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RPP25L Gene

protein-coding   GIFtS: 44
GCID: GC09M034610

Ribonuclease P/MRP 25kDa Subunit-Like

(Previous name: chromosome 9 open reading frame 23)
(Previous symbol: C9orf23)
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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
Ribonuclease P/MRP 25kDa Subunit-Like1 2     Chromosome 9 Open Reading Frame 231
C9orf231 2 3     Alba-Like Protein C9orf232
Rpp25-Like Protein2 3     bA296L22.52
RNase P Protein Subunit-Like P252 3     Ribonuclease P Protein Subunit P25-Like Protein2

External Ids:    HGNC: 199091   Entrez Gene: 1387162   Ensembl: ENSG000001649677   UniProtKB: Q8N5L83   

Export aliases for RPP25L gene to outside databases


(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 RPP25L Gene:
This gene encodes a protein that appears to belong to a family of evolutionarily related proteins (DUF78), that
may share one or more domains in common. Members of this family are small archaebacterial proteins with no known
function. Alternative splicing has been observed at this locus and two variants, both encoding the same protein,
have been identified. (provided by RefSeq, Jul 2008)

GeneCards Summary for RPP25L Gene:
RPP25L (ribonuclease P/MRP 25kDa subunit-like) is a protein-coding gene. GO annotations related to this gene include nucleic acid binding. An important paralog of this gene is RPP25.

UniProtKB/Swiss-Prot: RP25L_HUMAN, Q8N5L8
Function: May be a component of ribonuclease P or MRP




(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_000009.11  NC_018920.2  NT_008413.19  
Regulatory elements:
   Search for regulatory transcription factor binding sites for RPP25L
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for RPP25L

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RPP25L


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

Entrez Gene cytogenetic band: 9p13.3   Ensembl cytogenetic band:  9p13.3   HGNC cytogenetic band: 9p11.2

RPP25L Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RPP25L gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09M034610:  view genomic region     (about GC identifiers)

Start:
34,610,483 bp from pter      End:
34,612,101 bp from pter
Size:
1,619 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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: RP25L_HUMAN, Q8N5L8 (See protein sequence)
Recommended Name: Ribonuclease P protein subunit p25-like protein  
Size: 163 amino acids; 17631 Da
Secondary accessions: D3DRM5

Explore the universe of human proteins at neXtProt for RPP25L: NX_Q8N5L8

Explore proteomics data for RPP25L at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys86
  • Modification sites at PhosphoSitePlus

  • See RPP25L Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_680544.1  NP_680545.1  

    ENSEMBL proteins: 
     ENSP00000368242   ENSP00000297613  

    RPP25L Human Recombinant Protein Products:

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    Novus Biologicals RPP25L Lysates
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    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp.

     
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    Search eBioscience for ELISAs for RPP25L 


    (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:
     IPR002775 DNA/RNA-bd_Alba-like

    Graphical View of Domain Structure for InterPro Entry Q8N5L8

    ProtoNet protein and cluster: Q8N5L8

    1 Blocks protein domain: IPB002775 Alba

    UniProtKB/Swiss-Prot: RP25L_HUMAN, Q8N5L8
    Similarity: Belongs to the histone-like Alba family


    Find genes that share domains with RPP25L           About GenesLikeMe


    (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, 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: RP25L_HUMAN, Q8N5L8
    Function: May be a component of ribonuclease P or MRP

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding ----
    GO:0044822poly(A) RNA binding IDA--
         
    Find genes that share ontologies with RPP25L           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for RPP25L:
     Metaphase cells  Synthetic lethal with Ras 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for RPP25L
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       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for RPP25L

    miRNA
    Products:
        
    miRTarBase miRNAs that target RPP25L:
    hsa-mir-423-3p (MIRT042603), hsa-mir-27a-3p (MIRT028698), hsa-mir-124-3p (MIRT022708)

    Block miRNA regulation of human, mouse, rat RPP25L using miScript Target Protectors
    Search for qRT-PCR Assays for microRNAs that regulate RPP25L
    SwitchGear 3'UTR luciferase reporter plasmidRPP25L 3' UTR sequence
    Inhib. RNA
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    Browse Sino Biological Human cDNA Clones
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RPP25L


    (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
    RP25L_HUMAN, Q8N5L8: Nucleus (Probable)

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

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

    Find genes that share ontologies with RPP25L           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 RPP25L About    
    See pathways by source

    SuperPathContained pathways About
    1RNA transport
    RNA transport
    2Ribosome biogenesis in eukaryotes
    Ribosome biogenesis in eukaryotes


    Find genes that share SuperPaths with RPP25L           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways



    2 Kegg Pathways  (Kegg details for RPP25L):
        Ribosome biogenesis in eukaryotes
    RNA transport

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RPP25L
    Interactions:

        Search GeneGlobe Interaction Network for RPP25L

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    4 Interacting proteins for RPP25L (ENSP000002976134) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    EIF4EBP2ENSP000003623144STRING: ENSP00000362314
    EIF4EBP1ENSP000003406914STRING: ENSP00000340691
    UBCENSP000003448184STRING: ENSP00000344818
    TMEM203ENSP000003750534STRING: ENSP00000375053
    About this table

    (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 RPP25L (RP25L)



    (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 RPP25L gene (2 alternative transcripts): 
    NM_148178.2  NM_148179.2  

    Unigene Cluster for RPP25L:

    Ribonuclease P/MRP 25kDa subunit-like
    Hs.15961  [show with all ESTs]
    Unigene Representative Sequence: BM467200
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000378959(uc003zuv.3) ENST00000297613(uc003zuu.3)
    miRNA
    Products:
         
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    Search for qRT-PCR Assays for microRNAs that regulate RPP25L
    SwitchGear 3'UTR luciferase reporter plasmidRPP25L 3' UTR sequence
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for RPP25L
    Predesigned siRNA for gene silencing in human, mouse, rat RPP25L
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    Primer
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    OriGene qPCR primer pairs and template standards for RPP25L
    OriGene qSTAR qPCR primer pairs in human, mouse for RPP25L
    Search Pre-validated RT2 qPCR Primer Assays in human, mouse, rat RPP25L
      QuantiTect SYBR Green Assays in human, mouse, rat RPP25L
      QuantiFast Probe-based Assays in human, mouse, rat RPP25L

    Additional mRNA sequence: BC032136.2 

    3 DOTS entries:

    DT.75169832  DT.95272960  DT.86842596 

    Selected AceView cDNA sequences (see all 163):

    BU076428 BQ643214 AI419408 AA745778 CB117372 BU785062 BU684655 AA576695 
    BQ224958 AI761638 AA469996 AW131911 AI362001 BU732092 BI768478 CR619309 
    NM_148178 AW469200 NM_148179 CA433799 BQ070451 BU737577 BU785328 BU076706 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for RPP25L    About this scheme

    ExUns: 1a · 1b · 1c ^ 2a · 2b
    SP1:              -               
    SP2:                              


    ECgene alternative splicing isoforms for RPP25L

    (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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    RPP25L expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGGGAAGGGA
    RPP25L Expression
    About this image

    RPP25L Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RPP25L Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.15961
        Custom PCR Arrays for RPP25L
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RPP25L

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for RPP25L gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rpp25l1 , 5 RIKEN cDNA 2810432D09 gene5
    ribonuclease P/MRP 25 subunit-like1
    84.87(n)1
    94.74(a)1
      4 (21.97 cM)5
    699611  NM_027278.31  NP_081554.21 
     417120335 
    chicken
    (Gallus gallus)
    Aves C9ORF231 chromosome Z open reading frame, human C9orf23 59.66(n)
    55.07(a)
      427403  XM_424977.3  XP_424977.1 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    46(a)
    many ↔ many
    GL343482.1(124599-125093)
    zebrafish
    (Danio rerio)
    Actinopterygii rpp25l1 ribonuclease P/MRP 25 subunit-like 59.42(n)
    57.97(a)
      436813  NM_001002540.1  NP_001002540.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG94221 CG9422 49.38(n)
    40.74(a)
      35574  NM_165484.3  NP_724490.1 


    ENSEMBL Gene Tree for RPP25L (if available)
    TreeFam Gene Tree for RPP25L (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for RPP25L gene
    RPP252  
    1 SIMAP similar gene for RPP25L using alignment to 1 protein entry:     RP25L_HUMAN:
    RPP25

    Find genes that share paralogs with RPP25L           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)
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    Selected SNPs for RPP25L (see all 70)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1410222591,2
    --34610078(+) CTTATA/GTAATC 2 -- int10--------
    rs790764881,2
    C,F--34610234(+) TATACT/AATACT 2 -- int11Minor allele frequency- A:0.02WA 118
    rs1874381711,2
    --34610254(+) AGATGC/GAGAGA 2 -- int10--------
    rs1918474961,2
    --34610275(+) CTGGCA/C/TGTGTT 2 -- int10--------
    rs1448176131,2
    --34610298(+) CAAAGC/TAGGGG 2 -- int10--------
    rs748302021,2
    F--34610317(+) TATCCA/GGGGAA 2 -- int11Minor allele frequency- G:0.03WA 118
    rs70321271,2
    C,F,A,H--34610330(+) AGATAT/CATTCA 2 -- int111Minor allele frequency- C:0.08NS EA NA CSA WA 1211
    rs1141155471,2
    F--34610375(+) TCCCAG/CCACCG 2 -- int11Minor allele frequency- C:0.02WA 118
    rs1116647141,2
    C,F--34610554(+) GTTCAG/AATGCA 2 -- ut312Minor allele frequency- A:0.50CSA 4
    rs1399648471,2
    C--34610566(+) TGTAGA/GTAGAA 2 -- ut310--------

    HapMap Linkage Disequilibrium report for RPP25L (34610483 - 34612101 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for RPP25L: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing RPP25L
    DNA2.0 Custom Variant and Variant Library Synthesis for RPP25L

    (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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      --

    (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 RPP25L gene integrated from 10 sources:
    (articles sorted by number of sources associating them with RPP25L)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes. (PubMed id 16998185)1, 2, 3 Rosenblad M.A.... Samuelsson T. (Nucleic Acids Res. 2006)
    2. 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)
    3. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)1, 2 Humphray S.J.... Dunham I. (Nature 2004)
    4. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    5. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)
    6. 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)
    7. Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. (PubMed id 21145461)1 Bennett E.J....Harper J.W. (Cell 2010)
    8. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (Genomics 2007)
    9. Identification of genes related to Parkinson's disease using expressed sequence tags. (PubMed id 17213182)1 Kim J.M.... Kim N.S. (DNA Res. 2006)
    10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    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: 138716 HGNC: 19909 AceView: C9orf23 Ensembl:ENSG00000164967 euGenes: HUgn138716
    ECgene: RPP25L Kegg: 138716 H-InvDB: RPP25L

    (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 RPP25L 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 RPP25L gene:
    Search GeneIP for patents involving RPP25L

    GeneCards and IP:
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