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RPP38 Gene

protein-coding   GIFtS: 57
GCID: GC10P015140

Ribonuclease P/MRP 38kDa Subunit

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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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This gene clusters with an RNA gene
Subcategory (RNA class): antisense

Quality score for the ORGUL clustered with this gene is 3

Aliases
Ribonuclease P/MRP 38kDa Subunit1 2
RNaseP Protein P382 3
Ribonuclease P Protein Subunit P382
EC 3.1.26.53

External Ids:    HGNC: 303291   Entrez Gene: 105572   Ensembl: ENSG000001524647   OMIM: 6061165   UniProtKB: P783453   
ORGUL members:         

Export aliases for RPP38 gene to outside databases

Previous GC identifers: GC10P015121 GC10P015289 GC10P015143 GC10P015179 GC10P015050


(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 RPP38 Gene:
RPP38 (ribonuclease P/MRP 38kDa subunit) is a protein-coding gene. GO annotations related to this gene include ribonuclease P activity.

UniProtKB/Swiss-Prot: RPP38_HUMAN, P78345
Function: Component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their
5'-ends. RPP38 may associate transiently with RNase P RNA as a factor involved in the transport of H1 RNA to the
putative site of its assembly in the cell, the nucleolus

Gene Wiki entry for RPP38 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_000010.10  NT_008705.17  NC_018921.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the RPP38 gene promoter:
         p53   Pax-6   ATF-2   CUTL1   NF-kappaB   Evi-1   CRE-BP1   Egr-2   NRF-2   LyF-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRPP38 promoter sequence
   Search Chromatin IP Primers for RPP38

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RPP38


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

Entrez Gene cytogenetic band: 10p13   Ensembl cytogenetic band:  10p13   HGNC cytogenetic band: 10p13

RPP38 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RPP38 gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10P015140:  view genomic region     (about GC identifiers)

Start:
15,139,179 bp from pter      End:
15,181,817 bp from pter
Size:
42,639 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, 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: RPP38_HUMAN, P78345 (See protein sequence)
Recommended Name: Ribonuclease P protein subunit p38  
Size: 283 amino acids; 31834 Da
Subunit: RNase P consists of an RNA moiety and at least 8 protein subunits; POP1, RPP14, RPP20/POP7, RPP25,
RPP29/POP4, RPP30, RPP38 and RPP40. RPP38 is probably a dimer
Miscellaneous: Autoantibodies against RPP38 are found in sera from scleroderma patients
Secondary accessions: B3KPY0 D3DRT8 Q53F71 Q8NHS8

Explore the universe of human proteins at neXtProt for RPP38: NX_P78345

Explore proteomics data for RPP38 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See RPP38 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (4 alternative transcripts): 
    NP_001091059.1  NP_001252530.1  NP_006405.2  NP_892117.1  

    ENSEMBL proteins: 
     ENSP00000367445   ENSP00000367443   ENSP00000367444   ENSP00000367439   ENSP00000402635  

    RPP38 Human Recombinant Protein Products:

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    antibodies-online proteins for RPP38 (4 products) 

     
    antibodies-online peptides for RPP38

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    antibodies-online antibodies for RPP38 (14 products) 

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    antibodies-online kits for RPP38 (6 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR004038 Ribosomal_L7Ae/L30e/S12e/Gad45

    Graphical View of Domain Structure for InterPro Entry P78345

    ProtoNet protein and cluster: P78345

    1 Blocks protein domain: IPB004038 Ribosomal protein L7Ae/L30e/S12e/Gadd45

    UniProtKB/Swiss-Prot: RPP38_HUMAN, P78345
    Similarity: Belongs to the ribosomal protein L7Ae family


    Find genes that share domains with RPP38           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: RPP38_HUMAN, P78345
    Function: Component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their
    5'-ends. RPP38 may associate transiently with RNase P RNA as a factor involved in the transport of H1 RNA to the
    putative site of its assembly in the cell, the nucleolus
    Catalytic activity: Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor

         Enzyme Number (IUBMB): EC 3.1.26.51

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004526ribonuclease P activity IEA--
    GO:0005515protein binding IPI15096576
         
    Find genes that share ontologies with RPP38           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for RPP38:
     Synthetic lethal with Ras 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for RPP38

    miRNA
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    miRTarBase miRNAs that target RPP38:
    hsa-let-7b-5p (MIRT001597)

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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
    RPP38_HUMAN, P78345: Nucleus, nucleolus (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus4
    mitochondrion2
    cytosol1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus TAS9630247
    GO:0005655nucleolar ribonuclease P complex TAS9630247

    Find genes that share ontologies with RPP38           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 RPP38 About    
    See pathways by source

    SuperPathContained pathways About
    1RNA transport
    RNA transport
    2Ribosome biogenesis in eukaryotes
    Ribosome biogenesis in eukaryotes
    3Integrated Breast Cancer Pathway
    Integrated Breast Cancer Pathway


    Find genes that share SuperPaths with RPP38           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 BioSystems Pathway for RPP38
        Integrated Breast Cancer Pathway


    2 Kegg Pathways  (Kegg details for RPP38):
        Ribosome biogenesis in eukaryotes
    RNA transport

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RPP38
    Interactions:

        GeneGlobe Interaction Network for RPP38

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

    Selected Interacting proteins for RPP38 (P783451, 3 ENSP000003674394) via UniProtKB, MINT, STRING, and/or I2D (see all 56)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RPP21Q9H6333, ENSP000004038334I2D: score=1 STRING: ENSP00000403833
    ENSG00000239865Q9H6333I2D: score=1 
    ENSG00000239927Q9H6333I2D: score=1 
    ENSG00000241779Q9H6333I2D: score=1 
    ENSG00000241863Q9H6333I2D: score=1 
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008033tRNA processing IEA--
    GO:0090501RNA phosphodiester bond hydrolysis TAS9630247
    GO:0090502RNA phosphodiester bond hydrolysis, endonucleolytic TAS9630247

    Find genes that share ontologies with RPP38           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 RPP38



    (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 RPP38 gene (4 alternative transcripts): 
    NM_001097590.2  NM_001265601.1  NM_006414.4  NM_183005.4  

    Unigene Cluster for RPP38:

    Ribonuclease P/MRP 38kDa subunit
    Hs.94986  [show with all ESTs]
    Unigene Representative Sequence: NM_183005
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000378203(uc009xjm.3 uc001inx.4) ENST00000378201 ENST00000451677
    ENST00000378202 ENST00000378197(uc001iny.4) ENST00000441850
    miRNA
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      QuantiTect SYBR Green Assays in human, mouse, rat RPP38
      QuantiFast Probe-based Assays in human, mouse, rat RPP38

    Additional mRNA sequence: 

    AF079567.1 AK057006.1 AK223418.1 BC029494.1 CR541816.1 U77664.1 

    6 DOTS entries:

    DT.100008423  DT.309451  DT.99943905  DT.100648588  DT.121229568  DT.121229585 

    Selected AceView cDNA sequences (see all 80):

    BU180901 AW292674 AI638697 AW611895 BF222678 CA414693 AI433471 BE671046 
    BU616848 CR600741 AI434778 BM969850 AK057006 BU753917 BU521322 BM726307 
    NM_183005 CD050516 W94590 BX326988 BM680914 BM975685 AW002537 NM_006414 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for RPP38 (see all 6)    About this scheme

    ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b ^ 3 ^ 4
    SP1:                                -     -               
    SP2:                          -     -     -               
    SP3:                                      -               
    SP4:                                -     -     -         
    SP5:                                                      


    ECgene alternative splicing isoforms for RPP38

    (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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    RPP38 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TCATACAGTT
    RPP38 Expression
    About this image

    RPP38 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RPP38 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.94986
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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 chordates.

    Orthologs for RPP38 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rpp381 , 5 ribonuclease P/MRP 38 subunit (human)5
    ribonuclease P/MRP 38 subunit1
    79.62(n)1
    77.7(a)1
      2 (1.87 cM)5
    2275221  NM_001013376.21  NP_001013394.21 
     33289495 
    chicken
    (Gallus gallus)
    Aves RPP381 ribonuclease P/MRP 38kDa subunit 59.06(n)
    54.37(a)
      420530  NM_001199590.1  NP_001186519.1 
    African clawed frog
    (Xenopus laevis)
    Amphibia CA793682.12   -- 71.61(n)    CA793682.1 
    zebrafish
    (Danio rerio)
    Actinopterygii rpp381 ribonuclease P/MRP 38 subunit 50.46(n)
    49.4(a)
      436798  NM_001002525.2  NP_001002525.2 


    ENSEMBL Gene Tree for RPP38 (if available)
    TreeFam Gene Tree for RPP38 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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      --

    (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 RPP38 (see all 180)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 10 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs751970341,2
    C,F--15141446(+) GGCAAC/GAAAGC 4 -- int13Minor allele frequency- G:0.05WA NA EA 358
    rs1145424721,2
    F--15141524(+) GCTGGA/CGCACA 4 -- int11Minor allele frequency- C:0.05WA 118
    rs78977801,2
    C,F,A--15141845(+) agctaT/Ctcagc 4 -- int18Minor allele frequency- C:0.27WA CSA NA EA 366
    rs78977811,2
    C,F,A--15141852(+) cagcaT/Ggaggc 4 -- int12Minor allele frequency- G:0.06WA NA 238
    rs1843357271,2
    --15141871(+) GAGGAC/TTGCTT 4 -- int10--------
    rs1148058991,2
    F--15141874(+) GATTGC/TTTGAA 4 -- int11Minor allele frequency- T:0.01WA 118
    rs1165821421,2
    F--15141902(+) GCAGTG/AAGCCA 4 -- int11Minor allele frequency- A:0.03WA 118
    rs1886869001,2
    --15141912(+) ATGATC/TGAACG 4 -- int10--------
    rs1916401021,2
    --15141917(+) CGAACA/GACTGC 4 -- int10--------
    rs1387870141,2
    --15141963(+) AAAAGA/TGTTTG 4 -- int10--------

    HapMap Linkage Disequilibrium report for RPP38 (15139179 - 15181817 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for RPP38:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv831794CNV Loss17160897
    nsv894899CNV Gain21882294
    dgv618n71CNV Gain21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing RPP38
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 606116    OMIM disorders: --


    Find genes that share disorders with RPP38           About GenesLikeMe

    Genetic Association Database (GAD): RPP38
    Human Genome Epidemiology (HuGE) Navigator: RPP38 (1 document)

    Export disorders for RPP38 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 RPP38 gene, integrated from 10 sources (see all 32):
    (articles sorted by number of sources associating them with RPP38)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Characterization of two scleroderma autoimmune antigens that copurify with human ribonuclease P. (PubMed id 9037013)1, 2, 3, 9 Eder P.S.... Altman S. (Proc. Natl. Acad. Sci. U.S.A. 1997)
    2. Autoantigenic properties of some protein subunits of catalytically active complexes of human ribonuclease P. (PubMed id 9630247)1, 3, 9 Jarrous N.... Altman S. (RNA 1998)
    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. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    5. 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)
    6. The DNA sequence and comparative analysis of human chromosome 10. (PubMed id 15164054)1, 2 Deloukas P.... Rogers J. (Nature 2004)
    7. Localization in the nucleolus and coiled bodies of protein subunits of the ribonucleoprotein ribonuclease P. (PubMed id 10444065)1, 9 Jarrous N....Altman S. (J. Cell Biol. 1999)
    8. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    9. A high-throughput approach for measuring temporal changes in the interactome. (PubMed id 22863883)1 Kristensen A.R....Foster L.J. (Nat. Methods 2012)
    10. 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)

    (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: 10557 HGNC: 30329 AceView: RPP38 Ensembl:ENSG00000152464 euGenes: HUgn10557
    ECgene: RPP38 Kegg: 10557 H-InvDB: RPP38

    (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 RPP38 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 RPP38 gene:
    Search GeneIP for patents involving RPP38

    GeneCards and IP:
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