Stk40 (serine/threonine kinase 40)

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Gene: Stk40 (serine/threonine kinase 40) Rattus norvegicus

Analyze

Symbol:

Stk40

Name:

serine/threonine kinase 40

RGD ID:

727884

Description:

Predicted to enable ATP binding activity; protein serine kinase activity; and protein threonine kinase activity. Predicted to be involved in protein phosphorylation. Predicted to act upstream of or within several processes, including glycogen metabolic process; lung development; and respiratory system process. Predicted to be located in cytosol and nucleoplasm. Orthologous to human STK40 (serine/threonine kinase 40); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; aflatoxin B1.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

Lyk4; RGD1307310; Ser/Thr-like protein kinase lyk4; serine/threonine-protein kinase 40; serine/threonine-protein kinase lyk4

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	STK40 (serine/threonine kinase 40)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther
Mus musculus (house mouse):	Stk40 (serine/threonine kinase 40)	HGNC	EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Stk40 (serine/threonine kinase 40)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	STK40 (serine/threonine kinase 40)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	STK40 (serine/threonine kinase 40)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Stk40 (serine/threonine kinase 40)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	STK40 (serine/threonine kinase 40)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	STK40 (serine/threonine kinase 40)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Stk40 (serine/threonine kinase 40)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Stk40 (serine/threonine kinase 40)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Homo sapiens (human):	STK40 (serine/threonine kinase 40)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Danio rerio (zebrafish):	stk40 (serine/threonine kinase 40)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	5	138,380,049 - 138,417,802 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	5	138,381,159 - 138,417,796 (+)	Ensembl
Rnor_6.0	5	144,112,612 - 144,150,653 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	144,114,012 - 144,150,647 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	5	147,882,697 - 147,920,188 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	145,457,719 - 145,494,354 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	5	145,467,710 - 145,504,226 (+)	NCBI
Celera	5	136,891,355 - 136,927,933 (+)	NCBI		Celera
Cytogenetic Map	5	q36	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Charcot-Marie-Tooth disease dominant intermediate C (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-epigallocatechin 3-gallate (ISO)

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

2,4-dinitrotoluene (EXP)

2-methylcholine (ISO)

3,3',5,5'-tetrabromobisphenol A (ISO)

acrylamide (ISO)

aflatoxin B1 (EXP)

arsane (ISO)

arsenic atom (ISO)

benzene (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

carbamazepine (ISO)

chromium(6+) (ISO)

cobalt dichloride (EXP)

cocaine (EXP)

copper(II) sulfate (ISO)

Cuprizon (EXP)

cyclosporin A (ISO)

dibutyl phthalate (EXP,ISO)

doxorubicin (ISO)

entinostat (ISO)

fluoranthene (ISO)

furan (EXP)

gentamycin (EXP)

hydroquinone (ISO)

methylmercury chloride (ISO)

paracetamol (ISO)

phenobarbital (ISO)

pirinixic acid (ISO)

potassium chromate (ISO)

Soman (EXP)

sunitinib (ISO)

temozolomide (ISO)

tetrachloromethane (ISO)

tungsten (ISO)

valproic acid (ISO)

zinc atom (ISO)

zinc(0) (ISO)

zoledronic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

glycogen metabolic process (IEA,ISO)

lung alveolus development (IEA,ISO)

lung development (ISO)

lung morphogenesis (IEA,ISO)

multicellular organism growth (IEA,ISO)

negative regulation of apoptotic process (IEA,ISO)

protein phosphorylation (IEA)

regulation of gene expression (IEA,ISO)

regulation of MAPK cascade (IEA,ISO)

respiratory system process (IEA,ISO)

Cellular Component

cytoplasm (IEA)

cytosol (IEA,ISO)

nucleoplasm (IEA,ISO)

nucleus (IEA)

Molecular Function

ATP binding (IEA)

protein binding (ISO)

protein serine kinase activity (IEA)

protein serine/threonine kinase activity (IEA)

protein serine/threonine/tyrosine kinase activity (IEA)

References

References - curated


1.	NCBI rat LocusLink and RefSeq merged data October 15, 2003
2.	RGD automated data pipeline
3.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:12477932	PMID:15489334	PMID:23293024

Genomics

Comparative Map Data

Stk40
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	5	138,380,049 - 138,417,802 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	5	138,381,159 - 138,417,796 (+)	Ensembl
Rnor_6.0	5	144,112,612 - 144,150,653 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	144,114,012 - 144,150,647 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	5	147,882,697 - 147,920,188 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	145,457,719 - 145,494,354 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	5	145,467,710 - 145,504,226 (+)	NCBI
Celera	5	136,891,355 - 136,927,933 (+)	NCBI		Celera
Cytogenetic Map	5	q36	NCBI

STK40
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	1	36,339,624 - 36,385,924 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	1	36,339,628 - 36,385,924 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	1	36,805,229 - 36,851,525 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	36,577,812 - 36,624,072 (-)	NCBI	NCBI36		hg18	NCBI36
Celera	1	35,080,354 - 35,126,619 (-)	NCBI
Cytogenetic Map	1	p34.3	NCBI
HuRef	1	34,921,985 - 34,968,132 (-)	NCBI		HuRef
CHM1_1	1	36,921,399 - 36,967,662 (-)	NCBI		CHM1_1

Stk40
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	125,997,738 - 126,034,822 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	4	125,997,750 - 126,034,822 (+)	Ensembl
GRCm38	4	126,103,942 - 126,141,029 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	126,103,957 - 126,141,029 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	4	125,781,201 - 125,818,273 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	4	125,606,302 - 125,643,186 (+)	NCBI			mm8
Celera	4	124,434,390 - 124,471,601 (+)	NCBI		Celera
Cytogenetic Map	4	D2.2	NCBI

Stk40
(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_004955452	14,301,533 - 14,345,988 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955452	14,298,759 - 14,345,293 (-)	NCBI	ChiLan1.0	ChiLan1.0

STK40
(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	1	36,775,581 - 36,821,654 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	36,775,581 - 36,821,654 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	1	35,607,231 - 35,653,443 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

STK40
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	15	5,894,125 - 5,934,461 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	15	5,894,933 - 5,932,791 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	15	6,136,970 - 6,176,979 (+)	NCBI
ROS_Cfam_1.0	15	6,029,736 - 6,069,743 (+)	NCBI
UMICH_Zoey_3.1	15	5,883,149 - 5,923,136 (+)	NCBI
UNSW_CanFamBas_1.0	15	5,950,874 - 5,990,846 (+)	NCBI
UU_Cfam_GSD_1.0	15	5,965,960 - 6,005,961 (+)	NCBI

Stk40
(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_024405058	52,946,652 - 52,991,269 (-)	NCBI
SpeTri2.0	NW_004936474	18,771,434 - 18,816,086 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

STK40
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	92,424,984 - 92,483,709 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	92,441,231 - 92,484,363 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

STK40
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	20	96,473,456 - 96,520,683 (+)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	20	96,473,527 - 96,520,769 (+)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666033	20,217,574 - 20,265,834 (-)	NCBI	Vero_WHO_p1.0

Stk40
(Heterocephalus glaber - naked mole-rat)

Naked Mole-rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624764	19,255,300 - 19,298,956 (-)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

RH126883

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	138,417,353 - 138,417,547 (+)	MAPPER	mRatBN7.2
Rnor_6.0	5	144,150,205 - 144,150,398	NCBI	Rnor6.0
Rnor_5.0	5	147,919,740 - 147,919,933	UniSTS	Rnor5.0
RGSC_v3.4	5	145,493,911 - 145,494,104	UniSTS	RGSC3.4
Celera	5	136,927,490 - 136,927,683	UniSTS
Cytogenetic Map	5	q36	UniSTS

AA801260

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	138,417,574 - 138,417,802 (+)	MAPPER	mRatBN7.2
Rnor_6.0	5	144,150,426 - 144,150,653	NCBI	Rnor6.0
Rnor_5.0	5	147,919,961 - 147,920,188	UniSTS	Rnor5.0
RGSC_v3.4	5	145,494,132 - 145,494,359	UniSTS	RGSC3.4
Celera	5	136,927,711 - 136,927,938	UniSTS
Cytogenetic Map	5	q36	UniSTS

UniSTS:235027

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	138,416,435 - 138,416,653 (+)	MAPPER	mRatBN7.2
Rnor_6.0	5	144,149,287 - 144,149,504	NCBI	Rnor6.0
Rnor_5.0	5	147,918,822 - 147,919,039	UniSTS	Rnor5.0
RGSC_v3.4	5	145,492,993 - 145,493,210	UniSTS	RGSC3.4
Celera	5	136,926,572 - 136,926,789	UniSTS
Cytogenetic Map	5	q36	UniSTS

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1576314	Eutr1	Estrogen induced uterine response QTL 1			uterus integrity trait (VT:0010575)	pyometritis severity score (CMO:0002009)	5	2138965	166875058	Rat
1641912	Alcrsp18	Alcohol response QTL 18			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	5	35189153	141643988	Rat
1549845	Scl44	Serum cholesterol level QTL 44	6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	40128307	148607290	Rat
1578766	Tcas11	Tongue tumor susceptibility QTL 11	4.12		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	5	46711509	161317411	Rat
1576312	Emca8	Estrogen-induced mammary cancer QTL 8	4.1		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	50328551	141643988	Rat
61426	Scl2	Serum cholesterol level QTL 2	7.3	0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	59793399	143070159	Rat
61393	Bp7	Blood pressure QTL 7	4.5	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	60293434	161481680	Rat
1354598	Srn6	Serum renin concentration QTL 6	3.8		blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	5	69540295	151018848	Rat
1302790	Scl20	Serum cholesterol level QTL 20	6.4	0.0001	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	82394392	166664054	Rat
61452	Ciaa5	CIA Autoantibody QTL 5	3.5		blood autoantibody amount (VT:0003725)	calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)	5	94858972	143070159	Rat
1331796	Thshl2	Thyroid stimulating hormone level QTL 2	2.3		blood thyroid-stimulating hormone amount (VT:0005119)	serum thyroid stimulating hormone level (CMO:0001248)	5	97059760	147465714	Rat
1358187	Emca1	Estrogen-induced mammary cancer QTL 1	4.4		mammary gland integrity trait (VT:0010552)	post-insult time to mammary tumor formation (CMO:0000345)	5	99216724	148607142	Rat
1578673	Bmd13	Bone mineral density QTL 13	4.9		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	5	103689353	148689353	Rat
2317056	Wbc3	White blood cell count QTL 3	2.51	0.01	leukocyte quantity (VT:0000217)	white blood cell count (CMO:0000027)	5	105999803	150999803	Rat
7207488	Bss110	Bone structure and strength QTL 1	8.4		femur strength trait (VT:0010010)	femur stiffness (CMO:0001674)	5	106906205	151906205	Rat
7207491	Bss112	Bone structure and strength QTL 112	7		femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	5	106906205	151906205	Rat
7207481	Bss106	Bone structure and strength QTL 106	7.9		femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	5	106906205	151906205	Rat
7207486	Bss109	Bone structure and strength QTL 109			femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	5	106906205	151906205	Rat
1549838	Bss4	Bone structure and strength QTL 4	9.2		femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	5	106906205	151906205	Rat
1298089	Scl14	Serum cholesterol level QTL 14	5.8	0.0004	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	108845856	153845856	Rat
1598847	Cm62	Cardiac mass QTL 62	3.4		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	108845856	153845856	Rat
8657050	Bw146	Body weight QTL 146	19.84	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	5	108938288	153938288	Rat
8694441	Bw169	Body weight QTL 169	17.61	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	5	111416838	156416838	Rat
8694198	Abfw3	Abdominal fat weight QTL 3	16.13	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	5	111416838	156416838	Rat
8694389	Bw160	Body weight QTL 160	6.17	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	5	111416838	156416838	Rat
8552960	Pigfal15	Plasma insulin-like growth factor 1 level QTL 15			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	111416838	156416838	Rat
1581510	Cm54	Cardiac mass QTL 54	3.4	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	5	120740824	143608494	Rat
2293642	Bss37	Bone structure and strength QTL 37	4.64	0.0001	femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	5	120740824	151018848	Rat
1641920	Colcs1	Colorectal carcinoma susceptibility QTL 1	2.99	0.0055	intestine integrity trait (VT:0010554)	benign colorectal tumor surface area measurement (CMO:0001799)	5	121846814	166846814	Rat
10053720	Scort26	Serum corticosterone level QTL 26	2.06	0.0147	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	5	124965598	166875058	Rat
1300122	Wbc1	White blood cell count QTL 1	2.75		leukocyte quantity (VT:0000217)	total white blood cell count (CMO:0000365)	5	125392826	139989768	Rat
724525	Bp147	Blood pressure QTL 147	4.3	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	126424772	166875058	Rat
1598819	Bp292	Blood pressure QTL 292	4.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	127798274	166875058	Rat
1598861	Cm64	Cardiac mass QTL 64	2.9		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	127798274	166875058	Rat
8552908	Pigfal4	Plasma insulin-like growth factor 1 level QTL 4	6.6		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	128506074	166875058	Rat
8694169	Bw148	Body weight QTL 148	5	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	5	128506074	166875058	Rat
634349	Bp139	Blood pressure QTL 139		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	128924607	166875058	Rat
1331803	Rf32	Renal function QTL 32	2.798		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	5	129132428	143070159	Rat
70156	Niddm30	Non-insulin dependent diabetes mellitus QTL 30	3.98		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	5	129132447	151006154	Rat
738018	Anxrr4	Anxiety related response QTL 4	5.1		exploratory behavior trait (VT:0010471)	percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)	5	130130159	166875058	Rat
7794791	Mcs33	Mammary carcinoma susceptibility QTL 33	1.93		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	5	131345754	166875058	Rat
631505	Bp103	Blood pressure QTL 103	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	132717196	165560427	Rat
631562	Apr2	Acute phase response QTL 2	3.7		blood murinoglobulin 1 amount (VT:0010597)	plasma murinoglobulin 1 level (CMO:0001931)	5	135927956	166875058	Rat
61444	Strs2	Sensitivity to stroke QTL 2	4.7		cerebrum integrity trait (VT:0010549)	post-insult time to onset of cerebrovascular lesion (CMO:0002343)	5	135929696	166875058	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	540
Count of miRNA genes:	232
Interacting mature miRNAs:	307
Transcripts:	ENSRNOT00000035597
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	42	44	29	19	29	7	10	69	33	40	11	7
Low		1	13	12		12	1	1	5	2	1		1
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_183056	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006238881	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039110152	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC098381	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY336055	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC100062	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000162	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000035597 ⟹ ENSRNOP00000032827

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	138,381,159 - 138,417,796 (+)	Ensembl
Rnor_6.0 Ensembl	5	144,114,012 - 144,150,647 (+)	Ensembl

RefSeq Acc Id:

NM_183056 ⟹ NP_898879

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	138,381,159 - 138,417,797 (+)	NCBI
Rnor_6.0	5	144,114,012 - 144,150,648 (+)	NCBI
Rnor_5.0	5	147,882,697 - 147,920,188 (+)	NCBI
RGSC_v3.4	5	145,457,719 - 145,494,354 (+)	RGD
Celera	5	136,891,355 - 136,927,933 (+)	RGD

Sequence:

show sequence

GCGGCGGCGGCAGCTCTGGCGGCTGCGCTGGGAGGCGGCGGTGAGCGGCTCCCACGCCCCCGGC
CCGGCCCCGGCCACCGGGACGGAGCGCCGAGCAGCCCCGGCTCTGGGCTGCGGACTATGGGCAA
GCAGCGCTGATCCCCCGGGAAAGAACTGAGAATGAAGCGGAGAGCATCAGACAGAGGAGCTGGG
GAGACGTCGGCCAAGGCCCAGGCTCTAGGGACTGGCATTGCTGGAAATAATGCAAAGAGAGCAG
GACCGTTCATCCTGGGTCCCCGCCTGGGCAACTCACCGGTACCGAGCATTGTGCAATGTTTGGC
AAGGAAAGACGGCACGGACGACTTCTATCAGTTGAAGATCCTCACCCTTGAGGAGAGGGGCGAG
CAAGGAATTGAGAGCCAAGAGGAGAGGCAGGGCAAGATGCTGCTGCATACCGAGTACTCTCTGC
TGTCCCTGCTGCACACACAGGATGGCGTGGTCCACCACCATGGCCTCTTCCAGGACCGCACGTG
TGAAGCGGTCGAGGACACAGAGTCTGGGCGGATGGTAAAGAAGATGAAGAAACGCATTTGCCTT
GTCCTTGACTGCCTCTGTGCACACGACTTCAGTGACAAGACCGCTGACCTCATCAACCTACAGC
ACTACGTCATCAAAGAGAAGCGGCTCAGTGAGCGTGAGACTGTGGTCATTTTCTATGATGTAGT
CCGTGTGGTAGAAGCCCTGCACCAGAAAAACATCGTGCACAGAGACCTGAAGCTTGGGAACATG
GTGCTCAATAAAAGGACCCATCGGATAACTATCACCAACTTCTGCCTTGGAAAGCACCTTGTGA
GTGAGGGGGACCTGCTGAAGGACCAGAGGGGGAGCCCTGCCTACATCAGTCCTGATGTGCTCAG
CGGCCGGCCATACCGGGGGAAGCCTAGTGACATGTGGGCCTTGGGCGTGGTGCTCTTCACCATG
CTCTATGGCCAGTTCCCCTTCTACGACAGCATCCCACAGGAGCTCTTCCGCAAGATCAAGGCTG
CTGAGTACACCATCCCTGAGGATGGGCGAGTCTCTGAGAACACAGTGTGTCTTATCCGGAAACT
ACTGGTCCTTGACCCCCAGCAACGCCTGGCTGCTGCAGATGTCCTGGAGGCCCTCAGTGCCATC
ATTGCATCTTGGCAGTCCCTGTCCTCTCTGAGTGGGCCTTTGCAAGTGGTTCCTGACATCGATG
ACCAAATGAGCAGCTCTGACAGCTCCCAGGAGGCAAAGGTCACAGAGGAATGCTCCCAGTACGA
GTTTGAGAATTACATGCGACAGCAGCTGCTGCTGGCTGAAGAGAAGAGCTCCATTCACGAGGCC
CGGACCTGGGTACCCAAGCGGCAGTTTGGTAGCATGCCACCCGTCCGACGGCTAGGCCACGATG
CACAGCCAATGACCTCCTTGGACACAGCCATCCTGGCACAACGCTATCTGCGGAAATAGTGCCC
TCAGCTAGGGCACTAGCCCAGCACACCTCTCCTCGGCCCGCCTGAGGCCCAGCCATCAGGCCTG
CCTGGGCCCGGGCCCAGCAGTGCTGGACTGAGTCTCCCAGGCTGCAGTAGGGACAGGGCAGGGA
TAGGGACAGCCCAGGTCACAGCCAGGGTCAACAGAGGTACCACAAAGCTACCTTTTGGGATGAT
TGCTTGATTGTTTTTTTATCTGAGAATTCTAGATAGATACCTAATCTGCTTTTAATCATGACAT
TTTAATCTACCTCTGTCTCTTTAACCACGCTGTCTCTGGACTGAACGCTGGGAGGAAAGAGGGG
AGCCTACGCTCATATCCCAGGCACTGGAACAGCCTGGCTAGGCCACTGACCCCAGTCCATATAA
GCTGACCACGCAGCTCGCTGCTGGCCCCCAGTAAGCACCCCTTCCCACCGTTCACAGCCCCTCC
CTGGGGCTGCCCTCAGTCTAAGCTTTGGAACACTCTCACCTCACTTTCCACCCAAGTCAAATAT
ATTTATTTTTTTACTGAACCCAACTTGTATCTCTAGGTTCAGCCCATGGCCACTCTTCGCCCCT
GAGCCTGGCTGAATAACAGGGCCCAGGTGTGTAGGCTCCCTTCTCGCCCCAGGCACCCAGGAGC
CCTCTGGCCAGTTCCTCTGTCTGCTCTCAACCCCCCAGGCCCTCTGTTTCTAGCCTTGGCGCTT
TCTCTGTCCTAGCAGCTTCTCTGAGCGGCTGCACATTCGCATTAGTCCTGCCCACCTCCTCCAT
CTTTCATGTGGTACCCAGGTAACGCGGACGTAGTGTGAAGGGACCTGTGGCCAATTTCGGAGGA
TGCTCTGGGCCTACGGAGGACAGGACTGTGCTCAGAGACCCTCTCACCCTGCACAGAAGTGGTG
CCTCTCCCAGAAGACTCTGGGCAGATACCTACTTGAGGGTAGGACTTGGAGGGACTCTGTAGGG
ATCAGGGACCCACCCACCTTCCTGGCTTGAGAACAGCCCTGCTACCCCTTTTTGAGCCGAAATT
TTGAAGTGGATGCCCGTCTTGCCAGAAACGCTGTTCTCTCCAGAATGCCCCTCCCTGCACTGGA
CTTGGCGCACCCAGAACCAAGCAGAGACCCAACTCTGGAGGCCTACATCCTGTGTACCCTCAGG
AAGGGTGATGTCACCCTCCTGGTAGGTAGTCCTAGACCCTTCCTGCCTCTTGCTCTCCTATGGG
GAGACCATGTTTCCTAGAGTGTGAGCTGCCCCTCACCCCCTGAAAAGCTGACTCACTGTGAGTG
ACCTTGGGCAAGTTCCCAAACCTCCTTGTGCCTCAGTTTCCCCATCTGGAAAAAATGGGGCCAC
CTCTTGCCAGCAGTAGCAGGGCTGCCCGTGCCCCTTCCTCCCCGTGCCCCATATCCAGCCCTGG
GCACCTGTGCCTCTGTTCTGCTGGGTCTGTGGGAGCCCACCTGAGCCCAGTGGTTACTCCCCTG
GCACTCAGCTCTGCTTCTAGTTCAGCCATCCGGCCACTGAGAGTCAGGGCATGGTGCTGGGGCG
GGGTGGGGGAGGAGGGCTCTTTTCTATATTTATTTCATAGCGATAAGTCTCCGAAGGGAGCAGA
AATGCAGTCAGCCTGGGCCCCTAGCCCATGACTGCCCTCCAGTGAGGCTCTGAGGCCTGGCTAG
GGCCCTCCTGGGCAGAGCCCCTGCCTAGCCCCTCAGGCCTGATTCCACTTGCCCCCCTTTTAAA
AGCAATACCTTCAGGTCTGCAGCGCCATCAGCCAGCCTGGTTCCTTCTTAGGGTAACCTGGGTC
TGCTGGTGTTTCTGGCAATGCAGATGAGAGGAGGGTGGGCCTGCCCTCGCTGCTGTCAGGCACT
GAGAAGCCCTACGGTAAAGAAAAACAAAAACAAAAAAACAAACAAAATGGAAAAGTCACAAAAA
AGTTTGTATAAAGACGTATTTTTGTACTACATGGGGACTCTTCCTGCATGTCAGCAATAAAACT
TCCTGATCTGGAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_006238881 ⟹ XP_006238943

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	138,380,049 - 138,417,802 (+)	NCBI
Rnor_6.0	5	144,112,612 - 144,150,653 (+)	NCBI
Rnor_5.0	5	147,882,697 - 147,920,188 (+)	NCBI

Sequence:

show sequence

TAGAGGTTCCCTGACTGAGACCAGTGGGCATTTATAGGGTGTGGTGAGCTGGATGTGAAACTCT
TCGGGTCCTCCCAGAGTTGGTGTGATGTGTTATTCCCACTCAGACAATCAGGATTTACACTGAG
TTGCCTAGTTTGTAAGTGATACAACGGAGATTCAAGCGCTAGCCTTTTGGAATCCACCAAACTT
TATTTAAACCACAGTCCAACTATTATTAGCTGAGTGTCATGGCAAAGGTTCCCCTCTCTGAGTG
CTACCTTCTGCCTTTGTAAACAGGTCTCTAAAAATGCTTCCCAAAGCCAAGGCCTTGGGAGCTG
CTCTTATTACTAGTTTTTCAGCATTATCTGCAGCTGAGTGGCCACCAAGCATTCAAAGGGACTA
AGAAAGGATGCAGACTGGGACCTCATGAAGACCAGCCTTCCTGTCCCAGCAATACCTTGTGAAA
ATGTGACAAACATTTACTCCTAGCAGGGCTTAGTCGTGGCCACGTGAGTCTACACGTGGAAACA
GAATGACCCAGGGGAGGGGAGAAAAAAGCTGAGAGTCATCAAGTACACTTGTTAACTCTGAGAC
AAAGGAGTGGGACTATGGCCGCTGGTACTGCTGCCACCGAGCCCTTCTGGCCGCTTCTACACAG
CAGTGGACGGAAGCCAGGATTTTCGAGGGCCCCCAGTGAGTCACCAGACTGATGCAATCCCTTT
AAAGGGCTCATCTGCTGGTGCAAGAAGCTGATTCATGGAGGGCGTGGCTGCTGAAGGAGGAGAA
AGGGACGGAAACTGGCAGCAGGGAGTGAGGTAGACAGCCGGCTGAGATCGTTCATTGGAACTCT
TCACTGCAATCTCCCTGGACAAGACTCTAGGGATGTCCAAGAAGAACTAGGCCATCTTTGGGGT
TTCTGAAGGGCCCACAGTGAAATGAATTGTGACAGTAGCGACAGCAATTCGTGACTTCTCTTGA
ACCCAACTTCAGCGCTTTCCCACATAAATTTCCAGAAGCCGAGAAATGAGGAGCAAAGAAAGGC
CACTTTTCTAAAGAATGCAGTGCAGTTTGGCGGTTTTTGCAGCCACTTAGAGGTGTTCCCCAAC
CCCAGCAAGGAGAGCAGTAAGTCGACGAGGTTCTGCAGAGCCAAAGCGGGGCGGCGCCTCAGTC
CCAGTCTCACTGTAGATGTAGATTAGCGAACTGAGAATGAAGCGGAGAGCATCAGACAGAGGAG
CTGGGGAGACGTCGGCCAAGGCCCAGGCTCTAGGGACTGGCATTGCTGGAAATAATGCAAAGAG
AGCAGGACCGTTCATCCTGGGTCCCCGCCTGGGCAACTCACCGGTACCGAGCATTGTGCAATGT
TTGGCAAGGAAAGACGGCACGGACGACTTCTATCAGTTGAAGATCCTCACCCTTGAGGAGAGGG
GCGAGCAAGGAATTGAGAGCCAAGAGGAGAGGCAGGGCAAGATGCTGCTGCATACCGAGTACTC
TCTGCTGTCCCTGCTGCACACACAGGATGGCGTGGTCCACCACCATGGCCTCTTCCAGGACCGC
ACGTGTGAAGCGGTCGAGGACACAGAGTCTGGGCGGATGGTAAAGAAGATGAAGAAACGCATTT
GCCTTGTCCTTGACTGCCTCTGTGCACACGACTTCAGTGACAAGACCGCTGACCTCATCAACCT
ACAGCACTACGTCATCAAAGAGAAGCGGCTCAGTGAGCGTGAGACTGTGGTCATTTTCTATGAT
GTAGTCCGTGTGGTAGAAGCCCTGCACCAGAAAAACATCGTGCACAGAGACCTGAAGCTTGGGA
ACATGGTGCTCAATAAAAGGACCCATCGGATAACTATCACCAACTTCTGCCTTGGAAAGCACCT
TGTGAGTGAGGGGGACCTGCTGAAGGACCAGAGGGGGAGCCCTGCCTACATCAGTCCTGATGTG
CTCAGCGGCCGGCCATACCGGGGGAAGCCTAGTGACATGTGGGCCTTGGGCGTGGTGCTCTTCA
CCATGCTCTATGGCCAGTTCCCCTTCTACGACAGCATCCCACAGGAGCTCTTCCGCAAGATCAA
GGCTGCTGAGTACACCATCCCTGAGGATGGGCGAGTCTCTGAGAACACAGTGTGTCTTATCCGG
AAACTACTGGTCCTTGACCCCCAGCAACGCCTGGCTGCTGCAGATGTCCTGGAGGCCCTCAGTG
CCATCATTGCATCTTGGCAGTCCCTGTCCTCTCTGAGTGGGCCTTTGCAAGTGGTTCCTGACAT
CGATGACCAAATGAGCAGCTCTGACAGCTCCCAGGAGGCAAAGGTCACAGAGGAATGCTCCCAG
TACGAGTTTGAGAATTACATGCGACAGCAGCTGCTGCTGGCTGAAGAGAAGAGCTCCATTCACG
AGGCCCGGACCTGGGTACCCAAGCGGCAGTTTGGTAGCATGCCACCCGTCCGACGGCTAGGCCA
CGATGCACAGCCAATGACCTCCTTGGACACAGCCATCCTGGCACAACGCTATCTGCGGAAATAG
TGCCCTCAGCTAGGGCACTAGCCCAGCACACCTCTCCTCGGCCCGCCTGAGGCCCAGCCATCAG
GCCTGCCTGGGCCCGGGCCCAGCAGTGCTGGACTGAGTCTCCCAGGCTGCAGTAGGGACAGGGC
AGGGATAGGGACAGCCCAGGTCACAGCCAGGGTCAACAGAGGTACCACAAAGCTACCTTTTGGG
ATGATTGCTTGATTGTTTTTTTATCTGAGAATTCTAGATAGATACCTAATCTGCTTTTAATCAT
GACATTTTAATCTACCTCTGTCTCTTTAACCACGCTGTCTCTGGACTGAACGCTGGGAGGAAAG
AGGGGAGCCTACGCTCATATCCCAGGCACTGGAACAGCCTGGCTAGGCCACTGACCCCAGTCCA
TATAAGCTGACCACGCAGCTCGCTGCTGGCCCCCAGTAAGCACCCCTTCCCACCGTTCACAGCC
CCTCCCTGGGGCTGCCCTCAGTCTAAGCTTTGGAACACTCTCACCTCACTTTCCACCCAAGTCA
AATATATTTATTTTTTTACTGAACCCAACTTGTATCTCTAGGTTCAGCCCATGGCCACTCTTCG
CCCCTGAGCCTGGCTGAATAACAGGGCCCAGGTGTGTAGGCTCCCTTCTCGCCCCAGGCACCCA
GGAGCCCTCTGGCCAGTTCCTCTGTCTGCTCTCAACCCCCCAGGCCCTCTGTTTCTAGCCTTGG
CGCTTTCTCTGTCCTAGCAGCTTCTCTGAGCGGCTGCACATTCGCATTAGTCCTGCCCACCTCC
TCCATCTTTCATGTGGTACCCAGGTAACGCGGACGTAGTGTGAAGGGACCTGTGGCCAATTTCG
GAGGATGCTCTGGGCCTACGGAGGACAGGACTGTGCTCAGAGACCCTCTCACCCTGCACAGAAG
TGGTGCCTCTCCCAGAAGACTCTGGGCAGATACCTACTTGAGGGTAGGACTTGGAGGGACTCTG
TAGGGATCAGGGACCCACCCACCTTCCTGGCTTGAGAACAGCCCTGCTACCCCTTTTTGAGCCG
AAATTTTGAAGTGGATGCCCGTCTTGCCAGAAACGCTGTTCTCTCCAGAATGCCCCTCCCTGCA
CTGGACTTGGCGCACCCAGAACCAAGCAGAGACCCAACTCTGGAGGCCTACATCCTGTGTACCC
TCAGGAAGGGTGATGTCACCCTCCTGGTAGGTAGTCCTAGACCCTTCCTGCCTCTTGCTCTCCT
ATGGGGAGACCATGTTTCCTAGAGTGTGAGCTGCCCCTCACCCCCTGAAAAGCTGACTCACTGT
GAGTGACCTTGGGCAAGTTCCCAAACCTCCTTGTGCCTCAGTTTCCCCATCTGGAAAAAATGGG
GCCACCTCTTGCCAGCAGTAGCAGGGCTGCCCGTGCCCCTTCCTCCCCGTGCCCCATATCCAGC
CCTGGGCACCTGTGCCTCTGTTCTGCTGGGTCTGTGGGAGCCCACCTGAGCCCAGTGGTTACTC
CCCTGGCACTCAGCTCTGCTTCTAGTTCAGCCATCCGGCCACTGAGAGTCAGGGCATGGTGCTG
GGGCGGGGTGGGGGAGGAGGGCTCTTTTCTATATTTATTTCATAGCGATAAGTCTCCGAAGGGA
GCAGAAATGCAGTCAGCCTGGGCCCCTAGCCCATGACTGCCCTCCAGTGAGGCTCTGAGGCCTG
GCTAGGGCCCTCCTGGGCAGAGCCCCTGCCTAGCCCCTCAGGCCTGATTCCACTTGCCCCCCTT
TTAAAAGCAATACCTTCAGGTCTGCAGCGCCATCAGCCAGCCTGGTTCCTTCTTAGGGTAACCT
GGGTCTGCTGGTGTTTCTGGCAATGCAGATGAGAGGAGGGTGGGCCTGCCCTCGCTGCTGTCAG
GCACTGAGAAGCCCTACGGTAAAGAAAAACAAAAACAAAAAAACAAACAAAATGGAAAAGTCAC
AAAAAAGTTTGTATAAAGACGTATTTTTGTACTACATGGGGACTCTTCCTGCATGTCAGCAATA
AAACTTCCTGATCTGGAGCCAC

hide sequence

RefSeq Acc Id:

XM_039110152 ⟹ XP_038966080

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	138,401,861 - 138,410,374 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_898879	(Get FASTA)	NCBI Sequence Viewer
	XP_006238943	(Get FASTA)	NCBI Sequence Viewer
	XP_038966080	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI00063	(Get FASTA)	NCBI Sequence Viewer
	AAQ01589	(Get FASTA)	NCBI Sequence Viewer
	Q7TNL4	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_898879 ⟸ NM_183056

- UniProtKB:

Q7TNL4 (UniProtKB/Swiss-Prot), A0A0G2JST8 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MKRRASDRGAGETSAKAQALGTGIAGNNAKRAGPFILGPRLGNSPVPSIVQCLARKDGTDDFYQ
LKILTLEERGEQGIESQEERQGKMLLHTEYSLLSLLHTQDGVVHHHGLFQDRTCEAVEDTESGR
MVKKMKKRICLVLDCLCAHDFSDKTADLINLQHYVIKEKRLSERETVVIFYDVVRVVEALHQKN
IVHRDLKLGNMVLNKRTHRITITNFCLGKHLVSEGDLLKDQRGSPAYISPDVLSGRPYRGKPSD
MWALGVVLFTMLYGQFPFYDSIPQELFRKIKAAEYTIPEDGRVSENTVCLIRKLLVLDPQQRLA
AADVLEALSAIIASWQSLSSLSGPLQVVPDIDDQMSSSDSSQEAKVTEECSQYEFENYMRQQLL
LAEEKSSIHEARTWVPKRQFGSMPPVRRLGHDAQPMTSLDTAILAQRYLRK

hide sequence

RefSeq Acc Id:	XP_006238943 ⟸ XM_006238881
- Peptide Label:	isoform X1
- UniProtKB:	Q7TNL4 (UniProtKB/Swiss-Prot), A0A0G2JST8 (UniProtKB/TrEMBL)
- Sequence:	show sequence MKRRASDRGAGETSAKAQALGTGIAGNNAKRAGPFILGPRLGNSPVPSIVQCLARKDGTDDFYQ LKILTLEERGEQGIESQEERQGKMLLHTEYSLLSLLHTQDGVVHHHGLFQDRTCEAVEDTESGR MVKKMKKRICLVLDCLCAHDFSDKTADLINLQHYVIKEKRLSERETVVIFYDVVRVVEALHQKN IVHRDLKLGNMVLNKRTHRITITNFCLGKHLVSEGDLLKDQRGSPAYISPDVLSGRPYRGKPSD MWALGVVLFTMLYGQFPFYDSIPQELFRKIKAAEYTIPEDGRVSENTVCLIRKLLVLDPQQRLA AADVLEALSAIIASWQSLSSLSGPLQVVPDIDDQMSSSDSSQEAKVTEECSQYEFENYMRQQLL LAEEKSSIHEARTWVPKRQFGSMPPVRRLGHDAQPMTSLDTAILAQRYLRK hide sequence

RefSeq Acc Id:

ENSRNOP00000032827 ⟸ ENSRNOT00000035597

RefSeq Acc Id:	XP_038966080 ⟸ XM_039110152
- Peptide Label:	isoform X2

Protein Domains

Protein kinase

Transcriptome

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

Promoters

RGD ID:

13694028

Promoter ID:

EPDNEW_R4552

Type:

initiation region

Name:

Stk40_1

Description:

serine/threonine kinase 40

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	5	144,113,984 - 144,114,044	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (2019)

Visual

CSV

TAB

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

ACI/EurMcwi (MCW)

Visual

CSV

TAB

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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)

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

ACI/N (2020)

Visual

CSV

TAB

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

ACI/N (MCW)

Visual

CSV

TAB

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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)

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

BN-Lx/CubMcwi (2019)

Visual

CSV

TAB

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2019)

Visual

CSV

TAB

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2020)

Visual

CSV

TAB

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (2020)

Visual

CSV

TAB

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (MCW)

Visual

CSV

TAB

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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 (2020)

Visual

CSV

TAB

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH2/CubMcwi (2020)

Visual

CSV

TAB

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH3/CubMcwi (2020)

Visual

CSV

TAB

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

Buf/N (MCW)

Visual

CSV

TAB

Printer

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

COP/CrCrl (MCW & UW)

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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)

DA/OlaHsd (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/DuCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

F344/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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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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

FXLE16/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE18/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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/FarMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

HXB10/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB2/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB20/IpcvMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB31/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB4/IpcvMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (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/Crl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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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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

LEXF10A/StmMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF11/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1A/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1C/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF2B/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF3/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF4/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

LH/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

LL/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

LN/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

M520/NRrrcMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

MWF/Hsd (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

PVG/Seac (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

SHR/OlalpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHRSP/A3NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

WAG/RijCrl (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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:727884	AgrOrtholog
Ensembl Genes	ENSRNOG00000025679	Ensembl, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000032827	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000035597	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7124923	IMAGE-MGC_LOAD
InterPro	Kinase-like_dom_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Prot_kinase_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Ser/Thr_kinase_40	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Ser/Thr_kinase_AS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Tribbles/Ser_Thr_kinase_40	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:360230	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE	MGC:112582	IMAGE-MGC_LOAD
NCBI Gene	360230	ENTREZGENE
PANTHER	PTHR22961	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Pkinase	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Stk40	PhenoGen
PROSITE	PROTEIN_KINASE_DOM	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PROTEIN_KINASE_ST	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	S_TKc	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF56112	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A0G2JST8	ENTREZGENE, UniProtKB/TrEMBL
	Q7TNL4	ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary	Q498V1	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-02-25	Stk40	serine/threonine kinase 40	Lyk4	Ser/Thr-like protein kinase lyk4	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-10-12	Lyk4				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)

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Imported Disease Annotations - ClinVar