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

PRPF38A Gene

protein-coding   GIFtS: 48
GCID: GC01P052870

Pre-MRNA Processing Factor 38A

(Previous name: PRP38 pre-mRNA processing factor 38 (yeast) domain containing...)
  Search for PRPF38A
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Pre-MRNA Processing Factor 38A1
PRP38 Pre-MRNA Processing Factor 38 (Yeast) Domain Containing A1 2
Prp382
RP5-965L7.12
Pre-MRNA-Splicing Factor 38A2

External Ids:    HGNC: 259301   Entrez Gene: 849502   Ensembl: ENSG000001347487   UniProtKB: Q8NAV13   

Export aliases for PRPF38A gene to outside databases

Previous GC identifers: GC01P052583 GC01P052642 GC01P050986


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

GeneCards Summary for PRPF38A Gene: 
PRPF38A (pre-mRNA processing factor 38A) is a protein-coding gene. Among its related super-pathways are mRNA Splicing - Major Pathway.

UniProtKB/Swiss-Prot: PR38A_HUMAN, Q8NAV1
Function: May be required for pre-mRNA splicing (Potential)




(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NC_018912.2  NT_032977.9  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PRPF38A gene promoter:
         Pbx1a   POU3F2 (N-Oct-5b)   POU3F2 (N-Oct-5a)   STAT5A   POU3F2   Meis-1b   Gfi-1   Meis-1a   Meis-1   ATF6   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPRPF38A promoter sequence
   Search SABiosciences Chromatin IP Primers for PRPF38A

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PRPF38A


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

Entrez Gene cytogenetic band: 1p32.3   Ensembl cytogenetic band:  1p32.3   HGNC cytogenetic band: 1p32.3

PRPF38A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PRPF38A gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P052870:  view genomic region     (about GC identifiers)

Start:
52,870,219 bp from pter      End:
52,886,511 bp from pter
Size:
16,293 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: PR38A_HUMAN, Q8NAV1 (See protein sequence)
Recommended Name: Pre-mRNA-splicing factor 38A  
Size: 312 amino acids; 37477 Da
Subcellular location: Nucleus (Potential)
Sequence caution: Sequence=BAB55405.1; Type=Erroneous initiation;
Secondary accessions: Q96JW1 Q9BVZ8
Alternative splicing: 2 isoforms:  Q8NAV1-1   Q8NAV1-2   

Explore the universe of human proteins at neXtProt for PRPF38A: NX_Q8NAV1

Explore proteomics data for PRPF38A at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q8NAV1

  • PRPF38A Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    PRPF38A Protein Expression
    REFSEQ proteins: NP_116253.2  
    ENSEMBL proteins: 
     ENSP00000257181  

    Human Recombinant Protein Products for PRPF38A: 
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    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for PRPF38A 

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005681spliceosomal complex IEA--

    PRPF38A for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    2 InterPro protein domains:
     IPR024767 PRP38_C
     IPR005037 PRP38

    Graphical View of Domain Structure for InterPro Entry Q8NAV1

    ProtoNet protein and cluster: Q8NAV1

    UniProtKB/Swiss-Prot: PR38A_HUMAN, Q8NAV1
    Similarity: Belongs to the PRP38 family


    PRPF38A 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,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PR38A_HUMAN, Q8NAV1
    Function: May be required for pre-mRNA splicing (Potential)

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI--
         
    PRPF38A for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for PRPF38A:
     G2 arrest  Increased G2M DNA content 

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for PRPF38A 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for PRPF38A

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for PRPF38A 
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    miRTarBase miRNAs that target PRPF38A:
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    8/16 QIAGEN miScript miRNA Assays for microRNAs that regulate PRPF38A (see all 16):
    hsa-miR-15a hsa-miR-1257 hsa-miR-500a hsa-miR-3692 hsa-miR-424 hsa-miR-661 hsa-miR-1323 hsa-miR-195
    SwitchGear 3'UTR luciferase reporter plasmidPRPF38A 3' UTR sequence
    Inhib. RNA
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    (Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for PRPF38A About                                                                                                See pathways by source

    SuperPathContained pathways About
    1mRNA Splicing - Major Pathway
    Spliceosome0.31

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways



    1         Kegg Pathway  (Kegg details for PRPF38A):
        Spliceosome


    PRPF38A for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PRPF38A

    STRING Interaction Network Preview (showing 5 interactants - click image to see 15)

    5/19 Interacting proteins for PRPF38A (Q8NAV12, 3 ENSP000002571814) via UniProtKB, MINT, STRING, and/or I2D (see all 19)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    POLA2Q141812, 3MINT-65221 I2D: score=5 
    MAPK6Q166592, 3MINT-8261747 I2D: score=2 
    GTF3C1Q127892, 3, ENSP000003485104MINT-65220 I2D: score=5 STRING: ENSP00000348510
    PPIGQ134272, ENSP000002609704MINT-8336650 STRING: ENSP00000260970
    RNPS1Q152872, ENSP000003158594MINT-8336639 STRING: ENSP00000315859
    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:0006397mRNA processing IEA--
    GO:0008380RNA splicing IEA--

    PRPF38A for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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 PRPF38A (PR38A)

    Search CenterWatch for drugs/clinical trials and news about PRPF38A / PR38A

    (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,
    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, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for PRPF38A gene (2 alternative transcripts): 
    NM_032284.2  NM_032864.3  

    Unigene Cluster for PRPF38A:

    PRP38 pre-mRNA processing factor 38 (yeast) domain containing A
    Hs.5301  [show with all ESTs]
    Unigene Representative Sequence: NM_032864
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000257181(uc001ctv.4 uc001ctw.4) ENST00000487160 ENST00000474048

    miRNA
    Products:
         
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat PRPF38A
    8/16 QIAGEN miScript miRNA Assays for microRNAs that regulate PRPF38A (see all 16):
    hsa-miR-15a hsa-miR-1257 hsa-miR-500a hsa-miR-3692 hsa-miR-424 hsa-miR-661 hsa-miR-1323 hsa-miR-195
    SwitchGear 3'UTR luciferase reporter plasmidPRPF38A 3' UTR sequence
    Inhib. RNA
    Products:
         
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat PRPF38A
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat PRPF38A

    Additional mRNA sequence: 

    AK027842.1 AK092038.1 AK315621.1 BC000777.2 BC063655.1 BC105004.1 BC105006.1 

    8 DOTS entries:

    DT.95271536  DT.95107639  DT.95271537  DT.121336855  DT.92011978  DT.121280878  DT.75168164  DT.91652210 

    24/132 AceView cDNA sequences (see all 132):

    AX747327 BE313907 BE857095 AA255726 BX327847 BE646153 BF438551 CR607179 
    BC000777 NM_032284 BF197221 BM751076 AA255731 AA825904 AI421240 AA262655 
    BC063655 AI422906 AA354564 BU615655 BE672914 BE312273 BE326913 CB122845 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for PRPF38A    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b
    SP1:                    -                             -                                                   
    SP2:                                -     -     -     -     -                                             
    SP3:                                                                                                      
    SP4:                    -                                                                                 


    ECgene alternative splicing isoforms for PRPF38A

    (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

    PRPF38A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCCTCCTGTG
    PRPF38A Expression
    About this image


    See PRPF38A Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PRPF38A

    SOURCE GeneReport for Unigene cluster: Hs.5301
        SABiosciences Custom PCR Arrays for PRPF38A
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PRPF38A

    (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 eukaryotes.

    Orthologs for PRPF38A gene from 9/23 species (see all 23)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Prpf38a1 , 5 PRP38 pre-mRNA processing factor 38 (yeast) domain more1, 5 88.46(n)1
    98.72(a)1
      4 (50.64 cM)5
    2305961  NM_172697.31  NP_766285.21 
     1085631725 
    chicken
    (Gallus gallus)
    Aves PRPF38A1 PRP38 pre-mRNA processing factor 38 (yeast) domain more 79.59(n)
    97.76(a)
      771795  XM_001234244.2  XP_001234245.1 
    lizard
    (Anolis carolinensis)
    Reptilia PRPF38A6
    Uncharacterized protein
    96(a)
    1 ↔ 1
    4(114575187-114580026)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.18232 Xenopus laevis transcribed sequence with moderate similarity more 76.02(n)    CA973499.1 
    zebrafish
    (Danio rerio)
    Actinopterygii 570529392   -- 75.39(n)   334840  57052939 
    fruit fly
    (Drosophila melanogaster)
    Insecta Prp381 pre-mRNA processing factor 38 58.33(n)
    59.67(a)
      35934  NM_136619.2  NP_610463.2 
    worm
    (Caenorhabditis elegans)
    Secernentea CELE_D1054.141 Protein D1054.14 51.18(n)
    53.2(a)
      179499  NM_073361.2  NP_505762.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT2G406501 pre-mRNA-splicing factor 38A 52.9(n)
    51.94(a)
      818660  NM_129627.2  NP_565937.1 
    rice
    (Oryza sativa)
    Liliopsida Os.68132 Oryza sativa (japonica cultivar-group) cDNA clone0 more 73.4(n)    AK064099.1 


    ENSEMBL Gene Tree for PRPF38A (if available)
    TreeFam Gene Tree for PRPF38A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PRPF38A gene

    PRPF38A for paralogs           About GeneDecksing


    3 Pseudogenes.org Pseudogenes for PRPF38A
    PGOHUM00000238671 PGOHUM00000238679 PGOHUM00000260557


    (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) 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

    10/247 SNPs in PRPF38A are shown (see all 247)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1494148501,2
    C--52872210(+) TGGAG-/AGGTTA 1 -- int10--------
    rs1414586291,2
    --52872365(+) CTCGAC/GGAAAT 1 -- int10--------
    rs726668221,2
    --52872501(+) AGGAAA/GCTGAG 1 -- int10--------
    rs1474928871,2
    --52872566(+) TGGCTG/TCAGAG 1 -- int10--------
    rs1399987441,2
    --52872627(+) TTTCAA/GAAGCC 1 -- int10--------
    rs1829509411,2
    --52872637(+) CTCCTA/GGTTAC 1 -- int10--------
    rs1149945431,2
    F--52872695(+) CAACTC/GTTTTT 1 -- int11Minor allele frequency- G:0.04WA 118
    rs1437829081,2
    C--52872750(+) AGTGGC/TGCAGT 1 -- int10--------
    rs617825461,2
    C,F--52872758(+) AGTCTT/CGGCTC 1 -- int11Minor allele frequency- C:0.00NA 2
    rs1860298231,2
    --52872829(+) GGACTA/GCAGGC 1 -- int10--------

    HapMap Linkage Disequilibrium report for PRPF38A (52870219 - 52886511 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for PRPF38A: --
    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing PRPF38A
    DNA2.0 Custom Variant and Variant Library Synthesis for PRPF38A

    (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.)
    About This Section
      --

    (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 PRPF38A gene, integrated from 9 sources (see all 24):
    (articles sorted by number of sources associating them with PRPF38A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (2002)
    3. A Y2H-seq approach defines the human protein methyltransferase interactome. (PubMed id 23455924)1 Weimann M.... Stelzl U. (2013)
    4. Dynamic protein-protein interaction wiring of the huma n spliceosome. (PubMed id 22365833)1 Hegele A....Stelzl U. (2012)
    5. A bead-based approach for large-scale identification o f in vitro kinase substrates. (PubMed id 22113938)1 Zhang M....Zou H. (2011)
    6. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    7. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    8. A directed protein interaction network for investigat ing intracellular signal transduction. (PubMed id 21900206)1 Vinayagam A....Wanker E.E. (2011)
    9. The Brd4 extraterminal domain confers transcription a ctivation independent of pTEFb by recruiting multiple proteins, including NSD3. (PubMed id 21555454)1 Rahman S....Howley P.M. (2011)
    10. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (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)
    About This Section
    Entrez Gene: 84950 HGNC: 25930 AceView: FLJ14936 Ensembl:ENSG00000134748 euGenes: HUgn84950
    ECgene: PRPF38A Kegg: 84950 H-InvDB: PRPF38A

    (According to HUGE)
    About This Section
      --

    (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 PRPF38A Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for PRPF38A gene:
    Search GeneIP for patents involving PRPF38A

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



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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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