Gpc4 (glypican 4) - Rat Genome Database

Name: Gpc4
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Gpc4 (glypican 4) Rattus norvegicus

Analyze

Symbol:

Gpc4

Name:

glypican 4

RGD ID:

1359399

Description:

Involved in regulation of presynapse assembly. Localizes to anchored component of presynaptic membrane and glutamatergic synapse. Human ortholog(s) of this gene implicated in Keipert syndrome. Orthologous to human GPC4 (glypican 4); PARTICIPATES IN Hedgehog signaling pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

glypican-4; LOC317322; similar to glypican 4

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):	GPC4 (glypican 4)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Gpc4 (glypican 4)	HGNC	Treefam, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Gpc4 (glypican 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	GPC4 (glypican 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	GPC4 (glypican 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Gpc4 (glypican 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	GPC4 (glypican 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	GPC4 (glypican 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Gpc4 (glypican 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	GPC6 (glypican 6)	HGNC	OrthoDB
Alliance orthologs ³
Homo sapiens (human):	GPC4 (glypican 4)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Gpc4 (glypican 4)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	gpc6b (glypican 6b)	Alliance	DIOPT (InParanoid\|OMA\|OrthoInspector\|PANTHER)
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
Rnor_6.0	X	139,354,325 - 139,464,876 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	X	139,354,155 - 139,464,798 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	X	139,402,208 - 139,512,761 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	X	138,966,579 - 139,077,074 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	X	139,040,011 - 139,150,507 (-)	NCBI
Celera	X	130,559,646 - 130,670,213 (-)	NCBI		Celera
Cytogenetic Map	X	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

autistic disorder (ISO)

Craniofacial Abnormalities (ISO)

genetic disease (ISO)

Keipert syndrome (ISO)

nephroblastoma (ISO)

Simpson-Golabi-Behmel syndrome type 1 (ISO)

syndromic X-linked intellectual disability Lubs type (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,1-dichloroethene (ISO)

1,2-dimethylhydrazine (ISO)

17beta-estradiol (EXP,ISO)

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

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

2,4-dinitrotoluene (EXP)

4,4'-diaminodiphenylmethane (ISO)

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

5-aza-2'-deoxycytidine (ISO)

6-propyl-2-thiouracil (EXP)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

antirheumatic drug (ISO)

arsane (ISO)

arsenic atom (ISO)

arsenite(3-) (ISO)

arsenous acid (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

butanal (ISO)

cadmium dichloride (ISO)

cisplatin (ISO)

clofibrate (ISO)

crocidolite asbestos (ISO)

cyclosporin A (ISO)

dextran sulfate (ISO)

diarsenic trioxide (ISO)

dibutyl phthalate (EXP)

dorsomorphin (ISO)

doxorubicin (ISO)

endosulfan (EXP)

ethanol (ISO)

methapyrilene (EXP)

methylmercury chloride (ISO)

N-methyl-N'-nitro-N-nitrosoguanidine (ISO)

nickel atom (ISO)

nickel sulfate (ISO)

okadaic acid (ISO)

panobinostat (ISO)

paracetamol (ISO)

phenobarbital (ISO)

phenylmercury acetate (ISO)

phorbol 13-acetate 12-myristate (ISO)

pirinixic acid (ISO)

potassium dichromate (ISO)

pregnenolone 16alpha-carbonitrile (ISO)

Salinomycin (ISO)

SB 431542 (ISO)

sodium arsenate (ISO)

sodium arsenite (ISO)

sunitinib (ISO)

T-2 toxin (ISO)

tetrachloromethane (ISO)

titanium dioxide (ISO)

trichostatin A (ISO)

troglitazone (ISO)

urethane (ISO)

valproic acid (ISO)

vinclozolin (EXP)

zoledronic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

cell migration (IBA)

regulation of neurotransmitter receptor localization to postsynaptic specialization membrane (IBA,IDA,IMP)

regulation of presynapse assembly (IBA,IDA,IMP)

regulation of protein localization to membrane (IBA)

regulation of signal transduction (IEA)

synaptic membrane adhesion (IBA,ISO)

Wnt signaling pathway (ISO)

Cellular Component

anchored component of presynaptic membrane (IDA,IMP)

cell surface (IBA)

cellular_component (ND)

collagen-containing extracellular matrix (IEA)

external side of plasma membrane (ISO)

extracellular region (IBA)

glutamatergic synapse (IDA,IMP,ISO)

synapse (IBA,ISO)

Molecular Function

molecular_function (ND)

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

Hedgehog signaling pathway (ISO)

References

References - curated


1.	Allen NJ, etal., Nature. 2012 May 27;486(7403):410-4. doi: 10.1038/nature11059.
2.	de Wit J, etal., Neuron. 2013 Aug 21;79(4):696-711. doi: 10.1016/j.neuron.2013.06.049. Epub 2013 Aug 1.
3.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4.	GOA data from the GO Consortium
5.	Hagihara K, etal., Dev Dyn 2000 Nov;219(3):353-67.
6.	MGD data from the GO Consortium
7.	OMIM Disease Annotation Pipeline
8.	RGD automated data pipeline
9.	RGD automated import pipeline for gene-chemical interactions
10.	RGD comprehensive gene curation
11.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
12.	Williams EH, etal., Proc Natl Acad Sci U S A. 2010 Mar 30;107(13):5869-74. Epub 2010 Mar 15.

Additional References at PubMed

PMID:10585884	PMID:16452087	PMID:19199708	PMID:21630459	PMID:23376485	PMID:24006456	PMID:25624497	PMID:25931508	PMID:27425250	PMID:29276006

Genomics

Comparative Map Data

Gpc4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	X	139,354,325 - 139,464,876 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	X	139,354,155 - 139,464,798 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	X	139,402,208 - 139,512,761 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	X	138,966,579 - 139,077,074 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	X	139,040,011 - 139,150,507 (-)	NCBI
Celera	X	130,559,646 - 130,670,213 (-)	NCBI		Celera
Cytogenetic Map	X	q36	NCBI

GPC4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	X	133,300,103 - 133,415,489 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	X	133,300,103 - 133,415,489 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	X	132,433,815 - 132,549,205 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	X	132,262,730 - 132,376,871 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	X	132,160,583 - 132,274,725	NCBI
Celera	X	132,821,529 - 132,935,634 (-)	NCBI
Cytogenetic Map	X	q26.2	NCBI
HuRef	X	121,838,234 - 121,950,367 (-)	NCBI		HuRef
CHM1_1	X	132,346,513 - 132,460,631 (-)	NCBI		CHM1_1

Gpc4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	X	51,139,884 - 51,253,800 (-)	NCBI	GRCm39		mm39
GRCm38	X	52,051,007 - 52,164,923 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	X	52,053,021 - 52,165,252 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	X	49,406,195 - 49,518,100 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	X	48,297,547 - 48,409,879 (-)	NCBI			mm8
Celera	X	39,465,872 - 39,577,854 (-)	NCBI		Celera
Cytogenetic Map	X	A5	NCBI
cM Map	X	28.33	NCBI

Gpc4
(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_004955473	1,546,326 - 1,655,822 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955473	1,546,615 - 1,655,822 (+)	NCBI	ChiLan1.0	ChiLan1.0

GPC4
(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	X	132,746,525 - 132,860,422 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	X	132,746,519 - 132,860,420 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	X	122,441,290 - 122,555,192 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

GPC4
(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	X	104,100,571 - 104,216,103 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	X	104,098,316 - 104,215,883 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Gpc4
(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_004936691	1,564,872 - 1,676,378 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

GPC4
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	X	109,306,368 - 109,421,785 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	X	109,306,489 - 109,421,947 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	X	125,341,052 - 125,453,788 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

GPC4
(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	X	108,451,082 - 108,570,244 (-)	NCBI
ChlSab1.1 Ensembl	X	108,450,536 - 108,570,214 (-)	Ensembl

Gpc4
(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_004624797	13,005,310 - 13,116,414 (-)	NCBI

Position Markers

AI071251

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	X	139,354,573 - 139,354,792	NCBI	Rnor6.0
Rnor_5.0	X	139,402,456 - 139,402,675	UniSTS	Rnor5.0
RGSC_v3.4	X	138,966,773 - 138,966,992	UniSTS	RGSC3.4
Celera	X	130,559,840 - 130,560,059	UniSTS
Cytogenetic Map	X	q36	UniSTS
RH 3.4 Map	X	945.91	UniSTS

X83577

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	X	139,354,436 - 139,354,592	NCBI	Rnor6.0
Rnor_5.0	X	139,402,319 - 139,402,475	UniSTS	Rnor5.0
RGSC_v3.4	X	138,966,636 - 138,966,792	UniSTS	RGSC3.4
Celera	X	130,559,703 - 130,559,859	UniSTS
Cytogenetic Map	X	q36	UniSTS

RH143854

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	X	139,354,484 - 139,354,626	NCBI	Rnor6.0
Rnor_5.0	X	139,402,367 - 139,402,509	UniSTS	Rnor5.0
RGSC_v3.4	X	138,966,684 - 138,966,826	UniSTS	RGSC3.4
Celera	X	130,559,751 - 130,559,893	UniSTS
Cytogenetic Map	X	q36	UniSTS
RH 3.4 Map	X	949.12	UniSTS

AU048085

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	X	139,367,258 - 139,367,436	NCBI	Rnor6.0
Rnor_5.0	X	139,415,141 - 139,415,319	UniSTS	Rnor5.0
RGSC_v3.4	X	138,979,458 - 138,979,636	UniSTS	RGSC3.4
Celera	X	130,572,525 - 130,572,703	UniSTS
Cytogenetic Map	X	q36	UniSTS

UniSTS:471081

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	X	139,354,422 - 139,355,036	NCBI	Rnor6.0
Rnor_5.0	X	139,402,305 - 139,402,919	UniSTS	Rnor5.0
RGSC_v3.4	X	138,966,622 - 138,967,236	UniSTS	RGSC3.4
Celera	X	130,559,689 - 130,560,303	UniSTS
Cytogenetic Map	X	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
1598837	Memor13	Memory QTL 13	3.2		exploratory behavior trait (VT:0010471)	difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)	X	44320616	158345622	Rat
1598872	Memor14	Memory QTL 14	4.5		exploratory behavior trait (VT:0010471)	difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)	X	101333032	146333032	Rat
738025	Stresp3	Stress response QTL 3	4.61	0.0066	stress-related behavior trait (VT:0010451)	defensive burying - approach	X	107886746	152409805	Rat
1598809	Memor15	Memory QTL 15	4.4		exploratory behavior trait (VT:0010471)	difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)	X	110957467	155957467	Rat
1598856	Memor1	Memory QTL 1	1.9		exploratory behavior trait (VT:0010471)	total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)	X	110957467	155957467	Rat
10059603	Bw174	Body weight QTL 174	3.4	0.025	body mass (VT:0001259)	body weight (CMO:0000012)	X	118715462	159970021	Rat
738029	Stresp2	Stress response QTL 2	3.4	0.0004	stress-related behavior trait (VT:0010451)	defensive burying - approach	X	120045041	143145818	Rat
634346	Insul4	Insulin level QTL 4	0		blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	X	134627816	159970021	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	293
Count of miRNA genes:	189
Interacting mature miRNAs:	211
Transcripts:	ENSRNOT00000003282
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

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

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

Expression

RNA-SEQ Expression

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

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	3	42	43	35	1	35	8	11	62	35	41	11	8
Low		1	14	6	18	6			12
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001014108	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006257580	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AABR07041778	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01114675	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01114676	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01114677	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01114678	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01114679	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC081962	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473991	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000003282 ⟹ ENSRNOP00000003282

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	X	139,354,155 - 139,464,798 (-)	Ensembl

RefSeq Acc Id:

NM_001014108 ⟹ NP_001014130

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	X	139,354,379 - 139,464,833 (-)	NCBI
Rnor_5.0	X	139,402,208 - 139,512,761 (-)	NCBI
RGSC_v3.4	X	138,966,579 - 139,077,074 (-)	RGD
Celera	X	130,559,646 - 130,670,213 (-)	RGD

Sequence:

show sequence

GCTGAGAAGGGCACAGCCGTGCGGCCGAGGGCAGTGAGCTGAGCCGAGCTGGGTGAGCGGAGCA
GCGCCGGGTAGCTGGAGCCCCGCGCCAGCGATCACCCGCCGACGCCGCCCACACTCTGCTCTCC
TGCGACGCCTGCCACCTTCCCTTCCTTCCCTGAGCCCCTCCACCCCTGGCTAGCTGGCCCGGGT
TCTCTAGCCTTCAGAGTCCCGAGGTCACCGATCCTTTTCCTAGTCCCGCGCCCATTCCACGCCT
TTTCCCTTGTACCCCACCCCGGCTGGGCGCCTGGCACGGGGGACCGTTGCCTGACGCGAGGCCC
AGCTCCACTTTTCGCCTGGGTCTCCTCCTCCTCCTGTCCTCCTCCTCCTCCTTCACTACCAACT
CCAACTCCCCGGTTCACGCTCCGCTTGTGAGTGTTGACTCCGCGCCTCTTTGCCCGCTCCCGCA
GCGCTGCTTTGCATCCAGTCTCATTCTGTCCCCTAAAGGTGGGAGCGCGTCCGTCAGGGTCCGC
ACCATGGCACGGTTAGGCTTGCTCGCGCTTCTCTGCACTCTGGCGGCGCTCAGCGCCTCGCTGC
TGGCTGCGGAGCCCAAGTCGAAAAGTTGTTCGGAAGTGCGACGTCTCTACGTGTCCAAAGGCTT
CAACAAGAACGATGCCCCCCTCTATGAGATCAATGGTGACCATTTGAAGATCTGTTCCCAGGAT
TATACATGCTGTTCTCAAGAGATGGAGGAGAAGTACAGTCTGCAAAGTAAAGATGATTTCCAAA
CTGTGGTCAGCGAGCAGTGCAACCATTTGCAAGCCATCTTTGCATCCCGTTACAAGAAGTTTGA
TGAATTTTTCAAAGAACTTCTTGAAAATGCAGAGAAATCCCTGAATGATATGTTCGTGAAGACA
TACGGCCACTTATACATGCAAAATTCAGAGCTATTTAAAGATCTGTTCGTAGAGTTGAAGCGCT
ACTATGTGGCGGGAAACGTGAACCTGGAAGAAATGTTAAATGACTTCTGGGCTCGCCTTCTGGA
GCGCATGTTCCGCCTGGTGAACTCCCAGTACCATTTCACAGATGAGTACCTGGAATGTGTGAGC
AAATACACTGAGCAGCTGAAGCCTTTTGGAGACGTCCCTCGGAAACTGAAGCTCCAGGTTACCC
GTGCATTCGTTGCAGCCAGGACCTTCGCTCAAGGCTTAGCAGTTGCAAGGGATGTCGTGAACAG
AGTCTCTGTGGTGAATCCCACAGCTCAGTGCACCCAAGCACTGCTGAAGATGATCTACTGCTCT
CACTGCCGGGGCCTGGTGACTGTGAAGCCCTGTTACAACTATTGCTCAAACATCATGAGAGGCT
GTTTGGCCAACCAAGGAGACCTTGATTTAGAGTGGAACAATTTCATAGATGCCATGCTGATGGT
GGCAGAGAGGCTGGAGGGTCCTTTCAACATTGAGTCCGTTATGGATCCCATCGATGTGAAGATT
TCTGATGCTATCATGAACATGCAGGATAATAGTGTTCAGGTGTCTCAGAAGGTTTTCCAAGGCT
GTGGACCTCCAAAGCCTCTCCCGGCTGGACGAATTTCTCGTTCCATCTCTGAAAGTGCCTTCAG
TGCTCGATTCAGACCTTATCATCCAGAGCAACGCCCAACTACAGCAGCTGGCACTAGTTTGGAC
CGACTGGTTACTGATGTCAAAGAGAAACTGAAGCAAGCTAAGAAGTTCTGGTCCTCTCTCCCAA
GCACTGTCTGCAATGATGAGAGGATGGCAGCAGGAAATGAGAATGAGGATGACTGTTGGAACGG
GAAGAGCAAAAGCAGGTACCTGTTTGCAGTGACAGGAAACGGATTAGCCAACCAGGGCAACAAC
CCAGAAGTGCAGGTTGACACCAGCAAGCCGGACATTCTGATCCTTCGTCAAATCATGGCCCTTC
GGGTTATGACCAGTAAAATGAAGAATGCTTACAACGGAAATGACGTGGACTTCTTTGATATCAG
CGATGAGAGTAGTGGAGAGGGAAGCGGAAGCGGATGTGAATATCAGCAGTGCCCTTCAGAGTTT
GAGTACAACGCCACTGACCATTCTGGGAAGAGTGCCAACGAGAAAGCTGACAGTGCCGGTGGTG
CCCCTGCAGAGGCAAAGCCCTATCTCCTCGCTGCCCTCTGCATCCTGTTCCTCGCTGTGCAGGG
AGAGTGGAGATAATTGTCAAACTCTGAGTAAAAGTGTTCATCATCAGAAAGTTCAAAGGCACCA
GTTCTCACTTTTTTTTTTTTAATCATCCTAGTGACTTTGCTTTTAAATGAATGGACAACAATGT
ACAGTTTTTACTGTGTGGCCACTGGTTTAAGCAATGTTGACTTGTTGTTGACTTTGTTTTTCTC
ATTCAGTTTGAGGGGACAGGGGCCTCCTGCCTTCAAGTGTGTCCCTCCGCACTCCCCTCCTTTG
AGACTCGTGTTATGCGCGGCTAGCGGTGTAGTTACAGAACTGTAGTTAGTTGTGTATTGGTGAT
CTTGTTTTCTTTGTTGGTTTTTCTCATTTGTGGGGTTTTCCTTTTCCAATTATGGTCTCACCTT
GTTTCTCACAAGAAAACCAGGGTCGTTTCTTGGCATGTAACATGTACGTATTTCTGAAATATTA
AATAGCTGTACAGAAGCAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_006257580 ⟹ XP_006257642

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	X	139,354,325 - 139,464,876 (-)	NCBI
Rnor_5.0	X	139,402,208 - 139,512,761 (-)	NCBI

Sequence:

show sequence

CGGAGCCTCGCTGTGCAAGCCGGGCCAGTCAATCAGCGGCAGAGCTGAGAAGGGCACAGCCGTG
CGGCCGAGGGCAGTGAGCTGAGCCGAGCTGGGTGGGAGCGCGTCCGTCAGGGTCCGCACCATGG
CACGGTTAGGCTTGCTCGCGCTTCTCTGCACTCTGGCGGCGCTCAGCGCCTCGCTGCTGGCTGC
GGAGCCCAAGTCGAAAAGTTGTTCGGAAGTGCGACGTCTCTACGTGTCCAAAGGCTTCAACAAG
AACGATGCCCCCCTCTATGAGATCAATGGTGACCATTTGAAGATCTGTTCCCAGGATTATACAT
GCTGTTCTCAAGAGATGGAGGAGAAGTACAGTCTGCAAAGTAAAGATGATTTCCAAACTGTGGT
CAGCGAGCAGTGCAACCATTTGCAAGCCATCTTTGCATCCCGTTACAAGAAGTTTGATGAATTT
TTCAAAGAACTTCTTGAAAATGCAGAGAAATCCCTGAATGATATGTTCGTGAAGACATACGGCC
ACTTATACATGCAAAATTCAGAGCTATTTAAAGATCTGTTCGTAGAGTTGAAGCGCTACTATGT
GGCGGGAAACGTGAACCTGGAAGAAATGTTAAATGACTTCTGGGCTCGCCTTCTGGAGCGCATG
TTCCGCCTGGTGAACTCCCAGTACCATTTCACAGATGAGTACCTGGAATGTGTGAGCAAATACA
CTGAGCAGCTGAAGCCTTTTGGAGACGTCCCTCGGAAACTGAAGCTCCAGGTTACCCGTGCATT
CGTTGCAGCCAGGACCTTCGCTCAAGGCTTAGCAGTTGCAAGGGATGTCGTGAACAGAGTCTCT
GTGGTGAATCCCACAGCTCAGTGCACCCAAGCACTGCTGAAGATGATCTACTGCTCTCACTGCC
GGGGCCTGGTGACTGTGAAGCCCTGTTACAACTATTGCTCAAACATCATGAGAGGCTGTTTGGC
CAACCAAGGAGACCTTGATTTAGAGTGGAACAATTTCATAGATGCCATGCTGATGGTGGCAGAG
AGGCTGGAGGGTCCTTTCAACATTGAGTCCGTTATGGATCCCATCGATGTGAAGATTTCTGATG
CTATCATGAACATGCAGGATAATAGTGTTCAGGTGTCTCAGAAGGTTTTCCAAGGCTGTGGACC
TCCAAAGCCTCTCCCGGCTGGACGAATTTCTCGTTCCATCTCTGAAAGTGCCTTCAGTGCTCGA
TTCAGACCTTATCATCCAGAGCAACGCCCAACTACAGCAGCTGGCACTAGTTTGGACCGACTGG
TTACTGATGTCAAAGAGAAACTGAAGCAAGCTAAGAAGTTCTGGTCCTCTCTCCCAAGCACTGT
CTGCAATGATGAGAGGATGGCAGCAGGAAATGAGAATGAGGATGACTGTTGGAACGGGAAGAGC
AAAAGCAGGTACCTGTTTGCAGTGACAGGAAACGGATTAGCCAACCAGGGCAACAACCCAGAAG
TGCAGGTTGACACCAGCAAGCCGGACATTCTGATCCTTCGTCAAATCATGGCCCTTCGGGTTAT
GACCAGTAAAATGAAGAATGCTTACAACGGAAATGACGTGGACTTCTTTGATATCAGCGATGAG
AGTAGTGGAGAGGGAAGCGGAAGCGGATGTGAATATCAGCAGTGCCCTTCAGAGTTTGAGTACA
ACGCCACTGACCATTCTGGGAAGAGTGCCAACGAGAAAGCTGACAGTGCCGGTGGTGCCCCTGC
AGAGGCAAAGCCCTATCTCCTCGCTGCCCTCTGCATCCTGTTCCTCGCTGTGCAGGGAGAGTGG
AGATAATTGTCAAACTCTGAGTAAAAGTGTTCATCATCAGAAAGTTCAAAGGCACCAGTTCTCA
CTTTTTTTTTTTTAATCATCCTAGTGACTTTGCTTTTAAATGAATGGACAACAATGTACAGTTT
TTACTGTGTGGCCACTGGTTTAAGCAATGTTGACTTGTTGTTGACTTTGTTTTTCTCATTCAGT
TTGAGGGGACAGGGGCCTCCTGCCTTCAAGTGTGTCCCTCCGCACTCCCCTCCTTTGAGACTCG
TGTTATGCGCGGCTAGCGGTGTAGTTACAGAACTGTAGTTAGTTGTGTATTGGTGATCTTGTTT
TCTTTGTTGGTTTTTCTCATTTGTGGGGTTTTCCTTTTCCAATTATGGTCTCACCTTGTTTCTC
ACAAGAAAACCAGGGTCGTTTCTTGGCATGTAACATGTACGTATTTCTGAAATATTAAATAGCT
GTACAGAAGCAGGTTTATTTATCATGTTATCTTATTAAAAGAAAAAGCCCAAACAAGCTGAAAA
A

hide sequence

Protein Sequences


Protein RefSeqs	NP_001014130	(Get FASTA)	NCBI Sequence Viewer
	XP_006257642	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH81962	(Get FASTA)	NCBI Sequence Viewer
	EDM10951	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_001014130 ⟸ NM_001014108
- Peptide Label:	precursor
- UniProtKB:	Q642B0 (UniProtKB/TrEMBL)
- Sequence:	show sequence MARLGLLALLCTLAALSASLLAAEPKSKSCSEVRRLYVSKGFNKNDAPLYEINGDHLKICSQDY TCCSQEMEEKYSLQSKDDFQTVVSEQCNHLQAIFASRYKKFDEFFKELLENAEKSLNDMFVKTY GHLYMQNSELFKDLFVELKRYYVAGNVNLEEMLNDFWARLLERMFRLVNSQYHFTDEYLECVSK YTEQLKPFGDVPRKLKLQVTRAFVAARTFAQGLAVARDVVNRVSVVNPTAQCTQALLKMIYCSH CRGLVTVKPCYNYCSNIMRGCLANQGDLDLEWNNFIDAMLMVAERLEGPFNIESVMDPIDVKIS DAIMNMQDNSVQVSQKVFQGCGPPKPLPAGRISRSISESAFSARFRPYHPEQRPTTAAGTSLDR LVTDVKEKLKQAKKFWSSLPSTVCNDERMAAGNENEDDCWNGKSKSRYLFAVTGNGLANQGNNP EVQVDTSKPDILILRQIMALRVMTSKMKNAYNGNDVDFFDISDESSGEGSGSGCEYQQCPSEFE YNATDHSGKSANEKADSAGGAPAEAKPYLLAALCILFLAVQGEWR hide sequence

RefSeq Acc Id:	XP_006257642 ⟸ XM_006257580
- Peptide Label:	isoform X1
- UniProtKB:	Q642B0 (UniProtKB/TrEMBL)
- Sequence:	show sequence MARLGLLALLCTLAALSASLLAAEPKSKSCSEVRRLYVSKGFNKNDAPLYEINGDHLKICSQDY TCCSQEMEEKYSLQSKDDFQTVVSEQCNHLQAIFASRYKKFDEFFKELLENAEKSLNDMFVKTY GHLYMQNSELFKDLFVELKRYYVAGNVNLEEMLNDFWARLLERMFRLVNSQYHFTDEYLECVSK YTEQLKPFGDVPRKLKLQVTRAFVAARTFAQGLAVARDVVNRVSVVNPTAQCTQALLKMIYCSH CRGLVTVKPCYNYCSNIMRGCLANQGDLDLEWNNFIDAMLMVAERLEGPFNIESVMDPIDVKIS DAIMNMQDNSVQVSQKVFQGCGPPKPLPAGRISRSISESAFSARFRPYHPEQRPTTAAGTSLDR LVTDVKEKLKQAKKFWSSLPSTVCNDERMAAGNENEDDCWNGKSKSRYLFAVTGNGLANQGNNP EVQVDTSKPDILILRQIMALRVMTSKMKNAYNGNDVDFFDISDESSGEGSGSGCEYQQCPSEFE YNATDHSGKSANEKADSAGGAPAEAKPYLLAALCILFLAVQGEWR hide sequence

RefSeq Acc Id:

ENSRNOP00000003282 ⟸ ENSRNOT00000003282

Transcriptome

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

Promoters

RGD ID:

13702020

Promoter ID:

EPDNEW_R12543

Type:

initiation region

Name:

Gpc4_1

Description:

glypican 4

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	X	139,464,850 - 139,464,910	EPDNEW

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:1359399	AgrOrtholog
Ensembl Genes	ENSRNOG00000002413	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000003282	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000003282	ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7124728	IMAGE-MGC_LOAD
InterPro	Glypican	UniProtKB/TrEMBL
	Glypican-4	UniProtKB/TrEMBL
	Glypican_CS	UniProtKB/TrEMBL
KEGG Report	rno:317322	UniProtKB/TrEMBL
MGC_CLONE	MGC:94087	IMAGE-MGC_LOAD
NCBI Gene	317322	ENTREZGENE
PANTHER	Glypican	UniProtKB/TrEMBL
	PTHR10822:SF25	UniProtKB/TrEMBL
Pfam	Glypican	UniProtKB/TrEMBL
PhenoGen	Gpc4	PhenoGen
PROSITE	GLYPICAN	UniProtKB/TrEMBL
UniGene	Rn.19945	ENTREZGENE
UniProt	Q642B0	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2006-03-30	Gpc4	glypican 4	LOC317322	similar to glypican 4	Symbol and Name updated	1299863	APPROVED
2005-07-29	LOC317322	similar to glypican 4			Symbol and Name status set to provisional	70820	PROVISIONAL

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

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

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

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

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

RGD Manual Annotations