Hpcal4 (hippocalcin-like 4) - Rat Genome Database

Name: Hpcal4
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Hpcal4 (hippocalcin-like 4) Rattus norvegicus

Analyze

Symbol:

Hpcal4

Name:

hippocalcin-like 4

RGD ID:

708491

Description:

Exhibits calcium channel regulator activity; protein C-terminus binding activity; and protein domain specific binding activity. Predicted to be involved in signal transduction. Orthologous to human HPCAL4 (hippocalcin like 4); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 6-propyl-2-thiouracil; ammonium chloride.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

hippocalcin-like protein 4; neural visinin-like Ca2+-binding protein type 2; neural visinin-like protein 2; Nvjp2; NVL-2; NVP-2; VILIP-2; visinin-like protein 2

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):	HPCAL4 (hippocalcin like 4)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, PhylomeDB
Mus musculus (house mouse):	Hpcal4 (hippocalcin-like 4)	HGNC	NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Hpcal4 (hippocalcin like 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	HPCAL4 (hippocalcin like 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	HPCAL4 (hippocalcin like 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Hpcal4 (hippocalcin like 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	HPCAL4 (hippocalcin like 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	HPCAL4 (hippocalcin like 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Hpcal4 (hippocalcin like 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	HPCAL4 (hippocalcin like 4)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Mus musculus (house mouse):	Hpcal4 (hippocalcin-like 4)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Danio rerio (zebrafish):	hpcal4 (hippocalcin like 4)	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER\|PhylomeDB)
Saccharomyces cerevisiae (baker's yeast):	FRQ1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	CG7646	Alliance	DIOPT (Ensembl Compara\|PANTHER)
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	135,454,477 - 135,466,417 (+)	NCBI
Rnor_6.0 Ensembl	5	140,870,140 - 140,882,244 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	5	140,870,127 - 140,882,242 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	5	144,660,294 - 144,672,321 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	142,490,462 - 142,498,359 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	5	142,495,687 - 142,503,585 (+)	NCBI
Celera	5	133,994,080 - 134,001,954 (+)	NCBI		Celera
Cytogenetic Map	5	q36	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

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

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(S)-nicotine (ISO)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

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

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

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

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

2-methylcholine (ISO)

3,4-methylenedioxymethamphetamine (ISO)

3-methylcholanthrene (ISO)

6-propyl-2-thiouracil (EXP)

aflatoxin B1 (ISO)

aflatoxin B2 (ISO)

ammonium chloride (EXP)

antirheumatic drug (ISO)

benzo[a]pyrene (ISO)

benzo[b]fluoranthene (ISO)

bisphenol A (EXP,ISO)

butanal (ISO)

chloroprene (ISO)

clofibrate (ISO)

clozapine (EXP)

cocaine (EXP)

dichlorine (EXP)

entinostat (ISO)

ethanol (ISO)

fenvalerate (EXP)

haloperidol (EXP)

lead(0) (ISO)

lead(2+) (ISO)

methotrexate (ISO)

N-nitrosodiethylamine (EXP,ISO)

nicotine (ISO)

ozone (EXP)

paracetamol (ISO)

PCB138 (ISO)

pentanal (ISO)

phenethyl caffeate (EXP)

piperonyl butoxide (ISO)

pirinixic acid (ISO)

propanal (ISO)

testosterone undecanoate (ISO)

triclosan (ISO)

valproic acid (ISO)

vinclozolin (EXP)

zoledronic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

signal transduction (IEA)

Molecular Function

calcium channel regulator activity (IDA)

calcium ion binding (IEA)

protein binding (ISO)

protein C-terminus binding (IPI)

protein domain specific binding (IPI)

References

References - curated


1.	Kajimoto Y, etal., J Neurochem 1993 Sep;61(3):1091-6.
2.	Kobayashi M, etal., Biochem Biophys Res Commun 1992 Nov 30;189(1):511-7.
3.	Kuno T, etal., Biochem Biophys Res Commun 1992 May 15;184(3):1219-25.
4.	Lautermilch NJ, etal., J Neurosci. 2005 Jul 27;25(30):7062-70.
5.	MGD data from the GO Consortium
6.	Okazaki K, etal., Biochem Biophys Res Commun 1992 May 29;185(1):147-53.
7.	RGD automated data pipeline
8.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:16049184

Genomics

Comparative Map Data

Hpcal4
(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	135,454,477 - 135,466,417 (+)	NCBI
Rnor_6.0 Ensembl	5	140,870,140 - 140,882,244 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	5	140,870,127 - 140,882,242 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	5	144,660,294 - 144,672,321 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	142,490,462 - 142,498,359 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	5	142,495,687 - 142,503,585 (+)	NCBI
Celera	5	133,994,080 - 134,001,954 (+)	NCBI		Celera
Cytogenetic Map	5	q36	NCBI

HPCAL4
(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	39,678,648 - 39,691,485 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	1	39,678,648 - 39,691,433 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	1	40,144,320 - 40,157,105 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	39,917,232 - 39,929,676 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	1	39,813,738 - 39,826,182	NCBI
Celera	1	38,426,386 - 38,438,833 (-)	NCBI
Cytogenetic Map	1	p34.2	NCBI
HuRef	1	38,263,336 - 38,275,727 (-)	NCBI		HuRef
CHM1_1	1	40,259,703 - 40,272,820 (-)	NCBI		CHM1_1

Hpcal4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	123,077,297 - 123,088,492 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	4	123,077,020 - 123,088,494 (+)	Ensembl
GRCm38	4	123,183,504 - 123,194,699 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	123,183,227 - 123,194,701 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	4	122,860,747 - 122,871,942 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	4	122,685,807 - 122,697,002 (+)	NCBI			mm8
Celera	4	121,515,883 - 121,527,080 (+)	NCBI		Celera
Cytogenetic Map	4	D2.2	NCBI

Hpcal4
(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	17,193,242 - 17,205,603 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955452	17,193,505 - 17,205,174 (-)	NCBI	ChiLan1.0	ChiLan1.0

HPCAL4
(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	40,295,463 - 40,308,469 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	40,295,463 - 40,308,469 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	1	38,969,006 - 38,982,080 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

HPCAL4
(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	15	3,194,653 - 3,201,425 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	15	3,196,653 - 3,205,191 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Hpcal4
(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	21,561,544 - 21,568,230 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

HPCAL4
(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	95,502,679 - 95,515,850 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	95,502,679 - 95,515,892 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	88,590,972 - 88,604,172 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

HPCAL4
(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	93,287,035 - 93,298,310 (-)	NCBI

Hpcal4
(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	22,173,924 - 22,185,790 (-)	NCBI

Position Markers

RH130873

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	5	140,881,879 - 140,882,069	NCBI	Rnor6.0
Rnor_5.0	5	144,671,958 - 144,672,148	UniSTS	Rnor5.0
RGSC_v3.4	5	142,501,720 - 142,501,910	UniSTS	RGSC3.4
Celera	5	134,005,315 - 134,005,505	UniSTS
Cytogenetic Map	5	q36	UniSTS

AI846570

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	5	140,882,078 - 140,882,216	NCBI	Rnor6.0
Rnor_5.0	5	144,672,157 - 144,672,295	UniSTS	Rnor5.0
RGSC_v3.4	5	142,501,919 - 142,502,057	UniSTS	RGSC3.4
Celera	5	134,005,514 - 134,005,652	UniSTS
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
2317753	Glom24	Glomerulus QTL 24	3.1		kidney glomerulus integrity trait (VT:0010546)	kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)	5	101265591	141912026	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
7411722	Strs6	Sensitivity to stroke QTL 6	3.9		cerebrum integrity trait (VT:0010549)	percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)	5	140387005	143846157	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
1300122	Wbc1	White blood cell count QTL 1	2.75		leukocyte quantity (VT:0000217)	total white blood cell count (CMO:0000365)	5	130531300	145726262	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
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:	482
Count of miRNA genes:	246
Interacting mature miRNAs:	322
Transcripts:	ENSRNOT00000074347
Prediction methods:	Miranda, 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									52
Low	3	8	5	4		4	1	1	14	18	17	7	1
Below cutoff		14	19	8	11	8	5	5	8	13	22	4	5

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_017357	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006238829	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473968	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	D13125	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	D14819	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ212482	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000162	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000074347 ⟹ ENSRNOP00000066655

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	5	140,870,140 - 140,882,244 (+)	Ensembl

RefSeq Acc Id:

NM_017357 ⟹ NP_059053

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	135,454,796 - 135,462,693 (+)	NCBI
Rnor_6.0	5	140,870,551 - 140,878,518 (+)	NCBI
Rnor_5.0	5	144,660,294 - 144,672,321 (+)	NCBI
RGSC_v3.4	5	142,490,462 - 142,498,359 (+)	RGD
Celera	5	133,994,080 - 134,001,954 (+)	RGD

Sequence:

show sequence

TTTCACTTCAAGCCGAGTCCCCAGTTCAAGAAGGAGGTACGGCCGCCTCCTTACCCCCATCTCA
GGCCCACCATGGGGAAGAACAATAGCAAGCTGGCCCCTGAGGAGCTGGAAGATCTGGTCCAGAA
CACGGAGTTCAGCGAGCAGGAGCTAAAGCAGTGGTATAAGGGTTTCCTGAAGGACTGCCCCAGC
GGCATCCTCAACCTGGAGGAGTTTCAGCAACTCTACATCAAGTTCTTTCCTTACGGAGACGCCT
CCAAGTTTGCACAGCATGCTTTCCGCACCTTCGACAAGAACGGCGATGGCACCATCGACTTCCG
GGAGTTCATCTGCGCCCTTTCTGTCACCTCCCGTGGCAGCTTTGAGCAGAAGCTCAACTGGGCC
TTTGAGATGTACGACCTGGACGGTGATGGACGCATCACACGGCTGGAGATGCTGGAGATCATTG
AGGCTATCTATAAGATGGTGGGCACCGTGATCATGATGCGCATGAACCAGGATGGGCTCACGCC
CCAGCAGCGCGTAGACAAGATCTTCAAGAAGATGGACCAGGATAAGGATGACCAGATTACGCTG
GAGGAGTTCAAGGAGGCGGCCAAGAGTGACCCGTCCATCGTGTTGCTGTTGCAATGTGACATGC
AGAAGTAGGGCTGGTGAGGGGCA

hide sequence

RefSeq Acc Id:

XM_006238829 ⟹ XP_006238891

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	135,454,477 - 135,466,417 (+)	NCBI
Rnor_6.0	5	140,870,127 - 140,882,242 (+)	NCBI
Rnor_5.0	5	144,660,294 - 144,672,321 (+)	NCBI

Sequence:

show sequence

ACTCACAGGCCACCCCATCCCCACCTGAAACCCCGCCTGTCACTCGGTGCCAGCTGAACCAATC
GATGTCCAAAGTTGCGGAGAGGAGGCGGGCCTTATGCAAATCGTGTCGCCTTCGAGAAGCAAAT
AGTGATACAAGAACTGGGGAGGCGGCTTCGACGCGGACCCTACAGAGCCTGTCGTCCGCCCGAT
AGCCAGCTTCATCCCCGCGGACGTCCAGGCTCCGAGCCATCTAGCGACTCGGCGAGCGGCCTCA
GGTGGACAATCATCTGGAGAGCCCGCCTTGGGCCAGGGACTTTCACTTCAAGCCGAGTCCCCAG
TTCAAGAAGGAGGTACGGCCGCCTCCTTACCCCCAGCTCAGGCCCACCATGGGGAAGAACAATA
GCAAGCTGGCCCCTGAGGAGCTGGAAGATCTGGTCCAGAACACGGAGTTCAGCGAGCAGGAGCT
AAAGCAGTGGTATAAGGGTTTCCTGAAGGACTGCCCCAGCGGCATCCTCAACCTGGAGGAGTTT
CAGCAACTCTACATCAAGTTCTTTCCTTACGGAGACGCCTCCAAGTTTGCACAGCATGCTTTCC
GCACCTTCGACAAGAACGGCGATGGCACCATCGACTTCCGGGAGTTCATCTGCGCCCTTTCTGT
CACCTCCCGTGGCAGCTTTGAGCAGAAGCTCAACTGGGCCTTTGAGATGTACGACCTGGACGGT
GATGGACGCATCACACGGCTGGAGATGCTGGAGATCATTGAGGCTATCTATAAGATGGTGGGCA
CCGTGATCATGATGCGCATGAACCAGGATGGGCTCACGCCCCAGCAGCGTGTAGACAAGATCTT
CAAGAAGATGGACCAGGATAAGGATGACCAGATTACGCTGGAGGAGTTCAAGGAGGCGGCCAAG
AGTGACCCGTCCATCGTGTTGCTGTTGCAATGTGACATGCAGAAGTAGGGCTGGTGAGGGGCAG
GGCCCCTGGCCAGGAAAGGCGTGGCGCCTCCCAACCTGATGTCCTCTCTGCTGGCCCACCCCTG
GGGGGAGGGGCGTTCCAGCCTCACTCTCTAGCTCACCCATTCCTCTGCCCAAGCCTTTCTCTCC
TCAGTCAAGCTCCACGAGTGACCACCTCATCCTGCGAAGGAGACAGGTCCTCTCAAGTAGCCTG
TCCTCAGATAGTCTGCCATTAGCTCCACCTCTAGCCTTGGCCTAGAACCAACATCCTTTGGGCT
TAGGAGAGTTGGCTTTTGACCCTAGAGGCGAGGTTAAGGAGGGGATGAGGACTTGCTTTGCAAT
CCTGCTGTTCTCAGGATTATGGTCCAAATAAACAGTATGGTCCACGGGCCCCAGGTGGAAGGAC
CAAACCGGGTCTATCCTGGACTCTCCGGATTCCCTGAGAGGTGGTCTCTGCCCTGCCCCCTTGC
TCTACCTGGCTTCTCTGGCCCCAGCCTTTGGAACGTTCAATGAGTCCTTTCTTCAGCTAATGCT
TGTTGAGTACTTGCCCCATGCCAGGCACCTGACGGTGCTAAGAATACGGTTGTTTACAGAAACC
CATTCCATGCCCCCTGGAAGCCCACATGGTAACAAGACAACTTCCAAGGGTCTCGGTCTCAGAC
CGGGATGTGAAGCACAACAGGAGATGAGGGTGCGAGGCAGCTGGCGAGTTGTCAGAACTAGTGT
GTCCTCCAGTCGGTGCCACCCAAAGCTGCAGAAAGACCGAATGAAAAGCCTGAGGAAGCTTAGG
TGCCACGTGGGTGGAAACTTTAAGAAAAACAAAACAAAAAATTATGTAATATTTATTTTTTTAG
TGCCCTTTCGAAGAGATAAGATCATTTTATTAGACTATTAAAATATACTCTATATTACTTGATT
TCTTAAAAAAAAGATTTAAATGAATATAAAAATGCTAACGTTGGGGGTGGGGGGGACGTTTAGG
CAAAAGCGGTAGGGCTACCATCAGACCTGGAGAACCCGAGCTCTCACCACCAGCAGTTCCTGCT
GTCCTCTGCCACATCCCTTTATCTGCTTTTCATAGTTCCACGGGCGACTTTTCTGTCCCACGCT
TCGGGTGCTGGCGTCAGAGAACCAGGGGCAAGCGCAGTTCATACCCACGTCTTGGAAGCTTGTT
TCTGAGTTTGGGTTGGTTTGGTTGGCTTATCGTTTCACAGCCTAAGCTAGACGGAGCTAGAAGA
AAGGAATCCTGCAGCCGCTGTGCGTGCGGGCTTCTGGGCTCTGCTTATTTGTGAACCAAATGCT
TAAAGAATGTGCTGGATGTACTCCATACAAAAGGCTTTCCCTAAACCTTTCCATCCTAGATCTG
CCAGGTAATCTACTTCGTCCACCTCCAAGCTCACCAGCTTAGCTTTCTGAACTTTAAGGTCTCT
GAGCTAACTATTGTGCTGCATGCTTTCCAGAAAAAAAAAATCCACTTGCTTCTTCCAGCTCCAC
ACCTCACTTCCGCCCGCGCTTCCTTGTGATCAGAGGTTGGCTTTGACGTGCCATGACAGTTGGC
TTCCTCTTGAACTGCTGTGAAAACAGTCTAGTACAGAGATGCTGTCAGCTGGGGTGGGAGTTGA
GAGCGCTTGTGAAGCCGGGGCGTGTGCTGGCAAAGATTGCCCTGCAGAAGATACACGATTTGCC
ACTTCCGGGTGTTCATCTCCCTGCTGGTCGAAGTGTTTGTAGATTCTGACCTGTGGTCCGAAGT
TCTGTCTGACTTTCCTTCTTGTGGCCTTTGGAGGGAGCAAGTCACCTTCTTCCTGACCTGCCTA
CCCAGGCCATGTGGTGAGGCTGAGGAACTCTTAGCCTCAAGTGATAGTGGTAGGTGTTTATTTT
TTGGTGACGCTTCATGGGGCTGCTGCACAGCTCTCACAAACTGCCCGTTAAGCTTGTCTTGTGC
TGTCATCGCTGCGACAGATACATGAGTGCTCCACGGCCTAGCTCGGCTGGGACCTGAATCTTCT
AGTGAAAAGCTTTTCCTTGCCCCCAAATGTTTAATCTAGCCCGATTCACAACGACACAGAATTC
CTTGGCTTTCAAAGGCTTGTATCTGCCTGCATCTTGTTTTGTCCTCACAGCCCAGGGAGATAGG
GGTTTTCAGTACCTTTACCCAGGCTTGGAAGCTAAGGTTACAGGTTGAGGGTGAGAGGTCTCTT
GTATGAGAGACAATATTGAGACTCGAATGCAAGGCTCTCTAAGAGTCTCTTTTCTGCCCCACCT
GATTTCTCCAGATGCTAACTGCAAGACAAATTGACTTTGTCCTTTTAGAAGTTTCCTGCCTGCC
AAGAACTTTCTGAGGGGACAGTCTTCCAAAAAGGAGGAGGAGCTTGAAGTCGCTCCATTTTCTA
GCATCCTCTGGTTGCTTCAGGGCAGCTTTGCATGGACCAAAGCTGTTCTTGGAGGCTGCAAACC
AAATCCTGGAAGCACCTTGCTTGTCTTCCCCACTATCTTCCTTCCTAAGGGAATTACTTTTCTT
TTTCCAAGCTGGTCGGCAAGTTCTACTATGCGACAGATCACTCCAGGCTTCTGGTCACCCCCTC
ATGGGCAATATTTGCTACTTCGGCCAAGGGTTTCAGACAGCCCAGCAGGCCCCAAGCTGGCTCC
GCCCTCTTGCTGATGGGAGGAGCAACAGGCAGGTTAAGCCTCGCTCCCACATTCTCCTGGGTGT
CTAAACCTCAGCATATCCAGGAGACCACGTGGTAGAGTGCCCGTCCCTGCCTTGGGAAGAGAAA
GGTTTCCCATCTCTGCTCCAGCTTGAGAAGCGTCTTATCATGAAACACGAGGTCAGCAGAGATC
TGTGTGCGTGACTTGCACAGACATGGAAACATAAATGCAGTTAAAATGCTGACATATCAGATGT
GAGGTTCTGTATCCTCTTACAGAATGTGAATCTGGTGGTTCCAAATTTAGCCTTCTCACACCCC
CTATCCTCATTCATCCTCTCTGGCTAAGCGATGAGCCCCCTATTTCTCATCCCCAAAAAAATCC
CCAGCGTGGGCCGCTCTGTGCGCTGCTGTAGGCCACGCAGCTGCCTAATTACTAGCGAATCTTT
GAAATTAAGAGAAAGCCACGCCCATTGGCAAAGGCACTAATTCTTCTCTGCTCTGGCAATGGCA
GGACCCCAAAAGCAGAACTCCATTTTACGTAGGAGGTCGTGGGAGCAAGAAGAGGACAAGCTGG
TCTCCCTAGGCAGGGCAGTGAGCAGACACTGTAAATATTTTTACACAAAATTTTATTAAAGCAA
AAGTTATTTCCTGAAGATCCACCCTGGGTGAGGCTTTGTGTTGGCTTTAGAAATCACCTCGGGC
CTAAGAATACATTTCTTACATAGCTCCTTCATTGTGCTCAAAGAAAGCAAAGGATTCACGTGCT
CAATTTAAAAGTCTCCGAAAAACATGGGTTGTTTTTTTTTCCTAGACTTTTCAGGATTTTCTCT
TCTTAGCTTTGTCACAATGTGGGGTAGGACAGGGTCTCCCAGGATGCATGGGTCCCTCTGCTTG
GTGGAGGCTGTCCAGGCACTTGGTCTTCTAAGCAGTGAGGAAGCCTAGGTGTATCCCGGTTCAC
CATGGGAGCCCCCGTGTAGCTCCGACCCCTCCAGACATGCAACTTCTACTTGTGTTCACAGCGA
CCATCTTCACTGATCAACCCTGTGCCACGTGGTGTGTGTTTTCCCCACTGACAATGAATAAAAG
GTGTGACTGTA

hide sequence

Protein Sequences


Protein RefSeqs	NP_059053	(Get FASTA)	NCBI Sequence Viewer
	XP_006238891	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	BAA02427	(Get FASTA)	NCBI Sequence Viewer
	BAA03557	(Get FASTA)	NCBI Sequence Viewer
	EDL80371	(Get FASTA)	NCBI Sequence Viewer
	P35332	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_059053 ⟸ NM_017357
- UniProtKB:	P35332 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MGKNNSKLAPEELEDLVQNTEFSEQELKQWYKGFLKDCPSGILNLEEFQQLYIKFFPYGDASKF AQHAFRTFDKNGDGTIDFREFICALSVTSRGSFEQKLNWAFEMYDLDGDGRITRLEMLEIIEAI YKMVGTVIMMRMNQDGLTPQQRVDKIFKKMDQDKDDQITLEEFKEAAKSDPSIVLLLQCDMQK hide sequence

RefSeq Acc Id:	XP_006238891 ⟸ XM_006238829
- Peptide Label:	isoform X1
- UniProtKB:	P35332 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MGKNNSKLAPEELEDLVQNTEFSEQELKQWYKGFLKDCPSGILNLEEFQQLYIKFFPYGDASKF AQHAFRTFDKNGDGTIDFREFICALSVTSRGSFEQKLNWAFEMYDLDGDGRITRLEMLEIIEAI YKMVGTVIMMRMNQDGLTPQQRVDKIFKKMDQDKDDQITLEEFKEAAKSDPSIVLLLQCDMQK hide sequence

RefSeq Acc Id:

ENSRNOP00000066655 ⟸ ENSRNOT00000074347

Protein Domains

EF-hand

Transcriptome

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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

ACI/EurMcwi (RGD)

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

ACI/N (MCW)

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

BBDP/Wor (RGD)

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

BN/SsN (MCW)

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

Buf/N (MCW)

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

COP/CrCrl (MCW & UW)

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

F344/NCrl (RGD)

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

F344/NRrrc (MCW)

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

FHH/EurMcwi (MCW)

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

FHH/EurMcwi (RGD)

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

FHL/EurMcwi (MCW)

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

FHL/EurMcwi (RGD)

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

GH/OmrMcwi (MCW)

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

GK/Ox (RGD)

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

LE/Stm (RGD)

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

LEW/Crl (RGD)

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

LEW/NCrlBR (RGD)

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

LH/MavRrrc (RGD)

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

LL/MavRrrc (RGD)

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

LN/MavRrrc (RGD)

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

M520/N (MCW)

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

MHS/Gib (RGD)

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

MNS/Gib (RGD)

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

MR/N (MCW)

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

SBH/Ygl (MCW)

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

SBH/Ygl (RGD)

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

SBN/Ygl (MCW)

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

SBN/Ygl (RGD)

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

SHR/NHsd (RGD)

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

SHRSP/Gcrc (RGD)

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

SR/JrHsd (MCW)

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

SR/JrHsd (RGD)

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

SS/Jr (RGD)

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

SS/JrHsdMcwi (MCW)

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

SS/JrHsdMcwi (RGD)

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

WAG/Rij (RGD)

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

WKY/Gcrc (RGD)

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

WKY/N (MCW)

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

WKY/NCrl (RGD)

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

WKY/NHsd (RGD)

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

WN/N (MCW)

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:708491	AgrOrtholog
Ensembl Genes	ENSRNOG00000050983	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000066655	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000074347	UniProtKB/Swiss-Prot
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
	VILIP-2	UniProtKB/Swiss-Prot
KEGG Report	rno:50872	UniProtKB/Swiss-Prot
NCBI Gene	50872	ENTREZGENE
PANTHER	PTHR23055	UniProtKB/Swiss-Prot
	PTHR23055:SF84	UniProtKB/Swiss-Prot
Pfam	EF-hand_1	UniProtKB/Swiss-Prot
	EF-hand_7	UniProtKB/Swiss-Prot
PhenoGen	Hpcal4	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	HPCL4_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2005-07-08	Hpcal4	hippocalcin-like 4	Nvjp2	neural visinin-like Ca2+-binding protein type 2	Symbol and Name updated	1299863	APPROVED

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