Pde6d (phosphodiesterase 6D) - Rat Genome Database

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Gene: Pde6d (phosphodiesterase 6D) Rattus norvegicus
Analyze
Symbol: Pde6d
Name: phosphodiesterase 6D
RGD ID: 1306204
Description: Predicted to enable GTPase inhibitor activity and small GTPase binding activity. Predicted to be involved in visual perception. Predicted to be located in cytoplasmic vesicle and cytosol. Predicted to be active in cytoplasm. Human ortholog(s) of this gene implicated in Joubert syndrome 22. Orthologous to human PDE6D (phosphodiesterase 6D); PARTICIPATES IN purine metabolic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3H-1,2-dithiole-3-thione; 4,4'-sulfonyldiphenol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC363272; phosphodiesterase 6D, cGMP-specific, rod, delta; retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8994,640,932 - 94,685,918 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl994,640,932 - 94,685,918 (-)EnsemblGRCr8
mRatBN7.2987,192,989 - 87,237,979 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl987,192,983 - 87,237,969 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx995,609,761 - 95,654,513 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.09100,738,019 - 100,782,702 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0999,121,303 - 99,166,270 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0993,562,099 - 93,607,061 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl993,562,095 - 93,607,087 (-)Ensemblrn6Rnor6.0
Rnor_5.0993,290,035 - 93,335,020 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4985,307,907 - 85,352,836 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera984,608,306 - 84,653,222 (-)NCBICelera
RGSC_v3.1985,491,326 - 85,536,271 (-)NCBI
Cytogenetic Map9q35NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. 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.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
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
Additional References at PubMed
PMID:9712853   PMID:15979089  


Genomics

Comparative Map Data
Pde6d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8994,640,932 - 94,685,918 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl994,640,932 - 94,685,918 (-)EnsemblGRCr8
mRatBN7.2987,192,989 - 87,237,979 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl987,192,983 - 87,237,969 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx995,609,761 - 95,654,513 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.09100,738,019 - 100,782,702 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0999,121,303 - 99,166,270 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0993,562,099 - 93,607,061 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl993,562,095 - 93,607,087 (-)Ensemblrn6Rnor6.0
Rnor_5.0993,290,035 - 93,335,020 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4985,307,907 - 85,352,836 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera984,608,306 - 84,653,222 (-)NCBICelera
RGSC_v3.1985,491,326 - 85,536,271 (-)NCBI
Cytogenetic Map9q35NCBI
PDE6D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382231,732,433 - 231,781,282 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2231,732,354 - 231,786,272 (-)Ensemblhg38GRCh38
GRCh372232,597,143 - 232,645,992 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362232,305,391 - 232,354,218 (-)NCBIBuild 36Build 36hg18NCBI36
Build 342232,422,651 - 232,471,479NCBI
Celera2226,373,664 - 226,422,490 (-)NCBICelera
Cytogenetic Map2q37.1NCBI
HuRef2224,440,043 - 224,488,796 (-)NCBIHuRef
CHM1_12232,602,970 - 232,651,791 (-)NCBICHM1_1
T2T-CHM13v2.02232,217,003 - 232,265,853 (-)NCBIT2T-CHM13v2.0
Pde6d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39186,470,735 - 86,510,260 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl186,470,716 - 86,510,351 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38186,543,012 - 86,582,785 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl186,542,994 - 86,582,629 (-)Ensemblmm10GRCm38
MGSCv37188,439,590 - 88,479,076 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36188,374,186 - 88,413,672 (-)NCBIMGSCv36mm8
Celera189,512,736 - 89,552,068 (-)NCBICelera
Cytogenetic Map1C5NCBI
cM Map143.96NCBI
Pde6d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554533,992,160 - 4,024,695 (+)Ensembl
ChiLan1.0NW_0049554533,992,160 - 4,024,695 (+)NCBIChiLan1.0ChiLan1.0
PDE6D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v213134,357,185 - 134,405,908 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B134,372,155 - 134,420,873 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B118,984,666 - 119,033,525 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B237,772,529 - 237,821,044 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B237,772,529 - 237,821,044 (-)EnsemblpanPan2panpan1.1
PDE6D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12543,583,271 - 43,636,682 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2543,583,901 - 43,636,790 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2544,077,007 - 44,130,324 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02543,839,352 - 43,893,418 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2543,837,383 - 43,893,526 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12543,767,671 - 43,820,847 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02543,611,021 - 43,664,227 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02543,766,160 - 43,819,583 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Pde6d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303185,698,865 - 185,753,200 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365255,185,898 - 5,243,081 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365255,186,501 - 5,240,859 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDE6D
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15132,375,743 - 132,426,683 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.115132,376,117 - 132,426,678 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215146,142,941 - 146,193,486 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PDE6D
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110117,747,149 - 117,809,882 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl10117,746,686 - 117,809,824 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604081,629,156 - 81,690,453 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pde6d
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248434,741,220 - 4,776,381 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248434,741,211 - 4,776,404 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Pde6d
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v14158,677,857 - 158,721,878 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Pde6d
472 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:185
Count of miRNA genes:135
Interacting mature miRNAs:147
Transcripts:ENSRNOT00000025262
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
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)956047863101047863Rat
1582203Gluco19Glucose level QTL 193.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)963376862108376862Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)965657365108376720Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)986720043110356905Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94445825699506504Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)986720043121768150Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)964220169109220169Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)964220169109220169Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)944458256121768150Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)964220169109220169Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)968875497121768150Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)983161999118999486Rat
4889852Pur26Proteinuria QTL 26150.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)985262459109044727Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)985262459118999486Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)948718864108376862Rat
1578757Pur6Proteinuria QTL 63.30.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)964220169109220169Rat
4889943Bss90Bone structure and strength QTL 904.1tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)95450650499506504Rat

Markers in Region
RH128201  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2987,193,232 - 87,193,446 (+)MAPPERmRatBN7.2
Rnor_6.0993,562,342 - 93,562,555NCBIRnor6.0
Rnor_5.0993,290,279 - 93,290,492UniSTSRnor5.0
RGSC_v3.4985,308,149 - 85,308,362UniSTSRGSC3.4
Celera984,608,548 - 84,608,761UniSTS
Cytogenetic Map9q35UniSTS
RH140092  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2987,236,414 - 87,236,601 (+)MAPPERmRatBN7.2
Rnor_6.0993,605,517 - 93,605,703NCBIRnor6.0
Rnor_5.0993,333,453 - 93,333,639UniSTSRnor5.0
RGSC_v3.4985,351,325 - 85,351,511UniSTSRGSC3.4
Celera984,651,711 - 84,651,897UniSTS
Cytogenetic Map9q35UniSTS
RH140555  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2987,216,988 - 87,217,176 (+)MAPPERmRatBN7.2
Rnor_6.0993,586,091 - 93,586,278NCBIRnor6.0
Rnor_5.0993,314,027 - 93,314,214UniSTSRnor5.0
RGSC_v3.4985,331,899 - 85,332,086UniSTSRGSC3.4
Celera984,632,296 - 84,632,483UniSTS
Cytogenetic Map9q35UniSTS
RH140589  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2987,197,363 - 87,197,557 (+)MAPPERmRatBN7.2
Rnor_6.0993,566,473 - 93,566,666NCBIRnor6.0
Rnor_5.0993,294,410 - 93,294,603UniSTSRnor5.0
RGSC_v3.4985,312,280 - 85,312,473UniSTSRGSC3.4
Celera984,612,679 - 84,612,872UniSTS
Cytogenetic Map9q35UniSTS


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
17 12 75 187 91 90 59 114 59 6 414 222 11 174 108 99 31 28 28

Sequence


Ensembl Acc Id: ENSRNOT00000025262   ⟹   ENSRNOP00000025262
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl994,640,932 - 94,685,918 (-)Ensembl
mRatBN7.2 Ensembl987,192,983 - 87,237,969 (-)Ensembl
Rnor_6.0 Ensembl993,562,095 - 93,607,087 (-)Ensembl
RefSeq Acc Id: NM_001108806   ⟹   NP_001102276
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8994,640,932 - 94,685,918 (-)NCBI
mRatBN7.2987,192,989 - 87,237,979 (-)NCBI
Rnor_6.0993,562,100 - 93,607,028 (-)NCBI
Rnor_5.0993,290,035 - 93,335,020 (-)NCBI
RGSC_v3.4985,307,907 - 85,352,836 (-)RGD
Celera984,608,306 - 84,653,222 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102276 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL75597 (Get FASTA)   NCBI Sequence Viewer  
  EDL75598 (Get FASTA)   NCBI Sequence Viewer  
  EDL75599 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000025262
  ENSRNOP00000025262.6
RefSeq Acc Id: NP_001102276   ⟸   NM_001108806
- UniProtKB: D3ZRD3 (UniProtKB/TrEMBL),   A6JWI9 (UniProtKB/TrEMBL),   A6JWJ0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000025262   ⟸   ENSRNOT00000025262
Protein Domains
GMP phosphodiesterase delta subunit

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZRD3-F1-model_v2 AlphaFold D3ZRD3 1-150 view protein structure

Transcriptome

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

Promoters
RGD ID:13696825
Promoter ID:EPDNEW_R7350
Type:multiple initiation site
Name:Pde6d_1
Description:phosphodiesterase 6D
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0993,607,081 - 93,607,141EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306204 AgrOrtholog
BioCyc Gene G2FUF-26864 BioCyc
Ensembl Genes ENSRNOG00000018610 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000025262 ENTREZGENE
  ENSRNOT00000025262.8 UniProtKB/TrEMBL
Gene3D-CATH 2.70.50.40 UniProtKB/TrEMBL
InterPro GMP_PDE_delta UniProtKB/TrEMBL
  Ig_E-set UniProtKB/TrEMBL
  PDED_dom_sf UniProtKB/TrEMBL
  Rhodop-sen_GMP-Pdiesterase_dsu UniProtKB/TrEMBL
KEGG Report rno:363272 UniProtKB/TrEMBL
NCBI Gene 363272 ENTREZGENE
PANTHER RETINAL ROD RHODOPSIN-SENSITIVE CGMP 3',5'-CYCLIC PHOSPHODIESTERASE DELTA-SUBUNIT UniProtKB/TrEMBL
  RETINAL ROD RHODOPSIN-SENSITIVE CGMP 3',5'-CYCLIC PHOSPHODIESTERASE SUBUNIT DELTA UniProtKB/TrEMBL
Pfam GMP_PDE_delta UniProtKB/TrEMBL
PhenoGen Pde6d PhenoGen
PIRSF GMP-Pdiesterase_delta UniProtKB/TrEMBL
RatGTEx ENSRNOG00000018610 RatGTEx
Superfamily-SCOP Ig_E-set UniProtKB/TrEMBL
UniProt A6JWI9 ENTREZGENE, UniProtKB/TrEMBL
  A6JWJ0 ENTREZGENE, UniProtKB/TrEMBL
  D3ZRD3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-30 Pde6d  phosphodiesterase 6D  Pde6d  phosphodiesterase 6D, cGMP-specific, rod, delta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Pde6d  phosphodiesterase 6D, cGMP-specific, rod, delta   Pde6d_predicted  phosphodiesterase 6D, cGMP-specific, rod, delta (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Pde6d_predicted  phosphodiesterase 6D, cGMP-specific, rod, delta (predicted)      Symbol and Name status set to approved 70820 APPROVED