovarian Mesenchymal Stroma Cells Ovary Interstitium
             Oviduct
     
     Blood (Hematopoietic System)    fully expand to see all 2 entries
             Peripheral blood-derived hematopoietic stem cells (family)
     
     Bone (Muscoskeletal System)
             Bone Marrow
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
    RFX5 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RFX5 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.632472

    UniProtKB/Swiss-Prot: RFX5_HUMAN, P48382
    Tissue specificity: Ubiquitous

        Custom PCR Arrays for RFX5
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    QuantiTect SYBR Green Assays in human, mouse, rat RFX5
    QuantiFast Probe-based Assays in human, mouse, rat RFX5
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RFX5

    (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 animals and fungi.

    Orthologs for RFX5 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rfx55 regulatory factor X, 5 (influences HLA class II expression)   --   3 (40.74 cM) 94954075 
    chicken
    (Gallus gallus)
    Aves RFX56
    regulatory factor X, 5 (influences HLA class II ex...
    61(a)
    1 ↔ 1
    25(1848770-1850767)
    lizard
    (Anolis carolinensis)
    Reptilia RFX56
    regulatory factor X, 5 (influences HLA class II ex...
    61(a)
    1 ↔ 1
    GL343779.1(96597-106422)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.134932 Xenopus laevis transcribed sequence with weak similarity more 76.76(n)    BJ617558.1 
    zebrafish
    (Danio rerio)
    Actinopterygii rfx56
    regulatory factor X, 5
    31(a)
    1 ↔ 1
    19(8104467-8117542) ENSDARG00000063258
    fruit fly
    (Drosophila melanogaster)
    Insecta CG97276
    --
    7(a)
    1 → many
    3R(2277275-2282371)
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes RFX16
    Major transcriptional repressor of DNA-damage-regu...
    5(a)
    1 → many
    XII(507797-510232) YLR176C


    ENSEMBL Gene Tree for RFX5 (if available)
    TreeFam Gene Tree for RFX5 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for RFX5 gene
    RFX72  
    3 SIMAP similar genes for RFX5 using alignment to 14 protein entries:     RFX5_HUMAN (see all proteins):
    DKFZp586K091    RFX7    RFX4

    RFX5 for paralogs           About GeneDecksing



    (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 RFX5 (see all 210)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0155504
    Bare lymphocyte syndrome 2 (BLS2)4--see VAR_0155502 R Q mis40--------
    rs1133030341,2
    C,F--122699883(+) AGCACC/TGCCTT 2 -- us2k11Minor allele frequency- T:0.50CSA 2
    rs3725811701,2
    C--151312926(+) TGTCT-/AAAAAA 2 -- ds50010--------
    rs745769181,2
    F--157814383(+) TAACAT/CAGCTG 2 -- ds50011Minor allele frequency- C:0.01EA 120
    rs1432178651,2
    --157814396(+) CACAGA/GTGGCT 2 -- ds50010--------
    rs1814672051,2
    --157814426(+) CTTTGA/GGAGCC 2 -- ds50010--------
    rs1482972771,2
    --157814438(+) AAGGTA/GGGCAG 2 -- ds50010--------
    rs1409089281,2
    --157814507(+) ACTAAA/GAATAC 2 -- ds50010--------
    rs1868651411,2
    --157814649(+) ATAGAA/GTGAGA 2 -- ds50010--------
    rs1501621921,2
    C--157814653(+) AGTGAA/GACTGT 2 -- ds50010--------

    HapMap Linkage Disequilibrium report for RFX5 (151313116 - 151319833 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for RFX5:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv438026CNV Loss16468122
    nsv831581CNV Loss17160897
    esv34461CNV Gain17911159
    nsv522840CNV Gain19592680

    Human Gene Mutation Database (HGMD): RFX5
    Locus Specific Mutation Databases (LSDB): RFX5

    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: 601863   
    OMIM disorders: 209920  
    UniProtKB/Swiss-Prot: RFX5_HUMAN, P48382
  • 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

  • 18 diseases for RFX5:    
    About MalaCards
    bare lymphocyte syndrome    bare lymphocyte syndrome, type ii, complementation group e    bare lymphocyte syndrome, type ii, complementation group c    mhc class ii deficiency
    plasmodium falciparum malaria    severe combined immunodeficiency    acute graft versus host disease    graft versus host disease
    age related macular degeneration    malaria    tuberculosis    tonsillitis
    multiple myeloma    myeloma    thyroiditis    cerebritis
    endotheliitis    prostatitis

    1 disease from the University of Copenhagen DISEASES database for RFX5:
    Severe combined immunodeficiency

    RFX5 for disorders           About GeneDecksing

    3 Novoseek inferred disease relationships for RFX5 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    bare lymphocyte syndrome 96 6 10938133 (1), 15655668 (1), 9190936 (1), 10706293 (1) (see all 5)
    immunodeficiency 53.3 4 15655668 (1), 12618906 (1), 12498778 (1), 16848795 (1)
    severe combined immunodeficiency 41.7 1 10938133 (1)

    Genetic Association Database (GAD): RFX5
    Human Genome Epidemiology (HuGE) Navigator: RFX5 (2 documents)

    Export disorders for RFX5 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 RFX5 gene, integrated from 10 sources (see all 63):
    (articles sorted by number of sources associating them with RFX5)
        Utopia: connect your pdf to the dynamic
    world of online information

    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. (PubMed id 10779326)1, 2, 9 Villard J.... Reith W. (Mol. Cell. Biol. 2000)
    2. Analysis of mutations and chromosomal localisation of the gene encoding RFX5, a novel transcription factor affected in major histocompatibility complex class II deficiency. (PubMed id 9401005)1, 3, 9 Villard J....Mach B. (Hum. Mutat. 1997)
    3. A novel DNA-binding regulatory factor is mutated in primary MHC class II deficiency (bare lymphocyte syndrome). (PubMed id 7744245)1, 2, 9 Steimle V....Reith W. (Genes Dev. 1995)
    4. Mutations in the bare lymphocyte syndrome define critical steps in the assembly of the regulatory factor X complex. (PubMed id 10825209)1, 2, 9 Nekrep N.... Peterlin B.M. (Mol. Cell. Biol. 2000)
    5. Sequence-specific recognition of a PxLPxI/L motif by an ankyrin repeat tumbler lock. (PubMed id 22649097)1, 2 Xu C.... Min J. (Sci. Signal. 2012)
    6. 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)
    7. Association between the SERPING1 gene and age-related macular degeneration: a two-stage case-control study. (PubMed id 18842294)1, 4 Ennis S....Lotery A. (Lancet 2008)
    8. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (Nature 2006)
    9. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    10. 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)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 5993 HGNC: 9986 AceView: RFX5 Ensembl:ENSG00000143390 euGenes: HUgn5993
    ECgene: RFX5 Kegg: 5993 H-InvDB: RFX5

    (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 RFX5 Pharmacogenomics, SNPs, Pathways
    RFX5basehttp://bioinf.uta.fi/RFX5base/

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for RFX5 gene:
    Search GeneIP for patents involving RFX5

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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