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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-AMP phosphodiesterase activity and 3',5'-cyclic-GMP phosphodiesterase activity. Involved in retinal cell apoptotic process. Predicted to be located in photoreceptor outer segment. Predicted to be part of rod photoreceptor phosphodiesterase 6 complex. 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

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	PDE6B (phosphodiesterase 6B)	HGNC	EggNOG, Ensembl, HomoloGene, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Pde6b (phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Pde6b (phosphodiesterase 6B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PDE6B (phosphodiesterase 6B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	PDE6B (phosphodiesterase 6B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Pde6b (phosphodiesterase 6B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	PDE6B (phosphodiesterase 6B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	PDE6B (phosphodiesterase 6B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Pde6b (phosphodiesterase 6B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Pde6b (phosphodiesterase 6B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	PDE6A (phosphodiesterase 6A)	HGNC	OrthoDB
Alliance orthologs ³
Homo sapiens (human):	PDE6B (phosphodiesterase 6B)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Pde6b (phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Pde6	Alliance	DIOPT (Ensembl Compara\|PhylomeDB)
Xenopus tropicalis (tropical clawed frog):	pde6b	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Allele / Splice:

Pde6b^em1Baek ; Pde6b^em1Cgen

Genetic Models:

SD-Pde6b^em1Cgen ; SD-Pde6b^em1Baek

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	14	1,468,302 - 1,511,435 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	14	1,468,302 - 1,511,435 (-)	Ensembl				GRCr8
mRatBN7.2	14	1,323,310 - 1,366,450 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	14	1,323,310 - 1,366,450 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	14	1,205,011 - 1,248,120 (-)	NCBI	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	14	2,506,768 - 2,549,872 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	14	1,203,442 - 1,246,548 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd	14	1,197,663 - 1,240,766 (-)	NCBI
Lyon_Normotensive	14	1,196,535 - 1,239,640 (-)	NCBI
Lyon_Hypertensive	14	1,195,514 - 1,238,617 (-)	NCBI
F344_StmMcwi	14	1,477,527 - 1,520,657 (-)	NCBI
Rnor_6.0	14	2,328,690 - 2,371,913 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	14	2,328,750 - 2,371,883 (-)	Ensembl		Rnor_6.0 Ensembl	rn6	Rnor6.0
Rnor_5.0	14	2,327,104 - 2,370,811 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	14	1,871,037 - 1,914,170 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	14	1,345,195 - 1,388,316 (-)	NCBI		Celera
RGSC_v3.1	14	1,871,039 - 1,914,188 (-)	NCBI
Cytogenetic Map	14	p22	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

acute myeloid leukemia (ISO)

Animal Disease Models (ISO)

Breast Cancer, Familial (ISO)

cervical cancer (ISO)

cone-rod dystrophy (ISO)

cone-rod dystrophy 1 (ISO)

congenital stationary night blindness (ISO)

congenital stationary night blindness autosomal dominant 2 (ISO,ISS)

esophageal cancer (ISO)

fundus dystrophy (ISO)

genetic disease (ISO)

head and neck squamous cell carcinoma (ISO)

High Myopia (ISO)

macular degeneration (ISO)

melanoma (ISO)

night blindness (ISO)

nonpapillary renal cell carcinoma (ISO)

ovarian serous cystadenocarcinoma (ISO)

prostate cancer (ISO)

retinal degeneration (ISO,ISS)

retinitis pigmentosa (IMP,ISO,ISS)

retinitis pigmentosa 40 (ISO,ISS)

sarcoma (ISO)

thymoma (ISO)

Thyroid Carcinoma, Nonmedullary 1 (ISO)

uterine carcinosarcoma (ISO)

uterine corpus endometrial carcinoma (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

2,2',4,4'-Tetrabromodiphenyl ether (EXP)

acetamide (EXP)

acrylamide (ISO)

all-trans-retinoic acid (ISO)

arsane (ISO)

arsenic atom (ISO)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

cadmium dichloride (EXP,ISO)

CGP 52608 (ISO)

chlorpyrifos (ISO)

decabromodiphenyl ether (EXP)

Dibutyl phosphate (ISO)

dichloroacetic acid (ISO)

dorsomorphin (ISO)

imidacloprid (ISO)

indole-3-methanol (EXP)

lead(0) (ISO)

lidocaine (EXP)

manganese atom (EXP)

manganese(0) (EXP)

manganese(II) chloride (EXP)

methylmercury chloride (ISO)

mono(2-ethylhexyl) phthalate (ISO)

N-acetyl-L-cysteine (EXP)

N-ethyl-N-nitrosourea (ISO)

N-nitrosodiethylamine (EXP)

phenylmercury acetate (ISO)

SB 431542 (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

testosterone (ISO)

triptonide (ISO)

tris(2-butoxyethyl) phosphate (ISO)

trovafloxacin (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

detection of light stimulus (ISO)

entrainment of circadian clock by photoperiod (IEA,ISO)

negative regulation of cAMP/PKA signal transduction (IBA)

retina development in camera-type eye (IBA,ISO)

retinal cell apoptotic process (IMP)

signal transduction (IEA)

visual perception (IEA,ISO)

Cellular Component

membrane (IEA)

photoreceptor outer segment (IEA,ISO)

photoreceptor outer segment membrane (IBA,ISS)

rod photoreceptor disc membrane (IEA,ISO)

rod photoreceptor phosphodiesterase 6 complex (IEA,ISO)

Molecular Function

3',5'-cyclic-AMP phosphodiesterase activity (IBA)

3',5'-cyclic-GMP phosphodiesterase activity (IBA,IEA,ISO,ISS)

3',5'-cyclic-nucleotide phosphodiesterase activity (IEA)

phosphoric diester hydrolase activity (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

altered visual phototransduction pathway (ISO)

purine metabolic pathway (IEA)

retinitis pigmentosa pathway (ISO)

visual phototransduction pathway (IEA,ISO)

Phenotype Annotations Click to see Annotation Detail View

Mammalian Phenotype

abnormal retina blood vessel pattern (IMP)

increased retina apoptosis (IMP)

retina degeneration (IMP)

retina outer nuclear layer degeneration (IMP)

retina photoreceptor degeneration (IMP)

thin retina outer nuclear layer (IMP)

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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	14	1,468,302 - 1,511,435 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	14	1,468,302 - 1,511,435 (-)	Ensembl				GRCr8
mRatBN7.2	14	1,323,310 - 1,366,450 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	14	1,323,310 - 1,366,450 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	14	1,205,011 - 1,248,120 (-)	NCBI	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	14	2,506,768 - 2,549,872 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	14	1,203,442 - 1,246,548 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd	14	1,197,663 - 1,240,766 (-)	NCBI
Lyon_Normotensive	14	1,196,535 - 1,239,640 (-)	NCBI
Lyon_Hypertensive	14	1,195,514 - 1,238,617 (-)	NCBI
F344_StmMcwi	14	1,477,527 - 1,520,657 (-)	NCBI
Rnor_6.0	14	2,328,690 - 2,371,913 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	14	2,328,750 - 2,371,883 (-)	Ensembl		Rnor_6.0 Ensembl	rn6	Rnor6.0
Rnor_5.0	14	2,327,104 - 2,370,811 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	14	1,871,037 - 1,914,170 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	14	1,345,195 - 1,388,316 (-)	NCBI		Celera
RGSC_v3.1	14	1,871,039 - 1,914,188 (-)	NCBI
Cytogenetic Map	14	p22	NCBI

PDE6B
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	4	625,573 - 670,782 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	4	625,559 - 670,782 (+)	Ensembl		GRCh38.p14 Ensembl	hg38	GRCh38
GRCh37	4	619,362 - 664,571 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	4	609,373 - 654,571 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	4	609,394 - 654,542	NCBI
Celera	4	559,794 - 605,337 (+)	NCBI		Celera
Cytogenetic Map	4	p16.3	NCBI
HuRef	4	594,501 - 639,532 (+)	NCBI		HuRef
CHM1_1	4	619,152 - 664,469 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	4	586,384 - 670,456 (+)	NCBI		T2T-CHM13v2.0

Pde6b
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	108,536,239 - 108,579,609 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	5	108,536,243 - 108,580,263 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	5	108,388,373 - 108,431,743 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	108,388,391 - 108,432,397 (+)	Ensembl		GRCm38.p6 Ensembl	mm10	GRCm38
MGSCv37	5	108,817,392 - 108,860,762 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	5	108,628,742 - 108,672,038 (+)	NCBI		MGSCv36	mm8
Celera	5	105,508,147 - 105,551,677 (+)	NCBI		Celera
Cytogenetic Map	5	F	NCBI
cM Map	5	53.07	NCBI

Pde6b
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955514	234,972 - 279,420 (+)	Ensembl		ChiLan1.0 Ensembl
ChiLan1.0	NW_004955514	234,972 - 279,420 (+)	NCBI	ChiLan1.0	ChiLan1.0

PDE6B
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	3	866,524 - 979,062 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	4	831,856 - 936,701 (+)	NCBI		NHGRI_mPanPan1
PanPan1.1 Ensembl	4	646,516 - 701,680 (+)	Ensembl		PanPan1.1 Ensembl	panPan2	panpan1.1

PDE6B
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	3	91,746,571 - 91,775,372 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	3	91,746,571 - 91,775,372 (-)	Ensembl		CanFam3.1 Ensembl	canFam3	CanFam3.1
Dog10K_Boxer_Tasha	3	94,212,075 - 94,240,253 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	3	92,746,064 - 92,774,237 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	3	92,746,065 - 92,774,246 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	3	91,917,662 - 91,945,844 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	3	91,972,847 - 92,000,988 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	3	92,354,937 - 92,383,124 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Pde6b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mIctTri1.hap1	9	257,671 - 310,598 (+)	NCBI		mIctTri1.hap1
HiC_Itri_2	NW_024405285	68,717,209 - 68,770,451 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936477	22,417,453 - 22,472,185 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936477	22,418,037 - 22,472,251 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PDE6B
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	8	80,378 - 110,672 (+)	Ensembl		Sscrofa11.1 Ensembl	susScr11	Sscrofa11.1
Sscrofa11.1	8	80,378 - 111,960 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	8	131,905 - 148,422 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PDE6B
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mChlSab1.0.hap1	27	49,157,275 - 49,170,224 (-)	NCBI		mChlSab1.0.hap1
Vero_WHO_p1.0	NW_023666051	4,503,685 - 4,551,815 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0
ChlSab1.1	27	48,117,495 - 48,168,727 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	27	48,118,190 - 48,162,368 (-)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM

Pde6b
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624755	26,372,040 - 26,413,464 (-)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2
HetGla_female_1.0 Ensembl	NW_004624755	26,372,072 - 26,413,381 (-)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl

Pde6b
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	11	18,165,545 - 18,209,340 (+)	NCBI	Rrattus_CSIRO_v1	Rrattus_CSIRO_v1

Variants

Variants in Pde6b
421 total Variants

miRNA Target Status (No longer updated)

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 (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
7411573	Bw139	Body weight QTL 139	4.7	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	14	1	40068101	Rat
9589814	Gluco67	Glucose level QTL 67	4.54	0.001	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	14	1	40068101	Rat
634352	Apr6	Acute phase response QTL 6	3.7		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	14	1	41415516	Rat
71115	Niddm15	Non-insulin dependent diabetes mellitus QTL 15	4.8		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	14	1	11334906	Rat
71117	Niddm17	Non-insulin dependent diabetes mellitus QTL 17	2.35		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	14	1	17877928	Rat
70204	Niddm20	Non-insulin dependent diabetes mellitus QTL 20	5.1	0.000008	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	14	1	31893212	Rat

Genetic Models

This gene Pde6b is modified in the following models/strains:

SD-Pde6b^em1Cgen SD-Pde6b^em1Baek

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

adipose tissue	alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	entire extraembryonic component	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	pharyngeal arch	renal system	reproductive system	respiratory system	sensory system	visual system
28	39	86	130	2486	424	451	49	318	158	314	17	1212	400	160	2433	4	380	332	142	149	148

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001106024	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017599143	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_001841017	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC103314	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC106245	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474079	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000014	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000000077 ⟹ ENSRNOP00000000077

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	14	1,468,302 - 1,511,435 (-)	Ensembl
mRatBN7.2 Ensembl	14	1,323,310 - 1,366,450 (-)	Ensembl
Rnor_6.0 Ensembl	14	2,328,750 - 2,371,883 (-)	Ensembl

RefSeq Acc Id:

NM_001106024 ⟹ NP_001099494

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	14	1,468,302 - 1,511,435 (-)	NCBI
mRatBN7.2	14	1,323,310 - 1,366,450 (-)	NCBI
Dahl_SR_JrHsd	14	1,197,663 - 1,240,766 (-)	NCBI
Lyon_Normotensive	14	1,196,535 - 1,239,640 (-)	NCBI
Lyon_Hypertensive	14	1,195,514 - 1,238,617 (-)	NCBI
F344_StmMcwi	14	1,477,527 - 1,520,657 (-)	NCBI
Rnor_6.0	14	2,328,750 - 2,371,883 (-)	NCBI
Rnor_5.0	14	2,327,104 - 2,370,811 (-)	NCBI
RGSC_v3.4	14	1,871,037 - 1,914,170 (-)	RGD
Celera	14	1,345,195 - 1,388,316 (-)	RGD

Sequence:

show sequence

GAAAGCTCTGGGCACAGCAGGAGGAACACCATGAGCCTCAGTGAGGAACAAGTACGCAGCTTCC
TGGATGGGAACCCCACCTTTGCCCACCAATACTTTGAGAAGAAGCTGAGCCCTGAAAATGTGGC
AGGGGCCTGTGAAGGTGGTTGCCTGGTGGACTGTGGCAGCCTACGAGAGCTGTGCCAGGTGGAA
GAGAGTGCAGCGCTGTTTGAACTGGTGCAGGACATGCAAGAGAGCGTCAATATGGAACGCGTGG
TCTTCAAGGTTCTGCGGCGTCTCTGCACCATCCTGCATGCTGACCGCTGCAGCCTCTTTATGTA
CCGCCAGCGCAATGGCGTAGCTGAACTTGCTACTCGGCTCTTCAGTGTGCAGCCCGACAGCCTC
CTGGAGGATTGCCTGGTGCCCCCTGACTCTGAGATCGTCTTCCCTCTGGACATTGGGATTGTGG
GCCATGTGGCTCAGACCAAGAAGATGATAAACGTGCAGGATGTGGCAGAGTGTCCTCACTTCAG
CCCATTTGCCGATGAGCTCACCGACTACGTGACAAAGAACATTCTGTCCACGCCAATCATGAAT
GGCAAAGATGTTGTGGCTGTGATTATGGCAGTGAATAAATTGGATGGTCCATGCTTCACGAGCG
AAGACGAAGATGTTTTCACGAAGTACCTGAATTTTGCTACATTAAACCTGAAGATCTATCACCT
AAGCTACCTCCACAACTGTGAAACACGCAGAGGCCAGGTGCTTCTCTGGTCAGCCAATAAGGTA
TTTGAAGAACTGACAGACATTGAAAGACAGTTCCACAAGGCCTTCTACACTGTCCGGGCCTATC
TAAACTGTGACCGGTACTCAGTGGGCCTCCTGGACATGACCAAGGAGAAGGAATTCTTTGATGT
GTGGCCTGTGCTGATGGGGGAAGCCCAGCCATACTCGGGCCCACGAACACCAGATGGCCGGGAA
ATTGTCTTCTACAAAGTCATTGATTATATCCTCCATGGCAAAGAAGACATCAAAGTCATTCCCA
CACCTCCAGCTGATCACTGGGCCCTGACCAGTGGCCTTCCCACCTATGTGGCAGAAAGTGGCTT
TATCTGTAACATCATGAACGCTTCAGCTGATGAAATGTTCAACTTTCAGGAAGGGCCCCTGGAT
GAGTCAGGGTGGGTGATCAAGAATGTTCTCTCCATGCCCATTGTCAACAAGAAGGAGGAGATTG
TGGGGGTAGCCACCTTCTACAACAGGAAAGATGGAAAGCCCTTCGATGATCAAGATGAAGTCCT
TATGGAGTCTCTGACACAGTTCCTGGGATGGTCAGTGTTGAACACAGACACCTATGACAAGATG
AACAAGCTGGAGAACCGTAAGGACATCGCCCAGGACATGGTTCTGTACCATGTGAGATGCGACA
AGGATGAAATCCAGGAAATCTTGCCAACAAGGGATCGCCTGGGGAAGGAACCTGCTGACTGTGA
GGAGGATGAGCTGGGGAAAATCTTGAAGGAGGAACTTCCAGGGCCTACCAAGTTTGACATCTAT
GAGTTCCACTTCTCTGATCTGGAGTGCACCGAGCTGGAGCTAGTCAAATGTGGCATCCAGATGT
ACTACGAGCTGGGTGTAGTCCGAAAGTTCCAGATTCCCCAGGAGGTCCTTGTGCGCTTCCTATT
CTCTGTCAGCAAAGCTTACCGAAGAATCACCTACCATAACTGGCGCCATGGCTTCAATGTGGCC
CAGACCATGTTTACCCTACTCATGACAGGCAAACTGAAGAGCTATTACACAGACCTAGAGGCCT
TCGCCATGGTTACAGCTGGCCTGTGCCACGACATCGACCACCGTGGCACCAACAACCTGTACCA
GATGAAATCTCAGAATCCTCTAGCCAAACTACATGGCTCCTCAATTCTGGAAAGGCACCACTTG
GAGTTTGGGAAGTTTCTGTTGGCAGAGGAGAGCCTGAATATCTACCAGAACCTGAACCGGCGGC
AGCATGAACATGTGATCCACCTCATGGACATCGCCATCATTGCCACTGACCTGGCCCTCTACTT
CAAGAAGAGAACCATGTTCCAGAAGATTGTGGATGAATCTAAGAACTATGAAGATAAGAAGAGC
TGGGTTGAGTACTTGTCCCTAGAGACCACACGAAAGGAGATCGTCATGGCCATGATGATGACTG
CATGTGACCTGTCTGCTATCACCAAGCCCTGGGAAGTCCAGAGCAAGGTTGCTCTTCTGGTGGC
TGCTGAGTTCTGGGAACAGGGGGACCTGGAGAGGACTGTCCTGGACCAACAGCCCATTCCCATG
ATGGACCGGAACAAAGCAGCTGAGCTCCCCAAGCTACAAGTTGGCTTCATCGACTTCGTATGTA
CTTTCGTGTACAAGGAATTTTCTCGATTTCACGAAGAGATCCTGCCCATGTTTGACCGACTGCA
AAATAACAGAAAGGAGTGGAAAGCTCTAGCTGATGAGTATGAGGCCAAAGTCAAGGCACTGGAG
GAAGAGAAGAAGAAGGAAGAAGACAGAGTAGCAGCCAAGAAAGCGGGCACAGAAATTTGCAATG
GTGGTCCAGCACCCAAGTCCTCGACCTGCTGTATTCTATAAGCTCTATCTCATGGCTTTGTGTC
CCTCCTGCCACTCACCCACTGGGTATGGACTCTGCCTATAGCAGTTTGGTGTAAGATATTAGGA
ACAGGGGGGAGAAAAAGATCAAACTTTGGATGTTTTGAAACTTTAAAGGTGTTTTTACAAATTA
AAACCAACTATGAATAAGTT

hide sequence

Protein Sequences


Protein RefSeqs	NP_001099494	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	D3ZDI8	(Get FASTA)	NCBI Sequence Viewer
	EDL84006	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000000077
	ENSRNOP00000000077.5
	ENSRNOP00055038569
	ENSRNOP00060015232
	ENSRNOP00065015578

RefSeq Acc Id:

NP_001099494 ⟸ NM_001106024

- UniProtKB:

D3ZDI8 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MSLSEEQVRSFLDGNPTFAHQYFEKKLSPENVAGACEGGCLVDCGSLRELCQVEESAALFELVQ
DMQESVNMERVVFKVLRRLCTILHADRCSLFMYRQRNGVAELATRLFSVQPDSLLEDCLVPPDS
EIVFPLDIGIVGHVAQTKKMINVQDVAECPHFSPFADELTDYVTKNILSTPIMNGKDVVAVIMA
VNKLDGPCFTSEDEDVFTKYLNFATLNLKIYHLSYLHNCETRRGQVLLWSANKVFEELTDIERQ
FHKAFYTVRAYLNCDRYSVGLLDMTKEKEFFDVWPVLMGEAQPYSGPRTPDGREIVFYKVIDYI
LHGKEDIKVIPTPPADHWALTSGLPTYVAESGFICNIMNASADEMFNFQEGPLDESGWVIKNVL
SMPIVNKKEEIVGVATFYNRKDGKPFDDQDEVLMESLTQFLGWSVLNTDTYDKMNKLENRKDIA
QDMVLYHVRCDKDEIQEILPTRDRLGKEPADCEEDELGKILKEELPGPTKFDIYEFHFSDLECT
ELELVKCGIQMYYELGVVRKFQIPQEVLVRFLFSVSKAYRRITYHNWRHGFNVAQTMFTLLMTG
KLKSYYTDLEAFAMVTAGLCHDIDHRGTNNLYQMKSQNPLAKLHGSSILERHHLEFGKFLLAEE
SLNIYQNLNRRQHEHVIHLMDIAIIATDLALYFKKRTMFQKIVDESKNYEDKKSWVEYLSLETT
RKEIVMAMMMTACDLSAITKPWEVQSKVALLVAAEFWEQGDLERTVLDQQPIPMMDRNKAAELP
KLQVGFIDFVCTFVYKEFSRFHEEILPMFDRLQNNRKEWKALADEYEAKVKALEEEKKKEEDRV
AAKKAGTEICNGGPAPKSSTCCIL

hide sequence

Ensembl Acc Id:

ENSRNOP00000000077 ⟸ ENSRNOT00000000077

Protein Domains

GAF 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

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1311039	AgrOrtholog
BioCyc Gene	G2FUF-16674	BioCyc
Ensembl Genes	ENSRNOG00000000065	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOG00055027157	UniProtKB/Swiss-Prot
	ENSRNOG00060011473	UniProtKB/Swiss-Prot
	ENSRNOG00065012459	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000000077	ENTREZGENE
	ENSRNOT00000000077.7	UniProtKB/Swiss-Prot
	ENSRNOT00055046948	UniProtKB/Swiss-Prot
	ENSRNOT00060019415	UniProtKB/Swiss-Prot
	ENSRNOT00065020280	UniProtKB/Swiss-Prot
Gene3D-CATH	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	UniProtKB/Swiss-Prot
	3.30.450.40	UniProtKB/Swiss-Prot
InterPro	GAF	UniProtKB/Swiss-Prot
	GAF-like_dom_sf	UniProtKB/Swiss-Prot
	HD/PDEase_dom	UniProtKB/Swiss-Prot
	PDEase	UniProtKB/Swiss-Prot
	PDEase_catalytic_dom	UniProtKB/Swiss-Prot
	PDEase_catalytic_dom_sf	UniProtKB/Swiss-Prot
	PDEase_CS	UniProtKB/Swiss-Prot
KEGG Report	rno:289878	UniProtKB/Swiss-Prot
NCBI Gene	289878	ENTREZGENE
PANTHER	CYCLIC NUCLEOTIDE PHOSPHODIESTERASE	UniProtKB/Swiss-Prot
Pfam	GAF	UniProtKB/Swiss-Prot
	PDEase_I	UniProtKB/Swiss-Prot
PhenoGen	Pde6b	PhenoGen
PRINTS	PDIESTERASE1	UniProtKB/Swiss-Prot
PROSITE	GAF	UniProtKB/Swiss-Prot
	PDEASE_I_1	UniProtKB/Swiss-Prot
	PDEASE_I_2	UniProtKB/Swiss-Prot
RatGTEx	ENSRNOG00000000065	RatGTEx
	ENSRNOG00055027157	RatGTEx
	ENSRNOG00060011473	RatGTEx
	ENSRNOG00065012459	RatGTEx
SMART	GAF	UniProtKB/Swiss-Prot
	HDc	UniProtKB/Swiss-Prot
Superfamily-SCOP	GAF domain-like	UniProtKB/Swiss-Prot
	HD-domain/PDEase-like	UniProtKB/Swiss-Prot
UniProt	D3ZDI8	ENTREZGENE, UniProtKB/Swiss-Prot

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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIA

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - KEGG (archival)

Mammalian Phenotype

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIA

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - KEGG (archival)

Mammalian Phenotype