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

RPRD2 Gene

protein-coding   GIFtS: 50
GCID: GC01P150335

Regulation Of Nuclear Pre-MRNA Domain Containing 2

(Previous name: KIAA0460)
(Previous symbol: KIAA0460)
  Search for RPRD2
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
Regulation Of Nuclear Pre-MRNA Domain Containing 21 2
KIAA04601 2 3
Regulation Of Nuclear Pre-MRNA Domain-Containing Protein 22

External Ids:    HGNC: 290391   Entrez Gene: 232482   Ensembl: ENSG000001631257   OMIM: 6146955   UniProtKB: Q5VT523   

Export aliases for RPRD2 gene to outside databases

Previous GC identifers: GC01P148604 GC01P121715


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

GeneCards Summary for RPRD2 Gene: 
RPRD2 (regulation of nuclear pre-mRNA domain containing 2) is a protein-coding gene. An important paralog of this gene is RPRD1B.

Gene Wiki entry for RPRD2 (KIAA0460) 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NT_004487.19  NC_018912.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RPRD2 gene promoter:
         HOXA9B   HOXA9   SRF   SRF (504 AA)   Meis-1b   YY1   c-Rel   E2F-1   E2F   Meis-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRPRD2 promoter sequence
   Search SABiosciences Chromatin IP Primers for RPRD2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RPRD2


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

Entrez Gene cytogenetic band: 1q21.3   Ensembl cytogenetic band:  1q21.3   HGNC cytogenetic band: 1q21.2

RPRD2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RPRD2 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P150335:  view genomic region     (about GC identifiers)

Start:
150,335,567 bp from pter      End:
150,449,042 bp from pter
Size:
113,476 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: RPRD2_HUMAN, Q5VT52 (See protein sequence)
Recommended Name: Regulation of nuclear pre-mRNA domain-containing protein 2  
Size: 1461 amino acids; 156020 Da
Subunit: Associates with the RNA polymerase II complex
Sequence caution: Sequence=AAF28922.1; Type=Erroneous initiation; Sequence=AAH45623.2; Type=Erroneous initiation;
1 PDB 3D structure from and Proteopedia for RPRD2:
4FLB (3D)    
Secondary accessions: A8K6N8 B3KPT1 O75048 Q5VT51 Q5VT53 Q6MZL4 Q86XD2 Q9P0D7
Alternative splicing: 4 isoforms:  Q5VT52-1   Q5VT52-2   Q5VT52-3   Q5VT52-4   (Gene prediction based on EST data)

Explore the universe of human proteins at neXtProt for RPRD2: NX_Q5VT52

Explore proteomics data for RPRD2 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q5VT52

  • RPRD2 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    RPRD2 Protein Expression
    REFSEQ proteins: NP_056018.2  
    ENSEMBL proteins: 
     ENSP00000383785   ENSP00000358063   ENSP00000358064   ENSP00000445482  

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    Cloud-Clone Corp. Proteins for RPRD2 

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016591DNA-directed RNA polymerase II, holoenzyme IDA--

    RPRD2 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
    3 InterPro protein domains:
     IPR006903 RNA_pol_II-bd
     IPR006569 CID_dom
     IPR008942 ENTH_VHS

    Graphical View of Domain Structure for InterPro Entry Q5VT52

    ProtoNet protein and cluster: Q5VT52

    1 Blocks protein domain: IPB006569 Regulation of nuclear pre-mRNA protein

    UniProtKB/Swiss-Prot: RPRD2_HUMAN, Q5VT52
    Similarity: Contains 1 CID domain


    RPRD2 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

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for RPRD2 
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for RPRD2 
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    SwitchGear 3'UTR luciferase reporter plasmidRPRD2 3' UTR sequence
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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



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RPRD2

    STRING Interaction Network Preview (showing 5 interactants - click image to see 7)

    5/8 Interacting proteins for RPRD2 (Q5VT522, 3 ENSP000003580644) via UniProtKB, MINT, STRING, and/or I2D (see all 8)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    WWOXQ9NZC72, 3, ENSP000003861614MINT-72777 I2D: score=3 STRING: ENSP00000386161
    UPF1Q929003, ENSP000002628034I2D: score=2 STRING: ENSP00000262803
    MYCP011063, ENSP000003672074I2D: score=1 STRING: ENSP00000367207
    MAP4K4O958193I2D: score=1 
    SUMO2ENSP000004059654STRING: ENSP00000405965
    About this table

    (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 RPRD2

    Search CenterWatch for drugs/clinical trials and news about RPRD2

    (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 RPRD2 gene: 
    NM_015203.3  

    Unigene Cluster for RPRD2:

    Regulation of nuclear pre-mRNA domain containing 2
    Hs.213666  [show with all ESTs]
    Unigene Representative Sequence: NM_015203
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000492220 ENST00000401000(uc010pcc.1 uc009wlr.3 uc001eup.4)
    ENST00000369067 ENST00000369068 ENST00000539519
    miRNA
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    8/68 QIAGEN miScript miRNA Assays for microRNAs that regulate RPRD2 (see all 68):
    hsa-miR-1321 hsa-miR-607 hsa-miR-15a hsa-miR-4305 hsa-miR-30d hsa-miR-219-5p hsa-miR-519a hsa-miR-3162-5p
    SwitchGear 3'UTR luciferase reporter plasmidRPRD2 3' UTR sequence
    Inhib. RNA
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    Additional mRNA sequence: 

    AB007929.2 AF161362.1 AK022984.1 AK026120.1 AK056707.1 AK125864.1 AK291703.1 AK304380.1 
    AK308148.1 BC045623.1 BX641025.1 

    15 DOTS entries:

    DT.413298  DT.100818240  DT.213352  DT.100651833  DT.121404582  DT.102829594  DT.40221328  DT.100807449 
    DT.100818243  DT.75193037  DT.95086891  DT.100022887  DT.121404607  DT.40221269  DT.91746474 

    24/248 AceView cDNA sequences (see all 248):

    AA749025 AI039251 BU685478 BU552454 BM725312 F28811 BM803686 AA953472 
    AI613149 AL040995 BM472315 AA766918 AA356115 BX641025 BC045623 CA429841 
    AA485160 BM695188 AI246213 CB136587 AI688802 BI254416 AB007929 H15436 

    GeneLoc Exon Structure

    5/7 Alternative Splicing Database (ASD) splice patterns (SP) for RPRD2 (see all 7)    About this scheme

    ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18
    SP1:        -     -     -     -           -                 -           -     -                                                   
    SP2:                    -     -     -     -                 -           -                                                         
    SP3:                    -     -     -     -                 -           -     -                                                   
    SP4:                    -     -     -     -                                                                                       
    SP5:                          -     -     -                                                                                       


    ECgene alternative splicing isoforms for RPRD2

    (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

    RPRD2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAGGAGGAGG
    RPRD2 Expression
    About this image


    See RPRD2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RPRD2

    SOURCE GeneReport for Unigene cluster: Hs.213666
        SABiosciences Custom PCR Arrays for RPRD2
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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)
    About This Section

    This gene was present in the common ancestor of animals and fungi.

    Orthologs for RPRD2 gene from 8/15 species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rprd21 , 5 regulation of nuclear pre-mRNA domain containing 21, 5 90.51(n)1
    91.45(a)1
      3 (41.00 cM)5
    751371  NM_001081293.11  NP_001074762.11 
     957598735 
    chicken
    (Gallus gallus)
    Aves RPRD21 regulation of nuclear pre-mRNA domain containing 2 71.92(n)
    75.21(a)
      425074  NM_001012932.2  NP_001012950.2 
    lizard
    (Anolis carolinensis)
    Reptilia RPRD26
    Uncharacterized protein
    66(a)
    1 ↔ 1
    GL343802.1(84699-104349)
    African clawed frog
    (Xenopus laevis)
    Amphibia BX845340.12   -- 78.93(n)    BX845340.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufk52b122 wufk52b12 74.12(n)   334701  BC056830.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG151606
    --
    22(a)
    1 ↔ 1
    2L(18590897-18595431)
    worm
    (Caenorhabditis elegans)
    Secernentea cids-16
    CID domain-containing protein 1
    19(a)
    1 → many
    III(8244443-8245794)
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes RTT1036
    Protein that interacts with exonuclease Rat1p and ...
    14(a)
    1 → many
    IV(1038280-1039509)


    ENSEMBL Gene Tree for RPRD2 (if available)
    TreeFam Gene Tree for RPRD2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RPRD2 gene
    RPRD1B2  RPRD1A2  

    RPRD2 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) 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

    10/2386 SNPs in RPRD2 are shown (see all 2386)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs8287841,2
    C,F,A--150335240(-) gcagcT/Acaagt 1 -- us2k19Minor allele frequency- A:0.48NA WA CSA EA 369
    rs1839730771,2
    --150335250(+) CTGAGA/GCAGGA 1 -- us2k10--------
    rs1379766341,2
    --150335389(+) GTTCCA/GCTCCC 1 -- us2k10--------
    rs1900919801,2
    --150335394(+) GCTCCC/TCGTCT 1 -- us2k10--------
    rs354577291,2
    C--150335396(+) TCCCC-/GTCTCG 1 -- us2k12Minor allele frequency- G:0.00NA CSA 4
    rs774804581,2
    --150335396(+) TCCCCC/GTCTCG 1 -- us2k10--------
    rs1930725911,2
    --150335453(+) TCTTTC/GGAGAA 1 -- us2k10--------
    rs1448061321,2
    C--150335489(+) TTCTTA/GTACTG 1 -- us2k10--------
    rs115762891,2
    C,F,H--150335534(+) cgcacA/Gcacac 1 -- us2k12Minor allele frequency- G:0.24NA 126
    rs115762931,2
    C,F,H--150335536(+) cacacA/Gcacac 1 -- us2k12Minor allele frequency- G:0.25NA 124

    HapMap Linkage Disequilibrium report for RPRD2 (150335567 - 150449042 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10/11 variations for RPRD2 (see all 11):    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2658303CNV Deletion23128226
    esv2540817CNV Deletion19546169
    esv2717773CNV Deletion23290073
    esv2717784CNV Deletion23290073
    esv2670951CNV Deletion23128226
    esv989789CNV Deletion20482838
    esv2717795CNV Deletion23290073
    esv999047CNV Insertion20482838
    nsv831548CNV Loss17160897
    nsv872416CNV Loss21882294

    SABiosciences Cancer Mutation PCR Assays
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    (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

    RPRD2 for disorders           About MalaCards
    OMIM gene information: 614695    OMIM disorders: --


    RPRD2 for disorders           About GeneDecksing

    Genetic Association Database (GAD): RPRD2

    Export disorders for RPRD2 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)
    About This Section

    PubMed articles for RPRD2 gene, integrated from 9 sources (see all 29):
    (articles sorted by number of sources associating them with RPRD2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Control of the RNA polymerase II phosphorylation stat e in promoter regions by CTD interaction domain-containing proteins RPRD1A and RPRD1B. (PubMed id 22231121)1, 2, 3 Ni Z....Greenblatt J.F. (2011)
    2. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PubMed id 16964243)1, 2 Beausoleil S.A.... Gygi S.P. (2006)
    3. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (2006)
    4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (2006)
    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. (2004)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    7. Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones. (PubMed id 12168954)1, 2 Nakajima D.... Nagase T. (2002)
    8. Characterization of cDNA clones in size-fractionated cDNA libraries from human brain. (PubMed id 9455484)1, 2 Seki N.... Ohara O. (1997)
    9. Identification of UHRF1/2 as new N-methylpurine DNA gl ycosylase-interacting proteins. (PubMed id 23537643)1 Liang C....Zhang L. (2013)
    10. Protein phosphatase 1g isoforms linked interactions in the brain. (PubMed id 23080069)1 Esteves S.L....da Cruz e Silva E.F. (2013)

    (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: 23248 HGNC: 29039 AceView: KIAA0460 Ensembl:ENSG00000163125 euGenes: HUgn23248
    ECgene: RPRD2 H-InvDB: RPRD2

    (According to HUGE)
    About This Section
    HUGE: KIAA0460

    (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 RPRD2 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 RPRD2 gene:
    Search GeneIP for patents involving RPRD2

    GeneCards and IP:
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