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Aliases for RD3 Gene

Aliases for RD3 Gene

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

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) is a Protein Coding gene. Diseases associated with RD3 include leber congenital amaurosis 12 and leber congenital amaurosis. An important paralog of this gene is RD3L.

No data available for UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RD3 Gene

Genomics for RD3 Gene

Regulatory Elements for RD3 Gene

Enhancers for RD3 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around RD3 on UCSC Golden Path with GeneCards custom track

Genomic Location for RD3 Gene

Chromosome:
1
Start:
211,476,522 bp from pter
End:
211,492,917 bp from pter
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:
    No Data Available

neXtProt entry for RD3 Gene

Proteomics data for RD3 Gene at MOPED

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

Protein Domains for RD3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RD3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

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

No data available for Gene Families and UniProtKB/Swiss-Prot for RD3 Gene

Function for RD3 Gene

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

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Animal Models , Transcription Factor Targets and HOMER Transcription for RD3 Gene

Localization for RD3 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for RD3 Gene COMPARTMENTS Subcellular localization image for RD3 gene
Compartment Confidence
endoplasmic reticulum 2
mitochondrion 2
nucleus 2
cytosol 1
peroxisome 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for RD3 Gene

Pathways & Interactions for RD3 Gene

SuperPathways for RD3 Gene

No Data Available

Interacting Proteins for RD3 Gene

STRING Interaction Network Preview (showing 2 interactants - click image to see details)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000355969%0d%0a9606.ENSP00000416250%0d%0a9606.ENSP00000364687%0d%0a
Selected Interacting proteins: Q7Z3Z2-RD3_HUMAN ENSP00000355969 for RD3 Gene via UniProtKB STRING

Gene Ontology (GO) - Biological Process for RD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0050896 response to stimulus IEA --
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

Unigene Clusters for RD3 Gene

Retinal degeneration 3:
Representative Sequences:

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
ECgene alternative splicing isoforms for
RD3

Expression for RD3 Gene

mRNA expression in normal human tissues 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, PaxDb, and MOPED for RD3 Gene



SOURCE GeneReport for Unigene cluster for RD3 Gene Hs.632495

mRNA Expression by UniProt/SwissProt for RD3 Gene

Q7Z3Z2-RD3_HUMAN
Tissue specificity: Preferentially expressed in retina.
genes like me logo Genes that share expression patterns with RD3: view

Protein tissue co-expression partners for RD3 Gene

Primer Products

In Situ Assay Products

Orthologs for RD3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RD3 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia RD3 35
  • 85.57 (n)
  • 83.51 (a)
RD3 36
  • 83 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RD3 35
  • 84.85 (n)
  • 87.88 (a)
RD3 36
  • 61 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rd3 35
  • 83.25 (n)
  • 85.64 (a)
Rd3 16
Rd3 36
  • 54 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia RD3 35
  • 98.46 (n)
  • 98.97 (a)
RD3 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rd3 35
  • 84.79 (n)
  • 86.15 (a)
oppossum
(Monodelphis domestica)
Mammalia RD3 36
  • 74 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RD3 36
  • 66 (a)
OneToOne
chicken
(Gallus gallus)
Aves RD3 35
  • 69.26 (n)
  • 67.88 (a)
RD3 36
  • 66 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RD3 36
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rd3 35
  • 64.96 (n)
  • 60.51 (a)
zebrafish
(Danio rerio)
Actinopterygii rd3 35
  • 62.39 (n)
  • 58.29 (a)
rd3 36
  • 51 (a)
OneToOne
Species with no ortholog for RD3:
  • A. gosspyii yeast (Ashbya 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 squirt (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)

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 from dbSNP and Humsavar for RD3 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs34049451 - 211,481,277(-) GGGAG(C/T)GCAGC reference, missense
rs35649846 - 211,481,400(-) TCTCA(C/T)GGCTT reference, missense
rs34422496 - 211,481,347(-) GCTGA(C/G)ATGGT reference, missense
rs530024772 - 211,481,313(+) CTGCC(C/T)CGTCA reference, missense
VAR_031513 -

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

Variant ID Type Subtype PubMed ID
nsv832514 CNV Loss 17160897
esv2675306 CNV Deletion 23128226
esv29853 CNV Loss 19812545

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)

Relevant External Links for RD3 Gene

HapMap Linkage Disequilibrium report
RD3
Human Gene Mutation Database (HGMD)
RD3

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

Disorders for RD3 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
leber congenital amaurosis 12
  • amaurosis congenita of leber, type 12
leber congenital amaurosis
  • lca
rd3-related leber congenital amaurosis
retinal degeneration
  • degeneration of retina
retinitis pigmentosa
  • retinitis pigmentosa 1
- 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.

Relevant External Links for RD3

Genetic Association Database (GAD)
RD3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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. Identification and characterization of C1orf36, a transcript highly expressed in photoreceptor cells, and mutation analysis in retinitis pigmentosa. (PMID: 12914764) Lavorgna G. … Banfi S. (Biochem. Biophys. Res. Commun. 2003) 2 3 4 67
  2. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3
  3. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T. … Vidal M. (Cell 2014) 3
  4. Union makes strength: a worldwide collaborative genetic and clinical study to provide a comprehensive survey of RD3 mutations and delineate the associated phenotype. (PMID: 23308101) Perrault I. … Rozet J.M. (PLoS ONE 2013) 3
  5. Genome-wide association study of retinopathy in individuals without diabetes. (PMID: 23393555) Jensen R.A. … Wong T.Y. (PLoS ONE 2013) 3

Products for RD3 Gene

Sources for RD3 Gene

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