RD3 Gene
protein-coding GIFtS: 44
GCID: GC01M211649
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retinal degeneration 3(Previous name: chromosome 1 open reading frame 36 )
(Previous symbol: C1orf36)
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Aliases
for RD3 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| Retinal Degeneration 31 2 | | C1orf361 2 3 5 | | LCA121 2 5 | | Retinal Degeneration Protein 32 3 | | Chromosome 1 Open Reading Frame 361 | | Protein RD32 |
Export aliases for RD3 gene to outside databasesPrevious GC identifers: GC01M209717 GC01M182327 |
Summaries
for RD3 gene(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:
This gene encodes a retinal protein that is associated with promyelocytic leukemia-gene product (PML) bodies in thenucleus. Mutations in this gene cause Leber congenital amaurosis type 12, a disease that results in retinaldegeneration. Alternative splicing results in multiple transcript variants. (provided by RefSeq, Sep 2009)
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Genomic Views
for RD3 gene
(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 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000001.10 NC_018912.1 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
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: 1q32.3RD3 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 1 GeneLoc Exon Structure GeneLoc location for GC01M211649: view genomic region
(about GC identifiers)
Start:
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211,649,864 bp from pter |
End:
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211,666,259 bp from pter |
Size:
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16,396 bases |
Orientation:
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minus strand |
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Proteins
for RD3 gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
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
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
|
UniProtKB/Swiss-Prot: RD3_HUMAN, Q7Z3Z2 (See
protein sequence)Recommended Name: Protein RD3 Size: 195 amino acids; 22704 Da
Secondary accessions: A8K595Explore the universe of human proteins at neXtProt for RD3: NX_Q7Z3Z2
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q7Z3Z2
RD3 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins (2 alternative transcripts):
NP_001158160.1 NP_898882.1
ENSEMBL proteins: ENSP00000355969
Human Recombinant Protein Products for RD3:
RD3 Antibody Products:
Assay Products for RD3: |
Protein
Domains /
Families
for RD3 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
| ProtoNet protein and cluster: Q7Z3Z2 |
Function
for RD3 gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
inGenious Targeting Laboratory,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase,
shRNA from
OriGene,
Sirion Biotech,
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,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
Sirion Biotech,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Phenotypes:
2 MGI mutant phenotypes (inferred from 1 allele ) (MGI details for Rd3):
RD3 for phenotypes About GeneDecksing
Animal Models:
Clone
Products: |  | Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore | |  | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for RD3 (see all 4)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for RD3 (see all 2)
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling 
| |  | GenScript: all cDNA clones in your preferred vector (see all 2): RD3 (NM_000796) | |  | Browse Sino Biological Human cDNA Clones | |  | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for RD3 | |  | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RD3 |
In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RD3 |
|
Pathways & Interactions
for RD3 gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
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 Mar 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 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 | -- |
RD3 for ontologies About GeneDecksing
|
Drugs & Compounds
for RD3 gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
 Browse Tocris compounds for RD3
Search CenterWatch for drugs/clinical trials and news about RD3
|
Transcripts
for RD3 gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 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,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
Sirion Biotech,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
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_1830592 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000484910 ENST00000367002(uc001him.2 uc001hin.2 uc009xda.2)
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for RD3 (see all 4)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for RD3 (see all 2)
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector (see all 2): RD3 (NM_000796) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for RD3 | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RD3 |
Additional cDNA 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): BC065541 BC035651 BM451541 BU734167 AW963480 BQ637404 BM451791 AA364772 NM_183059 BM709674 AY191519 BQ423977 BU153642 AV722566 AA719822 BM450722 H56707 AA708109 BU176577 BE618160 BM478345 BU193531 BX647803 AV721413
GeneLoc Exon Structure
3 Alternative Splicing Database (ASD) splice patterns (SP) for RD3 About this scheme
| ExUns: | 1a | · | 1b | ^ | 2 | ^ | 3a | · | 3b | ^ | 4 |
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| SP1: | | | | | - | | | | | | | | |
| SP2: | | | | | - | | | | | | | | |
| SP3: | | | | | | | | | | | | |
ECgene alternative splicing isoforms for RD3
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Expression
for RD3 gene
(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)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: AGGGTCCAGA
About this image
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, Q7Z3Z2Tissue specificity: Preferentially expressed in retina
SABiosciences Custom PCR Arrays for RD3
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for RD3
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse, rat RD3 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat RD3 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat RD3 | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RD3 |
Orthologs
for RD3 gene
(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
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This gene was present in the common ancestor of chordates.
Orthologs for RD3 gene from 3/12 species (see all 12) About this table
ENSEMBL Gene Tree for RD3 (if available)
TreeFam Gene Tree for RD3 (if available) |
Paralogs
for RD3 gene(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
|
Genomic Variants
for RD3 gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, 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
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 1 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for RD3 (211649864 - 211666259 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for RD3
1 Indel: 65812
Human Gene Mutation Database (HGMD): RD3
| SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing RD3 |
|
Disorders
/ Diseases
for RD3 gene
(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.)
About This Section
|
RD3 for disorders About GeneDecksing
OMIM gene information: 180040
OMIM disorders: 610612
UniProtKB/Swiss-Prot: RD3_HUMAN, Q7Z3Z2
Defects in RD3 are the cause of Leber congenital amaurosis type 12 (LCA12) [MIM:610612]. LCA designates aclinically and genetically heterogeneous group of childhood retinal degenerations, generally inherited in an autosomalrecessive manner. Affected infants have little or no retinal photoreceptor function as tested by electroretinography.LCA represents the most common genetic cause of congenital visual impairment in infants and children
9  diseases for RD3: About MalaCardsretinal degeneration leber congenital amaurosis retinitis leber congenital amaurosis 12
supranuclear palsy progressive supranuclear palsy retinitis pigmentosa pick's disease
leukemia
3 diseases from the University of Copenhagen DISEASES database for RD3:Progressive supranuclear palsy Leber congenital amaurosis Pick's disease GeneTests: RD3
Leber Congenital Amaurosis
Export disorders for RD3 gene to outside databases
|
Publications
for RD3 gene (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:
(articles sorted by number of sources associating them with RD3) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- 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)
- 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)
- 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)
- 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)
- 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)
- 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)
- Mutation survey of known LCA genes and loci in the Saudi Arabian population. (PubMed id 18936139)1 Li Y....Chen R. (2009)
- Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)
- 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. (2002)
- Leber Congenital Amaurosis (PubMed id 20301475)1 Weleber R.G....Trzupek K.M. (1993)
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External Searches for RD3 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
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Genome Databases showing RD3 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing RD3 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing RD3 gene(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
|
| Name | Description |
| PharmGKB entry for RD3 | Pharmacogenomics, SNPs, Pathways |
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| | |
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
|
Products
for RD3 gene(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, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, LifeMap BioReagents, and Sirion Biotech, 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)
About This Section
|
 | |
 | |
 |
| | |  | Browse OriGene Antibodies | | OriGene shRNA RFP for RD3 | | | OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for RD3 | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for RD3 | | | OriGene Protein Over-expression Lysate for RD3 | | Browse OriGene Fluorogenic Cell Assay Kits | | | OriGene siRNA for RD3 | | OriGene 3'-UTR Clone for RD3 | | | OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for RD3 | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for RD3 | | | Browse OriGene GFP tagged cDNA clones in CMV expression vector | | Browse OriGene MicroRNA Expression Plasmids | | | Browse OriGene basic RS shRNAs | | Browse OriGene validated miRNA SYBR primer pairs | | | OriGene Purified Protein for RD3 | | OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling | | | OriGene Custom Antibody Services for RD3 | | OriGene Custom Protein Services for RD3 | | | OriGene Custom Immunoassay Development | | |
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| | | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat RD3 | | | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing RD3 | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RD3 | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat RD3 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat RD3 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat RD3 |
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| | | | Search Tocris compounds for RD3 |
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 | | | RD3 Proteins, Antibodies, CLIAs, and ELISAs |
| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RD3 |
|  |  |  |  | | | | Search ThermoFisher Antibodies for RD3 |
| | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RD3 |
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