PDE6B (phosphodiesterase 6B) - Rat Genome Database

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Gene: PDE6B (phosphodiesterase 6B) Canis lupus familiaris
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Symbol: PDE6B
Name: phosphodiesterase 6B
RGD ID: 12073166
Description: ENCODES a protein that exhibits 3',5'-cyclic-GMP phosphodiesterase activity (inferred); 3',5'-cyclic-nucleotide phosphodiesterase activity (inferred); hydrolase activity (inferred); INVOLVED IN detection of light stimulus (ortholog); entrainment of circadian clock by photoperiod (ortholog); retina development in camera-type eye (ortholog); PARTICIPATES IN altered visual phototransduction pathway; retinitis pigmentosa pathway; visual phototransduction pathway; ASSOCIATED WITH cone-rod dystrophy 1; retinitis pigmentosa 40; Animal Disease Models (ortholog); FOUND IN cell projection (inferred); membrane (inferred); photoreceptor outer segment (inferred)
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: GMP-PDE beta; PDBS; pde6B gene for cGMP phosphodiesterase beta subunit; PDEB; phosphodiesterase 6B, cGMP-specific, rod, beta (congenital stationary night blindness 3, autosomal dominant); RCD-1; rod cGMP phosphodiesterase beta subunit; rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:1323314   PMID:8387203   PMID:11124530   PMID:24045995  


Genomics

Comparative Map Data
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
(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
(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
(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
(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
428 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium 8
Low 3 6 1 9 3
Below cutoff 5 5 17 4 4 5 3 3 7 6

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001002934 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AAEX04000003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ277995 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ277997 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ277998 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ278000 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ278001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ278002 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ278003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ278005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAHUQ010000045 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAQRD010000074 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAUVH010000011 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L13262 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  REHQ01000003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X92839 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Z23014 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSCAFT00000026577   ⟹   ENSCAFP00000024683
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl391,746,571 - 91,775,372 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000081347   ⟹   ENSCAFP00000061190
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl391,746,571 - 91,775,372 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845002811   ⟹   ENSCAFP00845002234
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl392,746,065 - 92,774,246 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845002822   ⟹   ENSCAFP00845002245
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl392,746,065 - 92,774,246 (-)Ensembl
RefSeq Acc Id: NM_001002934   ⟹   NP_001002934
RefSeq Status: VALIDATED
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1391,746,571 - 91,775,372 (-)NCBI
Dog10K_Boxer_Tasha394,212,075 - 94,240,253 (-)NCBI
ROS_Cfam_1.0392,746,064 - 92,774,237 (-)NCBI
UMICH_Zoey_3.1391,917,662 - 91,945,844 (-)NCBI
UNSW_CanFamBas_1.0391,972,847 - 92,000,988 (-)NCBI
UU_Cfam_GSD_1.0392,354,937 - 92,383,124 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001002934 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA30882 (Get FASTA)   NCBI Sequence Viewer  
  CAA63425 (Get FASTA)   NCBI Sequence Viewer  
  CAA80557 (Get FASTA)   NCBI Sequence Viewer  
  CAB98144 (Get FASTA)   NCBI Sequence Viewer  
  P33726 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001002934   ⟸   NM_001002934
- UniProtKB: P33726 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSCAFP00000024683   ⟸   ENSCAFT00000026577
RefSeq Acc Id: ENSCAFP00000061190   ⟸   ENSCAFT00000081347
RefSeq Acc Id: ENSCAFP00845002234   ⟸   ENSCAFT00845002811
RefSeq Acc Id: ENSCAFP00845002245   ⟸   ENSCAFT00845002822
Protein Domains
GAF   PDEase


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000016782 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSCAFG00030021135 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSCAFG00040004174 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSCAFG00845001610 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSCAFP00000024683 UniProtKB/Swiss-Prot
  ENSCAFP00000061190.1 UniProtKB/TrEMBL
  ENSCAFP00030033913 UniProtKB/Swiss-Prot
  ENSCAFP00030033953.1 UniProtKB/TrEMBL
  ENSCAFP00040006969 UniProtKB/Swiss-Prot
  ENSCAFP00040006992 UniProtKB/TrEMBL
  ENSCAFP00845002234 ENTREZGENE
  ENSCAFP00845002234.1 UniProtKB/TrEMBL
  ENSCAFP00845002245.1 UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000026577 UniProtKB/Swiss-Prot
  ENSCAFT00000081347.2 UniProtKB/TrEMBL
  ENSCAFT00030038883 UniProtKB/Swiss-Prot
  ENSCAFT00030038931.1 UniProtKB/TrEMBL
  ENSCAFT00040007999 UniProtKB/Swiss-Prot
  ENSCAFT00040008024 UniProtKB/TrEMBL
  ENSCAFT00845002811 ENTREZGENE
  ENSCAFT00845002811.1 UniProtKB/TrEMBL
  ENSCAFT00845002822.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.1300.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.450.40 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro GAF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GAF-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HD/PDEase_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDEase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDEase_catalytic_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDEase_catalytic_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDEase_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report cfa:399653 UniProtKB/Swiss-Prot
NCBI Gene PDE6B ENTREZGENE
Pfam GAF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDEase_I UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS PDIESTERASE1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE PDEASE_I_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDEASE_I_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART GAF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HDc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8C0Q662_CANLF UniProtKB/TrEMBL
  A0A8I3MQ38_CANLF UniProtKB/TrEMBL
  A0A8I3RQ29_CANLF UniProtKB/TrEMBL
  A0A8P0PA79_CANLF UniProtKB/TrEMBL
  P33726 ENTREZGENE, UniProtKB/Swiss-Prot
  Q9MYV0_CANLF UniProtKB/TrEMBL
VGNC ID VGNC:44358 ENTREZGENE