Rd3 (RD3 regulator of GUCY2D) - Rat Genome Database

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Gene: Rd3 (RD3 regulator of GUCY2D) Rattus norvegicus
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Symbol: Rd3
Name: RD3 regulator of GUCY2D
RGD ID: 1593897
Description: Predicted to be involved in several processes, including negative regulation of guanylate cyclase activity; retina development in camera-type eye; and visual perception. Predicted to be located in several cellular components, including perinuclear region of cytoplasm; photoreceptor inner segment; and photoreceptor outer segment. Human ortholog(s) of this gene implicated in Leber congenital amaurosis; Leber congenital amaurosis 12; and retinal degeneration. Orthologous to human RD3 (RD3 regulator of GUCY2D); INTERACTS WITH 6-propyl-2-thiouracil; amitrole; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC684158; retinal degeneration 3; retinal degeneration 3, GUCY2D regulator; similar to chromosome 1 open reading frame 36
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr813106,060,657 - 106,097,063 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl13106,084,171 - 106,093,540 (+)EnsemblGRCr8
mRatBN7.213103,551,823 - 103,562,925 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl13103,552,857 - 103,562,622 (+)EnsemblmRatBN7.2
Rnor_6.013110,739,645 - 110,749,167 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13110,743,098 - 110,748,365 (+)Ensemblrn6Rnor6.0
Rnor_5.013115,288,392 - 115,307,827 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera13102,992,075 - 103,001,674 (+)NCBICelera
Cytogenetic Map13q27NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Premature truncation of a novel protein, RD3, exhibiting subnuclear localization is associated with retinal degeneration. Friedman JS, etal., Am J Hum Genet. 2006 Dec;79(6):1059-70. Epub 2006 Oct 23.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. RD3 gene delivery restores guanylate cyclase localization and rescues photoreceptors in the Rd3 mouse model of Leber congenital amaurosis 12. Molday LL, etal., Hum Mol Genet. 2013 Oct 1;22(19):3894-905. doi: 10.1093/hmg/ddt244. Epub 2013 Jun 4.
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. Mutations in RD3 are associated with an extremely rare and severe form of early onset retinal dystrophy. Preising MN, etal., Invest Ophthalmol Vis Sci. 2012 Jun 8;53(7):3463-72. doi: 10.1167/iovs.12-9519.
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:8486383   PMID:12477932   PMID:21052544   PMID:21078983   PMID:21928830   PMID:27471269   PMID:29030614   PMID:29515371   PMID:30559291  


Genomics

Comparative Map Data
Rd3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr813106,060,657 - 106,097,063 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl13106,084,171 - 106,093,540 (+)EnsemblGRCr8
mRatBN7.213103,551,823 - 103,562,925 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl13103,552,857 - 103,562,622 (+)EnsemblmRatBN7.2
Rnor_6.013110,739,645 - 110,749,167 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13110,743,098 - 110,748,365 (+)Ensemblrn6Rnor6.0
Rnor_5.013115,288,392 - 115,307,827 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera13102,992,075 - 103,001,674 (+)NCBICelera
Cytogenetic Map13q27NCBI
RD3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381211,476,522 - 211,492,162 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1211,476,522 - 211,492,162 (-)Ensemblhg38GRCh38
GRCh371211,649,864 - 211,665,504 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361209,717,404 - 209,732,882 (-)NCBIBuild 36Build 36hg18NCBI36
Celera1184,876,748 - 184,893,143 (-)NCBICelera
Cytogenetic Map1q32.3NCBI
HuRef1182,326,839 - 182,343,232 (-)NCBIHuRef
CHM1_11212,922,299 - 212,938,679 (-)NCBICHM1_1
T2T-CHM13v2.01210,722,616 - 210,738,242 (-)NCBIT2T-CHM13v2.0
Rd3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391191,688,574 - 191,725,497 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1191,709,331 - 191,720,244 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381191,956,490 - 191,988,282 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1191,977,370 - 191,988,283 (+)Ensemblmm10GRCm38
MGSCv371193,801,254 - 193,812,163 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361193,678,006 - 193,686,169 (+)NCBIMGSCv36mm8
Celera1198,918,619 - 198,929,618 (+)NCBICelera
Cytogenetic Map1H6NCBI
cM Map197.09NCBI
Rd3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955489896,964 - 903,855 (+)Ensembl
ChiLan1.0NW_004955489896,964 - 903,855 (+)NCBIChiLan1.0ChiLan1.0
RD3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2137,922,047 - 37,927,041 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1137,887,182 - 37,892,169 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01187,044,054 - 187,060,441 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11191,907,989 - 191,924,365 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1191,907,989 - 191,924,365 (-)EnsemblpanPan2panpan1.1
RD3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.179,876,003 - 9,887,267 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha79,451,711 - 9,465,821 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.079,579,585 - 9,593,687 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl79,579,448 - 9,582,414 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.179,502,556 - 9,516,383 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.079,603,610 - 9,618,587 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.079,728,937 - 9,742,788 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Rd3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934464,612,737 - 64,633,817 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365571,852,940 - 1,876,313 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365571,852,996 - 1,873,070 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RD3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9131,705,229 - 131,719,288 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.19131,712,858 - 131,716,179 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29144,740,850 - 144,751,535 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RD3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12518,011,865 - 18,029,392 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2518,025,451 - 18,027,916 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605518,550,003 - 18,554,269 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rd3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624807816,429 - 824,210 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624807815,027 - 824,294 (+)NCBIHetGla 1.0HetGla 1.0hetGla2

Variants

.
Variants in Rd3
80 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:85
Count of miRNA genes:74
Interacting mature miRNAs:77
Transcripts:ENSRNOT00000075086
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1366451204106807694Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1365103704106807694Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1365103704106807694Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1361825626106807694Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1380753256106807694Rat

Markers in Region
RH131777  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.213103,562,725 - 103,562,875 (+)MAPPERmRatBN7.2
Rnor_6.013110,748,972 - 110,749,121NCBIRnor6.0
Rnor_5.013115,307,632 - 115,307,781UniSTSRnor5.0
Celera13103,001,479 - 103,001,628UniSTS
RH 3.4 Map13748.4UniSTS
RH140801  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.213103,561,728 - 103,561,928 (+)MAPPERmRatBN7.2
Rnor_6.013110,747,975 - 110,748,174NCBIRnor6.0
Rnor_5.013115,306,635 - 115,306,834UniSTSRnor5.0
Celera13103,000,482 - 103,000,681UniSTS
RH 3.4 Map13748.8UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 10 37 141 54 53 22 48 22 6 201 108 4 120 47 75 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000075086   ⟹   ENSRNOP00000064931
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl13106,088,087 - 106,093,540 (+)Ensembl
mRatBN7.2 Ensembl13103,552,857 - 103,562,622 (+)Ensembl
Rnor_6.0 Ensembl13110,743,098 - 110,748,365 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000139943   ⟹   ENSRNOP00000099874
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl13106,084,171 - 106,092,657 (+)Ensembl
RefSeq Acc Id: XM_039091509   ⟹   XP_038947437
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr813106,085,263 - 106,097,063 (+)NCBI
mRatBN7.213103,554,280 - 103,562,925 (+)NCBI
RefSeq Acc Id: XM_063272732   ⟹   XP_063128802
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr813106,060,657 - 106,097,063 (+)NCBI
RefSeq Acc Id: XM_063272733   ⟹   XP_063128803
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr813106,085,253 - 106,092,339 (+)NCBI
Ensembl Acc Id: ENSRNOP00000064931   ⟸   ENSRNOT00000075086
RefSeq Acc Id: XP_038947437   ⟸   XM_039091509
- Peptide Label: isoform X1
- UniProtKB: M0R688 (UniProtKB/TrEMBL),   A6JH06 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063128802   ⟸   XM_063272732
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063128803   ⟸   XM_063272733
- Peptide Label: isoform X2
Ensembl Acc Id: ENSRNOP00000099874   ⟸   ENSRNOT00000139943

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R688-F1-model_v2 AlphaFold M0R688 1-195 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1593897 AgrOrtholog
BioCyc Gene G2FUF-16814 BioCyc
Ensembl Genes ENSRNOG00000050766 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000075086 ENTREZGENE
  ENSRNOT00000075086.3 UniProtKB/TrEMBL
  ENSRNOT00000139943 ENTREZGENE
InterPro RD3 UniProtKB/TrEMBL
NCBI Gene 684158 ENTREZGENE
PANTHER PROTEIN RD3 UniProtKB/TrEMBL
  PTHR28489 UniProtKB/TrEMBL
Pfam RD3 UniProtKB/TrEMBL
PhenoGen Rd3 PhenoGen
RatGTEx ENSRNOG00000050766 RatGTEx
UniProt A6JH06 ENTREZGENE, UniProtKB/TrEMBL
  M0R688 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-01-28 Rd3  RD3 regulator of GUCY2D  Rd3  retinal degeneration 3, GUCY2D regulator  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2018-07-20 Rd3  retinal degeneration 3, GUCY2D regulator  Rd3  retinal degeneration 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-13 Rd3  retinal degeneration 3  LOC684158  similar to chromosome 1 open reading frame 36  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-13 Rd3  retinal degeneration 3  Rd3  retinal degeneration 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC684158  similar to chromosome 1 open reading frame 36      Symbol and Name status set to provisional 70820 PROVISIONAL