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RRP1 Gene

protein-coding   GIFtS: 53
GCID: GC21P045209

Ribosomal RNA Processing 1

(Previous name: ribosomal RNA processing 1 homolog (S. cerevisiae))
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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
Ribosomal RNA Processing 11 2     Nnp1 Homolog1
Novel Nuclear Protein 12 3     Nucleolar Protein (Drosophila)1
Nucleolar Protein Nop522 3     Ribosomal RNA Processing 1 Homolog (S. Cerevisiae)1
D21S2056E2 3     Nnp1 Homolog, Nucleolar Protein2
NNP-12 3     Protein NNP-12
NOP522 3     Ribosomal RNA Processing 1 Homolog2
RRP1A2 3     Ribosomal RNA Processing Protein 1 Homolog A2
RRP1-Like Protein2 3     NNP13
DNA Segment On Chromosome 21 (Unique) 2056 Expressed Sequence1     

External Ids:    HGNC: 187851   Entrez Gene: 85682   Ensembl: ENSG000001602147   OMIM: 6106535   UniProtKB: P561823   

Export aliases for RRP1 gene to outside databases

Previous GC identifers: GC21P044035 GC21P030577


(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 RRP1 Gene:
The protein encoded by this gene is the putative homolog of the yeast ribosomal RNA processing protein RRP1. The
encoded protein is involved in the late stages of nucleologenesis at the end of mitosis, and may be required for
the generation of 28S rRNA. (provided by RefSeq, Jul 2008)

GeneCards Summary for RRP1 Gene:
RRP1 (ribosomal RNA processing 1) is a protein-coding gene. An important paralog of this gene is RRP1B.

UniProtKB/Swiss-Prot: RRP1_HUMAN, P56182
Function: Plays a critical role in the generation of 28S rRNA

Gene Wiki entry for RRP1 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_000021.8  NC_018932.2  NT_011512.12  
Regulatory elements:
   Regulatory transcription factor binding sites in the RRP1 gene promoter:
         SRF   USF1   SRF (504 AA)   USF2   AP-4   USF-1:USF-2   Max   USF-1   ATF   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRRP1 promoter sequence
   Search Chromatin IP Primers for RRP1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RRP1


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

Entrez Gene cytogenetic band: 21q22.3   Ensembl cytogenetic band:  21q22.3   HGNC cytogenetic band: 21q22.3

RRP1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RRP1 gene location

GeneLoc information about chromosome 21         GeneLoc Exon Structure

GeneLoc location for GC21P045209:  view genomic region     (about GC identifiers)

Start:
45,209,394 bp from pter      End:
45,225,174 bp from pter
Size:
15,781 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: RRP1_HUMAN, P56182 (See protein sequence)
Recommended Name: Ribosomal RNA processing protein 1 homolog A  
Size: 461 amino acids; 52839 Da
Subunit: Interacts with C1QBP
Secondary accessions: Q9NST5

Explore the universe of human proteins at neXtProt for RRP1: NX_P56182

Explore proteomics data for RRP1 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See RRP1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_003674.1  
    ENSEMBL proteins: 
     ENSP00000417464   ENSP00000426898  

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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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    1 InterPro protein domain:
     IPR010301 Nop52

    Graphical View of Domain Structure for InterPro Entry P56182

    ProtoNet protein and cluster: P56182

    1 Blocks protein domain: IPB010301 Nucleolar

    UniProtKB/Swiss-Prot: RRP1_HUMAN, P56182
    Similarity: Belongs to the RRP1 family


    Find genes that share domains with RRP1           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: RRP1_HUMAN, P56182
    Function: Plays a critical role in the generation of 28S rRNA

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0044822poly(A) RNA binding IDA--
         
    Find genes that share ontologies with RRP1           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for RRP1

    miRNA
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    miRTarBase miRNAs that target RRP1:
    hsa-mir-423-3p (MIRT042587), hsa-mir-615-3p (MIRT040457), hsa-mir-149-5p (MIRT045681), hsa-mir-92b-3p (MIRT040667)

    Block miRNA regulation of human, mouse, rat RRP1 using miScript Target Protectors
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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
    RRP1_HUMAN, P56182: Nucleus, nucleolus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2
    golgi apparatus1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus TAS9192856
    GO:0005730nucleolus IDA--
    GO:0030688preribosome, small subunit precursor IEA--

    Find genes that share ontologies with RRP1           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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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RRP1
    Interactions:

        Search GeneGlobe Interaction Network for RRP1

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

    Selected Interacting proteins for RRP1 (P561823 ENSP000004174644) via UniProtKB, MINT, STRING, and/or I2D (see all 155)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ESR2Q927313, ENSP000003439254I2D: score=1 STRING: ENSP00000343925
    GABARAPO951663I2D: score=1 
    MAP1LC3AQ9H4923I2D: score=1 
    RRP1BENSP000003391454STRING: ENSP00000339145
    BRIX1ENSP000003388624STRING: ENSP00000338862
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006364rRNA processing IEA--

    Find genes that share ontologies with RRP1           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 RRP1



    (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 RRP1 gene: 
    NM_003683.5  

    Unigene Cluster for RRP1:

    Ribosomal RNA processing 1 homolog (S. cerevisiae)
    Hs.110757  [show with all ESTs]
    Unigene Representative Sequence: BC000380
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000475534 ENST00000497547(uc011aez.1 uc002zds.2) ENST00000483896
    ENST00000492638 ENST00000473988 ENST00000467112(uc010gpl.1) ENST00000471909(uc010gpm.1)

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      QuantiTect SYBR Green Assays in human, mouse, rat RRP1
      QuantiFast Probe-based Assays in human, mouse, rat RRP1

    Additional mRNA sequence: 

    AK223185.1 AK223215.1 AK303000.1 AK313116.1 BC000380.2 BC014787.1 U79775.1 

    17 DOTS entries:

    DT.312327  DT.100794745  DT.100794748  DT.121139128  DT.40203772  DT.100794744  DT.92436490  DT.450248 
    DT.95311650  DT.121139140  DT.100667985  DT.100794741  DT.100794742  DT.121139139  DT.121139136  DT.91686845 
    DT.92443884 

    Selected AceView cDNA sequences (see all 204):

    BU158549 CR624766 CR603071 CR601038 BG403301 BQ439941 BP354134 BM468399 
    AI167158 BM811195 BM974024 BP339967 BU943979 BI223794 BU538262 CR594938 
    BM561572 BQ706649 BU535544 BE888594 BE796449 CB243970 CA388865 CB853658 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for RRP1 (see all 6)    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11a · 11b ^ 12 ^ 13
    SP1:                                                                    -                                             
    SP2:              -                                                     -                                             
    SP3:              -                                                     -                                             
    SP4:                                                                                                                  
    SP5:                                                                                                                  


    ECgene alternative splicing isoforms for RRP1

    (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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    RRP1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAGAGGAAGA
    RRP1 Expression
    About this image


    RRP1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Brain (Nervous System)    fully expand to see all 3 entries
             Cerebral Cortex
    RRP1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RRP1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.110757

    UniProtKB/Swiss-Prot: RRP1_HUMAN, P56182
    Tissue specificity: Ubiquitously expressed in fetal and adult tissues

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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 animals and fungi.

    Orthologs for RRP1 gene from Selected species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rrp15 ribosomal RNA processing 1 homolog (S. cerevisiae)   --   10 (39.72 cM) 78400362 
    chicken
    (Gallus gallus)
    Aves RRP1B6
    Gallus gallus ribosomal RNA processing 1 homolog B...
    28(a)
    1 → many
    1(109360240-109382258)
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    27(a)
    1 → many
    3(136735017-136765865)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.81752 Transcribed sequence with weak similarity to protein more 73.41(n)    141994033 
    zebrafish
    (Danio rerio)
    Actinopterygii rrp16
    ribosomal RNA processing 1 homolog (S. cerevisiae)...
    26(a)
    1 → many
    9(287537-296100) ENSDARG00000027515
    fruit fly
    (Drosophila melanogaster)
    Insecta Nnp-16
    Nnp-1
    15(a)
    1 → many
    2L(13363300-13366188)
    worm
    (Caenorhabditis elegans)
    Secernentea C47E12.71 C47E12.7 43.07(n)
    33.21(a)
      177853  NM_069397.5  NP_501798.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes RRP16
    Essential evolutionarily conserved nucleolar prote...
    25(a)
    1 → many
    IV(617470-618306) YDR087C


    ENSEMBL Gene Tree for RRP1 (if available)
    TreeFam Gene Tree for RRP1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for RRP1 gene
    RRP1B2  
    1 SIMAP similar gene for RRP1 using alignment to 3 protein entries:     RRP1_HUMAN (see all proteins):
    RRP1B

    Find genes that share paralogs with RRP1           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 RRP1 (see all 496)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 21 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2000614721,2
    C--30592001(+) CAGGGA/GAAGTG 1 -- ut310--------
    rs1448951851,2
    --45207423(+) GTTAAC/TATGAG 1 -- us2k10--------
    rs1387862671,2
    --45207430(+) TGAGGA/TCATGC 1 -- us2k10--------
    rs1404565271,2
    --45207623(+) AAACAC/GAAAAA 1 -- us2k10--------
    rs1504193091,2
    C--45207701(+) CAGCCC/TGGGCG 1 -- us2k10--------
    rs1129885561,2
    C--45207717(+) TGAAACT/-CTGTC 1 -- us2k11Minor allele frequency- -:0.00CSA 2
    rs1129947031,2
    C,F--45207845(+) GTGGCA/CGGATC 1 -- us2k12Minor allele frequency- C:0.00WA CSA 3
    rs1495958871,2
    C--45207908(+) CCTCCC/TGAGTA 1 -- us2k10--------
    rs124837061,2
    C,H--45208030(+) ccaccT/Cgcttt 1 -- us2k13Minor allele frequency- C:0.24NA CSA 124
    rs99849291,2
    C,F--45208097(+) CAACTT/GTTTAT 1 -- us2k11Minor allele frequency- G:0.09WA 118

    HapMap Linkage Disequilibrium report for RRP1 (45209394 - 45225174 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for RRP1 (see all 13):    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv509799CNV Insertion20534489
    nsv913885CNV Loss21882294
    nsv520305CNV Loss19592680
    nsv834108CNV Loss17160897
    nsv834107CNV Loss17160897
    nsv470904CNV Loss18288195
    nsv913882CNV Loss21882294
    esv33817CNV Loss17666407
    nsv522204CNV Loss19592680
    nsv913886CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing RRP1
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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: 610653    OMIM disorders: --


    Find genes that share disorders with RRP1           About GenesLikeMe

    Genetic Association Database (GAD): RRP1
    Human Genome Epidemiology (HuGE) Navigator: RRP1 (4 documents)

    Export disorders for RRP1 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 RRP1 gene, integrated from 10 sources (see all 27):
    (articles sorted by number of sources associating them with RRP1)
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    1. The nucleolar antigen Nop52, the human homologue of the yeast ribosomal RNA processing RRP1, is recruited at late stages of nucleologenesis. (PubMed id 10341208)1, 2, 3, 9 Savino T.M.... Hernandez-Verdun D. (J. Cell Sci. 1999)
    2. The DNA sequence of human chromosome 21. (PubMed id 10830953)1, 2, 3 Hattori M.... Yaspo M.-L. (Nature 2000)
    3. The NNP-1 gene (D21S2056E), which encodes a novel nuclear protein, maps in close proximity to the cystatin B gene within the EPM1 and APECED critical region on 21q22.3. (PubMed id 9192856)1, 2, 9 Jansen E.... Van de Ven W.J.M. (Genomics 1997)
    4. Splicing factor 2-associated protein p32 participates in ribosome biogenesis by regulating the binding of Nop52 and fibrillarin to preribosome particles. (PubMed id 21536856)1, 2 Yoshikawa H....Takahashi N. (Mol. Cell. Proteomics 2011)
    5. Transcriptomic and genetic studies identify IL-33 as a candidate gene for Alzheimer's disease. (PubMed id 19204726)1, 4 Chapuis J....Lambert J.C. (Mol. Psychiatry 2009)
    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. Functional proteomic analysis of human nucleolus. (PubMed id 12429849)1, 2 Scherl A.... Diaz J.-J. (Mol. Biol. Cell 2002)
    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. The P-body component USP52/PAN2 is a novel regulator of HIF1A mRNA stability. (PubMed id 23398456)1 Bett J.S....Hay R.T. (Biochem. J. 2013)
    10. Charting the landscape of tandem BRCT domain-mediated protein interactions. (PubMed id 22990118)1 Woods N.T....Monteiro A.N. (Sci Signal 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: 8568 HGNC: 18785 AceView: D21S2056E Ensembl:ENSG00000160214 euGenes: HUgn8568
    ECgene: RRP1 H-InvDB: RRP1

    (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 RRP1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    Patent Information for RRP1 gene:
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    GeneCards and IP:
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