Cnot6 (CCR4-NOT transcription complex, subunit 6)

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Gene: Cnot6 (CCR4-NOT transcription complex, subunit 6) Rattus norvegicus

Analyze

Symbol:

Cnot6

Name:

CCR4-NOT transcription complex, subunit 6

RGD ID:

1310783

Description:

Predicted to have poly(A)-specific ribonuclease activity. Predicted to be involved in several processes, including nuclear-transcribed mRNA catabolic process; positive regulation of cytoplasmic mRNA processing body assembly; and positive regulation of nuclear receptor transcription coactivator activity. Predicted to localize to CCR4-NOT complex; cytoplasm; and nucleus. Orthologous to human CNOT6 (CCR4-NOT transcription complex subunit 6); PARTICIPATES IN microRNA pathway; RNA degradation pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2-methoxyethanol.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

carbon catabolite repressor protein 4 homolog; CCR4; CCR4 carbon catabolite repression 4-like; CCR4-NOT transcription complex subunit 6; cytoplasmic deadenylase; LOC287249; RGD1310783; similar to CCR4

Orthologs:

Homo sapiens (human) : CNOT6 (CCR4-NOT transcription complex subunit 6) HGNC Alliance
Mus musculus (house mouse) : Cnot6 (CCR4-NOT transcription complex, subunit 6) MGI Alliance
Chinchilla lanigera (long-tailed chinchilla) : Cnot6 (CCR4-NOT transcription complex subunit 6)
Pan paniscus (bonobo/pygmy chimpanzee) : CNOT6 (CCR4-NOT transcription complex subunit 6)
Canis lupus familiaris (dog) : CNOT6 (CCR4-NOT transcription complex subunit 6)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Cnot6 (CCR4-NOT transcription complex subunit 6)
Sus scrofa (pig) : CNOT6 (CCR4-NOT transcription complex subunit 6)
Chlorocebus sabaeus (African green monkey) : CNOT6 (CCR4-NOT transcription complex subunit 6)
Heterocephalus glaber (naked mole-rat) : Cnot6 (CCR4-NOT transcription complex subunit 6)

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
Rnor_6.0	10	35,144,291 - 35,195,126 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	35,146,337 - 35,187,416 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	34,916,148 - 34,967,236 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	35,139,386 - 35,192,631 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	10	35,140,437 - 35,193,680 (-)	NCBI
Celera	10	33,337,338 - 33,387,801 (-)	NCBI		Celera
Cytogenetic Map	10	q21	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17beta-estradiol (EXP)

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

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

2-methoxyethanol (EXP)

4-hydroxyphenyl retinamide (ISO)

benzo[a]pyrene (ISO)

benzo[e]pyrene (ISO)

bisphenol A (EXP,ISO)

butanal (ISO)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

dibutyl phthalate (ISO)

dioxygen (ISO)

fenvalerate (EXP)

finasteride (EXP)

folic acid (ISO)

methapyrilene (ISO)

sulforaphane (ISO)

sulindac (EXP)

tetrachloromethane (ISO)

trichloroethene (EXP)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

exonucleolytic catabolism of deadenylated mRNA (IEA,ISO,ISS)

gene silencing by RNA (IEA)

nuclear-transcribed mRNA catabolic process, no-go decay (IEA,ISO,ISS)

nuclear-transcribed mRNA poly(A) tail shortening (IBA,IEA,ISO,ISS)

obsolete positive regulation of nuclear receptor transcription coactivator activity (IEA,ISO,ISS)

positive regulation of cell population proliferation (IEA,ISO)

positive regulation of cytoplasmic mRNA processing body assembly (IEA,ISO)

regulation of translation (IEA)

RNA phosphodiester bond hydrolysis, exonucleolytic (IEA)

Cellular Component

CCR4-NOT complex (IBA,IEA,ISO,ISS)

cellular_component (ND)

cytoplasm (IBA,IEA)

nucleus (IBA,IEA)

Molecular Function

3'-5'-exoribonuclease activity (IBA)

exoribonuclease activity (ISO,ISS)

metal ion binding (IEA)

molecular_function (ND)

poly(A)-specific ribonuclease activity (IBA,IEA,ISO,ISS)

protein binding (ISO)

RNA binding (IEA)

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.	Pipeline to import KEGG annotations from KEGG into RGD
3.	RGD automated data pipeline
4.	RGD automated import pipeline for gene-chemical interactions
5.	RGD comprehensive gene curation
6.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
7.	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:11889047	PMID:15314026	PMID:15489334	PMID:18180299	PMID:18377426	PMID:19558367	PMID:19946888	PMID:20065043	PMID:20595389	PMID:21233283

Genomics

Comparative Map Data

Cnot6
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	10	35,144,291 - 35,195,126 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	35,146,337 - 35,187,416 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	34,916,148 - 34,967,236 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	35,139,386 - 35,192,631 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	10	35,140,437 - 35,193,680 (-)	NCBI
Celera	10	33,337,338 - 33,387,801 (-)	NCBI		Celera
Cytogenetic Map	10	q21	NCBI

CNOT6
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	5	180,494,379 - 180,578,358 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	5	180,494,373 - 180,578,358 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	5	179,921,412 - 180,005,358 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	5	179,854,023 - 179,937,959 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	5	179,854,022 - 179,937,959	NCBI
Celera	5	175,544,212 - 175,628,139 (+)	NCBI
Cytogenetic Map	5	q35.3	NCBI
HuRef	5	174,644,736 - 174,728,395 (+)	NCBI		HuRef
CHM1_1	5	179,353,610 - 179,437,824 (+)	NCBI		CHM1_1

Cnot6
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	11	49,562,324 - 49,604,227 (-)	NCBI
GRCm38	11	49,671,497 - 49,713,401 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	11	49,671,503 - 49,712,723 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	11	49,488,200 - 49,526,212 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	11	49,518,121 - 49,556,133 (-)	NCBI			mm8
Celera	11	54,236,493 - 54,264,486 (-)	NCBI		Celera
Cytogenetic Map	11	B1.2	NCBI

Cnot6
(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_004955408	170,399 - 218,040 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955408	170,399 - 239,492 (-)	NCBI	ChiLan1.0	ChiLan1.0

CNOT6
(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	5	183,007,081 - 183,089,997 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	5	183,007,081 - 183,089,997 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	5	175,695,802 - 175,780,534 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

CNOT6
(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	11	1,212,546 - 1,270,997 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	11	1,209,732 - 1,277,435 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Cnot6
(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_004936739	308,117 - 384,600 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CNOT6
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	2	78,124,269 - 78,202,535 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	2	78,131,236 - 78,202,518 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	2	79,564,705 - 79,635,537 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CNOT6
(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 Ensembl	23	82,218,180 - 82,303,849 (+)	Ensembl
ChlSab1.1	23	82,218,170 - 82,303,552 (+)	NCBI

Cnot6
(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_004624733	43,137,751 - 43,195,004 (+)	NCBI

Position Markers

RH142065

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	10	35,190,812 - 35,191,015	NCBI	Rnor6.0
Rnor_5.0	10	34,962,922 - 34,963,125	UniSTS	Rnor5.0
RGSC_v3.4	10	35,188,317 - 35,188,520	UniSTS	RGSC3.4
Celera	10	33,383,481 - 33,383,684	UniSTS
Cytogenetic Map	10	q22	UniSTS
RH 3.4 Map	10	356.4	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
2293680	Bss40	Bone structure and strength QTL 40	5.66	0.0001	femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	10	1	35538813	Rat
634327	Hc4	Hypercalciuria QTL 4	2.4		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	10	1	38594330	Rat
7411611	Foco17	Food consumption QTL 17	18.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	10	1	42669970	Rat
10401803	Kidm50	Kidney mass QTL 50			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	10	1	44902893	Rat
631554	Bp133	Blood pressure QTL 133		0.005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	764421	66221621	Rat
2298544	Neuinf9	Neuroinflammation QTL 9	4.6		nervous system integrity trait (VT:0010566)	spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)	10	5877536	64401490	Rat
8662860	Vetf10	Vascular elastic tissue fragility QTL 10			artery integrity trait (VT:0010639)	number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)	10	6229095	75983805	Rat
631660	Hcar1	Hepatocarcinoma resistance QTL 1	3.4	0.0001	liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	10	6229289	36185929	Rat
61427	Cia16	Collagen induced arthritis QTL 16	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	6429075	99492409	Rat
1578761	Stresp21	Stress response QTL 21	3.3		thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	10	7521450	52521450	Rat
2303118	Mamtr7	Mammary tumor resistance QTL 7		0.003	mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	10	9841807	108540162	Rat
9590310	Scort19	Serum corticosterone level QTL 19	6.3	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	12639513	57639513	Rat
9590268	Scort13	Serum corticosterone level QTL 13	3.26	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	12639513	57639513	Rat
9589136	Insul27	Insulin level QTL 27	10.46	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	10	12639513	57639513	Rat
2301967	Cm73	Cardiac mass QTL 73	4.55		heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	10	14827894	92423564	Rat
631268	Cia21	Collagen induced arthritis QTL 21	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	14827894	107857673	Rat
2316949	Gluco60	Glucose level QTL 60	3.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	10	14827894	110992275	Rat
1354587	Kidm21	Kidney mass QTL 21	3.3		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	10	15375474	62469074	Rat
631564	Apr3	Acute phase response QTL 3	3.9		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	10	16468736	61468736	Rat
6893350	Bw99	Body weight QTL 99	0.87	0.16	body mass (VT:0001259)	body weight (CMO:0000012)	1	17121542	62121542	Rat
6893352	Bw100	Body weight QTL 100	0.33	0.6	body mass (VT:0001259)	body weight (CMO:0000012)	1	17121542	62121542	Rat
631532	Cm50	Cardiac mass QTL 50	6.6		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	10	18246394	53637634	Rat
1598852	Anxrr19	Anxiety related response QTL 19	5.07		body movement coordination trait (VT:0005424)	number of rearing movements in an experimental apparatus (CMO:0001752)	10	19402814	64402814	Rat
1554317	Bmd4	Bone mineral density QTL 4	9.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	10	20170031	102897474	Rat
70223	Bp57	Blood pressure QTL 57	5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	21523906	83549467	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	21523906	90312401	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	21523906	90312401	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	21523906	90312401	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	21523906	90312401	Rat
70198	BpQTLcluster9	Blood pressure QTL cluster 9	2.94		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	21523906	90312401	Rat
1581497	Esta1	Estrogen-induced thymic atrophy QTL 1			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	10	21707766	64648311	Rat
631531	Iresp2	Immunoglobin response QTL2	6.3		blood immunoglobulin E amount (VT:0002492)	serum total immunoglobulin E level (CMO:0001542)	10	22402817	38204229	Rat
724556	Pur2	Proteinuria QTL 2	5.5		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	10	22901497	93886300	Rat
1331762	Rf40	Renal function QTL 40	3.873		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	10	23861015	66539843	Rat
1331791	Cm31	Cardiac mass QTL 31	3.84606		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	10	23861015	112626471	Rat
631267	Cia20	Collagen induced arthritis QTL 20	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
61325	Aia5	Adjuvant induced arthritis QTL 5		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
61354	Pia10	Pristane induced arthritis QTL 10		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
634329	Pia15	Pristane induced arthritis QTL 15	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24884084	47487910	Rat
70224	Eae3	Experimental allergic encephalomyelitis QTL 3	4.1		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	10	27237530	64648311	Rat
1298069	Bp168	Blood pressure QTL 168	5.5		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	10	27237530	101482600	Rat
631542	Bp82	Blood pressure QTL 82	6.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	27237530	102427718	Rat
2300171	Bmd58	Bone mineral density QTL 58	4.9	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	10	28789280	73789280	Rat
1600371	Mcs21	Mammary carcinoma susceptibility QTL 21	3		mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	10	30021354	54057745	Rat
2292441	Bp308	Blood pressure QTL 308			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	30099909	75099909	Rat
10402859	Bp381	Blood pressure QTL 381		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	30099909	75099909	Rat
724527	Bp148	Blood pressure QTL 148		0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	30983805	75983805	Rat
1576311	Pia26	Pristane induced arthritis QTL 26			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	31919397	78343192	Rat
1578779	Tcas10	Tongue tumor susceptibility QTL 10	3.12		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	10	33179030	78179030	Rat
631557	Bp136	Blood pressure QTL 136		0.003	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	33343192	78343192	Rat
1576319	Cia29	Collagen induced arthritis QTL 29			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	35139424	80139424	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	176
Count of miRNA genes:	136
Interacting mature miRNAs:	150
Transcripts:	ENSRNOT00000003752
Prediction methods:	Microtar, 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	35	57	41	19	41	2	2	74	35	41	11	2
Low		8					6	9					6
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001013856	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017597073	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AABR07029573	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01063738	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01063739	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01063740	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01063741	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC079308	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473948	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ223171	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000078960 ⟹ ENSRNOP00000075273

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	10	35,148,022 - 35,175,647 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000084509 ⟹ ENSRNOP00000074431

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	10	35,146,337 - 35,187,416 (-)	Ensembl

RefSeq Acc Id:

NM_001013856 ⟹ NP_001013878

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	10	35,146,330 - 35,195,126 (-)	NCBI
Rnor_5.0	10	34,916,148 - 34,967,236 (-)	NCBI
RGSC_v3.4	10	35,139,386 - 35,192,631 (-)	RGD
Celera	10	33,337,338 - 33,387,801 (-)	RGD

Sequence:

show sequence

GAACTGCCTGGCATTGGACTCCCTGAAGTCTGATCCAGGTTGACAAAGTCAATGTGAACCAAGC
TTTCATTCTCATCTCTTCGTGGGTTGGCTTTGCTGCCTGGACACCTGCAGGATCCCCCTCATTG
GCAGACCTTCCTTAAAAGAATGGCTAAGGGAAGCTCTCCAGAACTGAAGAAAATGGTAGCTGAC
CCTTCTAAGAGGAAAACACAATGAGATCCCTGAGTTGCCCGGATAGTGATCCAGAATGACCTCC
AACTGGAGAAGATCATCCACAAAGGCATGCCCAAAGAAAAGTACGAGCCCCCTGACCCTCGGAG
GATGTACACAATTATGTCCTCTGAGGAAGCAGCAAATGGAAAGAAATCACATTGGGCAGAGCTT
GAAATAAGTGGAAAAGTAAGAAGCTTAAGCTCATCTTTGTGGTCACTAACTCACTTGACAGCTT
TGCATCTGAGTGACAATTCCCTGTCCTGTATTCCTTCAGACATTGCCAAGCTTCACAATCTGGT
ATATCTGGACCTGTCCCATAATCAAATCCAGAGTTTACCGGCAGAACTCGGAAACATGGTATCA
CTCAGGGAGCTCCATTTAAATTACAACCAGTTACGAGTTCTACCTTTTGAGCTGGGAAAACTGT
TTCAGTTGCAGACTTTAAGCCTGAAAGGAAATCCACTTACCCAGGATATATTGAACCTCTGTCT
GGAGCCAGATGGAACAAGAAGGCTACTGAACTACTTGCTCGATAATTTGTCAGGTACTGCAAAA
AGAATTTCAACAGAACAACCACCTCCAAGATCTTGGATCATGTTACAAGAACCAGACAGAACAA
GGCCAACAGCCTTGTTTTCTGTCATGTGCTATAATGTTCTTTGTGATAAATATGCGACCCGGCA
GTTATACGGCTACTGTCCATCATGGGCACTAAATTGGGACTACAGGAAAAAGGCCATTATTCAA
GAAATTTTGAGCTGCAATGCTGATATTATAAGTCTTCAGGAAGTTGAAACAGAGCAGTATTACA
GTTTTTTTCTGGTAGAACTGAAAGAACGTGGCTATAATGGATTCTTTAGTCCTAAGTCTCGAGC
TAGGACTATGTCTGAACAGGAAAGAAAGCATGTTGATGGCTGTGCAATATTCTTCAAGACTGAA
AAATTTACTTTGGTTCAGAAACACACGGTTGAATTTAATCAGCTAGCAATGGCGAATTCAGAAG
GGTCTGAAGCTATGTTGAACAGAGTCATGACAAAGGATAACATTGGAGTTGCCGTACTGCTAGA
ACTTCGAAAGGAATTGATTGAAATGTCATCTGGAAAACCACATCTGGGAACAGAAAAACAACTT
ATTCTTGTGGCTAATGCTCATATGCATTGGGACCCTGAATACTCAGACGTGAAGTTGGTGCAAA
CTATGATGTTCCTTTCAGAAGTGAAGAATATTATTGATAAAGCCTCTCGGAGCCTCAAATCCAG
TGTATTGGGAGAATGTGGAACTATTCCACTTGTGTTATGTGCAGATCTGAATTCTTTGCCAGAC
TCTGGTGTTGTAGAGTATTTGAGCACTGGTGGGGTAGAAACAAATCATAAAGACTTTAAGGAAC
TGAGATACAATGAAAGTCTTACAAACTTCAGCTGCAATGGGAAGAATGGGATGACCAATGGAAG
AATCACACATGGTTTCAAGTTAAAGAGTGCCTATGAGAATGGCCTGATGCCTTACACGAATTAC
ACATTTGATTTCAAGGGTATAATTGACTACATCTTCTATTCTAAACCTCAGCTGAATACTTTAG
CCATCCTGGGACCTCTGGACCACCATTGGCTAGTTGAGAATAACATCAGCGGCTGCCCACATCC
ACTTATTCCCTCCGACCACTTCTCACTTTTTGCACAATTGGAGCTCTTACTGCCTTTCCTGCCC
CAAGTTAATGGCATTCACCTTCCTGGCAGGAGGTAGTCATGTACTTTCAGAGGACCTCAGATTT
ACTTGTAAACTCGTGAAAATCTAAATATAGGGGAGTGAGGCAGTGGAGCAGAAGGACGCCGCGT
GGCACTAAAGTGAACTGTTGCGTGTTAACAGTTTTATACAGAGACTGAGCCATTTTGGATGACT
CAAAATTTTATGAGAAGACATTTAATTGCTTATGCTGTTTTTAAGAGGAAATAAAATTACATAC
TGTTTAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_017597073 ⟹ XP_017452562

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	10	35,144,291 - 35,176,054 (-)	NCBI

Sequence:

show sequence

GGCTTCCACATGCATGCACGCTTCTCCGTGCGTACATGAAGTGTGTATGCACATATAGATAGAT
AAATGTAAAAGACATTAAAAATGAAATTATGAATTCACTCAGTTTGTACTGTGCAGTTGTGGTT
ACTCGTTATGTTCAGATTTTCTTTCATTTGGCCAGTGGAACACTTCTAAAGCAAACAGCTATAT
TTTCTTCAATCACACCTTTATTAGCTCCAGAGTTTAATCATTCATATTCTAGAACTAAAAATCA
TTAAAAACTACATGGCACTCCTAGTTCTTTTTGGTAGCAAATCTATTTAATGATCCTAATACGT
CTGCTTTTTTTTTTTTTTTAAATACTTCTACTGATTTGATTCTTTATTATGTACTGATTGGTTT
CTTTTCTTCGTTTATTAACAGGCATGCCCAAAGAAAAGTACGAGCCCCCTGACCCTCGGAGGAT
GTACACAATTATGTCCTCTGAGGAAGCAGCAAATGGAAAGAAATCACATTGGGCAGAGCTTGAA
ATAAGTGGAAAAGTAAGAAGCTTAAGCTCATCTTTGTGGTCACTAACTCACTTGACAGCTTTGC
ATCTGAGTGACAATTCCCTGTCCTGTATTCCTTCAGACATTGCCAAGCTTCACAATCTGGTATA
TCTGGACCTGTCCCATAATCAAATCCAGAGTTTACCGGCAGAACTCGGAAACATGGTATCACTC
AGGGAGCTCCATTTAAATTACAACCAGTTACGAGTTCTACCTTTTGAGCTGGGAAAACTGTTTC
AGTTGCAGACTTTAAGCCTGAAAGGAAATCCACTTACCCAGGATATATTGAACCTCTGTCTGGA
GCCAGATGGAACAAGAAGGCTACTGAACTACTTGCTCGATAATTTGTCAGGTACTGCAAAAAGA
ATTCCAACAGAACAAACACCTCCAAGATCTTGGTCATGTTACAAGAACCGACATGAACAAGGAC
AACAGGTTGAAGTTATCTTTCCTACAGCCTTGTTTTCTGTCATGTGCTATAATGTTCTTTGTGA
TAAATATGCGACCCGGCAGTTATACGGCTACTGTCCATCATGGGCACTAAATTGGGACTACAGG
AAAAAGGCCATTATTCAAGAAATTTTGAGCTGCAATGCTGATATTATAAGTCTTCAGGAAGTTG
AAACAGAGCAGTATTACAGTTTTTTTCTGGTAGAACTGAAAGAACGTGGCTATAATGGATTCTT
TAGTCCTAAGTCTCGAGCTAGGACTATGTCTGAACAGGAAAGAAAGCATGTTGATGGCTGTGCA
ATATTCTTCAAGACTGAAAAATTTACTTTGGTTCAGAAACACACGGTTGAATTTAATCAGCTAG
CAATGGCGAATTCAGAAGGGTCTGAAGCTATGTTGAACAGAGTCATGACAAAGGATAACATTGG
AGTTGCCGTACTGCTAGAACTTCGAAAGGAATTGATTGAAATGTCATCTGGAAAACCACATCTG
GGAACAGAAAAACAACTTATTCTTGTGGCTAATGCTCATATGCATTGGGACCCTGAATACTCAG
ACGTGAAGTTGGTGCAAACTATGATGTTCCTTTCAGAAGTGAAGAATATTATTGATAAAGCCTC
TCGGAGCCTCAAATCCAGTGTATTGGGAGAATGTGGAACTATTCCACTTGTGTTATGTGCAGAT
CTGAATTCTTTGCCAGACTCTGGTGTTGTAGAGTATTTGAGCACTGGTGGGGTAGAAACAAATC
ATAAAGACTTTAAGGAACTGAGATACAATGAAAGTCTTACAAACTTCAGCTGCAATGGGAAGAA
TGGGATGACCAATGGAAGAATCACACATGGTTTCAAGTTAAAGAGTGCCTATGAGAATGGCCTG
ATGCCTTACACGAATTACACATTTGATTTCAAGGGTATAATTGACTACATCTTCTATTCTAAAC
CTCAGCTGAATACTTTAGCCATCCTGGGACCTCTGGACCACCATTGGCTAGTTGAGAATAACAT
CAGCGGCTGCCCACATCCACTTATTCCCTCCGACCACTTCTCACTTTTTGCACAATTGGAGCTC
TTACTGCCTTTCCTGCCCCAAGTTAATGGCATTCACCTTCCTGGCAGGAGGTAGTCATGTACTT
TCAGAGGACCTCAGATTTACTTGTAAACTCGTGAAAATCTAAATATAGGGGAGTGAGGTATGGC
CACTAGGGATTTTTCTCAATGATCATTTGGATTTTCAGTCTGGTTATTTGATAAAGGATATAGT
ATGAAAGCCAGGTGCTAGCAACAGACAGATTCTGAGCCCAGTGTACTTCATATACTGCTAGACA
GGGACTGGTGTGTTTACACCTATCTTTTAATTTGTTACAAATAATTTTCCTGTTTCTTCTCTCC
AATGTGTATTGTCATGCCTTGAAATAGGAAGATGTGTGAACAGTGTGTGTTTGCACAGAAGTCC
ACAGCACTGTTCTCTGAGGCCAGTAGTAACATCAGAGACCGTTCTTCCAGACTTTACTCCTTTT
TTTTTTCAGACTTGTTTGTAAAATGTAGAATTTGAATTTAGCCTTTATGATTGTATATGATCCA
CAGAAGACCTGATTTATGAAGTTTTCTACTAAAAAAAAGCAAAATCGAAAACAGTTGTATTGTA
AACTAAGGCTAATTTTTTTTAACCTGTGTCCTGTGTTCTGAAGGCCAGCTGGTAACAAAGTTGC
ATCAGACTTTCTCTGCAGTGATTTGCACTGTTAGGGTTTTGTTAGCCCTTTTATACTACTTTAT
TTTTAAATTGAAAACATTACTCTTTAAATGTAAGTTTGCTTAGACCTTGGGATATTTTCTTGGA
CCAGAGGCAACTTATGTATGAATTCCTGGATTTCTATGGAAACTTTGTACCAGGACAGATAAGC
TGATGTGTAGGCATTTAATGGACTGAATATGACAGTTGACATATGTACATTCTGCTATTTTTAA
GTCTTTCACTTTTTATGTTAAAAAATTACAGCTGCTTAGGTACAGCTTCTAAGTCGTCCTTTCT
GAGACATTTCTGTTCTGTCTCCACTGTGCCTGCCTAGATTTGTCCTCACCGAGCACTGCCTGTG
CATGCAGAGAAAATCTGTGCATCTTTTATATTTTTAAAAACTAACATTTGTGAGAATTTTATGG
AAATGCTTTTGTATGAGCTGTGGCTTTTCCTCGTTGTAAAGCGCTGGATAGCACATTCTGGAAC
ATGTTCCTGGGTCCTGGGTCTTTGCTCCCCAGACCCAAGCACTGCTTCTTGGTGTCATTGCGTC
CAGAGTGCCACTATCATGTGTATTCCTTATTCTCTTAATGTTTTTTAAAAAAATCATTCCTTTT
TTTAAGAAGAGTAATTTTCTGTTTATGAAGCAGTATAAATTAGACGCATTTTCAAAACAGTTAC
CCTAAGACAATTGTTTGGATCATTTTTAAAGTGACTAAGGAATTTTAGTATGTCAACCAAGATA
AAAGTTATACTGTACCCTATATTTTGCCCATAGTGCCATTAGTAGATTAGAGATTAAAGTCACT
TTTAACTTTACAAAGTTAACTTGTATATGTTCTGTTCTCGGTCGTTAGTTCTCTCAAAATCAAA
TGAATTCAGAGGGAACTTGTCTGGCTGCTTTTGTTTCAACTGCAGGCAGTGGAGCAGAAGGACG
CCGCGTGGCACTAAAGTGAACTGTTGCGTGTTAACAGTTTTATACAGAGACTGAGCCATTTTGG
ATGACTCAAAATTTTATGAGAAGACATTTAATTGCTTATGCTGTTTTTAAGAGGAAATAAAATT
ACATACTGTTTAAATAAATGAATTTTTTTCTTTTTAAAAAATTCTCTAGAAGGTCTTGATCTTG
AATCTGTCTTGGACCTTGTTTTTTCTTTAAGGTTTTTTGTTTTGTTTGTTTAATCTTAATTGTA
ATGTTGGGTTTGTTTGTTGTGGGTTTTTACTTTGTTTAAGTTGTGCTGGCACCAAACGCACCCA
GTTTGTAATCAGCAGGTTGGTGTAGAACCAGTACATAACTTCTAATGGCTTTTTGTCCTGTCTT
TCCCCCACCCCCTTGTCTCTGTCTCTGTCTCTTTCTTGTAAAGTGTGAATATAAGATGTGTTGA
CTCGATTTTCGTAAACACTGTGTTGGTAGTGTGCATCATGACAATTTCCAGTGAAGGTGAACTG
GAGCTGGTTGGACTGATGGGACTGAGGAATCCACTTTTCCTGTGACCTGCTTAGAGAAGCACAG
GTCCAGAGAGTGTGGTGTGAGGAGTGGGGAGGAGCACTTACTCATTTTTGCATTTGTTAGTGGA
AGACGTATTCCTTTCATGGATGCTGGAACTAGAGTGCACTTGTTAGATGCTAAAGGTTTGAGCT
TTACAGAGAACATTCATCTGTATTTGTAACTGTCTACACTATATTTGAATCTGGGGGCAGCATA
GTGAGATATAATTAATTGCCTGTTATGTCTTGAAAGTACTTGTTTTGCCTCTTTTAGGCGTACT
GCATTCTGTGGGTCAGTTTGAACATCCCCACCTGGGTTAGATAGTGGTGAGTTGAACGGAGAGT
GTAGATTTACAAGTATAATCTTCAAAAGAAAAATATTTTGAATCTATTGAGAATAAATGTTCAC
ACCAAAATAGACTGATACTTTGTTAAGCAAGGTTTTATGTTTTAAATGCTTTGTGTCCAAAATA
ATTTCCAAGAACCTATACTTCTTAAAATGCATAAAACTAGTCTGTTTTCATAATGTAGATTATT
TTGAAAGATACAGATTTTTGAAAAATTCTGTAATAAATATATGTAATGTTTTGCTATAATGTAA
TTTCAGTGTTCTTGATGATAAATACATCTTAGGAGTGTTTTACAGAATGTTTGGAATATGTTTC
CCTTTCTAAAGATGCAGATTGGAGGCACTCAAATCTTTGTAAATCTTATGAAGTACAGTTTACA
GTATTGGTGGTAATTATTTATGCTTTGAGAATTTAAATAATGTTCGTTGAAATTAATTTATGGC
ATAGTATAAACTGAAGTTCTAGAAGTAAATTGTTGATTGCAGCTTTAATAATCCCAGAACATAG
GCATCTCCAAAAATTTCGTTTTTGTTTGTACTTTGATTTGATTTGGTGTCAACTAGGAAAATTC
ATTTCATATTAGCACTTTGAAACCTAAAGACATAATTAAATTGGGTAGAATGCACTTCTAAATC
TTTAAATTATAATTGAAACCTCTAAGATTCCATTTTCCCATAATAGCACTCATGGTTTAGAGTT
CCACTTTTTCACTATTTAAACTGACTCTGAAGTTTGGTGGTCATGTCATATGTAGGCCAAAGCC
AACCCAGGCAAGACAATTAGAGGAGTTTGTCTTCCGAGAGTCAGCCATAATATCCAGGACCACA
GGTGTTGCAGATAATTTAGAGAACATAAGCAGGTGTCTCCAACCACAAGCAGTATTTTAAGATG
TTCGCTTTGTTCCTTTTGGTTACATAAATTTTAAAAACTGGTATGTTGATGTAGTGTCTAAAGT
AGAGTAGTCTTTATTCACAGTACATTATATGGTGTAATGCACTGGACTAACTCTTGTTTACCAT
TCGTGTAACAAAACCCAGCACACTTTCTGCACTAAGCTCAAGAACGTCATATCTGCCTAGGCAG
CTCTTTGATAAGGGTGATGAGAAACTGAATTTACACCATGTGGACTGGTGGTAACAAGGGCTTT
TACTGTTCTTTTCAGTGGGATTCTTCTTGGTCAAATTGTAACTAGCTAGTATTATATTTATATA
CAGGGTCTCTTTTCCTTACCGATGTATTTTCCTACTCATAGCCAACCAATAAATTCAATATCTG
TTTCAAATA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001013878	(Get FASTA)	NCBI Sequence Viewer
	XP_017452562	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH79308	(Get FASTA)	NCBI Sequence Viewer
	EDM04230	(Get FASTA)	NCBI Sequence Viewer
	EDM04231	(Get FASTA)	NCBI Sequence Viewer
	EDM04232	(Get FASTA)	NCBI Sequence Viewer
	EDM04233	(Get FASTA)	NCBI Sequence Viewer
	Q6AXU9	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001013878 ⟸ NM_001013856

- UniProtKB:

Q6AXU9 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MPKEKYEPPDPRRMYTIMSSEEAANGKKSHWAELEISGKVRSLSSSLWSLTHLTALHLSDNSLS
CIPSDIAKLHNLVYLDLSHNQIQSLPAELGNMVSLRELHLNYNQLRVLPFELGKLFQLQTLSLK
GNPLTQDILNLCLEPDGTRRLLNYLLDNLSGTAKRISTEQPPPRSWIMLQEPDRTRPTALFSVM
CYNVLCDKYATRQLYGYCPSWALNWDYRKKAIIQEILSCNADIISLQEVETEQYYSFFLVELKE
RGYNGFFSPKSRARTMSEQERKHVDGCAIFFKTEKFTLVQKHTVEFNQLAMANSEGSEAMLNRV
MTKDNIGVAVLLELRKELIEMSSGKPHLGTEKQLILVANAHMHWDPEYSDVKLVQTMMFLSEVK
NIIDKASRSLKSSVLGECGTIPLVLCADLNSLPDSGVVEYLSTGGVETNHKDFKELRYNESLTN
FSCNGKNGMTNGRITHGFKLKSAYENGLMPYTNYTFDFKGIIDYIFYSKPQLNTLAILGPLDHH
WLVENNISGCPHPLIPSDHFSLFAQLELLLPFLPQVNGIHLPGRR

hide sequence

RefSeq Acc Id:

XP_017452562 ⟸ XM_017597073

- Peptide Label:

isoform X1

- Sequence:

show sequence

MPKEKYEPPDPRRMYTIMSSEEAANGKKSHWAELEISGKVRSLSSSLWSLTHLTALHLSDNSLS
CIPSDIAKLHNLVYLDLSHNQIQSLPAELGNMVSLRELHLNYNQLRVLPFELGKLFQLQTLSLK
GNPLTQDILNLCLEPDGTRRLLNYLLDNLSGTAKRIPTEQTPPRSWSCYKNRHEQGQQVEVIFP
TALFSVMCYNVLCDKYATRQLYGYCPSWALNWDYRKKAIIQEILSCNADIISLQEVETEQYYSF
FLVELKERGYNGFFSPKSRARTMSEQERKHVDGCAIFFKTEKFTLVQKHTVEFNQLAMANSEGS
EAMLNRVMTKDNIGVAVLLELRKELIEMSSGKPHLGTEKQLILVANAHMHWDPEYSDVKLVQTM
MFLSEVKNIIDKASRSLKSSVLGECGTIPLVLCADLNSLPDSGVVEYLSTGGVETNHKDFKELR
YNESLTNFSCNGKNGMTNGRITHGFKLKSAYENGLMPYTNYTFDFKGIIDYIFYSKPQLNTLAI
LGPLDHHWLVENNISGCPHPLIPSDHFSLFAQLELLLPFLPQVNGIHLPGRR

hide sequence

RefSeq Acc Id:

ENSRNOP00000074431 ⟸ ENSRNOT00000084509

RefSeq Acc Id:

ENSRNOP00000075273 ⟸ ENSRNOT00000078960

Protein Domains

Endo/exonuclease/phosphatase

Transcriptome

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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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)

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CSV

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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)

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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)

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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)

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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)

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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)

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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)

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CSV

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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)

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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)

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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)

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CSV

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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)

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CSV

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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

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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)

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CSV

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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)

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CSV

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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)

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CSV

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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)

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CSV

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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)

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CSV

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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)

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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)

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CSV

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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)

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CSV

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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)

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CSV

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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)

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CSV

TAB

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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)

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CSV

TAB

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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:1310783	AgrOrtholog
Ensembl Genes	ENSRNOG00000054891	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000074431	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOP00000075273	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000078960	UniProtKB/TrEMBL
	ENSRNOT00000084509	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	3.60.10.10	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	3.80.10.10	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7134677	IMAGE-MGC_LOAD
InterPro	Cnot6	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Endo/exonu/phosph_ase_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Endo/exonuclease/phosphatase	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Leu-rich_rpt	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Leu-rich_rpt_typical-subtyp	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	LRR_dom_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:287249	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:94449	IMAGE-MGC_LOAD
NCBI Gene	287249	ENTREZGENE
Pfam	Exo_endo_phos	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	LRR_8	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Cnot6	PhenoGen
PROSITE	LRR	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	LRR_TYP	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF56219	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene	Rn.93562	ENTREZGENE
UniProt	A0A0G2K816_RAT	UniProtKB/TrEMBL
	A0A0G2KA59_RAT	UniProtKB/TrEMBL
	CNOT6_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-02-27	Cnot6	CCR4-NOT transcription complex, subunit 6	RGD1310783	similar to CCR4	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-12-06	RGD1310783	similar to CCR4	RGD1310783_predicted	similar to CCR4 (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-20	RGD1310783_predicted	similar to CCR4 (predicted)	LOC287249_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC287249_predicted	similar to CCR4 (predicted)			Symbol and Name status set to provisional	70820	PROVISIONAL

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)

RGD Manual Annotations

Imported Annotations - KEGG (archival)