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PRPF18 Gene

protein-coding   GIFtS: 54
GCID: GC10P013628

Pre-MRNA Processing Factor 18

(Previous names: PRP18 pre-mRNA processing factor 18 homolog (yeast), PRP18...)
Alzheimer's & Parkinson's Diseases Congress
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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
Pre-MRNA Processing Factor 181 2     Pre-MRNA-Splicing Factor 182
PRP18 Homolog2 3     PRP18 Pre-MRNA Processing Factor 18 Homolog2
PRP182 5     PRP18 Pre-MRNA Processing Factor 18 Homolog(PRPF18)2
PRP18 Pre-MRNA Processing Factor 18 Homolog (S. Cerevisiae)1     HPRP183
PRP18 Pre-MRNA Processing Factor 18 Homolog (Yeast)1     hPRP183
hPrp182     

External Ids:    HGNC: 173511   Entrez Gene: 85592   Ensembl: ENSG000001656307   OMIM: 6049935   UniProtKB: Q996333   

Export aliases for PRPF18 gene to outside databases

Previous GC identifers: GC10P013611 GC10P013779 GC10P013633 GC10P013669 GC10P013540


(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 PRPF18 Gene:
Pre-mRNA splicing occurs in 2 sequential transesterification steps. The protein encoded by this gene is found to
be essential for the catalytic step II in pre-mRNA splicing process. It is found in the spliceosome, and contains
seven WD repeats, which function in protein-protein interactions. This protein has a sequence similarity to the
yeast splicing factor Prp18. (provided by RefSeq, Jul 2008)

GeneCards Summary for PRPF18 Gene:
PRPF18 (pre-mRNA processing factor 18) is a protein-coding gene. Diseases associated with PRPF18 include pityriasis rubra pilaris, and exanthem. An important paralog of this gene is LOC101928524.

UniProtKB/Swiss-Prot: PRP18_HUMAN, Q99633
Function: Participates in the second step of pre-mRNA splicing




(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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Regulatory elements:
   Regulatory transcription factor binding sites in the PRPF18 gene promoter:
         Bach1   LHX3b/Lhx3b   GCNF   SREBP-1c   SREBP-1b   E47   SREBP-1a   POU2F1   POU2F1a   LHX3a/Lhx3a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPRPF18 promoter sequence
   Search Chromatin IP Primers for PRPF18

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PRPF18


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

Entrez Gene cytogenetic band: 10p13   Ensembl cytogenetic band:  10p13   HGNC cytogenetic band: 10p12.33

PRPF18 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PRPF18 gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10P013628:  view genomic region     (about GC identifiers)

Start:
13,628,927 bp from pter      End:
13,672,868 bp from pter
Size:
43,942 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, 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, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: PRP18_HUMAN, Q99633 (See protein sequence)
Recommended Name: Pre-mRNA-splicing factor 18  
Size: 342 amino acids; 39860 Da
Subunit: Heterodimer with PPIH. Interacts with PRPF4 and with the spliceosome. Part of a complex containing U4/U6
snRNPs
1 PDB 3D structure from and Proteopedia for PRPF18:
2DK4 (3D)    
Secondary accessions: Q5T9P9 Q9BUI9
Alternative splicing: 2 isoforms:  Q99633-1   Q99633-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for PRPF18: NX_Q99633

Explore proteomics data for PRPF18 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys5
  • Modification sites at PhosphoSitePlus

  • See PRPF18 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_003666.1  
    ENSEMBL proteins: 
     ENSP00000367835   ENSP00000392142   ENSP00000367824  

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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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    3 InterPro protein domains:
     IPR014906 PRP4-like
     IPR003648 SFM
     IPR004098 Prp18

    Graphical View of Domain Structure for InterPro Entry Q99633

    ProtoNet protein and cluster: Q99633

    UniProtKB/Swiss-Prot: PRP18_HUMAN, Q99633
    Similarity: Belongs to the PRP18 family


    PRPF18 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: PRP18_HUMAN, Q99633
    Function: Participates in the second step of pre-mRNA splicing

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0019870potassium channel inhibitor activity IEA--
         
    PRPF18 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for PRPF18:
     Decreased G3BP1 protein expres 

    Animal Models:
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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
    PRP18_HUMAN, Q99633: Nucleus speckle (By similarity). Note=Colocalizes with spliceosomal snRNPs (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus4
    cytosol2
    peroxisome2
    mitochondrion1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus TAS9000057
    GO:0005681spliceosomal complex IEA--
    GO:0016607nuclear speck IEA--

    PRPF18 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 PRPF18 About                                                                                                See pathways by source

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

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 BioSystems Pathway for PRPF18
        mRNA processing


    1 Kegg Pathway  (Kegg details for PRPF18):
        Spliceosome


    PRPF18 for pathways           About GeneDecksing

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PRPF18
    Interactions:

        GeneGlobe Interaction Network for PRPF18

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

    Selected Interacting proteins for PRPF18 (Q996333 ENSP000003678354) via UniProtKB, MINT, STRING, and/or I2D (see all 50)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PPIHO434473, ENSP000003066144I2D: score=2 STRING: ENSP00000306614
    CKBP122773I2D: score=5 
    SLU7ENSP000002971514STRING: ENSP00000297151
    SNRNP200ENSP000003171234STRING: ENSP00000317123
    CDC40ENSP000003043704STRING: ENSP00000304370
    About this table

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006397mRNA processing IEA--
    GO:0008380RNA splicing IEA--

    PRPF18 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 PRPF18 (PRP18)



    (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,
    Conferences by KenesGroup, 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 PRPF18 gene: 
    NM_003675.3  

    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000378572(uc001imp.3) ENST00000417658 ENST00000320054

    miRNA
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    Selected AceView cDNA sequences (see all 189):

    CA432267 U51990 CB157880 BF791404 BP368092 CR606297 BU177047 CA423849 
    BU852266 AI588999 AA702779 AL137400 CA429447 BP339860 NM_003675 BM678451 
    AI697476 BM824652 BE502519 BX647538 AI880181 BF057744 BU616913 BM721939 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for PRPF18    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b
    SP1:              -                                                                     
    SP2:                                                        -                           
    SP3:                                                                                    


    ECgene alternative splicing isoforms for PRPF18

    (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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    PRPF18 expression in normal human tissues (normalized intensities)      PRPF18 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGACCATTGA
    PRPF18 Expression
    About this image


    PRPF18 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 6) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Ovary (Reproductive System)
             Oviduct
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
     
     Liver (Hepatobiliary System)
             Hepatocytes Liver Lobule
    PRPF18 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PRPF18 Protein Expression
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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 eukaryotes.

    Orthologs for PRPF18 gene from Selected species (see all 20)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Prpf181 , 5 PRP18 pre-mRNA processing factor 18 homolog (yeast)1, 5 89.96(n)1
    99.12(a)1
      2 (2.79 cM)5
    672291  NM_026045.31  NP_080321.21 
     46220585 
    chicken
    (Gallus gallus)
    Aves PRPF181 PRP18 pre-mRNA processing factor 18 homolog (S. cerevisiae) 80.99(n)
    92.4(a)
      419036  XM_004937491.1  XP_004937548.1 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    90(a)
    1 → many
    5(90152592-90172728)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.136542 Xenopus laevis transcribed sequence with moderate similarity more 77.59(n)    BX847050.1 
    zebrafish
    (Danio rerio)
    Actinopterygii BM316634.12   -- 77.19(n)    BM316634.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Prp181 , 3 mRNA splicing pre-mRNA splicing factor3
    Prp181
    51(a)3
    54.75(n)1
    52.25(a)1
      91E43
    422851  NM_142519.11  NP_650776.11 
    worm
    (Caenorhabditis elegans)
    Secernentea F32B6.31 , 3 Human HPRP18 protein like3
    F32B6.31
    38(a)3
    50.05(n)1
    40.73(a)1
      IV(9882376-9884456)3
    1778401  NM_069375.41  NP_501776.21 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes PRP186
    Splicing factor involved in the positioning of the...
    25(a)
    1 → many
    VII(506070-506825) YGR006W
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT1G031401 AT1G03140 48.72(n)
    40.53(a)
      839567  NM_100196.2  NP_563676.1 
    rice
    (Oryza sativa)
    Liliopsida Os07g05719001 Os07g0571900 53.26(n)
    44.92(a)
      4343671  NM_001066589.1  NP_001060054.1 


    ENSEMBL Gene Tree for PRPF18 (if available)
    TreeFam Gene Tree for PRPF18 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PRPF18 gene
    LOC1019285242  
    1 SIMAP similar gene for PRPF18 using alignment to 4 protein entries:     PRP18_HUMAN (see all proteins):
    LOC101928497

    PRPF18 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 PRPF18 (see all 960)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 10 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1431562411,2
    --13626944(+) TTAAGC/TGTTTC 1 -- us2k10--------
    rs22553331,2
    C--13626964(+) cttttC/Tttttt 1 -- us2k1 trp35Minor allele frequency- T:0.10WA NA 10
    rs618352651,2
    F--13627013(+) CAGGCC/TGGAGT 1 -- us2k11Minor allele frequency- T:0.00NA 2
    rs79042801,2
    C--13627051(+) acctcC/Tgcctc 1 -- us2k10--------
    rs727675381,2
    C,F--13627254(+) GTGCCC/TGGCCT 1 -- us2k11Minor allele frequency- T:0.05NA 120
    rs1903134101,2
    --13627390(+) ATTCAG/TTGCAC 1 -- us2k10--------
    rs1834132251,2
    --13627409(+) ATAAAC/TGTAGA 1 -- us2k10--------
    rs1878973331,2
    --13627425(+) ATGAAA/CGTCTA 1 -- us2k10--------
    rs1932016971,2
    --13627428(+) AAAGTC/GTAAAA 1 -- us2k10--------
    rs1833893601,2
    --13627459(+) TGTAGC/TTAGTA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for PRPF18 (13628927 - 13672868 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for PRPF18:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv831790CNV Loss17160897
    nsv831789CNV Gain+Loss17160897

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing PRPF18
    DNA2.0 Custom Variant and Variant Library Synthesis for PRPF18

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 604993    OMIM disorders: --

    11 diseases for PRPF18:    About MalaCards
    pityriasis rubra pilaris    exanthem    palmoplantar keratosis    keratosis
    tonsillitis    alzheimer's disease    malaria    thyroiditis
    cerebritis    endotheliitis    prostatitis

    2 diseases from the University of Copenhagen DISEASES database for PRPF18:
    Pityriasis rubra pilaris     Palmoplantar keratosis

    PRPF18 for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:
    Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015
    Genetic Association Database (GAD): PRPF18
    Human Genome Epidemiology (HuGE) Navigator: PRPF18 (2 documents)

    Export disorders for PRPF18 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 PRPF18 gene, integrated from 10 sources (see all 15):
    (articles sorted by number of sources associating them with PRPF18)
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    1. A human protein required for the second step of pre-mRNA splicing is functionally related to a yeast splicing factor. (PubMed id 9000057)1, 2, 3, 9 Horowitz D.S. and Krainer A.R. (Genes Dev. 1997)
    2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    3. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PubMed id 16385451)1, 4 Grupe A....Goate A. (Am. J. Hum. Genet. 2006)
    4. 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)
    5. A cyclophilin functions in pre-mRNA splicing. (PubMed id 11823439)1, 2 Horowitz D.S.... Misteli T. (EMBO J. 2002)
    6. A genome-wide association study of chemotherapy-induced alopecia in breast cancer patients. (PubMed id 24025145)1 Chung S....Nakamura Y. (Breast Cancer Res. 2013)
    7. Solution structure of the splicing factor motif of the human Prp18 protein. (PubMed id 22213562)1 He F....Muto Y. (Proteins 2012)
    8. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (Cell 2012)
    9. N-terminal acetylome analyses and functional insights of the N- terminal acetyltransferase NatB. (PubMed id 22814378)2 Van Damme P....Aldabe R. (Proc. Natl. Acad. Sci. U.S.A. 2012)
    10. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)

    (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: 8559 HGNC: 17351 AceView: PRPF18 Ensembl:ENSG00000165630 euGenes: HUgn8559
    ECgene: PRPF18 Kegg: 8559 H-InvDB: PRPF18

    (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 PRPF18 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for PRPF18 gene:
    Search GeneIP for patents involving PRPF18

    GeneCards and IP:
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