Pde6h (phosphodiesterase 6H) - Rat Genome Database

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Gene: Pde6h (phosphodiesterase 6H) Rattus norvegicus
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Symbol: Pde6h
Name: phosphodiesterase 6H
RGD ID: 70933
Description: Predicted to enable 3',5'-cyclic-GMP phosphodiesterase activity and cGMP binding activity. Predicted to be involved in positive regulation of G protein-coupled receptor signaling pathway and positive regulation of epidermal growth factor receptor signaling pathway. Predicted to act upstream of or within positive regulation of MAPK cascade. Predicted to be active in photoreceptor outer segment membrane. Human ortholog(s) of this gene implicated in retinal cone dystrophy 3A. Orthologous to human PDE6H (phosphodiesterase 6H); PARTICIPATES IN visual phototransduction pathway; purine metabolic pathway; INTERACTS WITH 6-propyl-2-thiouracil; ammonium chloride; benzo[a]pyrene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: GMP-PDE gamma; Pde6g; phosphodiesterase 6G, cGMP-specific, rod, gamma; phosphodiesterase 6H, cGMP-specific, cone, gamma; retinal cone rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24169,857,793 - 169,872,969 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4169,857,812 - 169,872,969 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4176,164,525 - 176,169,238 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.04171,944,657 - 171,949,411 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.04170,570,202 - 170,574,915 (+)NCBIRnor_WKY
Rnor_6.04170,947,723 - 170,963,046 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4170,958,196 - 170,963,046 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04235,204,371 - 235,219,664 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44174,009,860 - 174,014,405 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14174,254,983 - 174,259,529 (+)NCBI
Celera4158,449,142 - 158,453,876 (+)NCBICelera
Cytogenetic Map4q43NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Characteristics of photoreceptor PDE (PDE6): similarities and differences to PDE5. Cote RH Int J Impot Res. 2004 Jun;16 Suppl 1:S28-33.
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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. KEGG: Kyoto Encyclopedia of Genes and Genomes KEGG
5. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
7. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
8. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
9. GOA pipeline RGD automated data pipeline
10. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
11. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
12. Comprehensive gene review and curation RGD comprehensive gene curation
13. The identification of the inhibitory gamma-subunits of the type 6 retinal cyclic guanosine monophosphate phosphodiesterase in non-retinal tissues: differential processing of mRNA transcripts. Tate RJ, etal., Genomics 2002 Apr;79(4):582-6.
14. PDE6 is an effector for the Wnt/Ca2+/cGMP-signalling pathway in development. Wang H, etal., Biochem Soc Trans 2004 Nov;32(Pt 5):792-6.
Additional References at PubMed
PMID:8889548   PMID:11502744   PMID:14502124  


Genomics

Comparative Map Data
Pde6h
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24169,857,793 - 169,872,969 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4169,857,812 - 169,872,969 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4176,164,525 - 176,169,238 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.04171,944,657 - 171,949,411 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.04170,570,202 - 170,574,915 (+)NCBIRnor_WKY
Rnor_6.04170,947,723 - 170,963,046 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4170,958,196 - 170,963,046 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04235,204,371 - 235,219,664 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44174,009,860 - 174,014,405 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14174,254,983 - 174,259,529 (+)NCBI
Celera4158,449,142 - 158,453,876 (+)NCBICelera
Cytogenetic Map4q43NCBI
PDE6H
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381214,973,042 - 14,981,865 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1214,973,042 - 14,981,865 (+)EnsemblGRCh38hg38GRCh38
GRCh371215,125,976 - 15,134,799 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361215,017,245 - 15,026,066 (+)NCBINCBI36Build 36hg18NCBI36
Build 341215,017,244 - 15,026,066NCBI
Celera1220,270,954 - 20,279,795 (+)NCBICelera
Cytogenetic Map12p12.3NCBI
HuRef1214,895,337 - 14,904,178 (+)NCBIHuRef
CHM1_11215,092,057 - 15,100,898 (+)NCBICHM1_1
T2T-CHM13v2.01214,850,375 - 14,859,197 (+)NCBIT2T-CHM13v2.0
Pde6h
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396136,929,216 - 136,940,483 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6136,900,830 - 136,945,863 (+)EnsemblGRCm39 Ensembl
GRCm386136,952,218 - 136,963,485 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6136,923,832 - 136,968,865 (+)EnsemblGRCm38mm10GRCm38
MGSCv376136,903,044 - 136,912,004 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366136,918,719 - 136,927,678 (+)NCBIMGSCv36mm8
Celera6139,997,648 - 140,006,582 (+)NCBICelera
Cytogenetic Map6G1NCBI
Pde6h
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541311,703,378 - 11,712,075 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541311,654,252 - 11,711,799 (+)NCBIChiLan1.0ChiLan1.0
PDE6H
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11215,372,413 - 15,381,249 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1215,372,413 - 15,381,249 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01214,890,192 - 14,984,542 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PDE6H
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12731,640,731 - 31,664,494 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2731,640,737 - 31,664,401 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2714,784,654 - 14,808,356 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02731,947,405 - 31,970,923 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2731,947,411 - 31,970,880 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12731,836,788 - 31,860,326 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02731,795,045 - 31,818,763 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02714,516,903 - 14,540,640 (+)NCBIUU_Cfam_GSD_1.0
Pde6h
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494592,778,204 - 92,786,504 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365872,506,585 - 2,514,157 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365872,505,755 - 2,514,103 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDE6H
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl557,556,149 - 57,594,423 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1557,555,448 - 57,582,324 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2560,944,506 - 60,978,007 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PDE6H
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11114,869,864 - 14,880,307 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1114,870,498 - 14,880,324 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606920,430,389 - 20,439,864 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pde6h
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475223,051,752 - 23,055,103 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475223,051,486 - 23,055,128 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pde6h
65 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:57
Count of miRNA genes:52
Interacting mature miRNAs:57
Transcripts:ENSRNOT00000007905
Prediction methods: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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4146565735175236377Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157710145182687754Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 2 13 1 1
Low 13 7 6 7 32 1 9 10
Below cutoff 26 22 18 18 3 3 28 22 21 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007905   ⟹   ENSRNOP00000007905
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4169,868,214 - 169,872,969 (+)Ensembl
Rnor_6.0 Ensembl4170,958,196 - 170,963,046 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000098707   ⟹   ENSRNOP00000088500
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4169,857,812 - 169,872,955 (+)Ensembl
RefSeq Acc Id: NM_053688   ⟹   NP_446140
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24169,868,214 - 169,872,969 (+)NCBI
Rnor_6.04170,958,196 - 170,963,046 (+)NCBI
Rnor_5.04235,204,371 - 235,219,664 (+)NCBI
RGSC_v3.44174,009,860 - 174,014,405 (+)RGD
Celera4158,449,142 - 158,453,876 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006237558   ⟹   XP_006237620
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24169,857,793 - 169,872,966 (+)NCBI
Rnor_6.04170,947,723 - 170,963,046 (+)NCBI
Rnor_5.04235,204,371 - 235,219,664 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_446140   ⟸   NM_053688
- UniProtKB: Q9EP63 (UniProtKB/Swiss-Prot),   P61250 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006237620   ⟸   XM_006237558
- Peptide Label: isoform X1
- UniProtKB: Q9EP63 (UniProtKB/Swiss-Prot),   P61250 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000007905   ⟸   ENSRNOT00000007905
RefSeq Acc Id: ENSRNOP00000088500   ⟸   ENSRNOT00000098707

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P61250-F1-model_v2 AlphaFold P61250 1-83 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:70933 AgrOrtholog
BioCyc Gene G2FUF-42588 BioCyc
Ensembl Genes ENSRNOG00000005947 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000007905 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000088500.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007905 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000098707.1 UniProtKB/TrEMBL
Gene3D-CATH 4.10.1120.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro PDE6_gamma UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDE6_gamma_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:114248 UniProtKB/Swiss-Prot
NCBI Gene 114248 ENTREZGENE
PANTHER PTHR12122 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PDE6_gamma UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pde6h PhenoGen
PIRSF 35-cGMP_Pdiase_g UniProtKB/Swiss-Prot
UniProt A0A8I6AAX4_RAT UniProtKB/TrEMBL
  CNCG_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q9EP63 ENTREZGENE
UniProt Secondary Q9D1Y6 UniProtKB/Swiss-Prot
  Q9EP63 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-30 Pde6h  phosphodiesterase 6H  Pde6h  phosphodiesterase 6H, cGMP-specific, cone, gamma  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-07-09 Pde6g  phosphodiesterase 6G, cGMP-specific, rod, gamma      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference