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

RD3 Gene

protein-coding   GIFtS: 46
GCID: GC01M211649

Retinal Degeneration 3

(Previous name: chromosome 1 open reading frame 36)
(Previous symbol: C1orf36)
  See 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)
About This Section

Aliases
Retinal Degeneration 31 2
C1orf361 2 3 5
Retinal Degeneration Protein 32 3
LCA122 5
Chromosome 1 Open Reading Frame 361
Protein RD32

External Ids:    HGNC: 196891   Entrez Gene: 3430352   Ensembl: ENSG000001985707   OMIM: 1800405   UniProtKB: Q7Z3Z23   

Export aliases for RD3 gene to outside databases

Previous GC identifers: GC01M209717 GC01M182327


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

Entrez Gene summary for RD3 Gene:
This gene encodes a retinal protein that is associated with promyelocytic leukemia-gene product (PML) bodies in
the nucleus. Mutations in this gene cause Leber congenital amaurosis type 12, a disease that results in retinal
degeneration. Alternative splicing results in multiple transcript variants. (provided by RefSeq, Sep 2009)

GeneCards Summary for RD3 Gene: 
RD3 (retinal degeneration 3) is a protein-coding gene. Diseases associated with RD3 include leber congenital amaurosis 12, and rd3-related leber congenital amaurosis. An important paralog of this gene is RD3L.




(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  NC_018912.2  NT_167186.1  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RD3 gene promoter:
         MEF-2A   RFX1   AP-4   aMEF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRD3 promoter sequence
   Search SABiosciences Chromatin IP Primers for RD3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RD3


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

Entrez Gene cytogenetic band: 1q32.3   Ensembl cytogenetic band:  1q32.3   HGNC cytogenetic band: 1q32.3

RD3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RD3 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M211649:  view genomic region     (about GC identifiers)

Start:
211,649,864 bp from pter      End:
211,666,259 bp from pter
Size:
16,396 bases      Orientation:
minus 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: RD3_HUMAN, Q7Z3Z2 (See protein sequence)
Recommended Name: Protein RD3  
Size: 195 amino acids; 22704 Da
Secondary accessions: A8K595

Explore the universe of human proteins at neXtProt for RD3: NX_Q7Z3Z2

Explore proteomics data for RD3 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q7Z3Z2

  • RD3 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    RD3 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_001158160.1  NP_898882.1  

    ENSEMBL proteins: 
     ENSP00000355969  

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

    ProtoNet protein and cluster: Q7Z3Z2


    (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

    Phenotypes:
         2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Rd3):
     nervous system  vision/eye 

    RD3 for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for RD3 
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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 RD3

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007601visual perception IEA--
    GO:0050896response to stimulus IEA--
    GO:0060041retina development in camera-type eye IEA--

    RD3 for ontologies           About GeneDecksing



    (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 RD3

    Search CenterWatch for drugs/clinical trials and news about RD3

    (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,
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    About This Section

    REFSEQ mRNAs for RD3 gene (2 alternative transcripts): 
    NM_001164688.1  NM_183059.2  

    Unigene Cluster for RD3:

    Retinal degeneration 3
    Hs.632495  [show with all ESTs]
    Unigene Representative Sequence: NM_183059
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000484910 ENST00000367002(uc001him.2 uc001hin.2 uc009xda.2)

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    hsa-miR-492 hsa-miR-103b hsa-miR-3651 hsa-miR-2278 hsa-miR-3647-3p hsa-miR-3150a-3p hsa-miR-182 hsa-miR-491-5p
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    Additional mRNA sequence: 

    AK291210.1 AY191519.1 BC035651.1 BC065541.1 BX647803.1 

    3 DOTS entries:

    DT.99941796  DT.102822814  DT.91668805 

    24/33 AceView cDNA sequences (see all 33):

    BU734167 BM451791 BQ637404 BM451541 AW963480 BM709674 BC065541 AY191519 
    AA364772 BC035651 NM_183059 BM450722 H56707 BX647803 AA708109 BE618160 
    AV722566 AA719822 BU176577 BM478345 BU193531 BQ423977 BU153642 BU734084 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for RD3    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4
    SP1:              -                     
    SP2:              -                     
    SP3:                                    


    ECgene alternative splicing isoforms for RD3

    (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

    RD3 expression in normal human tissues (normalized intensities)      RD3 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGGGTCCAGA
    RD3 Expression
    About this image


    RD3 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/1 selected tissues (see all 1) fully expand
     
     Eye (Sensory Organs)
             Adult Retinal Pigmented Epithelium Cells Retinal Pigmented Epithelium

    See RD3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RD3

    SOURCE GeneReport for Unigene cluster: Hs.632495

    UniProtKB/Swiss-Prot: RD3_HUMAN, Q7Z3Z2
    Tissue specificity: Preferentially expressed in retina

        SABiosciences Custom PCR Arrays for RD3
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RD3

    (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 chordates.

    Orthologs for RD3 gene from 4/9 species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rd31 , 5 retinal degeneration 31, 5 83.25(n)1
    85.64(a)1
      1 (97.09 cM)5
    740231  NM_023727.31  NP_076216.21 
     1919773735 
    chicken
    (Gallus gallus)
    Aves RD31 retinal degeneration 3 69.26(n)
    67.88(a)
      421378  XM_419438.3  XP_419438.1 
    lizard
    (Anolis carolinensis)
    Reptilia RD36
    Uncharacterized protein
    65(a)
    1 ↔ 1
    1(237921217-237949248)
    zebrafish
    (Danio rerio)
    Actinopterygii rd31 retinal degeneration 3 62.21(n)
    58.29(a)
      791149  NM_001080631.1  NP_001074100.1 


    ENSEMBL Gene Tree for RD3 (if available)
    TreeFam Gene Tree for RD3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RD3 gene
    RD3L2  

    RD3 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

    10/478 SNPs in RD3 are shown (see all 478)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0315144
    ----see VAR_0315142 R W mis40--------
    VAR_0315124
    ----see VAR_0315122 G R mis40--------
    VAR_0315134
    ----see VAR_0315132 G V mis40--------
    VAR_0315174
    ----see VAR_0315172 D V mis40--------
    VAR_0315154
    ----see VAR_0315152 K M mis40--------
    rs722471771,2
    C--182339651(+) GGTAT-/TTCTTTAG 4 -- int1 cds10--------
    rs1507917341,2
    C--182339651(+) GGTAT-/TTCTTTAG 2 -- int10--------
    rs2015216281,2
    C--182339653(-) CTAAAA/GANNNN 2 -- int10--------
    rs114636561,2
    C--182342273(+) CTCAAG/-ATTTT 2 -- ut511Minor allele frequency- -:0.00CSA 2
    rs75194961,2
    C,F,A--182344788(+) GCGTGC/TGTGTG 2 -- us2k15Minor allele frequency- T:0.22WA NA CSA 9

    HapMap Linkage Disequilibrium report for RD3 (211649864 - 211666259 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for RD3:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2675306CNV Deletion23128226
    nsv832514CNV Loss17160897
    esv29853CNV Loss19812545


    Human Gene Mutation Database (HGMD): RD3
    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
    OMIM gene information: 180040   
    OMIM disorders: 610612  
    UniProtKB/Swiss-Prot: RD3_HUMAN, Q7Z3Z2
  • Leber congenital amaurosis 12 (LCA12) [MIM:610612]: A severe dystrophy of the retina, typically becoming
    evident in the first years of life. Visual function is usually poor and often accompanied by nystagmus, sluggish
    or near-absent pupillary responses, photophobia, high hyperopia and keratoconus. Note=The disease is caused by
    mutations affecting the gene represented in this entry

  • 10 diseases for RD3:    About MalaCards
    leber congenital amaurosis 12    rd3-related leber congenital amaurosis    retinal degeneration    leber congenital amaurosis 1
    retinitis    leber congenital amaurosis    progressive supranuclear palsy    pick's disease
    retinitis pigmentosa    leukemia

    3 diseases from the University of Copenhagen DISEASES database for RD3:
    Progressive supranuclear palsy     Leber congenital amaurosis     Pick's disease

    RD3 for disorders           About GeneDecksing

    GeneTests: RD3
    GeneReviews: RD3
    Genetic Association Database (GAD): RD3

    Export disorders for RD3 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 RD3 gene, integrated from 9 sources (see all 13):
    (articles sorted by number of sources associating them with RD3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification and characterization of C1orf36, a transcript highly expressed in photoreceptor cells, and mutation analysis in retinitis pigmentosa. (PubMed id 12914764)1, 2, 3 Lavorgna G....Banfi S. (2003)
    2. Premature truncation of a novel protein, RD3, exhibiting subnuclear localization is associated with retinal degeneration. (PubMed id 17186464)1, 2 Friedman J.S.... Swaroop A. (2006)
    3. 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)
    4. Union makes strength: a worldwide collaborative geneti c and clinical study to provide a comprehensive survey of RD3 mutations and deli neate the associated phenotype. (PubMed id 23308101)1 Perrault I....Rozet J.M. (2013)
    5. Genome-wide association study of retinopathy in indivi duals without diabetes. (PubMed id 23393555)1 Jensen R.A....Wong T.Y. (2013)
    6. Mutations in RD3 are associated with an extremely rare and severe form of early onset retinal dystrophy. (PubMed id 22531706)1 Preising M.N....Lorenz B. (2012)
    7. Retinal degeneration 3 (RD3) protein inhibits catalyt ic activity of retinal membrane guanylyl cyclase (RetGC) and its stimulation by activating proteins. (PubMed id 21928830)1 Peshenko I.V....Dizhoor A.M. (2011)
    8. Interactions of pathological hallmark proteins: tubul in polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (2011)
    9. Mutation survey of known LCA genes and loci in the Saudi Arabian population. (PubMed id 18936139)1 Li Y....Chen R. (2009)
    10. A genome-wide association study of sporadic ALS in a homogenous Irish population. (PubMed id 18057069)4 Cronin S....Hardiman O. (2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    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)
    About This Section
    Entrez Gene: 343035 HGNC: 19689 AceView: C1orf36 Ensembl:ENSG00000198570 euGenes: HUgn343035
    ECgene: RD3 H-InvDB: RD3

    (According to HUGE)
    About This Section
      --

    (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 RD3 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 RD3 gene:
    Search GeneIP for patents involving RD3

    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    Category
    (GIFtS: 73)
    transforming growth factor, beta 1
    GIFtS Group
    The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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