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PRCD Gene

protein-coding   GIFtS: 38
GCID: GC17P074523

Progressive Rod-Cone Degeneration

  See PRCD-related diseases
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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This gene clusters with an RNA gene
Subcategory (RNA class): antisense

Quality score for the ORGUL clustered with this gene is 3

Aliases
Progressive Rod-Cone Degeneration1 2
RP362 5
Progressive Rod-Cone Degeneration Protein2

External Ids:    HGNC: 325281   Entrez Gene: 7682062   Ensembl: ENSG000002141407   OMIM: 6105985   UniProtKB: Q00LT13   
ORGUL members:         

Export aliases for PRCD gene to outside databases

Previous GC identifers: GC17U900816 GC17P072046 GC17P069951


(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 PRCD Gene:
This gene is predominantly expressed in the retina, and mutations in this gene are the cause of autosomal
recessive retinal degeneration in both humans and dogs. Alternatively spliced transcript variants have been found
for this gene. (provided by RefSeq, Mar 2010)

GeneCards Summary for PRCD Gene:
PRCD (progressive rod-cone degeneration) is a protein-coding gene. Diseases associated with PRCD include retinitis pigmentosa 36, and prcd-related retinitis pigmentosa.

UniProtKB/Swiss-Prot: PRCD_HUMAN, Q00LT1
Function: Involved in vision




(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_000017.10  NC_018928.2  NT_010783.16  
Regulatory elements:
   Regulatory transcription factor binding sites in the PRCD gene promoter:
         GATA-3   Sp1   RelA   XBP-1   NF-kappaB   HNF-3beta   Egr-2   ZIC2/Zic2   
         Other transcription factors

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

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


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

Entrez Gene cytogenetic band: 17q25.1   Ensembl cytogenetic band:  17q25.1   HGNC cytogenetic band: 17q25.1

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

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P074523:  view genomic region     (about GC identifiers)

Start:
74,523,668 bp from pter      End:
74,549,660 bp from pter
Size:
25,993 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for PRCD

(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: PRCD_HUMAN, Q00LT1 (See protein sequence)
Recommended Name: Progressive rod-cone degeneration protein  
Size: 54 amino acids; 6007 Da
Secondary accessions: B9EJD4

Explore the universe of human proteins at neXtProt for PRCD: NX_Q00LT1

Explore proteomics data for PRCD at MOPED


See PRCD Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001071088.1  
ENSEMBL proteins: 
 ENSP00000467661   ENSP00000465932  

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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:
 IPR027937 Rod_cone_degen

Graphical View of Domain Structure for InterPro Entry Q00LT1

ProtoNet protein and cluster: Q00LT1


Find genes that share domains with PRCD           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: PRCD_HUMAN, Q00LT1
Function: Involved in vision

Animal Models:

   genOway: Develop your customized and physiologically relevant rodent model for PRCD

miRNA
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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
PRCD_HUMAN, Q00LT1: Membrane; Single-pass membrane protein (Potential). Cytoplasm
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
extracellular2
mitochondrion2

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

GO IDQualified GO termEvidencePubMed IDs
GO:0005737cytoplasm IEA--
GO:0016021integral component of membrane IEA--

Find genes that share ontologies with PRCD           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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Interactions:

    Search GeneGlobe Interaction Network for PRCD

Gene Ontology (GO): 2 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0007601visual perception IEA--
GO:0050896response to stimulus IEA--

Find genes that share ontologies with PRCD           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 Tocris compounds for PRCD



(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 PRCD gene: 
NM_001077620.2  

Unigene Cluster for PRCD:

Progressive rod-cone degeneration
Hs.634380  [show with all ESTs]
Unigene Representative Sequence: AK125617
13 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000592432 ENST00000397633(uc002jrw.1) ENST00000590555 ENST00000465808
ENST00000592014 ENST00000586148 ENST00000397630(uc002jrx.2) ENST00000587813
ENST00000592340 ENST00000587289 ENST00000591317 ENST00000593023 ENST00000587063

miRNA
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hsa-miR-596 hsa-miR-4291 hsa-miR-3194-5p hsa-miR-1224-3p hsa-miR-1260b hsa-miR-30d hsa-miR-30a hsa-miR-637
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Additional mRNA sequence: 

AK125617.1 BC043413.1 BC146898.1 BC146904.1 DQ390338.1 NR_033357.1 

6 DOTS entries:

DT.101977118  DT.113708  DT.97771304  DT.209479  DT.100784263  DT.91971658 

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


PRCD expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 3) fully expand
 
 Eye (Sensory Organs)    fully expand to see all 2 entries
         Mature Rod Cells Outer Nuclear Layer
         Retina
 
 Neurons
         Mature Rod Cells Outer Nuclear Layer
 
 Ovary (Reproductive System)
PRCD Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

PRCD Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.634380
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In Situ
Assay Products:
 

 
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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 human and mouse.

Orthologs for PRCD gene from Selected species (see all 4)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Gm117445 predicted gene 11744   --   11 (81.46 cM) 116653534 


ENSEMBL Gene Tree for PRCD (if available)
TreeFam Gene Tree for PRCD (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 PRCD (see all 451)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 17 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
VAR_0311224
Retinitis pigmentosa 36 (RP36)4--see VAR_0311222 C Y mis40--------
VAR_0311244
Retinitis pigmentosa 36 (RP36)4--see VAR_0311242 V M mis40--------
rs1846326721,2
--69950417(+) GGGGCA/GCCCTT 1 -- us2k10--------
rs353234511,2
C--69950554(+) ATGGG-/C/GCGCCC 1 -- us2k10--------
rs352364191,2
C,F--69950627(+) TGGGAA/C/GAGGGG 1 -- us2k12NA WA 4
rs1130536111,2
C--69950667(+) TGGGGC/TGCCCT 1 -- us2k11Minor allele frequency- T:0.50NA 2
rs1135269541,2
C,F--69950704(+) CCTTGG/TTGTGG 1 -- us2k12Minor allele frequency- T:0.50NA WA 4
rs1123485951,2
C,F--69950781(+) TGGGGC/TGCCCT 1 -- us2k12Minor allele frequency- T:0.50NA WA 4
rs355213781,2
C,F--69950953(+) GGGGCA/GCCCTT 1 -- us2k19Minor allele frequency- G:0.44WA NA CSA EA 368
rs772531221,2
C--74522014(+) CTGAC-/TTTTTT 1 -- us2k10--------

HapMap Linkage Disequilibrium report for PRCD (74523668 - 74549660 bp)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for PRCD:    About this table    
Variant IDTypeSubtypePubMed ID
nsv908831CNV Loss21882294
nsv833549CNV Gain17160897

Human Gene Mutation Database (HGMD): PRCD
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing PRCD
DNA2.0 Custom Variant and Variant Library Synthesis for PRCD

(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: 610598   
OMIM disorders: 610599  
UniProtKB/Swiss-Prot: PRCD_HUMAN, Q00LT1
  • Retinitis pigmentosa 36 (RP36) [MIM:610599]: A retinal dystrophy belonging to the group of pigmentary
    retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination
    and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically
    have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose
    their far peripheral visual field and eventually central vision as well. Note=The disease is caused by mutations
    affecting the gene represented in this entry

  • 5 diseases for PRCD:    
    About MalaCards
    retinitis pigmentosa 36    prcd-related retinitis pigmentosa    membranous glomerulonephritis    retinal degeneration
    leber congenital amaurosis

    1 disease from the University of Copenhagen DISEASES database for PRCD:
    Retinal degeneration

    Find genes that share disorders with PRCD           About GenesLikeMe


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

    1. Identical mutation in a novel retinal gene causes progressive rod- cone degeneration in dogs and retinitis pigmentosa in humans. (PubMed id 16938425)1, 2, 3 Zangerl B.... Aguirre G.D. (Genomics 2006)
    2. Identification of a novel mutation in the PRCD gene causing autosomal recessive retinitis pigmentosa in a Turkish family. (PubMed id 23805042)1 Pach J....Zobor D. (Mol. Vis. 2013)
    3. Identification of a prevalent founder mutation in an Israeli Muslim Arab village confirms the role of PRCD in the aetiology of retinitis pigmentosa in humans. (PubMed id 20507925)1 Nevet M.J....Ben-Yosef T. (J. Med. Genet. 2010)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
    6. 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)
    7. Retinitis Pigmentosa Overview (PubMed id 20301590)1 Pagon R.A....Stephens K. (1993)

    (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: 768206 HGNC: 32528 Ensembl:ENSG00000214140 euGenes: HUgn768206 ECgene: PRCD
    H-InvDB: PRCD

    (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 PRCD 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 PRCD gene:
    Search GeneIP for patents involving PRCD

    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
    Advanced Cell Diagnostics, Animal models from genOway)
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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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