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RP9P Gene

pseudogene   GIFtS: 25
GCID: GC07M032922

Retinitis Pigmentosa 9 Pseudogene

  See RP9P-related disease
at  

(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
Retinitis Pigmentosa 9 Pseudogene1 2

External Ids:    HGNC: 339691   Entrez Gene: 4412122   Ensembl: ENSG000002057637   

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(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 RP9P Gene:
RP9P (retinitis pigmentosa 9 pseudogene) is a pseudogene. Diseases associated with RP9P include retinitis pigmentosa 9.


(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_000007.13  NC_018918.2  NT_007819.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the RP9P gene promoter:
         Pax-6   NRSF form 1   Pax-2   Pax-2a   NRSF form 2   PPAR-alpha   NRF-2   Nkx6-1   COMP1   HOXA5   
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RP9P


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

Entrez Gene cytogenetic band: 7p14.3   Ensembl cytogenetic band:  7p14.3   HGNC cytogenetic band: 7p14.3

RP9P Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RP9P gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07M032922:  view genomic region     (about GC identifiers)

Start:
32,956,427 bp from pter      End:
32,982,788 bp from pter
Size:
26,362 bases      Orientation:
minus strand

1 alternative location:
Chr7-,CRA_TCAG 33,000,944-33,027,306     

(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: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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  --

(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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Animal Models:
   genOway: Develop your customized and physiologically relevant rodent model for RP9P

miRNA
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miRTarBase miRNAs that target RP9P:
hsa-mir-192-5p (MIRT026467)

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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 COMPARTMENTS: 

CompartmentConfidence
nucleus2
cytosol1
extracellular1
mitochondrion1
plasma membrane1

(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 RP9P
Interactions:

    Search GeneGlobe Interaction Network for RP9P

(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 Tocris compounds for RP9P



(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 RP9P gene: 
NM_001039754.1  

Unigene Cluster for RP9P:

Retinitis pigmentosa 9 pseudogene
Hs.648086  [show with all ESTs]
Unigene Representative Sequence: BC050570
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000450133 ENST00000381639(uc003tdc.3 uc003tdd.3 uc011kaj.2)
ENST00000443264(uc003tdf.1)
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Additional mRNA sequence: 

AF274938.1 BC036907.1 BC050570.1 NR_003500.1 

15 DOTS entries:

DT.97814948  DT.92427536  DT.100697522  DT.121048563  DT.100721266  DT.97843207  DT.121048813  DT.101971471 
DT.121048558  DT.121048829  DT.75197056  DT.100045510  DT.100673832  DT.121048770  DT.86849308 

Selected AceView cDNA sequences (see all 210):

BC025928 BM931391 BC050570 CK299840 AI559377 AI369454 BC036907 AI333133 
AW615273 BF588527 AF007887 CA395366 AA737067 AW027943 BF438270 AI018332 
AI492167 AI658716 BM677345 AI299005 BE348450 AI221290 AI802000 C14383 

GeneLoc Exon Structure


(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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RP9P expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
RP9P Expression
About this image

RP9P Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

RP9P Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.648086
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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)
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  --

ENSEMBL Gene Tree for RP9P (if available)
TreeFam Gene Tree for RP9P (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 RP9P (see all 603)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 7 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1892022611,2
--32834704(+) ATTCCA/GAGGCC 1 -- int10--------
rs1925382541,2
--32834747(+) GAAGGA/GTCAGT 1 -- int10--------
rs3754080791,2
C--32834769(+) TGGCT-/GGTTCC 1 -- int10--------
rs349796861,2
C--32834781(+) AAAAAGGAG/-  
        
GGAGG
1 -- int11Minor allele frequency- -:0.50NA 2
rs678441431,2
C--32834782(+) AAAAG-/GGAG  
        
GAGGG
1 -- int10--------
rs1388175671,2
C--32834838(+) GGGACC/TCTGAC 1 -- int10--------
rs38013341,2
C,F,H--32834969(+) ACACCC/TTGGCC 1 -- int19Minor allele frequency- T:0.16EA NS NA 1954
rs38013351,2
C,F,A,H--32835099(+) GTACAG/CAAATC 1 -- int117Minor allele frequency- C:0.33NS EA NA WA CSA 770
rs1842678291,2
--32835339(+) CACATA/GAGGCC 1 -- nc-transcript-variant0--------
rs1891606981,2
--32835429(+) GCCACA/CCTGTG 1 -- nc-transcript-variant0--------

HapMap Linkage Disequilibrium report for RP9P (32956427 - 32982788 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for RP9P:    About this table    
Variant IDTypeSubtypePubMed ID
esv2734229CNV Deletion23290073
dgv1127e201CNV Deletion23290073
nsv436907CNV Insertion17901297

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing RP9P
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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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1 disease for RP9P:    
About MalaCards
retinitis pigmentosa 9


Find genes that share disorders with RP9P           About GenesLikeMe

Genetic Association Database (GAD): RP9P

Export disorders for RP9P 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 RP9P gene integrated from 10 sources:
(articles sorted by number of sources associating them with RP9P)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Chromosome 6p22 locus associated with clinically aggressive neuroblastoma. (PubMed id 18463370)4 Maris J.M....Hakonarson H. (N. Engl. J. Med. 2008)
  2. 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: 441212 HGNC: 33969 AceView: RP9 Ensembl:ENSG00000205763 euGenes: HUgn441212
ECgene: RP9P H-InvDB: RP9P

(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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  --

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for RP9P gene:
Search GeneIP for patents involving RP9P

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



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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