Pde6c (phosphodiesterase 6C) - Rat Genome Database

Name: Pde6c
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Pde6c (phosphodiesterase 6C) Rattus norvegicus

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Symbol:

Pde6c

Name:

phosphodiesterase 6C

RGD ID:

1309844

Description:

Predicted to enable 3',5'-cyclic-AMP phosphodiesterase activity and 3',5'-cyclic-GMP phosphodiesterase activity. Predicted to be involved in cAMP-mediated signaling and visual perception. Predicted to act upstream of or within phototransduction, visible light; retinal cone cell development; and sensory perception of light stimulus. Human ortholog(s) of this gene implicated in cone-rod dystrophy. Orthologous to human PDE6C (phosphodiesterase 6C); PARTICIPATES IN visual phototransduction pathway; purine metabolic pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'; LOC361752; phosphodiesterase 6C, cGMP specific, cone, alpha prime

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):	PDE6C (phosphodiesterase 6C)	HGNC	EggNOG, Ensembl, HomoloGene, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Pde6c (phosphodiesterase 6C, cGMP specific, cone, alpha prime)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Pde6c (phosphodiesterase 6C)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PDE6C (phosphodiesterase 6C)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	PDE6C (phosphodiesterase 6C)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Pde6c (phosphodiesterase 6C)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	PDE6C (phosphodiesterase 6C)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	PDE6C (phosphodiesterase 6C)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Pde6c (phosphodiesterase 6C)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	PDE6C (phosphodiesterase 6C)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Pde6c (phosphodiesterase 6C, cGMP specific, cone, alpha prime)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	pde6c (phosphodiesterase 6C, cGMP-specific, cone, alpha prime)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	PDE2	Alliance	DIOPT (Ensembl Compara\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	pde6c	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	245,322,015 - 245,377,874 (+)	NCBI		GRCr8
mRatBN7.2	1	235,909,583 - 235,965,435 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	235,909,775 - 235,965,315 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	244,331,176 - 244,387,526 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	251,226,959 - 251,282,404 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	244,065,193 - 244,120,646 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	256,822,099 - 256,885,879 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	256,822,334 - 256,877,810 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	264,302,622 - 264,358,510 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	242,459,653 - 242,515,102 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	1	242,652,932 - 242,727,438 (+)	NCBI
Celera	1	233,003,126 - 233,058,624 (+)	NCBI		Celera
Cytogenetic Map	1	q53	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

achromatopsia (ISO,ISS)

Achromatopsia 1 (ISO)

Achromatopsia 5 (ISO)

amphetamine abuse (ISO)

cone dystrophy (ISO)

Cone Dystrophy 4 (ISO)

cone-rod dystrophy (ISO)

Eye Abnormalities (ISO)

familial temporal lobe epilepsy 1 (ISO)

fundus dystrophy (ISO)

genetic disease (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

17beta-estradiol (EXP,ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,3,7,8-Tetrachlorodibenzofuran (EXP)

2-bromohexadecanoic acid (ISO)

4,4'-sulfonyldiphenol (ISO)

aflatoxin B1 (ISO)

Aflatoxin B2 alpha (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

benzo[b]fluoranthene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP)

bromobenzene (EXP)

cadmium atom (ISO)

cadmium dichloride (ISO)

carbon nanotube (ISO)

CGP 52608 (ISO)

folic acid (ISO)

formaldehyde (ISO)

furan (EXP)

genistein (EXP)

graphene oxide (ISO)

malathion (ISO)

metacetamol (ISO)

methamphetamine (ISO)

methyl methanesulfonate (ISO)

mono(2-ethylhexyl) phthalate (ISO)

monosodium L-glutamate (ISO)

N-nitrosodiethylamine (ISO)

paracetamol (ISO)

parathion (ISO)

perfluorohexanesulfonic acid (ISO)

perfluorooctanoic acid (ISO)

phenobarbital (ISO)

pioglitazone (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

streptozocin (ISO)

tetraphene (ISO)

thioacetamide (EXP)

triphenyl phosphate (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

cAMP-mediated signaling (IBA)

phototransduction, visible light (ISO)

retinal cone cell development (ISO)

sensory perception of light stimulus (ISO)

visual perception (IBA,ISO)

Molecular Function

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

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

metal ion binding (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

purine metabolic pathway (IEA)

visual phototransduction pathway (ISO)

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.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
5.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
6.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
7.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
9.	Comprehensive gene review and curation	RGD comprehensive gene curation

Additional References at PubMed

PMID:16723493	PMID:21052544	PMID:22937111

Genomics

Comparative Map Data

Pde6c
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	245,322,015 - 245,377,874 (+)	NCBI		GRCr8
mRatBN7.2	1	235,909,583 - 235,965,435 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	235,909,775 - 235,965,315 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	244,331,176 - 244,387,526 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	251,226,959 - 251,282,404 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	244,065,193 - 244,120,646 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	256,822,099 - 256,885,879 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	256,822,334 - 256,877,810 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	264,302,622 - 264,358,510 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	242,459,653 - 242,515,102 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	1	242,652,932 - 242,727,438 (+)	NCBI
Celera	1	233,003,126 - 233,058,624 (+)	NCBI		Celera
Cytogenetic Map	1	q53	NCBI

PDE6C
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	10	93,612,537 - 93,666,010 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	10	93,612,537 - 93,666,010 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	10	95,372,294 - 95,425,767 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	10	95,362,335 - 95,415,420 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	10	95,362,334 - 95,415,418	NCBI
Celera	10	89,113,470 - 89,166,556 (+)	NCBI		Celera
Cytogenetic Map	10	q23.33	NCBI
HuRef	10	89,000,108 - 89,053,208 (+)	NCBI		HuRef
CHM1_1	10	95,654,899 - 95,708,001 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	10	94,492,491 - 94,545,941 (+)	NCBI		T2T-CHM13v2.0

Pde6c
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	19	38,121,220 - 38,172,391 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	19	38,121,229 - 38,172,406 (+)	Ensembl		GRCm39 Ensembl
GRCm38	19	38,132,781 - 38,183,955 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	19	38,132,781 - 38,183,958 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	19	38,207,271 - 38,258,445 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	19	38,198,090 - 38,248,883 (+)	NCBI		MGSCv36	mm8
Celera	19	38,926,729 - 38,979,099 (+)	NCBI		Celera
Cytogenetic Map	19	C2	NCBI
cM Map	19	32.77	NCBI

Pde6c
(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_004955507	129,678 - 179,305 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955507	129,678 - 179,586 (+)	NCBI	ChiLan1.0	ChiLan1.0

PDE6C
(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	8	105,652,841 - 105,708,283 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	10	105,658,156 - 105,715,240 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	10	90,361,003 - 90,414,169 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	10	93,871,704 - 93,924,654 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	10	93,871,704 - 93,924,654 (+)	Ensembl	panpan1.1		panPan2

PDE6C
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	28	7,839,604 - 7,887,827 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	28	7,839,847 - 7,887,776 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	28	8,016,008 - 8,063,731 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	28	8,099,839 - 8,147,676 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	28	8,100,076 - 8,147,622 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	28	7,819,583 - 7,867,280 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	28	7,848,791 - 7,896,637 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	28	8,018,719 - 8,066,559 (+)	NCBI		UU_Cfam_GSD_1.0

Pde6c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024407213	39,709,403 - 39,760,997 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936601	1,341,658 - 1,393,377 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936601	1,343,538 - 1,393,605 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PDE6C
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	14	105,050,691 - 105,122,421 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	14	105,010,974 - 105,122,628 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	14	114,743,150 - 114,854,527 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PDE6C
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	9	86,850,500 - 86,904,853 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	9	86,851,867 - 86,904,481 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666048	47,626,964 - 47,680,050 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Pde6c
(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_female_1.0 Ensembl	NW_004624737	4,810,806 - 4,867,370 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624737	4,804,630 - 4,867,565 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Pde6c
525 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	27
Count of miRNA genes:	26
Interacting mature miRNAs:	27
Transcripts:	ENSRNOT00000022317
Prediction methods:	Miranda, Rnahybrid
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.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1578778	Pur4	Proteinuria QTL 4	3.3	0.003	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	1	150700247	252085048	Rat
1354646	Kidm18	Kidney mass QTL 18	5.7		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	151162512	256448636	Rat
1357335	Bw39	Body weight QTL 39	3.3		body mass (VT:0001259)	body weight (CMO:0000012)	1	197814409	242814409	Rat
2302375	Bw83	Body weight QTL 83	4.87	0.0002	body mass (VT:0001259)	body weight (CMO:0000012)	1	197697768	242697768	Rat
2293674	Bss39	Bone structure and strength QTL 39	7.1	0.0001	femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	1	201554356	246554356	Rat
1354652	Kidm20	Kidney mass QTL 20	4.3		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	177227632	256448636	Rat
2302378	Insul11	Insulin level QTL 11	3.25		blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	1	144267353	251128347	Rat
61455	Niddm7	Non-insulin dependent diabetes mellitus QTL 7	5.5		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	1	214537555	238757011	Rat
61327	Eae7	Experimental allergic encephalomyelitis QTL 7	5.6		body mass (VT:0001259)	change in body weight (CMO:0002045)	1	216255568	260522016	Rat
1600392	Bw123	Body weight QTL 123		0.001	body mass (VT:0001259)	body weight (CMO:0000012)	1	223201027	260522016	Rat
7794788	Mcs32	Mammary carcinoma susceptibility QTL 32	2.61		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	1	115540693	238914717	Rat
1600395	Niddm69	Non-insulin dependent diabetes mellitus QTL 69	4.14	0.0002	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	1	195804352	257091168	Rat
1578763	Kidm29	Kidney mass QTL 29	3.3	0.0001	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	1	179567751	260522016	Rat
1600396	Niddm68	Non-insulin dependent diabetes mellitus QTL 68	4.97	0.0003	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	195804352	257091168	Rat
1354624	Cm35	Cardiac mass QTL35	5.7		heart left ventricle mass (VT:0007031)	calculated heart weight (CMO:0000073)	1	177227632	256448636	Rat
1600397	Edcs4	Endometrial carcinoma susceptibility QTL 4	2.2		uterus morphology trait (VT:0001120)	percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)	1	206081677	251081677	Rat
1549837	Hcar15	Hepatocarcinoma resistance QTL 15		0.05	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	153136852	260522016	Rat
2293694	Bss38	Bone structure and strength QTL 38	7.05	0.0001	femur strength trait (VT:0010010)	femur stiffness (CMO:0001674)	1	201554356	246554356	Rat
1600388	Niddm67	Non-insulin dependent diabetes mellitus QTL 67	5.84	0.000004	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	195804352	257091168	Rat
1578759	Uae30	Urinary albumin excretion QTL 30	3.3	0.003	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	150700247	252085048	Rat
1300108	Rf8	Renal function QTL 8	3.75		renal blood flow trait (VT:2000006)	absolute change in renal vascular resistance (CMO:0001900)	1	228581588	259647894	Rat
8655655	Arrd2	Age-related retinal degeneration QTL 2	7.79		retinal layer morphology trait (VT:0003727)	percentage of study population developing retinopathy during a period of time (CMO:0002453)	1	183970203	243914901	Rat
734767	Niddm57	Non-insulin dependent diabetes mellitus QTL 57			body mass (VT:0001259)	body weight (CMO:0000012)	1	224054293	260122809	Rat
631215	Stl8	Serum triglyceride level QTL 8	9.27	0.0001	blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	1	225126575	260522016	Rat
1358898	Bp255	Blood pressure QTL 255	3.6		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	191019702	246062233	Rat
631843	Bw116	Body weight QTL 116	4.1	0.016	abdominal adipose amount (VT:1000220)	abdominal fat pad weight (CMO:0000088)	1	224054293	260122809	Rat
731175	Uae20	Urinary albumin excretion QTL 20	3.5	0.0018	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	221264111	259647894	Rat
2300175	Bmd40	Bone mineral density QTL 40	15.4	0.0001	femur mineral mass (VT:0010011)	bone mineral density (CMO:0001226)	1	201554356	246554356	Rat
724538	Kidm1	Kidney mass QTL 1	3.2		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	213707201	252085212	Rat
1354661	Bw33	Body weight QTL 33	5.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	151162512	256448636	Rat
2293655	Bss36	Bone structure and strength QTL 36	10.66	0.0001	femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	1	201554356	246554356	Rat
1298084	Thym4	Thymus enlargement QTL 4	10.68		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	1	197814409	242814409	Rat
724531	Uae5	Urinary albumin excretion QTL 5	4		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	1	150700142	252085212	Rat
8552891	Epfw5	Epididymal fat weight QTL 5	4.4		epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	1	193113876	238113876	Rat
734769	Niddm58	Non-insulin dependent diabetes mellitus QTL 58			body mass (VT:0001259)	body weight (CMO:0000012)	1	224569538	260122809	Rat
734768	Niddm59	Non-insulin dependent diabetes mellitus QTL 59			body mass (VT:0001259)	body weight (CMO:0000012)	1	213843987	258843987	Rat
724533	Rf51	Renal function QTL 51	5.3	0.0002	kidney plasma flow trait (VT:0005524)	renal plasma flow (CMO:0001914)	1	218753816	256448513	Rat
1358890	Bp259	Blood pressure QTL 259	3.06		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	210702053	260522016	Rat
1354580	Scort1	Serum corticosterone level QTL 1	3.4		blood corticosterone amount (VT:0005345)	blood corticosterone level (CMO:0001172)	1	156677124	256448636	Rat
634313	Niddm43	Non-insulin dependent diabetes mellitus QTL 43			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	199050459	259647894	Rat
1358292	Cm37	Cardiac mass QTL 37	6.2	8e-07	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	1	196248093	241248093	Rat
61376	Bp42	Blood pressure QTL 42	23.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	197814409	242814409	Rat
1549910	Bw54	Body weight QTL 54		0.05	body mass (VT:0001259)	body weight (CMO:0000012)	1	214647894	259647894	Rat
70211	Niddm24	Non-insulin dependent diabetes mellitus QTL 24	3.79		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	214647894	259647894	Rat
724552	Glom2	Glomerulus QTL 2	3.3	0.0001	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)	1	222363780	260522016	Rat
1357399	Bw45	Body weight QTL 45	3.05		body mass (VT:0001259)	body mass index (BMI) (CMO:0000105)	1	206329708	251329708	Rat
2316896	Gluco57	Glucose level QTL 57	7.2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	228985440	245907899	Rat
1357404	Bw42	Body weight QTL 42	4.49	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	1	206329708	251329708	Rat
10053715	Scort24	Serum corticosterone level QTL 24	2.13	0.0088	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	1	221414816	260522016	Rat
7421630	Bp362	Blood pressure QTL 362		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	118608292	241799120	Rat
1358916	Kidm22	Kidney mass QTL 22	3.32		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	1	210702053	240947965	Rat
634321	Hc1	Hypercalciuria QTL 1	2.91		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	1	178810256	240830002	Rat
61400	Niddm1	Non-insulin dependent diabetes mellitus QTL 1	11		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	218753689	245907899	Rat
2292216	Bw80	Body weight QTL 80	3.23	0.0019	body mass (VT:0001259)	body weight (CMO:0000012)	1	213533809	243914901	Rat
10059587	Bw173	Body weight QTL 173	3.23	0.025	body mass (VT:0001259)	body weight (CMO:0000012)	1	202069611	247069611	Rat
2292220	Bp306	Blood pressure QTL 306	3.47	0.00087	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	164310393	243914901	Rat
1641926	Teswt2	Testicular weight QTL 2	2.82		testis mass (VT:1000644)	both testes wet weight (CMO:0000175)	1	197697768	238755659	Rat
10059590	Kidm44	Kidney mass QTL 44	3.42	0.025	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	1	191033875	236033875	Rat
631658	Cm7	Cardiac mass QTL 7	5.32	0.0001	aorta mass (VT:0002845)	aorta weight (CMO:0000076)	1	196248093	241248093	Rat
2293700	Bmd27	Bone mineral density QTL 27	6.6	0.0001	femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	1	224054293	243747962	Rat
1354610	Bw34	Body weight QTL 34	4.1		body mass (VT:0001259)	body weight (CMO:0000012)	1	151162512	256448636	Rat
2293701	Bmd34	Bone mineral density QTL 34	8.3	0.0001	femur strength trait (VT:0010010)	femoral neck ultimate force (CMO:0001703)	1	224054293	243747962	Rat
8655855	Arrd3	Age-related retinal degeneration QTL 3	3.07		lens clarity trait (VT:0001304)	cataract incidence/prevalence measurement (CMO:0001585)	1	183970203	243914901	Rat
1600374	Mcs17	Mammary carcinoma susceptibility QTL 17	3		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	1	197670404	242670404	Rat
1581544	Rf52	Renal function QTL 52		0.05	urine total protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	1	232156370	259647894	Rat
1600363	Hc6	Hypercalciuria QTL 6	2.7		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	1	203995416	244113296	Rat
631536	Lnnr2	Liver neoplastic nodule remodeling QTL 2	2.9	0.0005	liver integrity trait (VT:0010547)	liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)	1	233948574	260522016	Rat
2302040	Pia35	Pristane induced arthritis QTL 35	3.8	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	1	216255568	260522016	Rat
738032	Hcas5	Hepatocarcinoma susceptibility QTL 5	3.12		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	176426412	257976495	Rat
1358191	Ept10	Estrogen-induced pituitary tumorigenesis QTL 10	3.8		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	1	192825253	243914732	Rat
631669	Iddm9	Insulin dependent diabetes mellitus QTL 9	2.8	0.039	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	1	233190394	258625266	Rat
1598821	Rf55	Renal function QTL 55	6.3		renal blood flow trait (VT:2000006)	ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)	1	218748008	257976495	Rat
7394701	Uae46	Urinary albumin excretion QTL 46	3.6	0.0056	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	201554356	246554356	Rat

Markers in Region

D1Got235

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	235,960,339 - 235,960,569 (+)	MAPPER	mRatBN7.2
Rnor_6.0	1	256,872,919 - 256,873,146	NCBI	Rnor6.0
Rnor_5.0	1	264,353,416 - 264,353,643	UniSTS	Rnor5.0
RGSC_v3.4	1	242,510,210 - 242,510,438	RGD	RGSC3.4
RGSC_v3.4	1	242,510,211 - 242,510,438	UniSTS	RGSC3.4
RGSC_v3.1	1	242,722,332 - 242,722,560	RGD
Celera	1	233,053,733 - 233,053,960	UniSTS
RH 3.4 Map	1	1581.2	UniSTS
RH 3.4 Map	1	1581.2	RGD
RH 2.0 Map	1	1219.7	RGD
Cytogenetic Map	1	q53	UniSTS

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			6		6
Low	10		143	117	53	117			11	4	23	21
Below cutoff	11	51	76	30	10	30	34	37	77	50	104	36	24

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001416003	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063268656	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_001835438	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC096330	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC107608	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473953	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000001	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000022317 ⟹ ENSRNOP00000022317

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	235,909,775 - 235,965,315 (+)	Ensembl
Rnor_6.0 Ensembl	1	256,822,334 - 256,877,810 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000117700 ⟹ ENSRNOP00000087890

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	235,909,775 - 235,965,315 (+)	Ensembl

RefSeq Acc Id:

NM_001416003 ⟹ NP_001402932

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	245,322,015 - 245,377,861 (+)	NCBI
mRatBN7.2	1	235,909,583 - 235,965,435 (+)	NCBI

RefSeq Acc Id:

XM_063268656 ⟹ XP_063124726

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	245,322,098 - 245,377,874 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001402932	(Get FASTA)	NCBI Sequence Viewer
	XP_063124726	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDM13214	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000022317.6
	ENSRNOP00000087890.1

Ensembl Acc Id:

ENSRNOP00000022317 ⟸ ENSRNOT00000022317

Ensembl Acc Id:

ENSRNOP00000087890 ⟸ ENSRNOT00000117700

RefSeq Acc Id:	NP_001402932 ⟸ NM_001416003
- UniProtKB:	D3ZLC7 (UniProtKB/TrEMBL), A6I183 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_063124726 ⟸ XM_063268656
- Peptide Label:	isoform X1
- UniProtKB:	A6I183 (UniProtKB/TrEMBL), A0A8I6A6R9 (UniProtKB/TrEMBL)

Protein Domains

PDEase

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D3ZLC7-F1-model_v2	AlphaFold	D3ZLC7	1-861	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:1309844	AgrOrtholog
BioCyc Gene	G2FUF-55791	BioCyc
Ensembl Genes	ENSRNOG00000016593	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000022317.6	UniProtKB/TrEMBL
	ENSRNOT00000117700.1	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
NCBI Gene	361752	ENTREZGENE
PANTHER	CONE CGMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE SUBUNIT ALPHA	UniProtKB/TrEMBL
	CYCLIC NUCLEOTIDE PHOSPHODIESTERASE	UniProtKB/TrEMBL
Pfam	GAF	UniProtKB/TrEMBL
	PDEase_I	UniProtKB/TrEMBL
PhenoGen	Pde6c	PhenoGen
PRINTS	PDIESTERASE1	UniProtKB/TrEMBL
PROSITE	PDEASE_I	UniProtKB/TrEMBL
	PDEASE_I_2	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000016593	RatGTEx
SMART	GAF	UniProtKB/TrEMBL
	HDc	UniProtKB/TrEMBL
Superfamily-SCOP	GAF domain-like	UniProtKB/TrEMBL
	HD-domain/PDEase-like	UniProtKB/TrEMBL
UniProt	A0A8I6A6R9	ENTREZGENE, UniProtKB/TrEMBL
	A6I183	ENTREZGENE, UniProtKB/TrEMBL
	D3ZLC7	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2015-11-30	Pde6c	phosphodiesterase 6C	Pde6c	phosphodiesterase 6C, cGMP specific, cone, alpha prime	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Pde6c	phosphodiesterase 6C, cGMP specific, cone, alpha prime	Pde6c_predicted	phosphodiesterase 6C, cGMP specific, cone, alpha prime (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Pde6c_predicted	phosphodiesterase 6C, cGMP specific, cone, alpha prime (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 - OMIM

RGD Manual Annotations

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - KEGG (archival)