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PRPF40A Gene

protein-coding   GIFtS: 51
GCID: GC02M153508

PRP40 Pre-MRNA Processing Factor 40 Homolog A (S. Cerevisiae)

(Previous names: formin-binding protein 3, formin binding protein 3, PRP4...)
(Previous symbol: FNBP3)
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(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
PRP40 Pre-MRNA Processing Factor 40 Homolog A (S. Cerevisiae)1 2     FLAF12 3
FNBP31 2 3 5     HIP-102 3
FBP112 3 5     HIP102 3
HYPA2 3 5     Huntingtin-Interacting Protein A2 3
Formin Binding Protein 31 2     PRP40 Pre-MRNA Processing Factor 40 Homolog A (Yeast)1
Formin-Binding Protein 31 3     FBP-112
Fas Ligand-Associated Factor 12 3     NY-REN-62
Formin-Binding Protein 112 3     Prp402
Huntingtin Yeast Partner A2 3     Fas-Ligand Associated Factor 12
Huntingtin-Interacting Protein 102 3     NY-REN-6 Antigen2
Renal Carcinoma Antigen NY-REN-62 3     Pre-MRNA-Processing Factor 40 Homolog A2

External Ids:    HGNC: 164631   Entrez Gene: 556602   Ensembl: ENSG000001965047   OMIM: 6129415   UniProtKB: O754003   

Export aliases for PRPF40A gene to outside databases

Previous GC identifers: GC02M153338 GC02M153216 GC02M145394


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for PRPF40A Gene:
PRPF40A (PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae)) is a protein-coding gene. GO annotations related to this gene include proline-rich region binding. An important paralog of this gene is PRPF40B.

UniProtKB/Swiss-Prot: PR40A_HUMAN, O75400
Function: Binds to WASL/N-WASP and suppresses its translocation from the nucleus to the cytoplasm, thereby
inhibiting its cytoplasmic function (By similarity). Plays a role in the regulation of cell morphology and
cytoskeletal organization. Required in the control of cell shape and migration. May play a role in cytokinesis.
May be involved in pre-mRNA splicing

Gene Wiki entry for PRPF40A 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_000002.11  NT_005403.18  NC_018913.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the PRPF40A gene promoter:
         HOXA9B   HOXA9   AP-1   AML1a   GATA-1   HEN1   Max   Meis-1a   c-Myc   Meis-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for PRPF40A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PRPF40A


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

Entrez Gene cytogenetic band: 2q23.3   Ensembl cytogenetic band:  2q23.3   HGNC cytogenetic band: 2q23.3

PRPF40A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PRPF40A gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M153508:  view genomic region     (about GC identifiers)

Start:
153,508,107 bp from pter      End:
153,574,511 bp from pter
Size:
66,405 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, 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: PR40A_HUMAN, O75400 (See protein sequence)
Recommended Name: Pre-mRNA-processing factor 40 homolog A  
Size: 957 amino acids; 108805 Da
Subunit: Interacts with the N-terminus of HTT. Interacts with the phosphorylated C-terminal domain of POLR2A.
Interacts with AKAP8L, SF1, SRPK1, CARD8, ATBF1 and MECP2 (By similarity). Interacts through the WW domains with
formin proline-rich regions and with WASL/N-WASP (By similarity)
Sequence caution: Sequence=AAC27501.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Sequence=AAC27502.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAC27506.1;
Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=AAD42862.1; Type=Frameshift;
Positions=953; Sequence=AAF36145.1; Type=Frameshift; Positions=Several; Sequence=AAH11788.1; Type=Miscellaneous
discrepancy; Note=Contaminating sequence. Potential poly-A sequence starting in position 409;
Sequence=BAA91277.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAB15016.1;
Type=Miscellaneous discrepancy;
Selected PDB 3D structures from and Proteopedia for PRPF40A (see all 10):
1UZC (3D)        1YWI (3D)        1YWJ (3D)        1ZR7 (3D)        2CQN (3D)        2DYF (3D)    
Secondary accessions: O43856 O75404 Q8TBQ1 Q9H782 Q9NWU9 Q9P0Q2 Q9Y5A8
Alternative splicing: 4 isoforms:  O75400-1   O75400-2   O75400-3   O75400-5   (Probable target of nonsense-mediated mRNA decay)

Explore the universe of human proteins at neXtProt for PRPF40A: NX_O75400

Explore proteomics data for PRPF40A at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys196, Lys718, Lys727
  • Modification sites at PhosphoSitePlus

  • See PRPF40A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_060362.3  
    ENSEMBL proteins: 
     ENSP00000386458   ENSP00000346332   ENSP00000444656   ENSP00000441656   ENSP00000406924  

    PRPF40A Human Recombinant Protein Products:

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    Novus Biologicals PRPF40A Protein
    Novus Biologicals PRPF40A Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp.

     
    Search eBioscience for Proteins for PRPF40A 

     
    antibodies-online proteins for PRPF40A (2 products) 

     
    antibodies-online peptides for PRPF40A

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    antibodies-online antibodies for PRPF40A (19 products) 

    PRPF40A Assay Products:

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    Browse CLIAs at Cloud-Clone Corp.
    Search eBioscience for ELISAs for PRPF40A 
    antibodies-online kits for PRPF40A (4 products) 


    (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:
     IPR002713 FF_domain
     IPR001202 WW_dom

    Graphical View of Domain Structure for InterPro Entry O75400

    ProtoNet protein and cluster: O75400

    UniProtKB/Swiss-Prot: PR40A_HUMAN, O75400
    Domain: The WW domains are essential for localization to nuclear speckles (By similarity)
    Similarity: Belongs to the PRPF40 family
    Similarity: Contains 6 FF domains
    Similarity: Contains 2 WW domains


    Find genes that share domains with PRPF40A           About GenesLikeMe


    (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: PR40A_HUMAN, O75400
    Function: Binds to WASL/N-WASP and suppresses its translocation from the nucleus to the cytoplasm, thereby
    inhibiting its cytoplasmic function (By similarity). Plays a role in the regulation of cell morphology and
    cytoskeletal organization. Required in the control of cell shape and migration. May play a role in cytokinesis.
    May be involved in pre-mRNA splicing

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI15383276
    GO:0044822poly(A) RNA binding IDA--
    GO:0070064proline-rich region binding IEA--
         
    Find genes that share ontologies with PRPF40A           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for PRPF40A:
     Increased gamma-H2AX phosphory  Upregulation of Wnt/beta-caten 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for PRPF40A

    miRNA
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    miRTarBase miRNAs that target PRPF40A:
    hsa-mir-30a-5p (MIRT005210), hsa-mir-455-3p (MIRT037858), hsa-mir-32-5p (MIRT028328), hsa-mir-34a-5p (MIRT025248)

    Block miRNA regulation of human, mouse, rat PRPF40A using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate PRPF40A (see all 115):
    hsa-miR-323-3p hsa-miR-549 hsa-miR-548j hsa-miR-3130-5p hsa-miR-607 hsa-miR-3607-3p hsa-miR-4272 hsa-miR-485-3p
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat PRPF40A

    Gene Editing
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PRPF40A


    (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
    PR40A_HUMAN, O75400: Nucleus speckle (By similarity). Nucleus matrix. Note=Colocalizes with AKAP8L in the nuclear
    matrix (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol1
    endoplasmic reticulum1
    mitochondrion1
    peroxisome1
    plasma membrane1

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005730NOT nucleolus IDA--
    GO:0005737cytoplasm IDA--
    GO:0016363nuclear matrix IDA16391387
    GO:0016607nuclear speck IEA--

    Find genes that share ontologies with PRPF40A           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 PRPF40A About    
    See pathways by source

    SuperPathContained pathways About
    1mRNA Splicing - Major Pathway
    mRNA processing0.44
    2Spliceosome
    Spliceosome


    Find genes that share SuperPaths with PRPF40A           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 BioSystems Pathway for PRPF40A
        mRNA processing


    1 Kegg Pathway  (Kegg details for PRPF40A):
        Spliceosome

        Pathway & Disease-focused RT2 Profiler PCR Array including PRPF40A: 
              Huntington's Disease in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for PRPF40A

    Selected Interacting proteins for PRPF40A (O754001, 2, 3) via UniProtKB, MINT, STRING, and/or I2D (see all 763)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HTTP428581, 2, 3EBI-473291,EBI-466029 MINT-3978265 MINT-3978367 MINT-7101607 MINT-7101726 MINT-3977892 MINT-7102030 MINT-7101739 MINT-7101642 MINT-7101687 MINT-7101453 MINT-7101586 MINT-7101713 I2D: score=5 
    CHD3Q128731, 2, 3EBI-473291,EBI-523590 MINT-7945693 MINT-3979432 MINT-3981738 I2D: score=4 
    SF3A1Q154591, 2, 3EBI-473291,EBI-1054743 MINT-8331514 MINT-7945693 MINT-8333163 I2D: score=2 
    BAG6P463792, 3MINT-61883 I2D: score=3 
    ENSG00000096155P463792, 3MINT-61883 I2D: score=3 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006397mRNA processing IEA--
    GO:0007010cytoskeleton organization IMP--
    GO:0007049cell cycle IEA--
    GO:0008360regulation of cell shape IMP--
    GO:0008380RNA splicing IEA--

    Find genes that share ontologies with PRPF40A           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 PRPF40A (PR40A)



    (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 PRPF40A gene: 
    NM_017892.3  

    Unigene Cluster for PRPF40A:

    PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae)
    Hs.643580  [show with all ESTs]
    Unigene Representative Sequence: NM_017892
    12 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000410080(uc002tyg.4 uc002tyh.4 uc010zcd.1) ENST00000471701
    ENST00000471167 ENST00000472760 ENST00000354363(uc002tyj.2) ENST00000545856(uc002tyi.2 uc002tyl.1)
    ENST00000493468 ENST00000448428 ENST00000467114 ENST00000489741 ENST00000450303
    ENST00000486100
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate PRPF40A (see all 115):
    hsa-miR-323-3p hsa-miR-549 hsa-miR-548j hsa-miR-3130-5p hsa-miR-607 hsa-miR-3607-3p hsa-miR-4272 hsa-miR-485-3p
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      QuantiTect SYBR Green Assays in human, mouse, rat PRPF40A
      QuantiFast Probe-based Assays in human, mouse, rat PRPF40A

    Additional mRNA sequence: 

    AF049523.1 AF049524.1 AF049528.1 AF151059.1 AF155096.1 AK000592.1 AK021621.1 AK024810.1 
    AK298547.1 AK315187.1 BC000273.1 BC011788.2 BC027178.1 BC029414.1 BC073138.1 U70667.1 

    Selected DOTS entries (see all 28):

    DT.121023714  DT.454961  DT.440682  DT.313645  DT.121023665  DT.65286973  DT.97838082  DT.95351232 
    DT.100754766  DT.97806522  DT.92425541  DT.100785283  DT.121023656  DT.455413  DT.87046748  DT.100785286 
    DT.100785288  DT.121023653  DT.65287736  DT.92432401  DT.95268820  DT.121023715  DT.40121185  DT.75185407 

    Selected AceView cDNA sequences (see all 367):

    BU902830 BQ025943 CB117805 AI868131 BF224280 AI743993 CB124551 U70667 
    BU183998 BC011788 T40740 AI050068 BU679640 BM313171 AI090511 W23623 
    AA244490 BU675147 AI015180 BC029414 AW131275 AA813099 CB129625 CA430244 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for PRPF40A (see all 7)    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^ 20
    SP1:                                                                                                                                                      
    SP2:                                                                                                                                                      
    SP3:                                                                                                                                                      
    SP4:                    -           -           -                                                                                                         
    SP5:                                -           -                                                                                                         


    ECgene alternative splicing isoforms for PRPF40A

    (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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    PRPF40A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGAGCAGGCT
    PRPF40A Expression
    About this image


    PRPF40A expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 4) fully expand
     
     Limb (Muscoskeletal System)
             Limb Bud
     
     Lung (Respiratory System)
             Stem Bronchi
     
     Kidney (Urinary System)
             Metanephros
     
     Neural Tube (Nervous System)
             Metencephalon
    PRPF40A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PRPF40A Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.643580

    UniProtKB/Swiss-Prot: PR40A_HUMAN, O75400
    Tissue specificity: Expressed in the brain cortex (at protein level). Widely expressed

        Pathway & Disease-focused RT2 Profiler PCR Array including PRPF40A: 
              Huntington's Disease in human mouse rat

    Primer
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    QuantiFast Probe-based Assays in human, mouse, rat PRPF40A
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PRPF40A

    (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

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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for PRPF40A gene from Selected species (see all 19)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Prpf40a1 , 5 PRP40 pre-mRNA processing factor 40 homolog A (yeast)1, 5 91.44(n)1
    96.49(a)1
      2 (30.69 cM)5
    561941  NM_018785.21  NP_061255.11 
     531347045 
    chicken
    (Gallus gallus)
    Aves PRPF40A1 PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) 80.02(n)
    87.7(a)
      373972  XM_003641632.2  XP_003641680.2 
    lizard
    (Anolis carolinensis)
    Reptilia PRPF40A6
    PRP40 pre-mRNA processing factor 40 homolog A (S. ...
    74(a)
    1 ↔ 1
    GL343296.1(1016271-1049930)
    African clawed frog
    (Xenopus laevis)
    Amphibia CB941857.12   -- 81.73(n)    CB941857.1 
    zebrafish
    (Danio rerio)
    Actinopterygii fnbp32 formin binding protein 3 77.03(n)   321555  BC049307.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG35426
    --
    44(a)
    1 → many
    2L(3023235-3026439)
    worm
    (Caenorhabditis elegans)
    Secernentea ZK1098.11 ZK1098.1 52.21(n)
    42.24(a)
      176343  NM_001268076.1  NP_001255005.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes PRP406
    U1 snRNP protein involved in splicing, interacts w...
    27(a)
    1 → many
    XI(418310-420061) YKL012W
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons PRP40B1 PRP40B 45.37(n)
    33.66(a)
      821504  NM_112857.5  NP_188601.4 


    ENSEMBL Gene Tree for PRPF40A (if available)
    TreeFam Gene Tree for PRPF40A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PRPF40A gene
    PRPF40B2  TCERG12  TCERG1L2  
    2 SIMAP similar genes for PRPF40A using alignment to 6 protein entries:     PR40A_HUMAN (see all proteins):
    FNBP3    PRPF40B

    Find genes that share paralogs with PRPF40A           About GenesLikeMe



    (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)
    About This Section

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    Selected SNPs for PRPF40A (see all 1334)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs615416991,2
    C--145428488(+) AAAAA-/AA/AAA
            
    CACGT
    1 -- int11NA 2
    rs668495461,2
    C,F--153507651(+) GGATGG/AAATGC 1 -- ds50017Minor allele frequency- A:0.10NA WA EA 368
    rs1858974021,2
    --153507714(+) CTCCCA/GCTTCA 1 -- ds50010--------
    rs1389232741,2
    --153507778(+) CTAGA-/AATAATAG 1 -- cds10--------
    rs1145511871,2
    F--153507959(+) CAGAAA/GTGTCT 1 -- ds50011Minor allele frequency- G:0.01NA 120
    rs1907013311,2
    --153508071(+) TGTACA/GTGAAA 1 -- ds50010--------
    rs2001017511,2
    --153508083(+) AGTGA-/TTGGGT 1 -- ds50010--------
    rs577044031,2
    C--153508084(+) ATGGGG/-TTTTT 1 -- ds50011Minor allele frequency- -:0.50CSA 2
    rs116852041,2
    C,A,H--153508088(+) ATGGGG/TTTTTT 1 -- ds50013Minor allele frequency- T:0.17NA 6
    rs725115611,2
    C--153508088(+) ATGGG-/G/TTTTTT 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for PRPF40A (153508107 - 153574511 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for PRPF40A:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv834420CNV Loss17160897
    nsv834421CNV Loss17160897
    esv34659CNV Loss17911159
    nsv7331OTHER Inversion18451855

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing PRPF40A
    DNA2.0 Custom Variant and Variant Library Synthesis for PRPF40A

    (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: 612941    OMIM disorders: --

    1 disease from the University of Copenhagen DISEASES database for PRPF40A:
    Rett syndrome

    Find genes that share disorders with PRPF40A           About GenesLikeMe

    2 Novoseek inferred disease relationships for PRPF40A gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    rett syndrome 62 1 15811376 (1)
    huntington disease 44.1 1 16391387 (1)

    Genetic Association Database (GAD): PRPF40A

    Export disorders for PRPF40A 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 PRPF40A gene, integrated from 10 sources (see all 68):
    (articles sorted by number of sources associating them with PRPF40A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Interaction of the nuclear matrix protein NAKAP with HypA and huntingtin: implications for nuclear toxicity in Huntington's disease pathogenesis. (PubMed id 16391387)1, 2, 9 Sayer J.A.... Coghlan V.M. (NeuroMolecular Med. 2005)
    2. Huntingtin interacts with a family of WW domain proteins. (PubMed id 9700202)1, 2, 9 Faber P.W....MacDonald M.E. (Hum. Mol. Genet. 1998)
    3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (Cell 2006)
    4. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)1, 2 Hillier L.W.... Wilson R.K. (Nature 2005)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    6. 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)
    7. Solution structure and ligand recognition of the WW domain pair of the yeast splicing factor Prp40. (PubMed id 12460579)1, 3 Wiesner S....Macias M.J. (J. Mol. Biol. 2002)
    8. The structure of an FF domain from human HYPA/FBP11. (PubMed id 12381297)1, 2 Allen M.... Bycroft M. (J. Mol. Biol. 2002)
    9. Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells. (PubMed id 11042152)1, 2 Zhang Q.-H.... Chen Z. (Genome Res. 2000)
    10. Antigens recognized by autologous antibody in patients with renal- cell carcinoma. (PubMed id 10508479)1, 2 Scanlan M.J....Old L.J. (Int. J. Cancer 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: 55660 HGNC: 16463 AceView: FNBP3 Ensembl:ENSG00000196504 euGenes: HUgn55660
    ECgene: PRPF40A Kegg: 55660 H-InvDB: PRPF40A

    (According to HUGE)
    About This Section

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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)
    About This Section

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    NameDescription
    PharmGKB entry for PRPF40A Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

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    Patent Information for PRPF40A gene:
    Search GeneIP for patents involving PRPF40A

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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