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] See more...

Aliases for RD3 Gene

Aliases for RD3 Gene

  • Retinal Degeneration 3, GUCY2D Regulator 2 3 5
  • Retinal Degeneration Protein 3 3 4
  • Retinal Degeneration 3 2 3
  • Protein RD3 3 4
  • C1orf36 3 4
  • LCA12 2 3
  • Chromosome 1 Open Reading Frame 36 2
  • RD3 5

External Ids for RD3 Gene

Previous HGNC Symbols for RD3 Gene

  • C1orf36

Previous GeneCards Identifiers for RD3 Gene

  • GC01M209717
  • GC01M211649
  • GC01M182327

Summaries for RD3 Gene

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, GUCY2D Regulator) is a Protein Coding gene. Diseases associated with RD3 include Leber Congenital Amaurosis 12 and Leber Plus Disease. An important paralog of this gene is RD3L.

UniProtKB/Swiss-Prot Summary for RD3 Gene

  • Plays a critical role in the regulation of enzymes involved in nucleotide cycle in photoreceptors (PubMed:29515371, PubMed:21928830, PubMed:21078983, PubMed:27471269, PubMed:30559291). Inhibits the basal catalytic activity and the GCAP-stimulated activity of GUCY2D and GUCY2F, two retinal guanylyl cyclases involved in the production of cGMP in photoreceptors (PubMed:21928830, PubMed:27471269, PubMed:29515371, PubMed:30559291). Involved in the transport of GUCY2D and GUCY2F to their target sites in the photoreceptor outer segment (PubMed:21078983). Up-regulates the activity of GUK1, a kinase that plays also an essential role for recycling GMP and indirectly, cGMP (PubMed:29515371). Plays an important role for the survival of rods and cones in the retina (By similarity).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RD3 Gene

Genomics for RD3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RD3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J211492 Promoter/Enhancer 0.9 EPDnew Ensembl 600.7 +0.6 616 0.6 RFX1 ZSCAN4 CTBP1 ZFHX2 RCOR1 SMARCA4 CHD2 EGR2 GATA2 ENSG00000223649 RD3 lnc-SLC30A1-2 lnc-RD3-3 TRAF5
GH01J211344 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 18 +148.5 148514 0.5 RFX1 LEF1 JUND SOX6 FOXJ2 MGA ZNF766 USF2 EGR1 CTBP1 RD3 TRAF5 lnc-RD3-1
GH01J211638 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE dbSUPER 11.4 -149.1 -149063 8 HNRNPL GATAD2A PRDM10 TFE3 SOX13 NFKBIZ RCOR2 FOXA1 RXRB PATZ1 LINC01693 SLC30A1 ENSG00000223649 RD3 NEK2 ENSG00000231057 ENSG00000260805 ENSG00000228792 lnc-TRAF5-4
GH01J211646 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 11.2 -155.7 -155716 4.7 TFE3 ZNF512 NFKBIZ CTCF JUND MTA2 RXRB REST RAD21 TRIM22 SNORA16B SLC30A1 ENSG00000223649 RD3 TRAF5 NEK2 ENSG00000231057 ENSG00000229832 ENSG00000228792 LINC01693
GH01J211334 Promoter/Enhancer 1.2 Ensembl ENCODE dbSUPER 11.3 +156.6 156561 3.4 FOXA1 PKNOX1 POLR2A EED RUNX3 TCF12 ZBTB17 FOSL1 ELF1 CEBPG ENSG00000223649 RD3 LINC00467 TRAF5 lnc-RD3-1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RD3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RD3

Top Transcription factor binding sites by QIAGEN in the RD3 gene promoter:
  • aMEF-2
  • AP-4
  • MEF-2A
  • RFX1

Genomic Locations for RD3 Gene

Genomic Locations for RD3 Gene
chr1:211,476,522-211,492,917
(GRCh38/hg38)
Size:
16,396 bases
Orientation:
Minus strand
chr1:211,649,864-211,666,259
(GRCh37/hg19)
Size:
16,396 bases
Orientation:
Minus strand

Genomic View for RD3 Gene

Genes around RD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RD3 Gene

Proteins for RD3 Gene

  • Protein details for RD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7Z3Z2-RD3_HUMAN
    Recommended name:
    Protein RD3
    Protein Accession:
    Q7Z3Z2
    Secondary Accessions:
    • A8K595

    Protein attributes for RD3 Gene

    Size:
    195 amino acids
    Molecular mass:
    22704 Da
    Quaternary structure:
    • Monomer (PubMed:30559291). Interacts with GUCY2D; negatively regulates its activity (PubMed:21928830, PubMed:26100624, PubMed:27471269, PubMed:30559291). The interaction with GUCY2D promotes the exit of GUCY2D from the endoplasmic reticulum and its trafficking to the photoreceptor outer segments (PubMed:21078983). Interacts with GUCY2F (By similarity). The interaction with GUCY2F negatively regulates GUCY2F activity (PubMed:29515371). The interaction with GUCY2F promotes the exit of GUCY2F from the endoplasmic reticulum and its trafficking to the photoreceptor outer segments (PubMed:21078983). Interacts with GUK1; up-regulates GUK1 activity (PubMed:29515371).

    Three dimensional structures from OCA and Proteopedia for RD3 Gene

neXtProt entry for RD3 Gene

Post-translational modifications for RD3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RD3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RD3 Gene

Domains & Families for RD3 Gene

Gene Families for RD3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for RD3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RD3 Gene

GenScript: Design optimal peptide antigens:
  • Protein RD3 (RD3_HUMAN)
genes like me logo Genes that share domains with RD3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for RD3 Gene

Function for RD3 Gene

Molecular function for RD3 Gene

UniProtKB/Swiss-Prot Function:
Plays a critical role in the regulation of enzymes involved in nucleotide cycle in photoreceptors (PubMed:29515371, PubMed:21928830, PubMed:21078983, PubMed:27471269, PubMed:30559291). Inhibits the basal catalytic activity and the GCAP-stimulated activity of GUCY2D and GUCY2F, two retinal guanylyl cyclases involved in the production of cGMP in photoreceptors (PubMed:21928830, PubMed:27471269, PubMed:29515371, PubMed:30559291). Involved in the transport of GUCY2D and GUCY2F to their target sites in the photoreceptor outer segment (PubMed:21078983). Up-regulates the activity of GUK1, a kinase that plays also an essential role for recycling GMP and indirectly, cGMP (PubMed:29515371). Plays an important role for the survival of rods and cones in the retina (By similarity).

Phenotypes From GWAS Catalog for RD3 Gene

Gene Ontology (GO) - Molecular Function for RD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21078983
genes like me logo Genes that share ontologies with RD3: view
genes like me logo Genes that share phenotypes with RD3: view

Human Phenotype Ontology for RD3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RD3

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for RD3 Gene

Localization for RD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RD3 Gene

Cell projection, cilium, photoreceptor outer segment. Photoreceptor inner segment. Endosome. Nucleus. Cytoplasm. Cytoplasm, perinuclear region. Note=Colocalizes with GUCY2E and GUCY2F in rods and cones photoreceptors. Colocalizes with GUK1 in photoreceptor inner segments and to a lesser extent in the outer plexiform layer (By similarity). Strong dot-like perinuclear staining in the epithelial cells (PubMed:29030614). {ECO:0000250 UniProtKB:Q8BRE0, ECO:0000269 PubMed:29030614}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RD3 gene
Compartment Confidence
nucleus 5
endosome 3
mitochondrion 2
endoplasmic reticulum 2
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
peroxisome 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for RD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001750 photoreceptor outer segment ISS --
GO:0001917 photoreceptor inner segment ISS --
GO:0005634 nucleus IEA,IDA 29030614
GO:0005737 cytoplasm IEA,IDA 29030614
GO:0005768 endosome IEA --
genes like me logo Genes that share ontologies with RD3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for RD3 Gene

Pathways & Interactions for RD3 Gene

PathCards logo

SuperPathways for RD3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007601 visual perception ISS --
GO:0015031 protein transport IMP 21928830
GO:0031283 negative regulation of guanylate cyclase activity IMP 21928830
GO:0050896 response to stimulus IEA --
GO:0060041 retina development in camera-type eye IEA,ISS --
genes like me logo Genes that share ontologies with RD3: view

No data available for Pathways by source and SIGNOR curated interactions for RD3 Gene

Drugs & Compounds for RD3 Gene

No Compound Related Data Available

Transcripts for RD3 Gene

mRNA/cDNA for RD3 Gene

2 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RD3

Alternative Splicing Database (ASD) splice patterns (SP) for RD3 Gene

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

Relevant External Links for RD3 Gene

GeneLoc Exon Structure for
RD3

Expression for RD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RD3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RD3 Gene

This gene is overexpressed in Esophagus - Gastroesophageal Junction (x4.4).

Protein differential expression in normal tissues from HIPED for RD3 Gene

This gene is overexpressed in Retina (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for RD3 Gene



Protein tissue co-expression partners for RD3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RD3

SOURCE GeneReport for Unigene cluster for RD3 Gene:

Hs.632495

mRNA Expression by UniProt/SwissProt for RD3 Gene:

Q7Z3Z2-RD3_HUMAN
Tissue specificity: Expressed in retina (PubMed:12914764). Widely expressed (at protein level) (PubMed:29030614). In the retina the strongest immunoreactivity is detected in the inner half of the cytoplasmic portion of the photoreceptor layer, where rods and cones are found, and the external half of the outer plexiform layer (at protein level) (PubMed:29030614).

Evidence on tissue expression from TISSUES for RD3 Gene

  • Eye(4.6)
  • Nervous system(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for RD3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • eye
  • head
  • olfactory bulb
  • skull
Abdomen:
  • liver
General:
  • blood
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with RD3: view

Orthologs for RD3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RD3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia RD3 30 31
  • 98.46 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia RD3 30 31
  • 85.57 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia RD3 30 31
  • 84.85 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Rd3 30
  • 84.79 (n)
Mouse
(Mus musculus)
Mammalia Rd3 30 17 31
  • 83.25 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia RD3 31
  • 74 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia RD3 31
  • 66 (a)
OneToOne
Chicken
(Gallus gallus)
Aves RD3 30 31
  • 69.26 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia RD3 31
  • 66 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia rd3 30
  • 64.96 (n)
Zebrafish
(Danio rerio)
Actinopterygii rd3 30 31
  • 62.39 (n)
OneToOne
Species where no ortholog for RD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for RD3 Gene

ENSEMBL:
Gene Tree for RD3 (if available)
TreeFam:
Gene Tree for RD3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RD3: view image

Paralogs for RD3 Gene

Paralogs for RD3 Gene

genes like me logo Genes that share paralogs with RD3: view

Variants for RD3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RD3 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
707006 Likely Benign: Leber congenital amaurosis 12 211,481,333(-) G/A MISSENSE_VARIANT
707391 Benign: Leber congenital amaurosis 12 211,479,124(-) C/T MISSENSE_VARIANT
707693 Benign: Leber congenital amaurosis 12 211,481,181(-) A/G SYNONYMOUS_VARIANT
707694 Benign: Leber congenital amaurosis 12 211,481,332(-) C/T SYNONYMOUS_VARIANT
707695 Benign: Leber congenital amaurosis 12 211,481,347(-) C/G MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for RD3 Gene

Structural Variations from Database of Genomic Variants (DGV) for RD3 Gene

Variant ID Type Subtype PubMed ID
esv2675306 CNV deletion 23128226
esv29853 CNV loss 19812545
esv3588733 CNV gain 21293372
esv3588734 CNV loss 21293372
nsv832514 CNV loss 17160897

Variation tolerance for RD3 Gene

Residual Variation Intolerance Score: 85% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.63; 56.62% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RD3 Gene

Human Gene Mutation Database (HGMD)
RD3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RD3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RD3 Gene

Disorders for RD3 Gene

MalaCards: The human disease database

(20) MalaCards diseases for RD3 Gene - From: OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
leber congenital amaurosis 12
  • lca12
leber plus disease
  • lca
retinal degeneration
  • degeneration of retina
noonan syndrome 4
  • ns4
spastic monoplegia
  • infantile monoplegic cerebral palsy
- elite association - COSMIC cancer census association via MalaCards
Search RD3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

RD3_HUMAN
  • 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. {ECO:0000269 PubMed:17186464}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for RD3

genes like me logo Genes that share disorders with RD3: view

No data available for Genatlas for RD3 Gene

Publications for RD3 Gene

  1. Retinal degeneration 3 (RD3) protein, a retinal guanylyl cyclase regulator, forms a monomeric and elongated four-helix bundle. (PMID: 30559291) Peshenko IV … Ames JB (The Journal of biological chemistry 2019) 2 3 4
  2. Retinal degeneration 3 (RD3) protein inhibits catalytic activity of retinal membrane guanylyl cyclase (RetGC) and its stimulation by activating proteins. (PMID: 21928830) Peshenko IV … Dizhoor AM (Biochemistry 2011) 2 3 4
  3. Identification and characterization of C1orf36, a transcript highly expressed in photoreceptor cells, and mutation analysis in retinitis pigmentosa. (PMID: 12914764) Lavorgna G … Banfi S (Biochemical and biophysical research communications 2003) 2 3 4
  4. Control of the Nucleotide Cycle in Photoreceptor Cell Extracts by Retinal Degeneration Protein 3. (PMID: 29515371) Wimberg H … Koch KW (Frontiers in molecular neuroscience 2018) 3 4
  5. Retinal Degeneration Protein 3 (RD3) in normal human tissues: Novel insights. (PMID: 29030614) Aravindan S … Aravindan N (Scientific reports 2017) 3 4

Products for RD3 Gene

Sources for RD3 Gene