Gpc2 (glypican 2) - Rat Genome Database

Name: Gpc2
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Gpc2 (glypican 2) Rattus norvegicus

Analyze

Symbol:

Gpc2

Name:

glypican 2

RGD ID:

621363

Description:

Involved in neuron differentiation; positive regulation of neuron projection development; and smoothened signaling pathway. Predicted to localize to cell surface; endoplasmic reticulum; and synapse. Orthologous to human GPC2 (glypican 2); PARTICIPATES IN Hedgehog signaling pathway; glypican signaling pathway; INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 2,2',5,5'-tetrachlorobiphenyl.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

cerebroglycan; glypican 2 (cerebroglycan); glypican-2; HSPG M13

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):	GPC2 (glypican 2)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Gpc2 (glypican 2 (cerebroglycan))	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Gpc2 (glypican 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	GPC2 (glypican 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	GPC2 (glypican 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Gpc2 (glypican 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	GPC2 (glypican 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	GPC2 (glypican 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Gpc2 (glypican 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	GPC2 (glypican 2)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Gpc2 (glypican 2 (cerebroglycan))	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)
Caenorhabditis elegans (roundworm):	gpn-1	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	dlp	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)

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	12	17,277,875 - 17,284,297 (-)	NCBI
Rnor_6.0 Ensembl	12	19,593,041 - 19,599,374 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	12	19,593,041 - 19,599,374 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	12	21,649,636 - 21,655,969 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	17,858,354 - 17,864,687 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	12	17,847,875 - 17,854,209 (-)	NCBI
Celera	12	19,202,336 - 19,208,665 (-)	NCBI		Celera
Cytogenetic Map	12	q11	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

pleomorphic xanthoastrocytoma (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

17alpha-ethynylestradiol (EXP)

17beta-estradiol (EXP,ISO)

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

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

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

6-propyl-2-thiouracil (EXP)

acetamide (EXP)

acrylamide (EXP,ISO)

ammonium chloride (EXP)

atrazine (ISO)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

butanal (ISO)

dexamethasone (ISO)

dorsomorphin (ISO)

exemestane (ISO)

folic acid (ISO)

glycidol (EXP)

monosodium L-glutamate (EXP)

O-methyleugenol (ISO)

paracetamol (ISO)

PCB138 (EXP,ISO)

pentanal (ISO)

phenylmercury acetate (ISO)

SB 431542 (ISO)

sunitinib (ISO)

testosterone (EXP)

titanium dioxide (ISO)

trichostatin A (ISO)

tunicamycin (ISO)

urethane (ISO)

valproic acid (ISO)

vorinostat (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cell migration (IBA)

neuron differentiation (IDA)

positive regulation of neuron projection development (IDA)

regulation of protein localization to membrane (IBA)

regulation of signal transduction (IEA)

smoothened signaling pathway (IBA,IMP)

Cellular Component

anchored component of plasma membrane (IEA)

cell surface (IBA)

cellular_component (ND)

collagen-containing extracellular matrix (IEA)

endoplasmic reticulum (IEA,ISO)

extracellular matrix (TAS)

extracellular space (IEA)

synapse (IBA)

Molecular Function

molecular_function (ND)

protein binding (IPI,ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

glypican signaling pathway (ISO)

Hedgehog signaling pathway (IMP)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	Kurosawa N, etal., Glycoconj J. 2001 Jun;18(6):499-507.
3.	MGD data from the GO Consortium
4.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
5.	Paveliev M, etal., Sci Rep. 2016 Sep 27;6:33916. doi: 10.1038/srep33916.
6.	Pipeline to import Pathway Interaction Database annotations from NCI into RGD
7.	RGD automated data pipeline
8.	RGD automated import pipeline for gene-chemical interactions
9.	RGD comprehensive gene curation
10.	Stipp CS, etal., J Cell Biol 1994 Jan;124(1-2):149-60.
11.	Williams EH, etal., Proc Natl Acad Sci U S A. 2010 Mar 30;107(13):5869-74. Epub 2010 Mar 15.

Genomics

Comparative Map Data

Gpc2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	12	17,277,875 - 17,284,297 (-)	NCBI
Rnor_6.0 Ensembl	12	19,593,041 - 19,599,374 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	12	19,593,041 - 19,599,374 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	12	21,649,636 - 21,655,969 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	17,858,354 - 17,864,687 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	12	17,847,875 - 17,854,209 (-)	NCBI
Celera	12	19,202,336 - 19,208,665 (-)	NCBI		Celera
Cytogenetic Map	12	q11	NCBI

GPC2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	7	100,169,606 - 100,177,381 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	7	100,169,606 - 100,177,381 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	7	99,767,229 - 99,775,004 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	7	99,605,165 - 99,612,926 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	7	99,411,879 - 99,419,641	NCBI
Celera	7	94,502,575 - 94,510,340 (-)	NCBI
Cytogenetic Map	7	q22.1	NCBI
HuRef	7	94,402,023 - 94,409,735 (-)	NCBI		HuRef
CHM1_1	7	99,697,303 - 99,705,068 (-)	NCBI		CHM1_1
CRA_TCAGchr7v2	7	99,127,317 - 99,135,078 (-)	NCBI

Gpc2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	138,271,918 - 138,278,288 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	5	138,271,917 - 138,278,267 (-)	Ensembl
GRCm38	5	138,273,657 - 138,280,026 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	138,273,655 - 138,280,005 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	138,714,888 - 138,721,165 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	5	138,503,448 - 138,509,725 (-)	NCBI			mm8
Celera	5	135,256,511 - 135,262,788 (-)	NCBI		Celera
Cytogenetic Map	5	G2	NCBI

Gpc2
(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_004955573	630,859 - 637,296 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955573	630,859 - 637,296 (+)	NCBI	ChiLan1.0	ChiLan1.0

GPC2
(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	7	105,637,059 - 105,645,115 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	7	105,637,682 - 105,644,888 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	7	92,204,355 - 92,213,750 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

GPC2
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	6	9,354,181 - 9,361,361 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	6	9,354,535 - 9,361,375 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	6	11,057,530 - 11,065,347 (+)	NCBI
ROS_Cfam_1.0	6	9,287,230 - 9,295,035 (+)	NCBI
UMICH_Zoey_3.1	6	9,139,687 - 9,147,491 (+)	NCBI
UNSW_CanFamBas_1.0	6	9,118,759 - 9,126,553 (+)	NCBI
UU_Cfam_GSD_1.0	6	9,299,810 - 9,307,638 (+)	NCBI

Gpc2
(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_024409344	133,606,525 - 133,612,846 (+)	NCBI
SpeTri2.0	NW_004936543	424,244 - 429,903 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

GPC2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	3	8,169,343 - 8,175,646 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	8,169,229 - 8,175,848 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	3	7,346,211 - 7,352,851 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

GPC2
(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	28	12,892,092 - 12,899,288 (+)	NCBI
ChlSab1.1 Ensembl	28	12,892,057 - 12,898,657 (+)	Ensembl
Vero_WHO_p1.0	NW_023666070	3,381,153 - 3,388,396 (-)	NCBI

Gpc2
(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_004624740	16,734,407 - 16,740,845 (+)	NCBI

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
2312418	Kidm41	Kidney mass QTL 41	3.7	0.0001	kidney mass (VT:0002707)	single kidney wet weight to body weight ratio (CMO:0000622)	12	1	22650917	Rat
10450854	Stl34	Serum triglyceride level QTL 34	3.5	0.05	blood LDL triglyceride amount (VT:0010699)	blood lipoprotein triglyceride level (CMO:0002685)	12	1	22853017	Rat
10755457	Coatc14	Coat color QTL 14		0.01759	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	12	1	23035872	Rat
6893681	Bw109	Body weight QTL 109	2.3	0.004	body mass (VT:0001259)	body weight (CMO:0000012)	12	1	23758197	Rat
1581516	Cm56	Cardiac mass QTL 56	4.2	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	12	1	30749723	Rat
1598855	Bp294	Blood pressure QTL 294	3.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	1	36919844	Rat
7387292	Kidm42	Kidney mass QTL 42	3.03	0.0004	kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	12	1	38334225	Rat
9590086	Insglur6	Insulin/glucose ratio QTL 6	18.97	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	12	150810	45150810	Rat
9590147	Scort7	Serum corticosterone level QTL 7	13.61	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	12	150810	45150810	Rat
7411545	Bw128	Body weight QTL 128	5.2	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	12	150810	45150810	Rat
7411586	Foco5	Food consumption QTL 5	5.4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	150810	45150810	Rat
7411660	Foco28	Food consumption QTL 28	10.9	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	150810	45150810	Rat
7411595	Foco9	Food consumption QTL 9	4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	150810	45150810	Rat
8694179	Bw150	Body weight QTL 150	2.9	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	12	150810	45150810	Rat
2303575	Insul14	Insulin level QTL 14	4		blood insulin amount (VT:0001560)	blood insulin level (CMO:0000349)	12	492578	45492578	Rat
737979	Pia22	Pristane induced arthritis QTL 22	53.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	2475687	47475687	Rat
634351	Apr5	Acute phase response QTL 5	6.7		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	12	2513442	47513442	Rat
2302042	Pia38	Pristane induced arthritis QTL 38	3.5	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	12	2513442	47513442	Rat
634350	Apr4	Acute phase response QTL 4	6		orosomucoid 1 amount (VT:0010541)	plasma orosomucoid 1 level (CMO:0001467)	12	4210051	49210051	Rat
1600391	Edcs2	Endometrial carcinoma susceptibility QTL2	3.5	0.01	uterus morphology trait (VT:0001120)	percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)	12	8249608	20590080	Rat
1302792	Scl21	Serum cholesterol level QTL 21	3.8	0.0011	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	12	8954593	27911196	Rat
7411547	Bw129	Body weight QTL 129		0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	6	9223626	52716770	Rat
7411588	Foco6	Food consumption QTL 6		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	9223626	52716770	Rat
7411597	Foco10	Food consumption QTL 10		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	9223626	52716770	Rat
7411641	Foco19	Food consumption QTL 19	27.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	9223626	52716770	Rat
8552918	Pigfal7	Plasma insulin-like growth factor 1 level QTL 7			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	9223626	52716770	Rat
8552964	Pigfal17	Plasma insulin-like growth factor 1 level QTL 17	3.5		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	9223626	52716770	Rat
8552912	Pigfal6	Plasma insulin-like growth factor 1 level QTL 6	5		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	9223630	52716770	Rat
10059594	Kidm46	Kidney mass QTL 46	3.79	0.025	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	12	9789834	52716770	Rat
2293086	Iddm30	Insulin dependent diabetes mellitus QTL 30	3.82		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	12	10175889	31975590	Rat
61331	Eau2	Experimental allergic uveoretinitis QTL 2		0.0005	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	12	10256890	31723732	Rat
1300157	Rf21	Renal function QTL 21	4.4		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	12	11764995	37522089	Rat
1331786	Kidm11	Kidney mass QTL 11	3.571		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	12	13127211	27285590	Rat
1331755	Bp219	Blood pressure QTL 219	3.041		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	12	13127211	31723688	Rat
1331761	Bp218	Blood pressure QTL 218	2.973		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	12	13127211	50320041	Rat
61404	Bw120	Body weight QTL 120	5.1		body mass (VT:0001259)	body mass index (BMI) (CMO:0000105)	12	14419775	52716770	Rat
1549829	Scl48	Serum cholesterol level QTL 48	5		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	12	15021986	52716770	Rat
7204484	Bp358	Blood pressure QTL 358		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	12	15085585	22283507	Rat
61416	Pia4	Pristane induced arthritis QTL 4	8.4		joint integrity trait (VT:0010548)	arthritic paw count (CMO:0001460)	12	15714609	35964508	Rat
61421	Cia12	Collagen induced arthritis QTL 12	4.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	15714609	41291738	Rat
2300186	Bmd59	Bone mineral density QTL 59	7.1	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	12	15908900	52716770	Rat
2293699	Bss49	Bone structure and strength QTL 49	5.61	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra trabecular cross-sectional area (CMO:0001692)	12	15908900	52716770	Rat
61443	Btemp2	Thermal response to stress QTL 2	3.3	0.000094	body temperature trait (VT:0005535)	core body temperature (CMO:0001036)	12	17114770	23839390	Rat
631543	Bp83	Blood pressure QTL 83	5.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	17185580	44098244	Rat
2293684	Bmd26	Bone mineral density QTL 26	4.4	0.0002	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	12	17960865	38409001	Rat
1641928	Alcrsp5	Alcohol response QTL 5			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	12	18342477	52716770	Rat
2303569	Gluco44	Glucose level QTL 44	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	12	18342477	52716770	Rat
2302060	Pia37	Pristane induced arthritis QTL 37	6.1	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	12	18729043	52716770	Rat
1549902	Bp269	Blood pressure QTL 269			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	18752593	52716770	Rat
1549912	Bp268	Blood pressure QTL 268			arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	10	18752593	52716770	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	433
Count of miRNA genes:	228
Interacting mature miRNAs:	269
Transcripts:	ENSRNOT00000001849
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

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

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

Expression

RNA-SEQ Expression

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

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium		2	4	4		4			53	20	25
Low	3	35	23	8	17	8	1	1	18	9	16	11	1
Below cutoff		6	30	29	2	29	7	10	3	6			7

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_138511	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039089051	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039089052	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039089053	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039089054	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH474107	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000225	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	L20468	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000001849 ⟹ ENSRNOP00000001849

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	12	19,593,041 - 19,599,374 (-)	Ensembl

RefSeq Acc Id:

NM_138511 ⟹ NP_612520

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	12	17,277,875 - 17,284,208 (-)	NCBI
Rnor_6.0	12	19,593,041 - 19,599,374 (-)	NCBI
Rnor_5.0	12	21,649,636 - 21,655,969 (-)	NCBI
RGSC_v3.4	12	17,858,354 - 17,864,687 (-)	RGD
Celera	12	19,202,336 - 19,208,665 (-)	RGD

Sequence:

show sequence

GATCATTGGCGGGCTCCAGCTTCGGGTCCCGCCCCCTGTCCCGCTCCCCGGCTCCCATTGTCTC
CGCAGATGCCTCCTAGTCCAGCTACCGTGCTGGGGCTGTTCAGTTTTGGGGGGGACGCTCGTAT
TCTTTTCTTCGAGACGTCCCGCGGCCGAGAACAGGATTTTAGAGTTCCGTGGACTCTTTTTTCC
TCCTTAGGACTCACTTTGCCCCGTCCCAGGAAGGAGAGCAGCTATGTCCGCGGTGCGACCTCTC
CTGCTTTTGCTGCTCCCTCTGTGTCCCGGTCCAGGACCGGGACATGGGAGTGAAGCAAAGGTCG
TCCGGAGTTGTGCAGAGACTCGGCAGGTGCTGGGGGCCCGGGGATATAGCTTAAACCTTATCCC
TCCCTCCCTCATCTCAGGTGAGCACCTTCAGATCTGTCCTCAGGAGTACACCTGCTGTTCCAGT
GAGACAGAGCAGAAGTTGATCCGGGATGCTGAGGTCACCTTCCGTGGCCTGGTGGAAGACAGTG
GCTCCTTCCTGATTCACACGCTGGCTGCCCGCCACAGAAAGTTTAACGAGTTTTTTCGGGAGAT
GCTGTCTATATCCCAGCATTCTTTGGCCCAGCTCTTCTCGCATTCCTATGGTCGCCTGTATTCC
CAGCATGCCGTCATCTTCAATAGCCTGTTCTCCGGCCTGCGGGACTACTATGAGAAGTCTGGTG
AGGGGTTAGATGACACCTTGGCAGACTTCTGGGCCCAGCTCCTGGAGAGAGCCTTCCCTTTGCT
GCACCCACAATACAGTTTCCCTCCTGATTTCCTGCTCTGCCTTACTCGGCTCACTTCAACTGCT
GATGGCTCTCTCCAGCCCTTCGGGGACTCGCCCCGCCGCCTCCGCCTACAGATAACCCGGGCAC
TGGTGGCAGCCCGGGCCTTGGTCCAGGGTCTGGAGACCGGAAGAAATGTGGTCAGCGAAGCACT
TAAGGTACCCATGTTGGAAGGCTGCAGACAGGCCCTCATGCGTCTGATCGGCTGCCCACTTTGT
CGGGGAGTACCCTCGCTTATGCCCTGCCGGGGCTTCTGCCTCAATGTGGCCCACGGCTGTCTCA
GCAGCAGGGGATTGGAGCCTGAATGGGGCGGATATCTGGATGGTCTCCTGCTGCTGGCTGAGAA
ACTCCAGGGACCCTTTTCCTTCGAGCTGGCTGCTGAGTCCATAGGGGTGAAGATCTCAGAAGGT
TTGATGCACTTGCAGGAAAACAGTGTAAAGGTGTCAGCCAAGGTGTTTCAGGAATGTGGGACGC
CTCACCCGGTGCAATCCCGTAACCGGCGAGCACCAGCACCCCGGGAAGAGACTAGCCGGTCTTG
GAGGTCGTCAGCTGAGGAAGAACGCCCCACAACAGCGGCAGGCACTAATCTGCACCGTCTGGTT
TGGGAGCTCCGAGAGAGGCTTAGCCGAGTGCGGGGCTTCTGGGCTGGACTTCCCGTTACGGTGT
GTGGGGACTCCCGCATGGCGGCAGATCTCTCCCAGGAGGCGGCACCCTGCTGGACTGGGGTTGG
GAGAGGCCGGTATATGTCGCCTGTGGTCGTGGGCTCCTTGAACGAGCAGCTCCATAACCCGGAG
TTGGATACTTCGAGTCCCGATGTCCCGACACGTCGGCGGAGGCTCCATCTCCGAGCAGCTACTG
CTCGAATGAAGGCGGCTGCGCTGGGCCAGGACCTTGACATGCATGATGCGGATGAAGACGCCAG
TGGCTCCGGAGGGGGACAGCAGTACGCAGACGACTGGAAAGCTGGGGCAGCGCCTGTGGTTCCC
CCAGCCAGGCCTCCAAGGCCACCTCGTCCTCCTCGAAGGGATGGTCTTGGAGTGAGAGGAGGAA
GTGGCAGTGCCAGATACAACCAGGGCCGAAGCAGGAATCTGGGGTCCTCTGTTGGCCTCCATGC
CCCACGTGTCTTCATTCTCCTCCCCTCAGCCCTGACCCTGCTTGGACTTCGATAACAAGCGAGG
GGCGCCCTAGCGTCAGGAGGCTTAGTGGCCTTTTCCTTCCACCTCCCTCAGCTGGGCATGAGGA
AGAATGGAAGGGGGCTACCGGGAGGGCAGAAAGGGACTTTGTAGGTAAATGGCTGGGGCCCCAA
ATCCAGGAGTTTCCTATTAGTGGGTTGGGAGGGGAGGTAGATGGGTGTTCATAATATTTATTTT
TTCATTTGGGAACTGGGGATATTTATTTAGGAAGGGATTGTGGTTCAGCTCTTTTAAGGCTTGG
GTCTCATTGATGCAAAAGGCAGGGGGTGGGGTTGGGATCGGGTTGAAGGAACTTGGAAGTGGGG
AGGGGTGGCACTATTGGCATGGGGGTACCTGATATTGAAAATGAACAAATAAACTAGCTGAGAG
TGATGTCACTTGCCTGTAAACCATTATTTTGGAGGCTGAGGCAGGAGGATTGAGCGTTGGAGAC
CCATAAAATTAGGTGCTGATAGTGGAACAGGCGGGGTGGGAGGTAGGACCTGAGTTTTATTGAC
TTTTAAAATCATCTGTTTCTTAAATATGGGGGAACCCATCTTGTGACCTTTGCTGTCTAATGTT
TCAGTGTTCACATCGGTGTTTATTGGTAAATAAACAATTTGACCATG

hide sequence

RefSeq Acc Id:

XM_039089051 ⟹ XP_038944979

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	12	17,278,637 - 17,284,297 (-)	NCBI

RefSeq Acc Id:

XM_039089052 ⟹ XP_038944980

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	12	17,277,875 - 17,283,123 (-)	NCBI

RefSeq Acc Id:

XM_039089053 ⟹ XP_038944981

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	12	17,277,875 - 17,283,116 (-)	NCBI

RefSeq Acc Id:

XM_039089054 ⟹ XP_038944982

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	12	17,277,875 - 17,281,414 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_612520	(Get FASTA)	NCBI Sequence Viewer
	XP_038944979	(Get FASTA)	NCBI Sequence Viewer
	XP_038944980	(Get FASTA)	NCBI Sequence Viewer
	XP_038944981	(Get FASTA)	NCBI Sequence Viewer
	XP_038944982	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA40961	(Get FASTA)	NCBI Sequence Viewer
	EDL83911	(Get FASTA)	NCBI Sequence Viewer
	EDL83912	(Get FASTA)	NCBI Sequence Viewer
	P51653	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_612520 ⟸ NM_138511
- Peptide Label:	precursor
- UniProtKB:	P51653 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MSAVRPLLLLLLPLCPGPGPGHGSEAKVVRSCAETRQVLGARGYSLNLIPPSLISGEHLQICPQ EYTCCSSETEQKLIRDAEVTFRGLVEDSGSFLIHTLAARHRKFNEFFREMLSISQHSLAQLFSH SYGRLYSQHAVIFNSLFSGLRDYYEKSGEGLDDTLADFWAQLLERAFPLLHPQYSFPPDFLLCL TRLTSTADGSLQPFGDSPRRLRLQITRALVAARALVQGLETGRNVVSEALKVPMLEGCRQALMR LIGCPLCRGVPSLMPCRGFCLNVAHGCLSSRGLEPEWGGYLDGLLLLAEKLQGPFSFELAAESI GVKISEGLMHLQENSVKVSAKVFQECGTPHPVQSRNRRAPAPREETSRSWRSSAEEERPTTAAG TNLHRLVWELRERLSRVRGFWAGLPVTVCGDSRMAADLSQEAAPCWTGVGRGRYMSPVVVGSLN EQLHNPELDTSSPDVPTRRRRLHLRAATARMKAAALGQDLDMHDADEDASGSGGGQQYADDWKA GAAPVVPPARPPRPPRPPRRDGLGVRGGSGSARYNQGRSRNLGSSVGLHAPRVFILLPSALTLL GLR hide sequence

RefSeq Acc Id:

ENSRNOP00000001849 ⟸ ENSRNOT00000001849

RefSeq Acc Id:	XP_038944980 ⟸ XM_039089052
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038944981 ⟸ XM_039089053
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038944982 ⟸ XM_039089054
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038944979 ⟸ XM_039089051
- Peptide Label:	isoform X1

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:621363	AgrOrtholog
Ensembl Genes	ENSRNOG00000001367	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000001849	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000001849	ENTREZGENE, UniProtKB/Swiss-Prot
InterPro	Glypican	UniProtKB/Swiss-Prot
	Glypican-2	UniProtKB/Swiss-Prot
	Glypican_CS	UniProtKB/Swiss-Prot
KEGG Report	rno:171517	UniProtKB/Swiss-Prot
NCBI Gene	171517	ENTREZGENE
PANTHER	PTHR10822	UniProtKB/Swiss-Prot
	PTHR10822:SF24	UniProtKB/Swiss-Prot
Pfam	Glypican	UniProtKB/Swiss-Prot
PhenoGen	Gpc2	PhenoGen
PROSITE	GLYPICAN	UniProtKB/Swiss-Prot
UniProt	GPC2_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-09-26	Gpc2	glypican 2	Gpc2	glypican 2 (cerebroglycan)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2004-09-10	Gpc2	glypican 2 (cerebroglycan)		cerebroglycan	Name updated	1299863	APPROVED
2002-08-07	Gpc2	cerebroglycan			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_domains	has five potential heparan sulfite attachment sites
gene_expression	expressed only in nerve tissue	728608
gene_expression	mRNA expressed in immature neurons, disappearing after completion of cell migration and axon outgrowth	728608
gene_product	member of integral membrane heparan sulfate proteoglycans (HSPGs), characterized by glycosylphosphatidylinositol (GPI) linkage and conserved structural motifs	728608
gene_protein	protein has predicted mass of 58.6 kDa	728608

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

RGD Manual Annotations

Imported Annotations - PID (archival)

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Imported Disease Annotations - ClinVar

RGD Manual Annotations

Imported Annotations - PID (archival)