Cnot3 (CCR4-NOT transcription complex, subunit 3)

	Submit Data \| Help \| Video Tutorials \| News \| Publications \| Download \| REST API \| Citing RGD \| Contact
	Search RGD Grant Resources Citing RGD About Us Contact Us Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) RatMine GViewer (Genome Viewer) Overgo Probe Designer ACP Haplotyper Genome Scanner Aging & Age-Related Disease Cancer Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease Find Models new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive Pathways Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
	Advanced Search (OLGA)

Gene: Cnot3 (CCR4-NOT transcription complex, subunit 3) Rattus norvegicus

Analyze

Symbol:

Cnot3

Name:

CCR4-NOT transcription complex, subunit 3

RGD ID:

1304771

Description:

Predicted to be involved in positive regulation of cold-induced thermogenesis; regulation of stem cell population maintenance; and trophectodermal cell differentiation. Predicted to localize to CCR4-NOT complex and P-body. Orthologous to human CNOT3 (CCR4-NOT transcription complex subunit 3); PARTICIPATES IN microRNA pathway; RNA degradation pathway; INTERACTS WITH bisphenol A; vinclozolin; 1,2-dimethylhydrazine (ortholog).

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

CCR4-NOT transcription complex subunit 3; LOC308311

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	65,555,924 - 65,572,167 (-)	NCBI
Rnor_6.0 Ensembl	1	64,130,908 - 64,147,251 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	64,130,823 - 64,147,066 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	63,123,105 - 63,139,396 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	63,868,853 - 63,885,095 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	63,945,601 - 63,961,798 (-)	NCBI
Celera	1	63,280,966 - 63,297,090 (-)	NCBI		Celera
Cytogenetic Map	1	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

Intellectual Developmental Disorder with Speech Delay, Autism, and Dysmorphic Facies (ISO)

intellectual disability (ISO)

Prostatic Neoplasms (ISO)

T-cell acute lymphoblastic leukemia (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

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

4,4'-diaminodiphenylmethane (ISO)

antirheumatic drug (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

benzo[e]pyrene (ISO)

bisphenol A (EXP,ISO)

cerium trichloride (ISO)

dicrotophos (ISO)

dorsomorphin (ISO)

entinostat (ISO)

lead(0) (ISO)

lead(2+) (ISO)

mercury atom (ISO)

mercury(0) (ISO)

methapyrilene (ISO)

methotrexate (ISO)

methylmercury chloride (ISO)

oxaliplatin (ISO)

phenobarbital (ISO)

propiconazole (ISO)

SB 431542 (ISO)

testosterone enanthate (ISO)

trichostatin A (ISO)

troglitazone (ISO)

tungsten (ISO)

urethane (ISO)

valproic acid (ISO)

vinclozolin (EXP)

vincristine (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

nuclear-transcribed mRNA poly(A) tail shortening (IBA)

positive regulation of cold-induced thermogenesis (ISO,ISS)

regulation of stem cell population maintenance (IBA,ISO)

regulation of transcription, DNA-templated (IEA)

trophectodermal cell differentiation (ISO)

Cellular Component

CCR4-NOT complex (ISO)

CCR4-NOT core complex (IBA)

cellular_component (ND)

nucleus (IEA)

P-body (IBA,ISO)

Molecular Function

molecular_function (ND)

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

microRNA pathway (ISO)

RNA degradation pathway (IEA)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	GOA data from the GO Consortium
3.	Li X, etal., FEBS Lett. 2017 Jan;591(2):358-368. doi: 10.1002/1873-3468.12550. Epub 2017 Jan 12.
4.	MGD data from the GO Consortium
5.	Pipeline to import KEGG annotations from KEGG into RGD
6.	RGD automated data pipeline
7.	RGD automated import pipeline for gene-chemical interactions
8.	RGD comprehensive gene curation
9.	Wahle E and Winkler GS, Biochim Biophys Acta. 2013 Jun-Jul;1829(6-7):561-70. doi: 10.1016/j.bbagrm.2013.01.003. Epub 2013 Jan 19.

Additional References at PubMed

PMID:19558367	PMID:20133598	PMID:22367759	PMID:30361391

Genomics

Comparative Map Data

Cnot3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	65,555,924 - 65,572,167 (-)	NCBI
Rnor_6.0 Ensembl	1	64,130,908 - 64,147,251 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	64,130,823 - 64,147,066 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	63,123,105 - 63,139,396 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	63,868,853 - 63,885,095 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	63,945,601 - 63,961,798 (-)	NCBI
Celera	1	63,280,966 - 63,297,090 (-)	NCBI		Celera
Cytogenetic Map	1	q12	NCBI

CNOT3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	19	54,137,749 - 54,155,681 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	19	54,137,689 - 54,155,690 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	19	54,641,478 - 54,659,419 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	19	59,333,261 - 59,351,239 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	19	59,333,260 - 59,351,239	NCBI
Celera	19	51,682,719 - 51,700,732 (+)	NCBI
Cytogenetic Map	19	q13.42	NCBI
HuRef	19	50,957,822 - 50,975,744 (+)	NCBI		HuRef
CHM1_1	19	54,642,739 - 54,660,727 (+)	NCBI		CHM1_1

Cnot3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	7	3,646,717 - 3,664,108 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	7	3,648,267 - 3,664,108 (+)	Ensembl
GRCm38	7	3,645,247 - 3,661,109 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	7	3,645,268 - 3,661,109 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	7	3,596,871 - 3,612,711 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	7	3,239,140 - 3,264,187 (+)	NCBI			mm8
Celera	7	3,557,188 - 3,573,023 (+)	NCBI		Celera
Cytogenetic Map	7	A1	NCBI

Cnot3
(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_004955604	109,340 - 122,001 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955604	109,522 - 122,001 (-)	NCBI	ChiLan1.0	ChiLan1.0

CNOT3
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	19	59,913,040 - 59,931,108 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	19	59,913,040 - 59,931,108 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	19	51,071,167 - 51,089,289 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

CNOT3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	1	103,057,542 - 103,066,887 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	1	103,057,392 - 103,070,612 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Cnot3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936994	256,022 - 271,235 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CNOT3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	55,973,591 - 55,991,287 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	55,975,628 - 55,993,140 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	53,227,109 - 53,243,171 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CNOT3
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	6	46,814,695 - 46,832,657 (+)	NCBI
ChlSab1.1 Ensembl	6	46,819,903 - 46,836,838 (+)	Ensembl

Cnot3
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624832	2,429,809 - 2,441,886 (-)	NCBI

Position Markers

AW533911

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	64,131,580 - 64,131,785	NCBI	Rnor6.0
Rnor_5.0	1	63,123,862 - 63,124,067	UniSTS	Rnor5.0
RGSC_v3.4	1	63,869,609 - 63,869,814	UniSTS	RGSC3.4
Celera	1	63,281,723 - 63,281,928	UniSTS
RH 3.4 Map	1	740.9	UniSTS
Cytogenetic Map	1	q12	UniSTS

BF396308

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	64,131,931 - 64,132,159	NCBI	Rnor6.0
Rnor_5.0	1	63,124,213 - 63,124,441	UniSTS	Rnor5.0
RGSC_v3.4	1	63,869,960 - 63,870,188	UniSTS	RGSC3.4
Celera	1	63,282,074 - 63,282,302	UniSTS
RH 3.4 Map	1	742.69	UniSTS
Cytogenetic Map	1	q12	UniSTS

BF397882

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	64,144,687 - 64,144,879	NCBI	Rnor6.0
Rnor_5.0	1	63,136,969 - 63,137,161	UniSTS	Rnor5.0
RGSC_v3.4	1	63,882,716 - 63,882,908	UniSTS	RGSC3.4
Celera	1	63,294,711 - 63,294,903	UniSTS
RH 3.4 Map	1	729.3	UniSTS
Cytogenetic Map	1	q12	UniSTS

CNOT3_7840

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	64,130,722 - 64,131,203	NCBI	Rnor6.0
Rnor_5.0	1	63,123,004 - 63,123,485	UniSTS	Rnor5.0
RGSC_v3.4	1	63,868,751 - 63,869,232	UniSTS	RGSC3.4
Celera	1	63,280,865 - 63,281,346	UniSTS
Cytogenetic Map	1	q12	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
738020	Pia8	Pristane induced arthritis QTL 8	4.7		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	1	1	64407321	Rat
1554320	Bmd1	Bone mineral density QTL 1	12.2	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	1	254393	86904217	Rat
631688	Hcas2	Hepatocarcinoma susceptibility QTL 2	3	0.0001	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	5655769	122614963	Rat
4889451	Eae29	Experimental allergic encephalomyelitis QTL 29	5.51		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis severity score (CMO:0001419)	1	5655772	85706974	Rat
1300167	Hrtrt2	Heart rate QTL 2	4.35		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	11314489	75844121	Rat
2313062	Bmd73	Bone mineral density QTL 73	3.9	0.0001	tibia mineral mass (VT:1000283)	cortical volumetric bone mineral density (CMO:0001730)	1	11314489	83657083	Rat
2313065	Bss67	Bone structure and strength QTL 67	3.1	0.0001	tibia area (VT:1000281)	tibia total energy absorbed before break (CMO:0001736)	1	11314489	83657083	Rat
2313069	Bss68	Bone structure and strength QTL 68	2.9	0.0001	tibia size trait (VT:0100001)	tibia total energy absorbed before break (CMO:0001736)	1	11314489	83657083	Rat
2313075	Bss66	Bone structure and strength QTL 66	3.4	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	11314489	83657083	Rat
2313077	Bss69	Bone structure and strength QTL 69	3.5	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	1	11314489	83657083	Rat
2313092	Bmd72	Bone mineral density QTL 72	2.5	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	1	11314489	83657083	Rat
2313097	Bss70	Bone structure and strength QTL 70	3.5	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	1	11314489	83657083	Rat
724520	Bp145	Blood pressure QTL 145	2.1	0.0024	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	21079305	66079305	Rat
1357400	Bw62	Body weight QTL62	4.05		inguinal fat pad mass (VT:0010424)	inguinal fat pad weight to body weight ratio (CMO:0001253)	1	23406428	68406428	Rat
631495	Bp96	Blood pressure QTL 96	4.52		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	23406428	108057505	Rat
1358192	Ept13	Estrogen-induced pituitary tumorigenesis QTL 13	3.4		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	1	24297799	78748000	Rat
1358359	Sradr1	Stress Responsive Adrenal Weight QTL 1	4.74		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	1	25951907	130917265	Rat
1331785	Rf27	Renal function QTL 27	4.643		urine sodium amount (VT:0006274)	urine sodium level (CMO:0000129)	1	31489454	79689689	Rat
1354643	Foco2	Food consumption QTL 2	7.17	0.0001	eating behavior trait (VT:0001431)	food intake rate (CMO:0000427)	1	34449112	79449112	Rat
1354599	Bw29	Body weight QTL 29	3.46	0.001	body mass (VT:0001259)	body weight (CMO:0000012)	1	34449112	79449112	Rat
70225	Bp58	Blood pressure QTL 58	3.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	34993530	173445086	Rat
1300172	Bp172	Blood pressure QTL 172	3.56		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	35377508	94364229	Rat
10059597	Bp377	Blood pressure QTL 377	3.42	0.025	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	35377692	217372257	Rat
9589820	Insglur3	Insulin/glucose ratio QTL 3	10.75	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	1	35854167	80854167	Rat
8552900	Pigfal1	Plasma insulin-like growth factor 1 level QTL 1	7.4		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	1	35854167	80854167	Rat
8552948	Pigfal11	Plasma insulin-like growth factor 1 level QTL 11	4.7		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	1	35854167	80854167	Rat
1331732	Srn4	Serum renin concentration QTL 4	4.467		renin activity (VT:0005581)	plasma renin activity level (CMO:0000116)	1	36033165	79689689	Rat
1331792	Rf29	Renal function QTL 29	4.589		urine potassium amount (VT:0010539)	urine potassium level (CMO:0000128)	1	36033165	79689689	Rat
2302059	Pia36	Pristane induced arthritis QTL 36	3.8	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	1	41907249	86907249	Rat
2313051	Bss57	Bone structure and strength QTL 57	3.7	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	1	43579208	126240667	Rat
2313059	Bss55	Bone structure and strength QTL 55	3.2	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	1	43579208	126240667	Rat
2313072	Bss53	Bone structure and strength QTL 53	4.3	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	43579208	126240667	Rat
2313078	Bss54	Bone structure and strength QTL 54	3.5	0.0001	tibia area (VT:1000281)	tibia midshaft cross-sectional area (CMO:0001717)	1	43579208	126240667	Rat
2313094	Bss58	Bone structure and strength QTL 58	3.7	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	1	43579208	126240667	Rat
2313098	Bmd70	Bone mineral density QTL 70	3.6	0.0001	tibia mineral mass (VT:1000283)	cortical volumetric bone mineral density (CMO:0001730)	1	43579208	126240667	Rat
2313099	Bss56	Bone structure and strength QTL 56	2.4	0.0001	tibia size trait (VT:0100001)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	1	43579208	126240667	Rat
1331778	Rf28	Renal function QTL 28	4.66		urine potassium amount (VT:0010539)	urine potassium excretion rate (CMO:0000761)	1	46113461	79689689	Rat
2313402	Anxrr24	Anxiety related response QTL 24			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	1	49147799	156446783	Rat
4889962	Bss94	Bone structure and strength QTL 94	3.8		tibia area (VT:1000281)	tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)	1	49547328	83657083	Rat
1578649	Bmd8	Bone mineral density QTL 8	4.9		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	1	49578577	94578577	Rat
1578654	Bss10	Bone structure and strength QTL 10	4		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	1	49578577	169852184	Rat
634314	Niddm44	Non-insulin dependent diabetes mellitus QTL 44			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	49578693	217054291	Rat
6903308	Scl36	Serum cholesterol QTL 36	2	0.0125	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	1	50522714	94225616	Rat
4889919	Bss86	Bone structure and strength QTL 86	4.1		tibia area (VT:1000281)	tibia midshaft total cross-sectional area (CMO:0001715)	1	53851348	83657083	Rat
4889929	Bss87	Bone structure and strength QTL 87	6.7		tibia area (VT:1000281)	tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)	1	53851348	83657083	Rat
61342	Bp27	Blood pressure QTL 27	3.4	0.0006	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	57761301	104391981	Rat
2300164	Bmd44	Bone mineral density QTL 44	5.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	1	58209327	103209327	Rat
2298545	Neuinf8	Neuroinflammation QTL 8	4.6		nervous system integrity trait (VT:0010566)	spinal cord beta-2 microglobulin mRNA level (CMO:0002125)	1	58354072	161711996	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	59
Count of miRNA genes:	51
Interacting mature miRNAs:	55
Transcripts:	ENSRNOT00000018017
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.

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	3	33	32	23	16	23			66	27	38	7
Low		10	25	18	3	18	8	11	8	8	3	4	8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001107471	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC103574	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC126217	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474101	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000026	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000088502 ⟹ ENSRNOP00000075261

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	64,130,908 - 64,147,251 (-)	Ensembl

RefSeq Acc Id:

NM_001107471 ⟹ NP_001100941

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	65,555,924 - 65,572,167 (-)	NCBI
Rnor_6.0	1	64,130,823 - 64,147,066 (-)	NCBI
Rnor_5.0	1	63,123,105 - 63,139,396 (-)	NCBI
RGSC_v3.4	1	63,868,853 - 63,885,095 (-)	RGD
Celera	1	63,280,966 - 63,297,090 (-)	NCBI

Sequence:

show sequence

GGCCCGTTCAGCTTCCGTGGAGCCGTCGGCAGCCGCTGCCAGGCCTTTCCTTGATCCCTGAATC
CCCTACTCGGTCGTCTAGAACAATCCCGGGCTCACTTCCTCTATCAACAACCCAACCCCACTTC
CGGCTTTCGCGCCCTCTTATCGCGATAGCGCCCGGACTCGGGGCGCGAGGAAAGAGGAAAAAAA
AAAAAAGGCGGCGGGCGGGCGCTCGCCTCTCTCTCCCCCCTCCTCGCCTGTCGCGATACGCTCC
GCAGCGGCGGCGCCAGCTCCTGCGCGTCCGTTTCTAAGAGAGTATGAAGAGAGTGCGTCTGTAG
GGCAGGGAAGATGGCGGACAAGCGCAAACTCCAAGGTGAGATTGATCGCTGCCTCAAGAAGGTG
TCCGAAGGTGTGGAGCAGTTTGAAGATATTTGGCAAAAGCTCCACAATGCAGCCAACGCGAACC
AGAAAGAAAAGTATGAGGCTGACCTAAAGAAGGAGATTAAGAAGCTACAACGGCTGAGGGACCA
GATCAAGACATGGGTAGCATCCAATGAGATCAAGGACAAAAGGCAGCTTATCGAAAACCGCAAG
CTCATTGAAACGCAAATGGAACGGTTCAAAGTTGTGGAACGAGAGACCAAAACCAAAGCCTATA
GCAAGGAGGGTCTCGGTCTGGCTCAGAAGGTGGACCCTGCCCAGAAGGAGAAGGAAGAGGTTGG
CCAGTGGCTCACGAACACCATTGACACCTTAAATATGCAGGTGGACCAGTTTGAGAGTGAGGTG
GAGTCACTGTCAGTACAGACGCGCAAGAAGAAAGGCGATAAGGATAAGCAGGACCGGATTGAGG
GCTTGAAGCGGCACATCGAGAAGCACCGCTACCATGTACGTATGCTGGAGACCATCCTGCGCAT
GCTGGACAATGACTCCATCCTGGTTGATGCCATCCGCAAGATCAAGGATGATGTAGAGTACTAC
GTTGACTCATCCCAGGACCCCGACTTTGAAGAGAATGAGTTCCTCTATGACGACCTGGACCTCG
AGGACATTCCACAGGCGCTGGTCGCCACCTCCCCCCCCAGCCACAGCCACATGGAGGACGAGAT
CTTCAACCAGTCTAGCAGTACACCCACCTCAACAACCTCCAGCTCTCCCATCCCACCCAGCCCA
GCTAACTGCACTACGGAAAACTCTGAAGATGATAAGAAGAGAGGCCGCTCTACAGATAGTGAAG
TCAGCCAGTCTCCAGCCAAAAATGGCTCCAAGCCTGTCCACAGCAACCAGCACCCCCAGTCCCC
AGCTGTGCCGCCCACCTACCCCTCTGGCCCCCCACCTGCCACTTCTGCCTTGAGCTCCACCCCT
GGCAACAATGGGGCCTCTACCCCAGCAGCACCTCCAAGTGCCCTGGGCCCTAAGGCCAGTCCAG
CTCCCAGCCACAACTCGGGTACTCCTGCCCCCTATGCCCAGGCTGTGGCCCCACCCAATGCCAG
CGGGCCCAGCAATGCCCAGCCCCGGCCCCCCAGTGCCCAGCCAAGCGGGGGAAGTGGTGGTGGC
AGCGGAGGGAGCAGCAGCAATAGTAACAGTGGCACAGGCGGAGGGGCTGGCAAGCAGAACGGTG
CCACCAGCTATAGTTCGGTTGTGGCAGACAGCCCTGCAGAGGTGGCCCTGAGTAGCAGTGGGGG
CAGCAGTGCCAGCAGCCAAGCCCTGGGGCCCACATCGGGCCCTCATAACCCAGCTCCCAGCACC
TTAAAGGAATCCAGTACAGCAGCCCCATCCGGGGCTGGGAGTGTGGCTTCAGGCTCAGGGAACA
ACTCAGGGGGACCCAGCCTCTTGGTGCCACTGCCTGTAAATCCCCCCAGTTCTCCAACGCCCAG
CTTCAGTGAAGCCAAGGCAGCTGGCACTCTTCTTAATGGTCCCCCACAGTTTAGCACCACCCCA
GAAATCAAGGCCCCTGAACCTCTGAGCTCTCTGAAATCCATGGCAGAACGGGCAGCTATCAGCT
CTGGTATTGAGGACCCTGTGCCAACGTTACACCTAACTGATAGAGACATCATCCTGAGCAGCAC
ATCAGCACCACCCACCTCATCCCAGCCACCCCTGCAGCTATCAGAGGTGAACATACCATTGTCA
CTGGGCGTCTGTCCATTGGGGCCAGTGTCCCTCACCAAGGAGCAGCTATACCAACAGGCCATGG
AAGAGGCCGCCTGGCACCACATGCCCCACCCCTCTGACTCCGAGCGCATTCGGCAGTACCTTCC
CCGGAACCCTTGCCCGACACCCCCCTACCACCACCAGATGCCACCCCCGCACTCGGACACTGTG
GAGTTCTACCAGCGCCTGTCAACTGAGACGCTCTTCTTCATCTTCTACTATCTGGAGGGAACCA
AGGCACAGTACTTGGCAGCCAAGGCCCTAAAGAAGCAGTCCTGGCGATTCCACACCAAGTATAT
GATGTGGTTTCAGAGGCATGAGGAGCCCAAGACCATCACAGATGAGTTTGAGCAGGGCACCTAC
ATCTACTTTGACTACGAGAAGTGGGGCCAGCGGAAGAAGGAAGGCTTCACCTTTGAGTATCGCT
ACCTGGAGGACCGGGACCTCCAGTGACACCGGCCCCCTTTACCCTCCCCCTCCCCCGCATGCTG
ATCCCCCTGCCCAGGTGAGGGCCCTGCCCTGGAAGACTGGGGGAGGCCCAAGGCCATGGGACAC
CCTCCCGCCCCAGGAAGCAGAGAAGGGATAGGGAAGTTTTCTCTTCCTCTCTGCCCTACCCTGG
GGGCCTGGGGGCAAGGGCTGCCCCCTCCTCCCCTCCCCAGTGAGGGACATTTTTTGGTAAACCT
ATTTTCATTTTGGAAAATATTTATGAATAAATAGTTTTATATGACGGCTGGCA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001100941	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL84932	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001100941 ⟸ NM_001107471

- UniProtKB:

D3ZUV9 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MADKRKLQGEIDRCLKKVSEGVEQFEDIWQKLHNAANANQKEKYEADLKKEIKKLQRLRDQIKT
WVASNEIKDKRQLIENRKLIETQMERFKVVERETKTKAYSKEGLGLAQKVDPAQKEKEEVGQWL
TNTIDTLNMQVDQFESEVESLSVQTRKKKGDKDKQDRIEGLKRHIEKHRYHVRMLETILRMLDN
DSILVDAIRKIKDDVEYYVDSSQDPDFEENEFLYDDLDLEDIPQALVATSPPSHSHMEDEIFNQ
SSSTPTSTTSSSPIPPSPANCTTENSEDDKKRGRSTDSEVSQSPAKNGSKPVHSNQHPQSPAVP
PTYPSGPPPATSALSSTPGNNGASTPAAPPSALGPKASPAPSHNSGTPAPYAQAVAPPNASGPS
NAQPRPPSAQPSGGSGGGSGGSSSNSNSGTGGGAGKQNGATSYSSVVADSPAEVALSSSGGSSA
SSQALGPTSGPHNPAPSTLKESSTAAPSGAGSVASGSGNNSGGPSLLVPLPVNPPSSPTPSFSE
AKAAGTLLNGPPQFSTTPEIKAPEPLSSLKSMAERAAISSGIEDPVPTLHLTDRDIILSSTSAP
PTSSQPPLQLSEVNIPLSLGVCPLGPVSLTKEQLYQQAMEEAAWHHMPHPSDSERIRQYLPRNP
CPTPPYHHQMPPPHSDTVEFYQRLSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFHTKYMMWF
QRHEEPKTITDEFEQGTYIYFDYEKWGQRKKEGFTFEYRYLEDRDLQ

hide sequence

RefSeq Acc Id:

ENSRNOP00000075261 ⟸ ENSRNOT00000088502

Protein Domains

NOT2_3_5 Not3

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13689662

Promoter ID:

EPDNEW_R187

Type:

multiple initiation site

Name:

Cnot3_1

Description:

CCR4-NOT transcription complex, subunit 3

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	1	64,147,077 - 64,147,137	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN/SsN (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Buf/N (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

Visual

CSV

TAB

Printer

Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

F344/NCrl (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

FHH/EurMcwi (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

GH/OmrMcwi (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/Ox (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LE/Stm (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrc (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrc (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrc (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

M520/N (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MHS/Gib (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

SBH/Ygl (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHRSP/Gcrc (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/Gcrc (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1304771	AgrOrtholog
Ensembl Genes	ENSRNOG00000053234	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000075261	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000088502	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	2.30.30.1020	UniProtKB/TrEMBL
InterPro	CCR4-NOT_su2/3/5_N_sf	UniProtKB/TrEMBL
	CCR4-NOT_su3/5	UniProtKB/TrEMBL
	NOT	UniProtKB/TrEMBL
	Not2/3/5	UniProtKB/TrEMBL
	Not_N	UniProtKB/TrEMBL
KEGG Report	rno:308311	UniProtKB/TrEMBL
NCBI Gene	308311	ENTREZGENE
PANTHER	PTHR23326	UniProtKB/TrEMBL
Pfam	NOT2_3_5	UniProtKB/TrEMBL
	Not3	UniProtKB/TrEMBL
PhenoGen	Cnot3	PhenoGen
PIRSF	NOT_su_3_5	UniProtKB/TrEMBL
UniProt	D3ZUV9	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-04-30	Cnot3	CCR4-NOT transcription complex, subunit 3	Cnot3_predicted	CCR4-NOT transcription complex, subunit 3 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Cnot3_predicted	CCR4-NOT transcription complex, subunit 3 (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 - OMIM

RGD Manual Annotations

Imported Annotations - KEGG (archival)