Hpca (hippocalcin) - Rat Genome Database

Name: Hpca
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Hpca (hippocalcin) Rattus norvegicus

Analyze

Symbol:

Hpca

Name:

hippocalcin

RGD ID:

620060

Description:

Exhibits calcium ion binding activity and kinase binding activity. Involved in several processes, including activation of phospholipase D activity; cellular response to electrical stimulus; and regulation of protein transport. Localizes to several cellular components, including dendrite; neuronal cell body membrane; and perikaryon. Human ortholog(s) of this gene implicated in torsion dystonia 2. Orthologous to human HPCA (hippocalcin); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; ammonium chloride.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

calcium-binding protein; MGC105450; neuron-specific calcium-binding protein hippocalcin; P23K

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):	HPCA (hippocalcin)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Hpca (hippocalcin)	HGNC	Treefam, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Hpca (hippocalcin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	HPCA (hippocalcin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	HPCA (hippocalcin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Hpca (hippocalcin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	HPCA (hippocalcin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	HPCA (hippocalcin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Hpca (hippocalcin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	HPCA (hippocalcin)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Hpca (hippocalcin)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	hpca (hippocalcin)	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER\|PhylomeDB)
Saccharomyces cerevisiae (baker's yeast):	FRQ1	Alliance	DIOPT (Hieranoid\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	Nca	Alliance	DIOPT (Hieranoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	ncs-2	Alliance	DIOPT (Ensembl Compara\|PANTHER)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	5	141,455,616 - 141,466,252 (-)	NCBI
Rnor_6.0 Ensembl	5	147,294,820 - 147,303,346 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	5	147,295,124 - 147,305,757 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	5	151,029,882 - 151,040,514 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	148,267,898 - 148,276,223 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	5	148,277,936 - 148,286,262 (-)	NCBI
Celera	5	139,935,623 - 139,943,977 (-)	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)

colorectal adenocarcinoma (ISO)

Huntington's disease (ISO)

isolated growth hormone deficiency (ISO)

torsion dystonia 2 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(S)-nicotine (ISO)

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

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

4,4'-sulfonyldiphenol (ISO)

8-Br-cAMP (ISO)

ammonium chloride (EXP)

arsenous acid (ISO)

benzo[a]pyrene (ISO)

butanal (ISO)

calcium atom (ISO)

calcium(0) (ISO)

carvedilol (EXP)

copper(II) sulfate (ISO)

diarsenic trioxide (ISO)

ethanol (ISO)

fenvalerate (EXP)

furan (EXP)

genistein (ISO)

gentamycin (EXP)

isoprenaline (EXP)

kainic acid (ISO)

ketamine (EXP)

lead(0) (ISO)

lead(2+) (ISO)

methamphetamine (EXP)

morphine (ISO)

nicotine (ISO)

propanal (ISO)

propranolol (EXP)

Soman (EXP)

thapsigargin (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

activation of phospholipase D activity (IDA)

brain development (IEP)

calcium-mediated signaling (IEP)

cellular response to calcium ion (ISO,ISS)

cellular response to electrical stimulus (IEP)

cellular response to monosodium glutamate (IDA)

inner ear development (ISO)

negative regulation of guanylate cyclase activity (IDA)

positive regulation of adenylate cyclase activity (IDA)

positive regulation of phospholipase activity (IDA)

positive regulation of protein targeting to membrane (IDA)

regulation of postsynaptic neurotransmitter receptor internalization (IDA,IMP)

regulation of voltage-gated calcium channel activity (ISO,ISS)

response to Aroclor 1254 (IEP)

response to ketamine (IEP)

response to L-glutamate (IEP)

response to organic cyclic compound (IEP)

retina development in camera-type eye (IEP)

Cellular Component

axon (IDA)

cytoplasm (ISO)

cytosol (IDA)

dendrite cytoplasm (IDA)

dendrite membrane (IDA)

dendritic spine head (IDA)

extrinsic component of membrane (IDA)

glutamatergic synapse (IDA,IMP)

neuronal cell body membrane (IDA)

perikaryon (IDA)

postsynapse (IDA,IMP)

Molecular Function

actin binding (ISO,ISS)

calcium ion binding (IDA,ISO)

identical protein binding (ISO,ISS)

kinase binding (IPI)

protein binding (IPI,ISO)

References

References - curated


1.	Bastianelli E, etal., Exp Eye Res. 1995 Mar;60(3):257-66.
2.	Bernstein HG, etal., Neurosci Lett. 2003 Mar 20;339(2):95-8.
3.	Conesa-Zamora P, etal., Int J Cancer. 2013 Jan 15;132(2):297-307. doi: 10.1002/ijc.27674. Epub 2012 Jun 28.
4.	Dovgan AV, etal., Eur J Neurosci. 2010 Aug;32(3):347-58. doi: 10.1111/j.1460-9568.2010.07303.x.
5.	Haynes LP, etal., Proteomics. 2006 Mar;6(6):1822-32.
6.	Hyun JK, etal., Mol Cells. 2000 Dec 31;10(6):669-77.
7.	Jo J, etal., Nat Neurosci. 2010 Oct;13(10):1216-24. doi: 10.1038/nn.2636. Epub 2010 Sep 19.
8.	Kobayashi M, etal., Biochem Biophys Res Commun 1992 Nov 30;189(1):511-7.
9.	Kobayashi M, etal., Biochem Biophys Res Commun. 2012 Dec 14;429(3-4):142-7. doi: 10.1016/j.bbrc.2012.10.125. Epub 2012 Nov 6.
10.	Kobayashi M, etal., J Biol Chem. 1993 Sep 5;268(25):18898-904.
11.	Mammen A, etal., Biochem Biophys Res Commun. 2004 Oct 1;322(4):1131-9.
12.	MGD data from the GO Consortium
13.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
14.	OMIM Disease Annotation Pipeline
15.	RGD automated data pipeline
16.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
17.	RGD automated import pipeline for gene-chemical interactions
18.	Royland JE and Kodavanti PR, Toxicol Appl Pharmacol. 2008 Sep 1;231(2):179-96. Epub 2008 May 6.
19.	Rudinskiy N, etal., J Neurochem. 2009 Oct;111(2):460-72. doi: 10.1111/j.1471-4159.2009.06344.x. Epub 2009 Aug 17.
20.	Saitoh S, etal., Brain Res Dev Brain Res. 1994 Jul 15;80(1-2):199-208.
21.	Saitoh S, etal., Neurosci Lett. 1993 Jul 9;157(1):107-10.
22.	Sugisaki T, etal., Brain Res. 1994 Nov 28;665(1):101-6.
23.	Takamatsu K, etal., Biochem Biophys Res Commun 1994 Apr 15;200(1):606-11.
24.	Takamatsu K, etal., Biochem Biophys Res Commun. 1992 Feb 28;183(1):245-51.

Additional References at PubMed

PMID:8240319	PMID:8938744	PMID:11964161	PMID:12477932	PMID:12657681	PMID:15489334	PMID:16102532	PMID:16294323	PMID:21795542	PMID:22639951	PMID:28398555	PMID:29061397
PMID:31301343

Genomics

Comparative Map Data

Hpca
(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	141,455,616 - 141,466,252 (-)	NCBI
Rnor_6.0 Ensembl	5	147,294,820 - 147,303,346 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	5	147,295,124 - 147,305,757 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	5	151,029,882 - 151,040,514 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	148,267,898 - 148,276,223 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	5	148,277,936 - 148,286,262 (-)	NCBI
Celera	5	139,935,623 - 139,943,977 (-)	NCBI		Celera
Cytogenetic Map	5	q36	NCBI

HPCA
(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	32,885,994 - 32,898,441 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	1	32,885,965 - 32,894,646 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	1	33,352,092 - 33,360,247 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	33,124,685 - 33,132,834 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	1	33,021,190 - 33,029,339	NCBI
Celera	1	31,620,733 - 31,628,882 (+)	NCBI
Cytogenetic Map	1	p35.1	NCBI
HuRef	1	31,467,222 - 31,475,369 (+)	NCBI		HuRef
CHM1_1	1	33,467,533 - 33,475,680 (+)	NCBI		CHM1_1

Hpca
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	129,005,363 - 129,019,712 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	4	129,005,363 - 129,015,829 (-)	Ensembl
GRCm38	4	129,111,570 - 129,125,919 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	129,111,570 - 129,122,036 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	4	128,788,819 - 128,798,984 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	4	128,613,879 - 128,621,062 (-)	NCBI			mm8
Celera	4	127,451,599 - 127,461,862 (-)	NCBI		Celera
Cytogenetic Map	4	D2.2	NCBI

Hpca
(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	11,140,373 - 11,154,261 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955452	11,142,282 - 11,150,798 (+)	NCBI	ChiLan1.0	ChiLan1.0

HPCA
(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	33,362,921 - 33,371,524 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	33,363,673 - 33,371,524 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	1	32,176,465 - 32,185,133 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

HPCA
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	2	68,465,280 - 68,473,310 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	2	68,464,631 - 68,473,661 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Hpca
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936474	15,786,171 - 15,794,830 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

HPCA
(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	89,186,670 - 89,200,441 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	89,187,544 - 89,197,049 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	83,214,827 - 83,224,104 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

HPCA
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	20	99,974,952 - 99,983,194 (-)	NCBI
ChlSab1.1 Ensembl	20	99,975,742 - 99,980,728 (-)	Ensembl

Hpca
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624764	15,990,910 - 15,999,617 (+)	NCBI

Position Markers

D5Wox35

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	5	147,295,243 - 147,295,443	NCBI	Rnor6.0
Rnor_5.0	5	151,030,004 - 151,030,204	UniSTS	Rnor5.0
RGSC_v3.4	5	148,267,965 - 148,268,165	UniSTS	RGSC3.4
Celera	5	139,935,690 - 139,935,890	UniSTS
Cytogenetic Map	5	q36	UniSTS

PMC126259P4

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	5	147,296,005 - 147,296,287	NCBI	Rnor6.0
Rnor_5.0	5	151,030,766 - 151,031,048	UniSTS	Rnor5.0
RGSC_v3.4	5	148,268,727 - 148,269,009	UniSTS	RGSC3.4
Cytogenetic Map	5	q36	UniSTS

PMC126259P5

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	5	147,296,005 - 147,296,264	NCBI	Rnor6.0
Rnor_5.0	5	151,030,766 - 151,031,025	UniSTS	Rnor5.0
RGSC_v3.4	5	148,268,727 - 148,268,986	UniSTS	RGSC3.4
Cytogenetic Map	5	q36	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1298089	Scl14	Serum cholesterol level QTL 14	5.8	0.0004	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	114140832	159140832	Rat
631562	Apr2	Acute phase response QTL 2	3.7		blood murinoglobulin 1 amount (VT:0010597)	plasma murinoglobulin 1 level (CMO:0001931)	5	142307322	173707219	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	136354114	173707219	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	116767924	161767924	Rat
7794791	Mcs33	Mammary carcinoma susceptibility QTL 33	1.93		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	5	136640731	173707219	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	134712342	173707219	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	116767924	161767924	Rat
8694389	Bw160	Body weight QTL 160	6.17	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	5	116767924	161767924	Rat
631505	Bp103	Blood pressure QTL 103	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	138154677	172402610	Rat
634349	Bp139	Blood pressure QTL 139		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	134197905	173707219	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	116767924	161767924	Rat
8694169	Bw148	Body weight QTL 148	5	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	5	134712342	173707219	Rat
7207488	Bss110	Bone structure and strength QTL 1	8.4		femur strength trait (VT:0010010)	femur stiffness (CMO:0001674)	5	112279412	157279412	Rat
7207491	Bss112	Bone structure and strength QTL 112	7		femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	5	112279412	157279412	Rat
7207481	Bss106	Bone structure and strength QTL 106	7.9		femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	5	112279412	157279412	Rat
7207486	Bss109	Bone structure and strength QTL 109			femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	5	112279412	157279412	Rat
10053720	Scort26	Serum corticosterone level QTL 26	2.06	0.0147	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	5	131077716	173707219	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	134502121	149030144	Rat
1302790	Scl20	Serum cholesterol level QTL 20	6.4	0.0001	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	84963058	173504662	Rat
1354598	Srn6	Serum renin concentration QTL 6	3.8		blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	5	71552569	157225114	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	112279412	157279412	Rat
1549845	Scl44	Serum cholesterol level QTL 44	6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	40777918	154732375	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	102945579	154732228	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	125455818	149568944	Rat
1641912	Alcrsp18	Alcohol response QTL 18			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	5	35788756	147487820	Rat
1598819	Bp292	Blood pressure QTL 292	4.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	133943857	173707219	Rat
1576312	Emca8	Estrogen-induced mammary cancer QTL 8	4.1		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	51418671	147487820	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	47745646	167946134	Rat
1578673	Bmd13	Bone mineral density QTL 13	4.9		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	5	107119214	152119214	Rat
61393	Bp7	Blood pressure QTL 7	4.5	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	61612600	168109659	Rat
61426	Scl2	Serum cholesterol level QTL 2	7.3	0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	61086525	149030144	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	142309061	173707219	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	134502140	157212422	Rat
724525	Bp147	Blood pressure QTL 147	4.3	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	132551937	173707219	Rat
2317056	Wbc3	White blood cell count QTL 3	2.51	0.01	leukocyte quantity (VT:0000217)	white blood cell count (CMO:0000027)	5	111278451	156278451	Rat
1598861	Cm64	Cardiac mass QTL 64	2.9		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	133943857	173707219	Rat
2293642	Bss37	Bone structure and strength QTL 37	4.64	0.0001	femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	5	125455818	157225114	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	100723739	153577831	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	128687766	173687766	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	97921932	149030144	Rat
1598847	Cm62	Cardiac mass QTL 62	3.4		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	114140832	159140832	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	126
Count of miRNA genes:	92
Interacting mature miRNAs:	110
Transcripts:	ENSRNOT00000009153
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									64
Low	3		2	2		2			10	8	24
Below cutoff		11	16	14	2	14	4	4		13	12	3	4

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_017122	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006238920	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006238921	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC141171	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY442172	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC087632	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	D12573	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000162	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	X96993	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000009153 ⟹ ENSRNOP00000009153

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	5	147,294,820 - 147,303,346 (-)	Ensembl

RefSeq Acc Id:

NM_017122 ⟹ NP_058818

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	141,455,668 - 141,463,993 (-)	NCBI
Rnor_6.0	5	147,295,176 - 147,303,501 (-)	NCBI
Rnor_5.0	5	151,029,882 - 151,040,514 (-)	NCBI
RGSC_v3.4	5	148,267,898 - 148,276,223 (-)	RGD
Celera	5	139,935,623 - 139,943,977 (-)	RGD

Sequence:

show sequence

GAGTGTGTGGTCTGGGGCCACCTCTCTCTTTTTGGGTCAAATGAGAGTTTGGGGTATCTTGTGT
CTGAGGGCCCTTCTGGAGTAGTGTCAAGGGACTAAAAGGATGTAACCATTGCTCTCTCCTTTCA
CTTCCTTTGGTTGGGGGGAACCCAGGTGGGACTTGGCTCTTCTGCCATGGGCAAGCAGAATAGC
AAGCTGCGGCCAGAGATGCTGCAGGACCTGCGAGAGAACACCGAGTTCTCTGAGCTGGAGCTTC
AGGAGTGGTACAAGGGCTTCCTGAAGGACTGCCCGACTGGCATCCTCAACGTGGATGAGTTCAA
GAAGATCTACGCCAACTTCTTCCCCTACGGCGATGCCTCCAAGTTCGCCGAGCATGTCTTCCGC
ACTTTTGACACCAACAGCGACGGCACCATCGACTTCCGGGAGTTCATCATCGCTCTGAGCGTGA
CCTCGCGTGGCCGCCTGGAGCAGAAGCTCATGTGGGCCTTCAGCATGTACGACCTGGACGGCAA
TGGCTACATCAGCCGGGAGGAGATGCTAGAAATTGTGCAGGCCATTTACAAGATGGTTTCGTCC
GTGATGAAGATGCCTGAGGATGAGTCTACCCCGGAAAAGAGGACTGAGAAAATCTTCCGCCAAA
TGGACACAAACAATGACGGCAAGCTGTCACTGGAGGAGTTCATCCGCGGGGCCAAAAGCGACCC
ATCGATCGTGCGCCTGCTGCAATGCGATCCCAGCAGCGCTTCCCAGTTCTGAGCTGAGAGGAGC
CAGCTCGCCTCCCTGCCTTCACCGGCCCTCCGGCTCTCAGCTTCCTCTCCCTCGTGTCTATCCA
GGCTGGGGAATCCCCTTCTGGGTCTGCACTGTGGGGGGGCCTCTGGAGAAGCGAACCCTGCAAG
GAAGGGGCTAAGCAAGGCAGCCGTTAGTCCCCACGGCCTAAGAGGCAGAATCTCCCTTAGTGGA
CCGAGATTACCCCCGGGTCAGGTTCTGTATCTTTCCCCAGACAGCTGATCACCTTCCACGCCAC
CCACAACCCGAGGCTCTTCCACAACACGGGAAGAGGGGCTAGGTCCTTCTTGGGTGGTCCTCAG
CCTGGAGGGAGGTGGGGATTTGTGCCAAGGTGAAGAGTCTTTTTGTTTGTTTTGGTGGGGAAGA
CCGGAGGATTACTGGGCTGTGGGACTTTGAAGAAGTTCCCTGATCTACTTCCCTGCAGAAGAAC
ACTTCCTGTCCCAGCTCTTGCTGCTGGAGGCATGGTAAAAAGAAGATCTCCCAGGATTCCAACT
GGGGGTCCCCAAACCCAGCCTGCCTCTTTGCACTTGGATAACACAGATTTACCCGTCTGTCCTC
TGTATTTCTCTCTCCTTCCCCACCTCACACACGCACGGGGCCGCGCGACATGCGCGCGCAACAC
ACACACACACACACACGCACGATATGCACGCACACATGCACAGCACCCGCGCACACAGAGGCCG
GCAGACAGATGAGCAGAGCCCCTCCACAGCGTTCTGTGTGGGAAAGAAGTGCAGCCCCTGCCAA
GCCCCATGTCCCTCTGCATGCGCCG

hide sequence

RefSeq Acc Id:

XM_006238920 ⟹ XP_006238982

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	141,455,616 - 141,466,252 (-)	NCBI
Rnor_6.0	5	147,295,124 - 147,305,757 (-)	NCBI
Rnor_5.0	5	151,029,882 - 151,040,514 (-)	NCBI

Sequence:

show sequence

GGCGTCTCCTTCACAGTCTCGCCCGCCCCTCTGGCCGCCTCTGCCGCCGCGCGCCGCAGCAGCG
CCGCCTTCCCTGCGCAGTCGGTGTCTCGGCGTTGCTGGGTGGGACTTGGCTCTTCTGCCATGGG
CAAGCAGAATAGCAAGCTGCGGCCAGAGATGCTGCAGGACCTGCGAGAGAACACCGAGTTCTCT
GAGCTGGAGCTTCAGGAGTGGTACAAGGGCTTCCTGAAGGACTGCCCGACTGGCATCCTCAACG
TGGATGAGTTCAAGAAGATCTACGCCAACTTCTTCCCCTACGGCGATGCCTCCAAGTTCGCCGA
GCATGTCTTCCGCACTTTTGACACCAACAGCGACGGCACCATCGACTTCCGGGAGTTCATCATC
GCTCTGAGCGTGACCTCGCGTGGCCGCCTGGAGCAGAAGCTCATGTGGGCCTTCAGCATGTACG
ACCTGGACGGCAATGGCTACATCAGCCGGGAGGAGATGCTAGAAATTGTGCAGGCCATTTACAA
GATGGTTTCGTCCGTGATGAAGATGCCTGAGGATGAGTCTACCCCGGAAAAGAGGACTGAGAAA
ATCTTCCGCCAAATGGACACAAACAATGACGGCAAGCTGTCACTGGAGGAGTTCATCCGCGGGG
CCAAAAGCGACCCATCGATCGTGCGCCTGCTGCAATGCGATCCCAGCAGCGCTTCCCAGTTCTG
AGCTGAGAGGAGCCAGCTCGCCTCCCTGCCTTCACCGGCCCTCCGGCTCTCAGCTTCCTCTCCC
TCGTGTCTATCCAGGCTGGGGAATCCCCTTCTGGGGTCTGCACTGTGGGGGGGCCTCTGGAGAA
GCGAACCCTGCAAGGAAGGGGCTAAGCAAGGCAGCCGTTAGTCCCCACGGCCTAAGAGGCAGAA
TCTCCCTTAGTGGGACCGAGATTACCCCCGGGTCAGGTTCTGTATTCTTTCCCCAGACAGCTGG
ATCACCTTCCACCCACCCACAACCCGGAGGCTCTTCCACAACACGGGGAAGAGGGTCCTTCTTG
GGTGGTCCTCAGCCTGGAGGGAGGTGGGGATTTGTGCCAAGGTGAAGAGTCTTTTTGTTTGTTT
GGTGGGGAGACCCGGAGGATTACTGGGCTGTGGGACTTTGAAGAAGTTCCCTGATCTACTTCCC
TGCAGAAGAACACTTCCTGTCCCAGCTCTTGCTGGCTGGAGGCCATGGTAAAAAGAAGATCTCC
CAGGATTCCAACTGGGGGTCCCCAAACCCAGCCTGCCTCTTTGCACTTGGATAACCACAGATTT
ACCCGTCTGTCCTCTGTATTTCTCTCTCCTTCCCCCACCTCACACACGCACGGGCGCGCGCGCA
CATGCGCGCGCAACACACACACACACACACACACGCACGCATATGCACGCACACATGCACACGC
ACCCGCGCACACAGAGGCCGGCAGACAGATGAGCAGAGCCCCTCCACAGCGTTCTGTGTGGGAA
AGAAGTGCAGGCCCCTGGCCAAGCCCCATGTCCCTCTGCATGCGCCACACGGAGCGTCTTTGTT
CTTTTTAATAACTTCAAAATAAAGTCTTGTTTCA

hide sequence

RefSeq Acc Id:

XM_006238921 ⟹ XP_006238983

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	141,455,616 - 141,466,047 (-)	NCBI
Rnor_6.0	5	147,295,124 - 147,305,488 (-)	NCBI
Rnor_5.0	5	151,029,882 - 151,040,514 (-)	NCBI

Sequence:

show sequence

TCTCCAGGGTCCTGACCGCCAAGTGGCCGGCTCCCGGGAGTCGCGCGTCGACCGTCCCGGGCGC
CCCCTCCAGGAGGTGGGACTTGGCTCTTCTGCCATGGGCAAGCAGAATAGCAAGCTGCGGCCAG
AGATGCTGCAGGACCTGCGAGAGAACACCGAGTTCTCTGAGCTGGAGCTTCAGGAGTGGTACAA
GGGCTTCCTGAAGGACTGCCCGACTGGCATCCTCAACGTGGATGAGTTCAAGAAGATCTACGCC
AACTTCTTCCCCTACGGCGATGCCTCCAAGTTCGCCGAGCATGTCTTCCGCACTTTTGACACCA
ACAGCGACGGCACCATCGACTTCCGGGAGTTCATCATCGCTCTGAGCGTGACCTCGCGTGGCCG
CCTGGAGCAGAAGCTCATGTGGGCCTTCAGCATGTACGACCTGGACGGCAATGGCTACATCAGC
CGGGAGGAGATGCTAGAAATTGTGCAGGCCATTTACAAGATGGTTTCGTCCGTGATGAAGATGC
CTGAGGATGAGTCTACCCCGGAAAAGAGGACTGAGAAAATCTTCCGCCAAATGGACACAAACAA
TGACGGCAAGCTGTCACTGGAGGAGTTCATCCGCGGGGCCAAAAGCGACCCATCGATCGTGCGC
CTGCTGCAATGCGATCCCAGCAGCGCTTCCCAGTTCTGAGCTGAGAGGAGCCAGCTCGCCTCCC
TGCCTTCACCGGCCCTCCGGCTCTCAGCTTCCTCTCCCTCGTGTCTATCCAGGCTGGGGAATCC
CCTTCTGGGGTCTGCACTGTGGGGGGGCCTCTGGAGAAGCGAACCCTGCAAGGAAGGGGCTAAG
CAAGGCAGCCGTTAGTCCCCACGGCCTAAGAGGCAGAATCTCCCTTAGTGGGACCGAGATTACC
CCCGGGTCAGGTTCTGTATTCTTTCCCCAGACAGCTGGATCACCTTCCACCCACCCACAACCCG
GAGGCTCTTCCACAACACGGGGAAGAGGGTCCTTCTTGGGTGGTCCTCAGCCTGGAGGGAGGTG
GGGATTTGTGCCAAGGTGAAGAGTCTTTTTGTTTGTTTGGTGGGGAGACCCGGAGGATTACTGG
GCTGTGGGACTTTGAAGAAGTTCCCTGATCTACTTCCCTGCAGAAGAACACTTCCTGTCCCAGC
TCTTGCTGGCTGGAGGCCATGGTAAAAAGAAGATCTCCCAGGATTCCAACTGGGGGTCCCCAAA
CCCAGCCTGCCTCTTTGCACTTGGATAACCACAGATTTACCCGTCTGTCCTCTGTATTTCTCTC
TCCTTCCCCCACCTCACACACGCACGGGCGCGCGCGCACATGCGCGCGCAACACACACACACAC
ACACACACGCACGCATATGCACGCACACATGCACACGCACCCGCGCACACAGAGGCCGGCAGAC
AGATGAGCAGAGCCCCTCCACAGCGTTCTGTGTGGGAAAGAAGTGCAGGCCCCTGGCCAAGCCC
CATGTCCCTCTGCATGCGCCACACGGAGCGTCTTTGTTCTTTTTAATAACTTCAAAATAAAGTC
TTGTTTCA

hide sequence

Protein Sequences


Protein RefSeqs	NP_058818	(Get FASTA)	NCBI Sequence Viewer
	XP_006238982	(Get FASTA)	NCBI Sequence Viewer
	XP_006238983	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH87632	(Get FASTA)	NCBI Sequence Viewer
	AAR14053	(Get FASTA)	NCBI Sequence Viewer
	BAA02122	(Get FASTA)	NCBI Sequence Viewer
	CAA65718	(Get FASTA)	NCBI Sequence Viewer
	P84076	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_058818 ⟸ NM_017122
- UniProtKB:	P84076 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MGKQNSKLRPEMLQDLRENTEFSELELQEWYKGFLKDCPTGILNVDEFKKIYANFFPYGDASKF AEHVFRTFDTNSDGTIDFREFIIALSVTSRGRLEQKLMWAFSMYDLDGNGYISREEMLEIVQAI YKMVSSVMKMPEDESTPEKRTEKIFRQMDTNNDGKLSLEEFIRGAKSDPSIVRLLQCDPSSASQ F hide sequence

RefSeq Acc Id:	XP_006238982 ⟸ XM_006238920
- Peptide Label:	isoform X1
- UniProtKB:	P84076 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MGKQNSKLRPEMLQDLRENTEFSELELQEWYKGFLKDCPTGILNVDEFKKIYANFFPYGDASKF AEHVFRTFDTNSDGTIDFREFIIALSVTSRGRLEQKLMWAFSMYDLDGNGYISREEMLEIVQAI YKMVSSVMKMPEDESTPEKRTEKIFRQMDTNNDGKLSLEEFIRGAKSDPSIVRLLQCDPSSASQ F hide sequence

RefSeq Acc Id:	XP_006238983 ⟸ XM_006238921
- Peptide Label:	isoform X1
- UniProtKB:	P84076 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MGKQNSKLRPEMLQDLRENTEFSELELQEWYKGFLKDCPTGILNVDEFKKIYANFFPYGDASKF AEHVFRTFDTNSDGTIDFREFIIALSVTSRGRLEQKLMWAFSMYDLDGNGYISREEMLEIVQAI YKMVSSVMKMPEDESTPEKRTEKIFRQMDTNNDGKLSLEEFIRGAKSDPSIVRLLQCDPSSASQ F hide sequence

RefSeq Acc Id:

ENSRNOP00000009153 ⟸ ENSRNOT00000009153

Protein Domains

EF-hand

Transcriptome

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

Promoters

RGD ID:

13694055

Promoter ID:

EPDNEW_R4580

Type:

single initiation site

Name:

Hpca_1

Description:

hippocalcin

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	147,303,382 - 147,303,442	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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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)

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CSV

TAB

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

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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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/SsN (MCW)

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CSV

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

Buf/N (MCW)

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

COP/CrCrl (MCW & UW)

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

F344/NCrl (RGD)

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CSV

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

F344/NRrrc (MCW)

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CSV

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

FHH/EurMcwi (MCW)

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CSV

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

FHH/EurMcwi (RGD)

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CSV

TAB

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

FHL/EurMcwi (MCW)

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CSV

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

FHL/EurMcwi (RGD)

Visual

CSV

TAB

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

GH/OmrMcwi (MCW)

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CSV

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

GK/Ox (RGD)

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CSV

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

LE/Stm (RGD)

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CSV

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

LEW/Crl (RGD)

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CSV

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

LEW/NCrlBR (RGD)

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CSV

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

LH/MavRrrc (RGD)

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CSV

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

LL/MavRrrc (RGD)

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CSV

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

LN/MavRrrc (RGD)

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CSV

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

M520/N (MCW)

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

MHS/Gib (RGD)

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CSV

TAB

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

MNS/Gib (RGD)

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CSV

TAB

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

MR/N (MCW)

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CSV

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

SBH/Ygl (MCW)

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CSV

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

SBH/Ygl (RGD)

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

SBN/Ygl (MCW)

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

SBN/Ygl (RGD)

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

SHR/NHsd (RGD)

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

SHRSP/Gcrc (RGD)

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

SR/JrHsd (MCW)

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

SR/JrHsd (RGD)

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

SS/Jr (RGD)

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

SS/JrHsdMcwi (MCW)

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

SS/JrHsdMcwi (RGD)

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

WAG/Rij (RGD)

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

WKY/Gcrc (RGD)

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

WKY/N (MCW)

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

WKY/NCrl (RGD)

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

WKY/NHsd (RGD)

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

WN/N (MCW)

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:620060	AgrOrtholog
Ensembl Genes	ENSRNOG00000006979	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000009153	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000009153	ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7319524	IMAGE-MGC_LOAD
InterPro	EF-hand-dom_pair	UniProtKB/Swiss-Prot
	EF_Hand_1_Ca_BS	UniProtKB/Swiss-Prot
	EF_hand_dom	UniProtKB/Swiss-Prot
	Recoverin	UniProtKB/Swiss-Prot
KEGG Report	rno:29177	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:105450	IMAGE-MGC_LOAD
NCBI Gene	29177	ENTREZGENE
PANTHER	PTHR23055	UniProtKB/Swiss-Prot
Pfam	EF-hand_7	UniProtKB/Swiss-Prot
	EF-hand_8	UniProtKB/Swiss-Prot
PhenoGen	Hpca	PhenoGen
PROSITE	EF_HAND_1	UniProtKB/Swiss-Prot
	EF_HAND_2	UniProtKB/Swiss-Prot
SMART	EFh	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF47473	UniProtKB/Swiss-Prot
UniProt	HPCA_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary	P32076	UniProtKB/Swiss-Prot
	P41211	UniProtKB/Swiss-Prot
	P70510	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2004-02-26	Hpca	hippocalcin			Symbol and Name status set to approved	625702	APPROVED
2002-08-07	Hpca				Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_domains	contains three EF-hand calcium-binding domains	727521
gene_protein	195 amino acids; 22.6 kDa	727521

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

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

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

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

Imported Disease Annotations - ClinVar

Imported Disease Annotations - OMIM