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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
  • Protein RD3 3
  • 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 Rd3-Related Leber Congenital Amaurosis. An important paralog of this gene is RD3L.

No data available for CIViC summary , 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 Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01G211344 1.4 FANTOM5 ENCODE dbSUPER 18 +148.5 148515 0.5 KLF1 LEF1 DDX20 ZNF644 FOSL1 ZNF766 GATA2 EGR1 NFE2 CREM RD3 TRAF5 LINC00467
GH01G211646 1.8 FANTOM5 Ensembl ENCODE dbSUPER 11.2 -155.7 -155717 4.7 SIN3A ARID4B GATA2 ZNF143 FOS NFYC REST PPARG TBX21 MIER3 SNORA16B SLC30A1 ENSG00000223649 RD3 LOC91548 NEK2 ENSG00000228792 FDPSP8
GH01G211641 1.5 Ensembl ENCODE dbSUPER 11.2 -150.6 -150554 4.3 ATF1 MLX ARID4B FEZF1 ZNF48 YY1 TCF12 ZNF121 SLC30A9 GLIS2 SLC30A1 RD3 ENSG00000223649 NEK2 LOC91548 ENSG00000228792 FDPSP8
GH01G211638 1.3 Ensembl ENCODE dbSUPER 11.4 -146.7 -146727 2.6 GTF2F1 TBP MXI1 TAF1 JUN MAX KLF17 RAD21 GTF3C2 POLR2A SLC30A1 RCOR3 ENSG00000223649 RD3 NEK2 LOC91548 ENSG00000260805 LINC01693 LOC105372903
GH01G211334 1.2 Ensembl ENCODE dbSUPER 11.3 +156.6 156562 3.4 PKNOX1 KLF1 YY2 NR2F1 HLF FEZF1 CEBPG FOSL1 POLR2A EED ENSG00000223649 RD3 LINC00467 TRAF5
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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

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

Gene Ontology (GO) - Molecular Function for RD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
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

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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

Localization for RD3 Gene

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
mitochondrion 2
nucleus 2
endoplasmic reticulum 2
peroxisome 1
cytosol 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

No Data Available

Gene Ontology (GO) - Biological Process for RD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007601 visual perception IEA --
GO:0050896 response to stimulus IEA --
GO:0060041 retina development in camera-type eye 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

Transcripts for RD3 Gene

Unigene Clusters for RD3 Gene

Retinal degeneration 3:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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 from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, and MOPED for RD3 Gene



Protein tissue co-expression partners for RD3 Gene

NURSA nuclear receptor signaling pathways regulating expression of RD3 Gene:

RD3

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.

Evidence on tissue expression from TISSUES for RD3 Gene

  • Eye(4.5)

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
Organs:
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

Primer 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
chimpanzee
(Pan troglodytes)
Mammalia RD3 34 35
  • 98.46 (n)
cow
(Bos Taurus)
Mammalia RD3 34 35
  • 85.57 (n)
dog
(Canis familiaris)
Mammalia RD3 34 35
  • 84.85 (n)
rat
(Rattus norvegicus)
Mammalia Rd3 34
  • 84.79 (n)
mouse
(Mus musculus)
Mammalia Rd3 34 16 35
  • 83.25 (n)
oppossum
(Monodelphis domestica)
Mammalia RD3 35
  • 74 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RD3 35
  • 66 (a)
OneToOne
chicken
(Gallus gallus)
Aves RD3 34 35
  • 69.26 (n)
lizard
(Anolis carolinensis)
Reptilia RD3 35
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rd3 34
  • 64.96 (n)
zebrafish
(Danio rerio)
Actinopterygii rd3 34 35
  • 62.39 (n)
Species where no ortholog for RD3 was found in the sources mined by GeneCards:
  • 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
rs386834260 Pathogenic 211,481,119(-) CTCAG(A/G)TGAGC splice-donor-variant
rs762631020 Pathogenic 211,481,236(+) CAGCT(A/G/T)TAGTC reference, synonymous-codon
rs786205148 Pathogenic 211,481,304(-) AGATG(C/T)GAGAG reference, stop-gained
rs786205149 Pathogenic 211,481,278(-) GCGGG(-/AG)CGCAG reference, frameshift-variant
rs786205150 Pathogenic 211,481,280(-) AGCGG(G/T)AGCGC reference, stop-gained

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)

Relevant External Links for RD3 Gene

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

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

Disorders for RD3 Gene

MalaCards: The human disease database

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

- 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 64
  2. Premature truncation of a novel protein, RD3, exhibiting subnuclear localization is associated with retinal degeneration. (PMID: 17186464) Friedman J.S. … Swaroop A. (Am. J. Hum. Genet. 2006) 3 4 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  4. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3 64
  5. RD3 loss dictates high-risk aggressive neuroblastoma and poor clinical outcomes. (PMID: 26375249) Khan F.H. … Aravindan N. (Oncotarget 2015) 3 64

Products for RD3 Gene

Sources for RD3 Gene

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