Cdk5rap3 (CDK5 regulatory subunit associated protein 3)

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Gene: Cdk5rap3 (CDK5 regulatory subunit associated protein 3) Rattus norvegicus

Analyze

Symbol:

Cdk5rap3

Name:

CDK5 regulatory subunit associated protein 3

RGD ID:

620002

Description:

Predicted to have several functions, including MDM2/MDM4 family protein binding activity; NF-kappaB binding activity; and enzyme binding activity. Involved in negative regulation of cyclin-dependent protein serine/threonine kinase activity. Predicted to colocalize with microtubule. Orthologous to human CDK5RAP3 (CDK5 regulatory subunit associated protein 3); INTERACTS WITH 1,2,4-trimethylbenzene; 17alpha-ethynylestradiol; acrylamide.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

C53; CDK5 activator-binding protein C53; CDK5 regulatory subunit-associated protein 3

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	10	81,894,393 - 81,903,581 (-)	NCBI
Rnor_6.0 Ensembl	10	84,780,608 - 84,789,832 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	10	84,780,644 - 84,789,800 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	10	84,571,933 - 84,581,074 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	10	80,656,149 - 80,665,286 (-)	NCBI		Celera
Cytogenetic Map	10	q31	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

1,2,4-trimethylbenzene (EXP)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (EXP)

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

3,4-methylenedioxymethamphetamine (ISO)

3-isobutyl-1-methyl-7H-xanthine (ISO)

acrolein (ISO)

acrylamide (EXP)

alendronic acid (EXP)

alpha-pinene (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP)

bisphenol F (ISO)

butan-1-ol (ISO)

cisplatin (ISO)

clofibrate (ISO)

copper atom (ISO)

copper(0) (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

dibutyl phthalate (ISO)

dicrotophos (ISO)

disulfiram (ISO)

hydrogen peroxide (ISO)

hypochlorous acid (ISO)

indometacin (ISO)

ozone (ISO)

paracetamol (ISO)

pirinixic acid (ISO)

raloxifene (EXP)

resveratrol (ISO)

silicon dioxide (ISO)

sodium fluoride (ISO)

tetrachloroethene (ISO)

thapsigargin (ISO)

triptonide (ISO)

troglitazone (ISO)

tunicamycin (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

apoptotic nuclear changes (IEA,ISO,ISS)

brain development (TAS)

cell population proliferation (IEA,ISO,ISS)

definitive erythrocyte differentiation (IEA,ISO,ISS)

endoplasmic reticulum unfolded protein response (IEA,ISO,ISS)

liver development (IEA,ISO,ISS)

mitotic G2 DNA damage checkpoint signaling (IEA,ISO,ISS)

mitotic G2/M transition checkpoint (ISO,ISS)

negative regulation of cellular protein catabolic process (IEA,ISO,ISS)

negative regulation of cyclin-dependent protein serine/threonine kinase activity (IDA)

negative regulation of MAP kinase activity (IEA,ISO,ISS)

negative regulation of NF-kappaB transcription factor activity (IEA,ISO,ISS)

negative regulation of protein kinase activity by regulation of protein phosphorylation (IEA,ISO,ISS)

negative regulation of protein phosphorylation (ISO,ISS)

negative regulation of protein serine/threonine kinase activity (ISO,ISS)

positive regulation of protein localization to nucleus (IEA,ISO,ISS)

positive regulation of protein ubiquitination (IEA,ISO,ISS)

positive regulation of signal transduction by p53 class mediator (IEA,ISO,ISS)

positive regulation of transcription by RNA polymerase II (IEA,ISO)

positive regulation of ubiquitin-dependent protein catabolic process (ISO,ISS)

protein ufmylation (IEA,ISO,ISS)

regulation of cyclin-dependent protein serine/threonine kinase activity (IBA,IDA)

regulation of mitotic cell cycle (IBA)

regulation of phosphatase activity (IEA,ISO,ISS)

response to endoplasmic reticulum stress (ISO,ISS)

Cellular Component

cellular_component (ND)

centrosome (IEA,ISO,ISS)

cytoplasm (ISO,ISS)

cytosol (IEA,ISO)

intracellular membrane-bounded organelle (ISO)

microtubule (IEA,ISO,ISS)

nucleolus (IEA,ISO)

nucleus (ISO,ISS)

protein-containing complex (IEA,ISO)

Molecular Function

cyclin binding (IEA,ISO)

MDM2/MDM4 family protein binding (IEA,ISO)

mitogen-activated protein kinase binding (IEA,ISO)

NF-kappaB binding (IEA,ISO)

protein binding (ISO)

protein kinase binding (ISO)

protein-containing complex binding (IDA)

ubiquitin-like protein ligase binding (IEA,ISO,ISS)

References

References - curated


1.	Ching YP, etal., Gene 2000 Jan 25;242(1-2):285-94.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	GOA data from the GO Consortium
4.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
5.	RGD automated data pipeline
6.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7.	RGD automated import pipeline for gene-chemical interactions
8.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
9.	Wang X, etal., J Biol Chem 2000 Oct 13;275(41):31763-9.

Additional References at PubMed

PMID:12054757	PMID:15790566	PMID:16012757	PMID:16173922	PMID:17785205	PMID:19223857	PMID:19946888	PMID:20228063	PMID:20531390	PMID:21283629	PMID:21494687	PMID:23152784
PMID:23478299	PMID:30954448

Genomics

Comparative Map Data

Cdk5rap3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	10	81,894,393 - 81,903,581 (-)	NCBI
Rnor_6.0 Ensembl	10	84,780,608 - 84,789,832 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	10	84,780,644 - 84,789,800 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	10	84,571,933 - 84,581,074 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	10	80,656,149 - 80,665,286 (-)	NCBI		Celera
Cytogenetic Map	10	q31	NCBI

CDK5RAP3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	17	47,967,810 - 47,981,781 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	17	47,967,904 - 47,981,781 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	17	46,047,894 - 46,059,147 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	17	43,403,428 - 43,414,146 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	17	43,403,427 - 43,414,146	NCBI
Celera	17	42,501,248 - 42,511,966 (+)	NCBI
Cytogenetic Map	17	q21.32	NCBI
HuRef	17	41,416,597 - 41,427,853 (+)	NCBI		HuRef
CHM1_1	17	46,112,862 - 46,124,122 (+)	NCBI		CHM1_1

Cdk5rap3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	11	96,798,251 - 96,807,359 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	11	96,798,252 - 96,807,322 (-)	Ensembl
GRCm38	11	96,907,425 - 96,916,531 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	11	96,907,426 - 96,916,496 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	11	96,769,100 - 96,777,795 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	11	96,723,876 - 96,732,571 (-)	NCBI			mm8
Celera	11	106,553,602 - 106,563,974 (-)	NCBI		Celera
Cytogenetic Map	11	D	NCBI

Cdk5rap3
(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_004955451	13,120,761 - 13,170,073 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955451	13,160,811 - 13,170,012 (-)	NCBI	ChiLan1.0	ChiLan1.0

CDK5RAP3
(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	17	9,738,144 - 9,748,989 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	17	9,738,141 - 9,749,302 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	17	9,556,313 - 9,567,099 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

CDK5RAP3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	9	24,276,660 - 24,286,273 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	9	24,276,768 - 24,286,272 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	9	23,742,863 - 23,752,452 (+)	NCBI
ROS_Cfam_1.0	9	25,070,151 - 25,079,744 (+)	NCBI
UMICH_Zoey_3.1	9	23,840,058 - 23,849,636 (+)	NCBI
UNSW_CanFamBas_1.0	9	24,101,046 - 24,110,629 (+)	NCBI
UU_Cfam_GSD_1.0	9	24,227,612 - 24,237,208 (+)	NCBI

Cdk5rap3
(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_024405602	23,719,423 - 23,729,698 (+)	NCBI
SpeTri2.0	NW_004936490	13,345,443 - 13,355,841 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CDK5RAP3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	12	24,224,256 - 24,234,467 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	12	24,224,262 - 24,234,468 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	12	24,044,526 - 24,053,777 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CDK5RAP3
(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	16	68,367,591 - 68,382,000 (+)	NCBI
ChlSab1.1 Ensembl	16	68,370,483 - 68,382,022 (+)	Ensembl

Cdk5rap3
(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_004624795	4,594,131 - 4,602,435 (+)	NCBI

Position Markers

RH130138

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	10	84,780,742 - 84,780,961	NCBI	Rnor6.0
Rnor_5.0	10	84,572,029 - 84,572,248	UniSTS	Rnor5.0
Celera	10	80,656,247 - 80,656,466	UniSTS
RH 3.4 Map	10	731.9	UniSTS

RH65642

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	10	84,784,837 - 84,785,546	NCBI	Rnor6.0
Rnor_5.0	10	84,576,124 - 84,576,833	UniSTS	Rnor5.0
Celera	10	80,660,323 - 80,661,032	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
61427	Cia16	Collagen induced arthritis QTL 16	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	6429075	99492409	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
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
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
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	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)	systolic blood pressure (CMO:0000004)	1	21523906	90312401	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
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
724556	Pur2	Proteinuria QTL 2	5.5		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	10	22901497	93886300	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
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
631552	Vetf2	Vascular elastic tissue fragility QTL 2	4.5	0.0002	aorta elastic tissue integrity trait (VT:0010556)	artery internal elastic lamina non-tumorous lesion count (CMO:0001913)	10	36185929	95845311	Rat
2317042	Aia20	Adjuvant induced arthritis QTL 20	3.38		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	10	40514044	85514044	Rat
2317043	Aia7	Adjuvant induced arthritis QTL 7	3.82		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	10	40514044	85514044	Rat
1576308	Schws1	Schwannoma susceptibility QTL 1		0.0041	nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	10	41260363	106105607	Rat
631269	Cia22	Collagen induced arthritis QTL 22	8.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	41260363	107857673	Rat
631270	Cia23	Collagen induced arthritis QTL 23	3.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	41260363	107857673	Rat
1298078	Stresp5	Stress response QTL 5	2.99	0.00025	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	43289657	108540162	Rat
61463	Bp12	Blood pressure QTL 12	6.3	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	43704955	88704955	Rat
2300218	Hpcl2	Hepatic cholesterol level QTL 2			liver cholesterol amount (VT:0010498)	liver cholesterol level (CMO:0001597)	10	46593021	98939209	Rat
9589030	Epfw9	Epididymal fat weight QTL 9	19.24	0.001	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	10	46848346	91848346	Rat
7411614	Foco18	Food consumption QTL 18		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	10	46848346	91848346	Rat
8694173	Bw149	Body weight QTL 149	4.38	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	10	46848346	91848346	Rat
631547	Bp87	Blood pressure QTL 87	4.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	50638337	95638337	Rat
1549846	Scl47	Serum cholesterol level QTL 47	3.6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	10	53104718	98104718	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	10	53621375	112626471	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	53621375	112626471	Rat
631530	Tls3	T-lymphoma susceptibility QTL 3	0	0.0001	thymus integrity trait (VT:0010555)	percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)	10	53625815	98939209	Rat
631535	Cm51	Cardiac mass QTL 51	3		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	10	53637485	94807701	Rat
1359017	Hrtrt21	Heart rate QTL 21	2.4		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	10	55224855	100224855	Rat
70171	Cari1	Carrageenan-induced inflammation QTL 1	4.9	0.0005	hypodermis integrity trait (VT:0010550)	inflammatory exudate volume (CMO:0001429)	10	55678976	112626471	Rat
70164	Bw21	Body weight QTL 21	4.36	0.00005	body mass (VT:0001259)	body weight (CMO:0000012)	10	55679084	102427604	Rat
1354608	Cm33	Cardiac mass QTL 33	2.8		heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	10	56698730	101698730	Rat
1549831	Bss6	Bone structure and strength QTL 6	4		lumbar vertebra strength trait (VT:0010574)	vertebra ultimate force (CMO:0001678)	10	60450007	105450007	Rat
2312662	Slep8	Serum leptin concentration QTL 8		0.05	blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	10	60875260	105875260	Rat
2312668	Scl65	Serum cholesterol level QTL 65		0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	10	60875260	105875260	Rat
2312672	Insul15	Insulin level QTL 15		0.01	blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	10	60875260	105875260	Rat
2293698	Bss43	Bone structure and strength QTL 43	5.33	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra cross-sectional area (CMO:0001689)	10	62096293	107096293	Rat
2306970	Anxrr22	Anxiety related response QTL 22	5.95		fear/anxiety-related behavior trait (VT:1000241)	number of periods of voluntary immobility (CMO:0001045)	10	64648175	101691360	Rat
1558643	Cm44	Cardiac mass QTL 44	4.8	0.0000368	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	10	64648175	102149713	Rat
6893336	Cm75	Cardiac mass QTL 75	0.1	0.87	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	10	64648175	102149713	Rat
61402	Niddm3	Non-insulin dependent diabetes mellitus QTL 3	4.58		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	10	64648311	85513822	Rat
61449	Ciaa2	CIA Autoantibody QTL 2	7.1		blood autoantibody amount (VT:0003725)	calculated serum anti-type 2 collagen antibody titer (CMO:0001279)	10	65590122	110590122	Rat
2313103	Bss80	Bone structure and strength QTL 80	2	0.0001	tibia strength trait (VT:1000284)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	10	65992275	110992275	Rat
2313105	Bss79	Bone structure and strength QTL 79	1.8	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	10	65992275	110992275	Rat
7387312	Bw125	Body weight QTL 125	3	0.0047	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight (CMO:0000356)	10	67880046	112626471	Rat
1581559	Eae18	Experimental allergic encephalomyelitis QTL 18		0.00002	nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis severity score (CMO:0001419)	10	67988218	110992091	Rat
2298481	Eau9	Experimental allergic uveoretinitis QTL 9		0.0169	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	10	68305037	85514044	Rat
1357344	Bp249	Blood pressure QTL 249		0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	69123603	101482600	Rat
2317029	Aia19	Adjuvant induced arthritis QTL 19	2.98		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	10	69385595	112626471	Rat
2317039	Aia6	Adjuvant induced arthritis QTL 6	4.31		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	10	69385595	112626471	Rat
10450498	Bp384	Blood pressure QTL 384		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	70166960	112626471	Rat
1642980	Bp300	Blood pressure QTL 300			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	70800069	112626471	Rat
61396	Bp9	Blood pressure QTL 9	4.8	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	71692298	112626471	Rat
2300172	Bmd57	Bone mineral density QTL 57	9.8	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	10	73008136	112626471	Rat
2293646	Bss25	Bone structure and strength QTL 25	10.96	0.0001	femur morphology trait (VT:0000559)	femur cross-sectional area (CMO:0001661)	10	73008136	112626471	Rat
2293663	Bss33	Bone structure and strength QTL 33	9.34	0.0001	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	10	73008136	112626471	Rat
6893366	Bw106	Body weight QTL 106	0.3	0.47	body mass (VT:0001259)	body weight (CMO:0000012)	10	73467158	112626471	Rat
2306793	Ean5	Experimental allergic neuritis QTL 5	4.7		nervous system integrity trait (VT:0010566)	IFNG-secreting splenocyte count (CMO:0002122)	10	75045391	97308358	Rat
70193	Mcs7	Mammary carcinoma susceptibility QTL 7	2.38		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	10	75544754	112626471	Rat
2298548	Neuinf7	Neuroinflammation QTL 7	3.4		nervous system integrity trait (VT:0010566)	spinal cord RT1-B protein level (CMO:0002132)	10	75544754	112626471	Rat
12880053	Cm104	Cardiac mass QTL 104		0.009	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	10	75983662	86419171	Rat
1358188	Ept9	Estrogen-induced pituitary tumorigenesis QTL 9	3.9		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	10	75983805	99492217	Rat
2292617	Ept18	Estrogen-induced pituitary tumorigenesis QTL 18	3.9		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	10	75983805	99492217	Rat
12880050	Am10	Aortic mass QTL 10		0.016	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	10	77055741	86962563	Rat
1579919	Bp281	Blood pressure QTL 281		0.01	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	77055741	98282519	Rat
631537	Oia4	Oil induced arthritis QTL 4			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	78343027	90042115	Rat
2325836	Bp346	Blood pressure QTL 346		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	78970279	86962563	Rat
10450495	Bp383	Blood pressure QTL 383		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	78970279	98282519	Rat
2292438	Bp311	Blood pressure QTL 311			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	78970279	112626471	Rat
1302404	Cia27	Collagen induced arthritis QTL 27	2.6	0.0045	joint integrity trait (VT:0010548)	experimental arthritis severity measurement (CMO:0001459)	10	79927661	112626471	Rat
4889492	Pancm2	Pancreatic morphology QTL 2	3.2		pancreatic beta cell morphology trait (VT:0005217)	ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)	10	80239190	112626471	Rat
724516	Uae17	Urinary albumin excretion QTL 17	3.6		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	10	80946110	88200662	Rat
1300107	Rf18	Renal function QTL 18	3.41		urine output (VT:0003620)	timed urine volume (CMO:0000260)	10	81515116	101758478	Rat
1358915	Stresp7	Stress response QTL 7	3.52		blood norepinephrine amount (VT:0005663)	plasma norepinephrine level (CMO:0001010)	10	81649775	90297007	Rat
634354	Rends3	Renal damage susceptibility QTL 3		0.05	kidney blood vessel morphology trait (VT:0000530)	organ lesion measurement (CMO:0000677)	10	82675233	88141097	Rat
631555	Bp134	Blood pressure QTL 134		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	83389828	94488181	Rat
6893357	Bw102	Body weight QTL 102	0.5	0.36	body mass (VT:0001259)	body weight (CMO:0000012)	10	83389828	104994768	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	150
Count of miRNA genes:	118
Interacting mature miRNAs:	126
Transcripts:	ENSRNOT00000071719
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	43	57	41	19	41	6	9	74	35	41	11	6
Low							2	2					2
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_024488	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039086923	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039086924	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AF177476	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC081793	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473948	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000220	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000071719 ⟹ ENSRNOP00000065240

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	10	84,780,608 - 84,789,832 (-)	Ensembl

RefSeq Acc Id:

NM_024488 ⟹ NP_077814

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	81,894,397 - 81,903,555 (-)	NCBI
Rnor_6.0	10	84,780,644 - 84,789,800 (-)	NCBI
Rnor_5.0	10	84,571,933 - 84,581,074 (-)	NCBI
Celera	10	80,656,149 - 80,665,286 (-)	NCBI

Sequence:

show sequence

GGCCGGTTTGTTTCTGAATTGAGGCTCAGGCACGCCGGCTCAGGATTGGTGCTGGGCCGGGCCG
GGGTCTTTGGCCGGAAGCGGAAGTGGAAAAAGGATGCAGGACCATCAGCACGTGCCCATCGACA
TCCAGACCAGCAAGCTGCTCGATTGGCTGGTGGACAGAAGACACTGCAACTTAAAATGGCAAAG
CCTGGTGCTGACCATCCGGGAAAAGATCAACACCGCCATCCAGGACATGCCAGAGAGCCAAGAG
ATTGCCCAGCTGCTCTCTGGTTCCTACATCCACTACTTCCACTGCCTAAGAATAGTGGACCTTC
TTAAAGGTACCGAGGCTTCCACCAAAAATATTTTTGGCCGCTACTCTTCACAGCGGATGAAGGA
TTGGCAGGAGATCATAAGCCTGTATGAGAAGGACAACACCTATTTAGTGGAACTCTCTAGCCTC
CTGGTTCGGAATGTCAACTATGAGATCCCCTCTCTGAAGAAGCAGATTGCCAAGTGCCAGCAAC
TGCAGCAAGACTACAGCCGCAAGGAGGAGGAGGGCCAGGCTGGGGCTGCTGAGATGCGAGAGCA
GTTCTACCACTCCTGCAAACAGTACGGCATCACGGGAGACAATGTCCGACGAGAGCTTCTGGCC
CTGGTGAAGGACCTGCCAAGTCAGCTGGCTGAGATAGGAGCGGGAGCTCAGTCCCTGGGGGAAG
CCATCGACCTGTACCAGGCCTGTGTGGAGTTTGTATGTGACAGCCCCACAGAGCAGGTGCTGCC
CATGCTGCGGTACGTTCAGAAGAAGGGAAACTCCACGGTGTATGAGTGGAGGACAGGGACAGAG
CCCTCTGTGGTAGAGCGGCCACAACTGGAGGACCCTCCCGAGCAGGTGCAAGAAGACGAGATCG
ACTGGGGCGACTTTGGCCTGGAGGCTGTTTCTGACTCTGGAAACATCATCTCTGCTGAGACCCC
TGGGATAGACTGGGGTATCTCCCTGGAGTCAGAGTCCAAGGATGCTGGGGCTGACAAGATAGAC
TGGGGTGACAATGCTGTTGCTTCGGAGATCACCGTGCTGGAGACAGGAACGGAGGCTCCAGAGG
GTGTTGCTAGGGGCTCAGACGCTCTGACTCTCCTTGAATACCCTGAGACTCGGAATCAGTTCAT
CGATGAGCTCATGGAGCTTGAGATCTTCTTGTCTCAGAGAGCAGTAGAGATGAGTGAGGAGGCT
GACATCCTGTCCGTGAGCCAGTTCCAGCTGGCTCCTGCCATCCTTCAGGGCCAGACCAAGGAGA
AGATGCTCAGCCTGGTGTCCACACTGCAGCATCTGATTGGCCAGCTCACCAGTCTCCGGATGCA
GCACCTGTTTATGATTCTGGCCTCACCGAGGTATGTGGACCGGGTGACAGAGCTCCTCCAGCAG
AAGCTGAAGCAGTCCCAGCTGTTGGCTCTGAAGAAGGACCTGATGGTGGAGAAGCAGCAGGAGG
CGCTTCAGGAGCAGGCAGCGCTGGAGCCCAAGCTGGACCTGCTGCTGGAGAAGACCAGAGAGCT
GCAGAAGCTGATTGAAGCTGACATCTCCAAGAGATACAACGGCCGTCCTGTGAACCTGATGGGG
ACCTCTGTGTGACGTGCTCCCTCTGTGTCCTCCACCCAGCTTCCTGGTGGGGGGTGGGACAGCC
CAGGCTGGTATTGCTGGACCTCACCAGCAAGAAGCCAGCAGACCTGGAGGCAGAGCCACAAGGA
AGGGCCACCTGAGTGGTGGCACCAGCATTCATTGTGACCTCTGCAAGAAGTCTGAGTGGCTCTG
TGGCTCTCAGCCTAAGGCACAGTTGCTTCTTCTGGTTATCAAGGAAGGCTTAATAAAAAAAGGA
AGTGACTCTCAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_039086923 ⟹ XP_038942851

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	81,894,393 - 81,903,581 (-)	NCBI

RefSeq Acc Id:

XM_039086924 ⟹ XP_038942852

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	81,894,393 - 81,903,448 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_077814	(Get FASTA)	NCBI Sequence Viewer
	XP_038942851	(Get FASTA)	NCBI Sequence Viewer
	XP_038942852	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAF60222	(Get FASTA)	NCBI Sequence Viewer
	AAH81793	(Get FASTA)	NCBI Sequence Viewer
	EDM05826	(Get FASTA)	NCBI Sequence Viewer
	EDM05827	(Get FASTA)	NCBI Sequence Viewer
	EDM05828	(Get FASTA)	NCBI Sequence Viewer
	EDM05829	(Get FASTA)	NCBI Sequence Viewer
	Q9JLH7	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_077814 ⟸ NM_024488

- UniProtKB:

Q642E3 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MQDHQHVPIDIQTSKLLDWLVDRRHCNLKWQSLVLTIREKINTAIQDMPESQEIAQLLSGSYIH
YFHCLRIVDLLKGTEASTKNIFGRYSSQRMKDWQEIISLYEKDNTYLVELSSLLVRNVNYEIPS
LKKQIAKCQQLQQDYSRKEEEGQAGAAEMREQFYHSCKQYGITGDNVRRELLALVKDLPSQLAE
IGAGAQSLGEAIDLYQACVEFVCDSPTEQVLPMLRYVQKKGNSTVYEWRTGTEPSVVERPQLED
PPEQVQEDEIDWGDFGLEAVSDSGNIISAETPGIDWGISLESESKDAGADKIDWGDNAVASEIT
VLETGTEAPEGVARGSDALTLLEYPETRNQFIDELMELEIFLSQRAVEMSEEADILSVSQFQLA
PAILQGQTKEKMLSLVSTLQHLIGQLTSLRMQHLFMILASPRYVDRVTELLQQKLKQSQLLALK
KDLMVEKQQEALQEQAALEPKLDLLLEKTRELQKLIEADISKRYNGRPVNLMGTSV

hide sequence

RefSeq Acc Id:

ENSRNOP00000065240 ⟸ ENSRNOT00000071719

RefSeq Acc Id:	XP_038942851 ⟸ XM_039086923
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038942852 ⟸ XM_039086924
- Peptide Label:	isoform X1

Transcriptome

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

Promoters

RGD ID:

13697637

Promoter ID:

EPDNEW_R8161

Type:

initiation region

Name:

Cdk5rap3_1

Description:

CDK5 regulatory subunit associated protein 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	10	84,789,809 - 84,789,869	EPDNEW

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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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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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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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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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)

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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

GH/OmrMcwi (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)

GK/Ox (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

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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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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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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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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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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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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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:620002	AgrOrtholog
Ensembl Genes	ENSRNOG00000048747	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000065240	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000071719	ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7190258	IMAGE-MGC_LOAD
InterPro	CDK5RAP3	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:80278	UniProtKB/TrEMBL
MGC_CLONE	MGC:93406	IMAGE-MGC_LOAD
NCBI Gene	80278	ENTREZGENE
PANTHER	PTHR14894	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	DUF773	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Cdk5rap3	PhenoGen
UniProt	CK5P3_RAT	UniProtKB/Swiss-Prot
	Q642E3	ENTREZGENE, UniProtKB/TrEMBL
	Q9JLH7	ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2005-01-20	Cdk5rap3	CDK5 regulatory subunit associated protein 3			Symbol and Name updated	1299863	APPROVED
2005-01-12	Cdk5rap3	CDK5 regulatory subunit associated protein 3	C53		Data Merged	1299863	APPROVED
2004-12-02	Cdk5rap3	CDK5 regulatory subunit associated protein 3	C53	CDK5 activator-binding protein C53	Symbol and Name updated	1299863	APPROVED
2002-08-07	C53	CDK5 activator-binding protein C53			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference

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)

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