Pde6b (phosphodiesterase 6B) - Rat Genome Database

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Gene: Pde6b (phosphodiesterase 6B) Rattus norvegicus
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Symbol: Pde6b
Name: phosphodiesterase 6B
RGD ID: 1311039
Description: Predicted to enable 3',5'-cyclic-nucleotide phosphodiesterase activity. Involved in retinal cell apoptotic process. Predicted to be located in photoreceptor outer segment. Predicted to be active in photoreceptor outer segment membrane. Used to study retinitis pigmentosa. Human ortholog(s) of this gene implicated in congenital stationary night blindness autosomal dominant 2 and retinitis pigmentosa 40. Orthologous to human PDE6B (phosphodiesterase 6B); PARTICIPATES IN altered visual phototransduction pathway; retinitis pigmentosa pathway; visual phototransduction pathway; INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; acetamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC289878; phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide; phosphodiesterase 6B, cGMP-specific, rod, beta; rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta
RGD Orthologs
Human
Mouse
Chinchilla
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Pde6bem1Baek   Pde6bem1Cgen  
Genetic Models: SD-Pde6bem1Cgen SD-Pde6bem1Baek
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2141,323,310 - 1,366,450 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl141,323,310 - 1,366,450 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx141,205,011 - 1,248,120 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0142,506,768 - 2,549,872 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0141,203,442 - 1,246,548 (-)NCBIRnor_WKY
Rnor_6.0142,328,690 - 2,371,913 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl142,328,750 - 2,371,883 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0142,327,104 - 2,370,811 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4141,871,037 - 1,914,170 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1141,871,039 - 1,914,188 (-)NCBI
Celera141,345,195 - 1,388,316 (-)NCBICelera
Cytogenetic Map14p22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. Two mouse retinal degenerations caused by missense mutations in the beta-subunit of rod cGMP phosphodiesterase gene. Chang B, etal., Vision Res. 2007 Mar;47(5):624-33. Epub 2007 Jan 30.
2. Characteristics of photoreceptor PDE (PDE6): similarities and differences to PDE5. Cote RH Int J Impot Res. 2004 Jun;16 Suppl 1:S28-33.
3. Genes and mutations causing retinitis pigmentosa. Daiger SP, etal., Clin Genet. 2013 Aug;84(2):132-41. doi: 10.1111/cge.12203. Epub 2013 Jun 19.
4. 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.
5. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
6. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
7. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
8. Online Mendelian Inheritance in Man, OMIM (TM). Online Mendelian Inheritance in Man, OMIM (TM).
9. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
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. A novel homozygous Ile535Asn mutation in the rod cGMP phosphodiesterase beta-subunit gene in two brothers of a Japanese family with autosomal recessive retinitis pigmentosa. Saga M, etal., Curr Eye Res. 1998 Mar;17(3):332-5.
14. Photoreceptor degeneration: genetic and mechanistic dissection of a complex trait. Wright AF, etal., Nat Rev Genet. 2010 Apr;11(4):273-84. doi: 10.1038/nrg2717.
15. Development of a Pde6b Gene Knockout Rat Model for Studies of Degenerative Retinal Diseases. Yeo JH, etal., Invest Ophthalmol Vis Sci. 2019 Apr 1;60(5):1519-1526. doi: 10.1167/iovs.18-25556.
Additional References at PubMed
PMID:11747369   PMID:21052544   PMID:22183407  


Genomics

Comparative Map Data
Pde6b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2141,323,310 - 1,366,450 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl141,323,310 - 1,366,450 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx141,205,011 - 1,248,120 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0142,506,768 - 2,549,872 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0141,203,442 - 1,246,548 (-)NCBIRnor_WKY
Rnor_6.0142,328,690 - 2,371,913 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl142,328,750 - 2,371,883 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0142,327,104 - 2,370,811 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4141,871,037 - 1,914,170 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1141,871,039 - 1,914,188 (-)NCBI
Celera141,345,195 - 1,388,316 (-)NCBICelera
Cytogenetic Map14p22NCBI
PDE6B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384625,573 - 670,782 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl4625,573 - 670,782 (+)EnsemblGRCh38hg38GRCh38
GRCh374619,362 - 664,571 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 364609,373 - 654,571 (+)NCBINCBI36Build 36hg18NCBI36
Build 344609,394 - 654,542NCBI
Celera4559,794 - 605,337 (+)NCBICelera
Cytogenetic Map4p16.3NCBI
HuRef4594,501 - 639,532 (+)NCBIHuRef
CHM1_14619,152 - 664,469 (+)NCBICHM1_1
T2T-CHM13v2.04624,854 - 670,456 (+)NCBIT2T-CHM13v2.0
Pde6b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395108,536,239 - 108,579,609 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5108,536,257 - 108,580,263 (+)EnsemblGRCm39 Ensembl
GRCm385108,388,373 - 108,431,743 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5108,388,391 - 108,432,397 (+)EnsemblGRCm38mm10GRCm38
MGSCv375108,817,392 - 108,860,762 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv365108,628,742 - 108,672,038 (+)NCBIMGSCv36mm8
Celera5105,508,147 - 105,551,677 (+)NCBICelera
Cytogenetic Map5FNCBI
cM Map553.07NCBI
Pde6b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955514234,972 - 279,420 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955514234,972 - 279,420 (+)NCBIChiLan1.0ChiLan1.0
PDE6B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1391,746,571 - 91,775,372 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl391,746,571 - 91,775,372 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha394,212,075 - 94,240,253 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0392,746,064 - 92,774,237 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl392,746,065 - 92,774,246 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1391,917,662 - 91,945,844 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0391,972,847 - 92,000,988 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0392,354,937 - 92,383,124 (-)NCBIUU_Cfam_GSD_1.0
Pde6b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528568,717,209 - 68,770,451 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647722,417,453 - 22,472,185 (-)EnsemblSpeTri2.0
SpeTri2.0NW_00493647722,418,037 - 22,472,251 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDE6B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl880,378 - 110,672 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1880,378 - 111,960 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28131,905 - 148,422 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PDE6B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12748,117,495 - 48,168,727 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2748,118,190 - 48,162,368 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660514,503,685 - 4,551,815 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pde6b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475526,372,072 - 26,413,381 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475526,372,040 - 26,413,464 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pde6b
132 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:22
Count of miRNA genes:22
Interacting mature miRNAs:22
Transcripts:ENSRNOT00000000077
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
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
619619Rf4Renal disease susceptibility QTL 44.10.002urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
71115Niddm15Non-insulin dependent diabetes mellitus QTL 154.8blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14121760611030812Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14121760616960180Rat


Genetic Models
This gene Pde6b is modified in the following models/strains

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
Low 8 17 10 7
Below cutoff 3 7 27 19 2 19 8 9 23 9 8 3 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000077   ⟹   ENSRNOP00000000077
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl141,323,310 - 1,366,450 (-)Ensembl
Rnor_6.0 Ensembl142,328,750 - 2,371,883 (-)Ensembl
RefSeq Acc Id: NM_001106024   ⟹   NP_001099494
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,323,310 - 1,366,450 (-)NCBI
Rnor_6.0142,328,750 - 2,371,883 (-)NCBI
Rnor_5.0142,327,104 - 2,370,811 (-)NCBI
RGSC_v3.4141,871,037 - 1,914,170 (-)RGD
Celera141,345,195 - 1,388,316 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001099494 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL84006 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001099494   ⟸   NM_001106024
- UniProtKB: D3ZDI8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000000077   ⟸   ENSRNOT00000000077
Protein Domains
PDEase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZDI8-F1-model_v2 AlphaFold D3ZDI8 1-856 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:1311039 AgrOrtholog
BioCyc Gene G2FUF-16674 BioCyc
Ensembl Genes ENSRNOG00000000065 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000000077 ENTREZGENE
  ENSRNOP00000000077.5 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000077 ENTREZGENE
  ENSRNOT00000000077.6 UniProtKB/TrEMBL
Gene3D-CATH 1.10.1300.10 UniProtKB/TrEMBL
  3.30.450.40 UniProtKB/TrEMBL
InterPro GAF UniProtKB/TrEMBL
  GAF_dom_like UniProtKB/TrEMBL
  Metal-dep_PHydrolase_HD_dom UniProtKB/TrEMBL
  PDEase UniProtKB/TrEMBL
  PDEase UniProtKB/TrEMBL
  PDEase_catalytic_dom_sf UniProtKB/TrEMBL
  PDEase_CS UniProtKB/TrEMBL
KEGG Report rno:289878 UniProtKB/TrEMBL
NCBI Gene 289878 ENTREZGENE
Pfam GAF UniProtKB/TrEMBL
  PDEase_I UniProtKB/TrEMBL
PhenoGen Pde6b PhenoGen
PRINTS PDIESTERASE1 UniProtKB/TrEMBL
PROSITE PDEASE_I UniProtKB/TrEMBL
  PDEASE_I_2 UniProtKB/TrEMBL
SMART GAF UniProtKB/TrEMBL
  HDc UniProtKB/TrEMBL
UniProt D3ZDI8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-30 Pde6b  phosphodiesterase 6B  Pde6b  phosphodiesterase 6B, cGMP-specific, rod, beta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-08-29 Pde6b  phosphodiesterase 6B, cGMP-specific, rod, beta  Pde6b  phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Pde6b  phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide   Pde6b_predicted  phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Pde6b_predicted  phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide (predicted)      Symbol and Name status set to approved 70820 APPROVED