Itpka (inositol-trisphosphate 3-kinase A)

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Gene: Itpka (inositol-trisphosphate 3-kinase A) Rattus norvegicus

Analyze

Symbol:

Itpka

Name:

inositol-trisphosphate 3-kinase A

RGD ID:

619950

Description:

Enables calmodulin-dependent protein kinase activity and inositol-1,4,5-trisphosphate 3-kinase activity. Predicted to be involved in inositol phosphate biosynthetic process and phosphatidylinositol phosphate biosynthetic process. Predicted to act upstream of or within inositol metabolic process and regulation of synaptic plasticity. Predicted to be active in cytoplasm and nucleus. Orthologous to human ITPKA (inositol-trisphosphate 3-kinase A); PARTICIPATES IN inositol metabolic pathway; inositol phosphate metabolic pathway; calcium/calcium-mediated signaling pathway; INTERACTS WITH (+)-schisandrin B; 1,3,5-trinitro-1,3,5-triazinane; 2,4-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

inositol 1,4,5-triphosphate 3-kinase; inositol 1,4,5-trisphosphate 3-kinase A; inositol 145-triphosphate 3-kinase; insP 3-kinase A; IP3 3-kinase A; IP3K A

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):	ITPKA (inositol-trisphosphate 3-kinase A)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Itpka (inositol 1,4,5-trisphosphate 3-kinase A)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Itpka (inositol-trisphosphate 3-kinase A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	ITPKA (inositol-trisphosphate 3-kinase A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	ITPKA (inositol-trisphosphate 3-kinase A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Itpka (inositol-trisphosphate 3-kinase A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	ITPKA (inositol-trisphosphate 3-kinase A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	ITPKA (inositol-trisphosphate 3-kinase A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Itpka (inositol-trisphosphate 3-kinase A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	ITPKA (inositol-trisphosphate 3-kinase A)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Itpka (inositol 1,4,5-trisphosphate 3-kinase A)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	itpka (inositol-trisphosphate 3-kinase A)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)
Caenorhabditis elegans (roundworm):	lfe-2	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoInspector\|PANTHER)
Drosophila melanogaster (fruit fly):	IP3K2	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)

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	3	106,726,036 - 106,734,601 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	3	106,726,036 - 106,734,600 (+)	Ensembl
Rnor_6.0	3	111,545,007 - 111,553,605 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	111,545,007 - 111,553,604 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	118,093,293 - 118,102,060 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	106,257,482 - 106,266,160 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	3	106,153,909 - 106,162,588 (+)	NCBI
Celera	3	105,636,919 - 105,645,481 (+)	NCBI		Celera
Cytogenetic Map	3	q35	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Bloom syndrome (ISO)

colon cancer (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

1,3,5-trinitro-1,3,5-triazinane (EXP)

2,2',4,4',5,5'-hexachlorobiphenyl (ISO)

2,2',5,5'-tetrachlorobiphenyl (ISO)

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

2,4-dinitrotoluene (EXP)

4,4'-diaminodiphenylmethane (ISO)

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

aristolochic acid (ISO)

arsane (ISO)

arsenic atom (ISO)

benzo[a]pyrene (ISO)

benzo[e]pyrene (ISO)

bisphenol A (EXP,ISO)

butanal (ISO)

carbon nanotube (ISO)

cefaloridine (EXP)

choline (ISO)

cisplatin (EXP)

copper(II) sulfate (ISO)

Cuprizon (EXP)

cyclosporin A (ISO)

dextran sulfate (ISO)

diazinon (ISO)

dibenz[a,h]anthracene (ISO)

dibutyl phthalate (ISO)

endosulfan (EXP)

ethanol (ISO)

fluoxetine (EXP)

folic acid (ISO)

ketamine (EXP)

L-methionine (ISO)

metacetamol (ISO)

methapyrilene (ISO)

methotrexate (ISO)

paracetamol (ISO)

paraquat (EXP)

PCB138 (ISO)

perfluorononanoic acid (ISO)

perfluorooctane-1-sulfonic acid (EXP)

perfluorooctanoic acid (ISO)

phenobarbital (ISO)

pirinixic acid (ISO)

quercetin (ISO)

S-nitroso-N-acetyl-D-penicillamine (EXP)

sodium arsenate (ISO)

Soman (EXP)

sunitinib (ISO)

tetrachloroethene (ISO)

tetrachloromethane (EXP)

titanium dioxide (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

actin cytoskeleton organization (IGI,IMP)

dendritic spine maintenance (IMP)

inositol metabolic process (ISO)

inositol phosphate biosynthetic process (IBA)

phosphatidylinositol phosphate biosynthetic process (IBA)

positive regulation of dendritic spine morphogenesis (IMP)

protein phosphorylation (IEA)

regulation of synaptic plasticity (ISO)

Cellular Component

cytoplasm (IBA)

dendritic spine (IDA)

nucleus (IBA)

Molecular Function

ATP binding (IEA)

calmodulin binding (IEA)

calmodulin-dependent protein kinase activity (IDA)

inositol hexakisphosphate kinase activity (IBA)

inositol-1,4,5-trisphosphate 3-kinase activity (IDA,IMP)

kinase activity (IBA)

small GTPase binding (IDA)

Molecular Pathway Annotations Click to see Annotation Detail View

calcium/calcium-mediated signaling pathway (IEA)

inositol metabolic pathway (ISO)

inositol phosphate metabolic pathway (IEA,ISO)

phosphatidylinositol 3-kinase signaling pathway (IEA)

References

References - curated


1.	Choi KY, etal., Science 1990 Apr 6;248(4951):64-6.
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.	KEGG
5.	Kim IH, etal., J Neurosci. 2009 Nov 4;29(44):14039-49. doi: 10.1523/JNEUROSCI.2483-09.2009.
6.	MGD data from the GO Consortium
7.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
8.	Pipeline to import KEGG annotations from KEGG into RGD
9.	Pipeline to import SMPDB annotations from SMPDB into RGD
10.	RGD automated data pipeline
11.	RGD automated import pipeline for gene-chemical interactions
12.	Takazawa K, etal., Biochem J 1990 Nov 15;272(1):107-12.

Additional References at PubMed

PMID:7646431	PMID:8889548	PMID:10454357	PMID:12527368	PMID:15093681	PMID:15350215	PMID:15537642	PMID:19292454	PMID:19846664	PMID:20131911	PMID:22384237	PMID:22389500
PMID:30053369

Genomics

Comparative Map Data

Itpka
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	3	106,726,036 - 106,734,601 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	3	106,726,036 - 106,734,600 (+)	Ensembl
Rnor_6.0	3	111,545,007 - 111,553,605 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	111,545,007 - 111,553,604 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	118,093,293 - 118,102,060 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	106,257,482 - 106,266,160 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	3	106,153,909 - 106,162,588 (+)	NCBI
Celera	3	105,636,919 - 105,645,481 (+)	NCBI		Celera
Cytogenetic Map	3	q35	NCBI

ITPKA
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	15	41,493,393 - 41,503,551 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	15	41,493,874 - 41,503,555 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	15	41,786,072 - 41,795,749 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	15	39,573,414 - 39,583,039 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	15	39,573,413 - 39,583,037	NCBI
Celera	15	18,554,082 - 18,563,706 (+)	NCBI
Cytogenetic Map	15	q15.1	NCBI
HuRef	15	18,634,270 - 18,643,970 (+)	NCBI		HuRef
CHM1_1	15	41,904,654 - 41,914,323 (+)	NCBI		CHM1_1

Itpka
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	119,572,818 - 119,581,734 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	2	119,572,818 - 119,581,744 (+)	Ensembl
GRCm38	2	119,742,337 - 119,751,253 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	119,742,337 - 119,751,263 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	119,568,073 - 119,576,989 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	2	119,433,778 - 119,442,694 (+)	NCBI			mm8
Celera	2	120,898,643 - 120,907,740 (+)	NCBI		Celera
Cytogenetic Map	2	E5	NCBI

Itpka
(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_004955416	8,299,318 - 8,309,865 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955416	8,300,059 - 8,310,225 (+)	NCBI	ChiLan1.0	ChiLan1.0

ITPKA
(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	15	38,663,857 - 38,685,172 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	15	38,675,600 - 38,684,779 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	15	20,434,532 - 20,444,389 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

ITPKA
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	30	8,532,191 - 8,541,273 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	30	8,532,284 - 8,541,285 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	30	8,591,175 - 8,600,076 (+)	NCBI
ROS_Cfam_1.0	30	8,666,590 - 8,675,492 (+)	NCBI
UMICH_Zoey_3.1	30	8,587,903 - 8,596,796 (+)	NCBI
UNSW_CanFamBas_1.0	30	8,695,316 - 8,704,204 (+)	NCBI
UU_Cfam_GSD_1.0	30	8,827,050 - 8,835,956 (+)	NCBI

Itpka
(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_024408640	86,992,042 - 87,000,822 (+)	NCBI
SpeTri2.0	NW_004936471	4,840,113 - 4,848,881 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

ITPKA
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1	1	129,867,261 - 129,877,762 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	144,939,082 - 144,947,563 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

ITPKA
(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	26	41,502,417 - 41,512,131 (-)	NCBI	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666048	99,468,986 - 99,479,279 (+)	NCBI	Vero_WHO_p1.0

Itpka
(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_004624804	8,655,762 - 8,664,599 (+)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

RH130923

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	106,734,384 - 106,734,572 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	111,553,389 - 111,553,576	NCBI	Rnor6.0
Rnor_5.0	3	118,101,844 - 118,102,031	UniSTS	Rnor5.0
RGSC_v3.4	3	106,265,955 - 106,266,142	UniSTS	RGSC3.4
Celera	3	105,645,265 - 105,645,452	UniSTS
RH 3.4 Map	3	917.7	UniSTS
Cytogenetic Map	3	q35	UniSTS

BE106366

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	106,734,718 - 106,734,882 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	111,553,723 - 111,553,886	NCBI	Rnor6.0
Rnor_5.0	3	118,102,178 - 118,102,341	UniSTS	Rnor5.0
RGSC_v3.4	3	106,266,289 - 106,266,452	UniSTS	RGSC3.4
Celera	3	105,645,599 - 105,645,762	UniSTS
RH 3.4 Map	3	921.1	UniSTS
Cytogenetic Map	3	q35	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
2312659	Slep7	Serum leptin concentration QTL 7		0.001	blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	3	98535255	168026850	Rat
2312670	Bw94	Body weight QTL 94		0.01	inguinal fat pad mass (VT:0010424)	inguinal fat pad weight to body weight ratio (CMO:0001253)	3	98535255	168026850	Rat
2312673	Scl63	Serum cholesterol level QTL 63		0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	3	98535255	168026850	Rat
737818	Hcar12	Hepatocarcinoma resistance QTL 12	2.6		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	3	29463235	118376539	Rat
631649	Bp123	Blood pressure QTL 123	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	89772419	134772419	Rat
8694437	Bw167	Body weight QTL 167	22.46	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	3	91797474	136797474	Rat
631841	Niddm39	Non-insulin dependent diabetes mellitus QTL 39	3.36		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	94856903	159898684	Rat
8662816	Vetf4	Vascular elastic tissue fragility QTL 4	4		renal artery integrity trait (VT:0010642)	number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)	3	59242096	157323038	Rat
1300111	Rf12	Renal function QTL 12	3.78		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	3	61017749	121056321	Rat
1358362	Srcrt2	Stress Responsive Cort QTL 2	2.78		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	38192233	133483320	Rat
1354611	Despr2	Despair related QTL 2	3.03	0.0028	locomotor behavior trait (VT:0001392)	amount of time spent in voluntary immobility (CMO:0001043)	3	97084464	142084464	Rat
1358186	Ept2	Estrogen-induced pituitary tumorigenesis QTL 2	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	47233430	110362260	Rat
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	Rat
1559282	Emca5	Estrogen-induced mammary cancer QTL 5	3.9		mammary gland integrity trait (VT:0010552)	percentage of study population developing mammary tumors during a period of time (CMO:0000948)	3	43827364	169034231	Rat
1581503	Cm58	Cardiac mass QTL 58	2.7	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	43827364	121056321	Rat
1581546	Pur13	Proteinuria QTL 13	2.93	0.0335	total urine protein amount (VT:0000032)	urine protein excretion rate (CMO:0000759)	3	78196190	146592722	Rat
1581568	Rf53	Renal function QTL 53			total urine protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	3	56395968	161299569	Rat
1600376	Arunc5	Aerobic running capacity QTL 5		0.21	exercise endurance trait (VT:0002332)	maximum distance run on treadmill (CMO:0001406)	3	73376539	118376539	Rat
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	31172320	163586636	Rat
2292591	Esta4	Estrogen-induced thymic atrophy QTL 4			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	3	47233211	147415807	Rat
2292613	Ept16	Estrogen-induced pituitary tumorigenesis QTL 16	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	47233430	110362260	Rat
2293087	Iddm27	Insulin dependent diabetes mellitus QTL 27	2.68		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	97551417	147415807	Rat
724523	Tsu1	Thymus enlargement suppressive QTL 1	3.84		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	3	50437504	115638231	Rat
2301971	Cm71	Cardiac mass QTL 71	4.63		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	3	41874578	155617519	Rat
2302373	Gluco39	Glucose level QTL 39	5.01		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	3	98535386	161695835	Rat
1582221	Kidm30	Kidney mass QTL 30	3.5	0.0008	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	3	64655305	115665732	Rat
1582218	Bw74	Body weight QTL 74	3.9	0.0021	body mass (VT:0001259)	body weight (CMO:0000012)	3	53184593	115665732	Rat
2302273	Gluco35	Glucose level QTL 35	5.3	0.001	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	80800231	114297550	Rat
1582216	Bw65	Body weight QTL 65	6.3		body mass (VT:0001259)	body weight (CMO:0000012)	3	102200529	115665732	Rat
1582238	Bw68	Body weight QTL 68	3.2	0.0064	body mass (VT:0001259)	body weight (CMO:0000012)	3	53184593	115665732	Rat
2301970	Bw81	Body weight QTL 81	5.19		body mass (VT:0001259)	body weight (CMO:0000012)	3	41874578	155617519	Rat
1582219	Bw63	Body weight QTL 63	3.8	0.001	body mass (VT:0001259)	body weight (CMO:0000012)	3	96127817	115665732	Rat
1582210	Bw71	Body weight QTL 71	3.3	0.0012	body mass (VT:0001259)	body weight (CMO:0000012)	3	64655305	115665732	Rat
2301414	Kidm37	Kidney mass QTL 37		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	70653097	121056321	Rat
1582239	Epfw1	Epididymal fat weight QTL 1	4.5	0.0006	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	3	53184593	115665732	Rat
12879848	Bw181	Body weght QTL 181		0.015	body mass (VT:0001259)	body weight (CMO:0000012)	3	70348525	121056321	Rat
724532	Cm17	Cardiac mass QTL 17	2		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	3	95735366	140735366	Rat
631665	Bw8	Body weight QTL 8	5.5		body mass (VT:0001259)	body weight (CMO:0000012)	3	50437042	119183768	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	61
Count of miRNA genes:	49
Interacting mature miRNAs:	56
Transcripts:	ENSRNOT00000007247
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	2								25		7
Low	1	28	57	41	11	41			32	25	34	11
Below cutoff		15			8		6	7	15	10			6

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_031045	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039105917	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC107565	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BQ204027	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473949	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000118	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	M29787	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	X56917	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000007247 ⟹ ENSRNOP00000007247

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	3	106,726,036 - 106,734,600 (+)	Ensembl
Rnor_6.0 Ensembl	3	111,545,007 - 111,553,604 (+)	Ensembl

RefSeq Acc Id:

NM_031045 ⟹ NP_112307

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	106,726,036 - 106,734,601 (+)	NCBI
Rnor_6.0	3	111,545,007 - 111,553,605 (+)	NCBI
Rnor_5.0	3	118,093,293 - 118,102,060 (+)	NCBI
RGSC_v3.4	3	106,257,482 - 106,266,160 (+)	RGD
Celera	3	105,636,919 - 105,645,481 (+)	NCBI

Sequence:

show sequence

CGCGCCGCGGGCTGGTGGGCTCGGCTGCCGCTCCGGTGTCGGGAGATGACCCTGCCCGGACACC
CGACGGGCATGGCGCGACCACGGGGCGCGGGGCCCTGCAGCCCCGGGTTGGAGCGGGCTCCGCG
CCGGAGCGTCGGGGAGCTGCGCCTGCTCTTCGAAGCGCGCTGCGCCGCAGTCGCCGCCGCAGCG
GCCGCAGGGGAGCCCCGGGCCCGCGGGGCCAAGCGGCGTGGGGGACAAGTGCCTAACGGGCTCC
CGCGTGCTGCCCCTGCTCCGGTGATCCCGCAGCTCACTGTGACAAGCGAGGAGGATGTGGCCCC
GGCCAGCCCCGGGCCGCCGGACCGGGAGGGGAACTGGCTCCCAGCTGCGGGGTCGCACCTGCAG
CAGCCACGCCGCCTCTCCACCTCGTCCCTCTCCTCCACCGGCTCCTCGTCGCTGCTCGAGGACT
CGGAGGACGACCTGCTGAGCGACAGCGAGAGCCGGAGCCGCGGCAACGTGCAGCTGGAAACCAG
CGAAGACGTGGGGCAGAAAAGCCATTGGCAGAAGATCCGTACCATGGTCAACCTGCCTGTCATG
AGTCCTTTCAAAAAGCGCTACTCCTGGGTGCAGTTAGCAGGGCACACAGGGAGTTTCAAAGCTG
CGGGCACCAGCGGCCTGATCCTGAAGCGCAGCTCGGAGCCTGAACACTACTGCCTGGTGCGGTT
GATGGCTGATGTGCTGCGTGGGTGTGTGCCGGCCTTCCACGGTGTGGTCGAGCGGGATGGTGAA
AGCTACTTACAGTTACAGGACCTGCTTGATGGCTTCGATGGACCTTGCGTGCTTGACTGCAAGA
TGGGTGTCAGAACTTACCTGGAAGAAGAGCTGACCAAAGCCCGAGAACGGCCCAAGCTGCGAAA
GGACATGTATAAGAAAATGCTGGCCGTGGACCCCGAGGCACCTACTGAGGAGGAGCATGCGCAG
CGTGCCGTCACAAAACCTCGATACATGCAATGGCGCGAAGGCATCAGCTCCAGCACTACACTCG
GCTTCCGCATCGAGGGCATCAAGAAAGCCGATGGATCTTGCAGTACTGATTTCAAAACTACACG
AAGCAGAGAGCAAGTGACTCGAGTCTTTGAGGAGTTCATGCAAGGAGATGCTGAAGTGCTGAAG
AGGTATCTGAACCGCCTACAGCAGATCCGGGATACCCTGGAGATCTCTGATTTCTTTAGACGGC
ACGAGGTGATTGGCAGCTCACTCCTCTTCGTGCATGACCATTGCCATCGCGCTGGTGTGTGGCT
CATCGATTTTGGCAAGACCACGCCTCTCCCCGATGGCCAGATCCTGGATCATCGGAGGCCCTGG
GAGGAGGGCAATCGTGAGGACGGCTATTTGCTGGGGCTGGACAATCTCATTGGCATCTTGGCCA
ACCTGGCTGAGAGATGAGGCTGGGCCCTTTTCCCTCAGCTTGGGCCAGCTGGTCAGAGATGTGG
ACCTGTGGCTGCATCCCCACCATGCATGCCGGCAAGAGACTGGAACCCCGCTGGGCGGGCAGTT
CACATGGTCCTGGAGGACCAGGTGCCATCCACTAAGGGGGTGTAGTACATTAGGAGCTGGCTTC
TACACAAGCCTGTCTCCCAGAGCTGAATGACACTAATTTATAGGAGAGGAAGGAAACAGTGGGC
TTCTCCCCCAGCCTTGTCAAGTGACTTTGCACCTCTCCAGAGGGTCCCGATCCAGAATTGTACT
TCACAGTTATATAGACTTACTGGTCTAACTTCCTACACTACCATGGACACCCTTCCTAATAAAA
CTCAAAGATTCAGCTTCTGTGAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_039105917 ⟹ XP_038961845

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	106,726,744 - 106,734,593 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_112307	(Get FASTA)	NCBI Sequence Viewer
	XP_038961845	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA41457	(Get FASTA)	NCBI Sequence Viewer
	CAA40248	(Get FASTA)	NCBI Sequence Viewer
	EDL79923	(Get FASTA)	NCBI Sequence Viewer
	EDL79924	(Get FASTA)	NCBI Sequence Viewer
	P17105	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_112307 ⟸ NM_031045

- UniProtKB:

P17105 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MTLPGHPTGMARPRGAGPCSPGLERAPRRSVGELRLLFEARCAAVAAAAAAGEPRARGAKRRGG
QVPNGLPRAAPAPVIPQLTVTSEEDVAPASPGPPDREGNWLPAAGSHLQQPRRLSTSSLSSTGS
SSLLEDSEDDLLSDSESRSRGNVQLETSEDVGQKSHWQKIRTMVNLPVMSPFKKRYSWVQLAGH
TGSFKAAGTSGLILKRSSEPEHYCLVRLMADVLRGCVPAFHGVVERDGESYLQLQDLLDGFDGP
CVLDCKMGVRTYLEEELTKARERPKLRKDMYKKMLAVDPEAPTEEEHAQRAVTKPRYMQWREGI
SSSTTLGFRIEGIKKADGSCSTDFKTTRSREQVTRVFEEFMQGDAEVLKRYLNRLQQIRDTLEI
SDFFRRHEVIGSSLLFVHDHCHRAGVWLIDFGKTTPLPDGQILDHRRPWEEGNREDGYLLGLDN
LIGILANLAER

hide sequence

RefSeq Acc Id:

ENSRNOP00000007247 ⟸ ENSRNOT00000007247

RefSeq Acc Id:	XP_038961845 ⟸ XM_039105917
- Peptide Label:	isoform X1

Transcriptome

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

Promoters

RGD ID:

13692335

Promoter ID:

EPDNEW_R2858

Type:

initiation region

Name:

Itpka_1

Description:

inositol-trisphosphate 3-kinase A

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	3	111,544,998 - 111,545,058	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/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

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 (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

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-Lx/CubMcwi (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

BN/NHsdMcwi (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

BN/NHsdMcwi (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

BN/SsN (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

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 (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

BXH2/CubMcwi (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

BXH3/CubMcwi (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

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)

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:619950	AgrOrtholog
Ensembl Genes	ENSRNOG00000005284	Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000007247	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000007247	UniProtKB/Swiss-Prot
Gene3D-CATH	1.10.510.50	UniProtKB/Swiss-Prot
InterPro	IPK	UniProtKB/Swiss-Prot
	IPK_sf	UniProtKB/Swiss-Prot
KEGG Report	rno:81677	UniProtKB/Swiss-Prot
NCBI Gene	81677	ENTREZGENE
PANTHER	PTHR12400	UniProtKB/Swiss-Prot
Pfam	IPK	UniProtKB/Swiss-Prot
PhenoGen	Itpka	PhenoGen
UniProt	IP3KA_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2011-08-02	Itpka	inositol-trisphosphate 3-kinase A	Itpka	inositol 1,4,5-trisphosphate 3-kinase A	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2004-09-10	Itpka	inositol 1,4,5-trisphosphate 3-kinase A		inositol 1,4,5-triphosphate 3-kinase	Name updated	1299863	APPROVED
2002-08-07	Itpka	inositol 1,4,5-triphosphate 3-kinase			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_domains	contains calmodulin-binding site and six regions with amino acid compositions (PEST regions) common to proteins that are susceptible to calpain	633125
gene_regulation	activity stimulated by Ca2+ in the presence of calmodulin	633124

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)