Rapsn (receptor-associated protein of the synapse)

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Gene: Rapsn (receptor-associated protein of the synapse) Rattus norvegicus

Analyze

Symbol:

Rapsn

Name:

receptor-associated protein of the synapse

RGD ID:

1311592

Description:

Exhibits ionotropic glutamate receptor binding activity. Involved in establishment of protein localization to postsynaptic membrane; positive regulation of neuromuscular synaptic transmission; and regulation of postsynaptic membrane organization. Localizes to neuromuscular junction. Human ortholog(s) of this gene implicated in congenital myasthenic syndrome 11 and fetal akinesia deformation sequence syndrome 2. Orthologous to human RAPSN (receptor associated protein of the synapse); PARTICIPATES IN acetylcholine signaling pathway via nicotinic acetylcholine receptor; INTERACTS WITH bisphenol A; cadmium dichloride; cyclophosphamide.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

43 kDa receptor-associated protein of the synapse; LOC362161; rapsyn; receptor-associated protein of the synapse, 43 kDa

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

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	3	77,014,699 - 77,024,373 (+)	NCBI
Rnor_6.0 Ensembl	3	79,860,179 - 79,869,524 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	3	79,859,815 - 79,869,486 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	3	86,568,568 - 86,578,239 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	75,396,836 - 75,406,115 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	3	75,293,208 - 75,302,485 (+)	NCBI
Celera	3	76,223,882 - 76,233,161 (+)	NCBI		Celera
Cytogenetic Map	3	q24	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autoimmune disease (ISO)

congenital disorder of glycosylation type IIc (ISO)

congenital myasthenic syndrome (ISO)

congenital myasthenic syndrome 11 (ISO)

congenital myasthenic syndrome 4C (ISO)

Congenital Myasthenic Syndrome, with Facial Dysmorphism, associated with Acetylcholine Receptor Deficiency (ISO)

Developmental Disabilities (ISO)

Experimental Autoimmune Myasthenia Gravis (IEP)

fetal akinesia deformation sequence syndrome 1 (ISO)

fetal akinesia deformation sequence syndrome 2 (ISO)

Hydrops Fetalis (ISO)

hypertrophic cardiomyopathy (ISO)

intellectual disability (ISO)

muscular disease (ISO)

myopathy (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

17alpha-ethynylestradiol (ISO)

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

benzo[a]pyrene (ISO)

bisphenol A (EXP)

cadmium dichloride (EXP)

cyclophosphamide (EXP)

endosulfan (EXP)

fenvalerate (EXP)

folic acid (ISO)

furan (EXP)

gentamycin (EXP)

phenylephrine (EXP)

quercetin (ISO)

tamoxifen (ISO)

tetrachloromethane (ISO)

titanium dioxide (ISO)

triptonide (ISO)

urethane (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

establishment of protein localization to postsynaptic membrane (IMP)

positive regulation of neuromuscular synaptic transmission (IMP)

positive regulation of neuron apoptotic process (ISO)

regulation of postsynaptic membrane organization (IMP)

synaptic transmission, cholinergic (ISO)

Cellular Component

centrosome (IEA,ISO)

cytosol (IEA,ISO)

Golgi apparatus (ISO)

membrane (ISO)

neuromuscular junction (IDA,ISO)

plasma membrane (ISO)

postsynaptic specialization membrane (ISO)

synapse (ISO)

Molecular Function

acetylcholine receptor binding (ISO)

ionotropic glutamate receptor binding (IPI)

metal ion binding (IEA)

protein binding (ISO)

protein-membrane adaptor activity (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

acetylcholine signaling pathway via nicotinic acetylcholine receptor (ISO)

References

References - curated


1.	Francolini M, etal., J Neuropathol Exp Neurol. 2009 Oct;68(10):1103-15.
2.	GOA data from the GO Consortium
3.	Martinez-Martinez P, etal., Neurobiol Dis. 2009 Jul;35(1):14-23. doi: 10.1016/j.nbd.2009.03.008. Epub 2009 Apr 1.
4.	MGD data from the GO Consortium
5.	OMIM Disease Annotation Pipeline
6.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7.	RGD automated import pipeline for gene-chemical interactions
8.	Witzemann V, etal., Mech Dev. 2013 Jun-Aug;130(6-8):402-11. doi: 10.1016/j.mod.2012.09.004. Epub 2012 Sep 29.

Additional References at PubMed

PMID:8416841	PMID:11312299	PMID:12388596	PMID:12486121	PMID:17119023	PMID:18420419	PMID:20053883	PMID:27225759

Genomics

Comparative Map Data

Rapsn
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	3	77,014,699 - 77,024,373 (+)	NCBI
Rnor_6.0 Ensembl	3	79,860,179 - 79,869,524 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	3	79,859,815 - 79,869,486 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	3	86,568,568 - 86,578,239 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	75,396,836 - 75,406,115 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	3	75,293,208 - 75,302,485 (+)	NCBI
Celera	3	76,223,882 - 76,233,161 (+)	NCBI		Celera
Cytogenetic Map	3	q24	NCBI

RAPSN
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	11	47,437,764 - 47,449,143 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	11	47,437,764 - 47,449,136 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	11	47,459,315 - 47,470,688 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	11	47,415,891 - 47,427,306 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	11	47,415,890 - 47,427,306	NCBI
Celera	11	47,601,051 - 47,612,463 (-)	NCBI
Cytogenetic Map	11	p11.2	NCBI
HuRef	11	47,159,075 - 47,170,494 (-)	NCBI		HuRef
CHM1_1	11	47,458,570 - 47,469,991 (-)	NCBI		CHM1_1

Rapsn
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	90,865,810 - 90,876,074 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	2	90,865,965 - 90,876,074 (+)	Ensembl
GRCm38	2	91,035,472 - 91,045,729 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	91,035,620 - 91,045,729 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	90,875,784 - 90,885,886 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	2	90,836,478 - 90,846,568 (+)	NCBI			mm8
Celera	2	92,420,152 - 92,430,248 (+)	NCBI		Celera
Cytogenetic Map	2	E1	NCBI
cM Map	2	50.44	NCBI

Rapsn
(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_004955422	826,727 - 834,289 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955422	826,556 - 834,483 (+)	NCBI	ChiLan1.0	ChiLan1.0

RAPSN
(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	11	47,940,530 - 47,951,667 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	11	47,940,530 - 47,951,667 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	11	47,387,324 - 47,398,579 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

RAPSN
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	18	42,199,160 - 42,210,668 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	18	42,199,412 - 42,210,673 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	18	40,930,029 - 40,941,208 (+)	NCBI
ROS_Cfam_1.0	18	42,855,197 - 42,866,378 (+)	NCBI
UMICH_Zoey_3.1	18	42,341,801 - 42,352,980 (+)	NCBI
UNSW_CanFamBas_1.0	18	41,896,689 - 41,907,866 (+)	NCBI
UU_Cfam_GSD_1.0	18	42,626,215 - 42,637,394 (+)	NCBI

Rapsn
(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_024404947	19,680,416 - 19,692,511 (+)	NCBI
SpeTri2.0	NW_004936562	1,796,087 - 1,804,153 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

RAPSN
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	2	15,066,547 - 15,193,085 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	2	15,166,968 - 15,181,011 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	2	16,382,739 - 16,387,663 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

RAPSN
(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	1	17,867,721 - 17,887,162 (+)	NCBI
ChlSab1.1 Ensembl	1	17,868,888 - 17,887,164 (+)	Ensembl

Rapsn
(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_004624767	1,350,820 - 1,358,107 (+)	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
2290452	Scl56	Serum cholesterol level QTL 56	2.26		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	3	1	95176874	Rat
1358905	Hrtrt17	Heart rate QTL 17	5.9	0.000014	heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	10094081	93415837	Rat
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	10639528	127023997	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	10639528	127023997	Rat
737818	Hcar12	Hepatocarcinoma resistance QTL 12	2.6		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	3	30114912	123700444	Rat
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	30846101	172879276	Rat
1354589	Bw31	Body weight QTL 31	3.3		body mass (VT:0001259)	body weight (CMO:0000012)	3	33477354	81136227	Rat
1354604	Bw36	Body weight QTL 36	2.9		body mass (VT:0001259)	body weight (CMO:0000012)	3	33477354	108914061	Rat
61419	Cia11	Collagen induced arthritis QTL 11	5.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	3	34394121	103141944	Rat
1358362	Srcrt2	Stress Responsive Cort QTL 2	2.78		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	39248391	140271184	Rat
738019	Anxrr10	Anxiety related response QTL 10	3.9		exploratory behavior trait (VT:0010471)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	3	40422921	85422921	Rat
1331777	Bw24	Body weight QTL 24	3.503		body mass (VT:0001259)	body weight (CMO:0000012)	3	40523593	92654473	Rat
1331795	Rf30	Renal function QTL 30	3.708		urine potassium amount (VT:0010539)	urine potassium level (CMO:0000128)	3	40523593	92654473	Rat
1354597	Kidm13	Kidney mass QTL 13	2.9		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	3	43295930	108914061	Rat
2301970	Bw81	Body weight QTL 81	5.19		body mass (VT:0001259)	body weight (CMO:0000012)	3	43295930	163640485	Rat
2301971	Cm71	Cardiac mass QTL 71	4.63		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	3	43295930	163640485	Rat
1300178	Hrtrt4	Heart rate QTL 4	3.74		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	45406058	94467785	Rat
1581503	Cm58	Cardiac mass QTL 58	2.7	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	45406058	127023997	Rat
1559282	Emca5	Estrogen-induced mammary cancer QTL 5	3.9		mammary gland integrity trait (VT:0010552)	percentage of study population developing mammary tumors during a period of time (CMO:0000948)	3	45406058	177699992	Rat
2292591	Esta4	Estrogen-induced thymic atrophy QTL 4			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	3	48561928	155263151	Rat
1358186	Ept2	Estrogen-induced pituitary tumorigenesis QTL 2	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	48562146	115249962	Rat
2292613	Ept16	Estrogen-induced pituitary tumorigenesis QTL 16	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	48562146	115249962	Rat
631665	Bw8	Body weight QTL 8	5.5		body mass (VT:0001259)	body weight (CMO:0000012)	3	51821836	124513579	Rat
724523	Tsu1	Thymus enlargement suppressive QTL 1	3.84		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	3	51822008	120917851	Rat
1582218	Bw74	Body weight QTL 74	3.9	0.0021	body mass (VT:0001259)	body weight (CMO:0000012)	3	54630948	119830094	Rat
1582238	Bw68	Body weight QTL 68	3.2	0.0064	body mass (VT:0001259)	body weight (CMO:0000012)	3	54630948	119830094	Rat
1582239	Epfw1	Epididymal fat weight QTL 1	4.5	0.0006	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	3	54630948	119830094	Rat
61377	Edpm3	Estrogen-dependent pituitary mass QTL 3	7.05	0.038	pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	54631046	93415673	Rat
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	55245276	95176874	Rat
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	3	55245276	95176874	Rat
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	55245276	95176874	Rat
1358293	Bw38	Body weight QTL 38	6	0.0000031	body mass (VT:0001259)	body weight (CMO:0000012)	3	56735995	101735995	Rat
1581568	Rf53	Renal function QTL 53			total urine protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	3	58204463	170534769	Rat
8662816	Vetf4	Vascular elastic tissue fragility QTL 4	4		renal artery integrity trait (VT:0010642)	number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)	3	61241033	165369047	Rat
1300111	Rf12	Renal function QTL 12	3.78		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	3	62922868	127023997	Rat
631200	Cm25	Cardiac mass QTL 25	4.8	0.0001	heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	3	63049050	92654302	Rat
1582221	Kidm30	Kidney mass QTL 30	3.5	0.0008	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	3	66711607	119830094	Rat
1582210	Bw71	Body weight QTL 71	3.3	0.0012	body mass (VT:0001259)	body weight (CMO:0000012)	3	66711607	119830094	Rat
12879848	Bw181	Body weght QTL 181		0.015	body mass (VT:0001259)	body weight (CMO:0000012)	3	72672290	127023997	Rat
2301414	Kidm37	Kidney mass QTL 37		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	72973445	127023997	Rat
1600376	Arunc5	Aerobic running capacity QTL 5		0.21	exercise endurance trait (VT:0002332)	maximum distance run on treadmill (CMO:0001406)	3	78700444	123700444	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	76
Count of miRNA genes:	65
Interacting mature miRNAs:	72
Transcripts:	ENSRNOT00000068444
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

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

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

Expression

RNA-SEQ Expression

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

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium		15					5	8		8	3		5
Low	2	28	26	10	18	10	3	3	54	27	38	11	3
Below cutoff	1		30	30	1	30			20

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001108584	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006234528	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039105428	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039105429	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473949	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000118	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000068444 ⟹ ENSRNOP00000060958

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	3	79,860,207 - 79,869,486 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000081160 ⟹ ENSRNOP00000075166

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	3	79,860,179 - 79,869,524 (+)	Ensembl

RefSeq Acc Id:

NM_001108584 ⟹ NP_001102054

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	77,015,094 - 77,024,373 (+)	NCBI
Rnor_6.0	3	79,860,207 - 79,869,486 (+)	NCBI
Rnor_5.0	3	86,568,568 - 86,578,239 (+)	NCBI
RGSC_v3.4	3	75,396,836 - 75,406,115 (+)	RGD
Celera	3	76,223,882 - 76,233,161 (+)	RGD

Sequence:

show sequence

TGTTCCCAGGGTGGCGCCCGTTGTCCATCCAGGCCCTGCTTAGCTTTTGCCTGGTGTTGCTTTT
CCCTCCCAGAGATCAGCTGGCACTGTGGGTCCAACACCATGAAGGTCTAAAGACACCTAGCCAA
CCACGGTCTTTCCGAGTGGCCAGACTGTGGGAGGATGGGGCAGGACCAGACAAAGCAACAGATC
GAAAAAGGACTGCAGCTGTACCAGTCCAACCAGACAGAGAAGGCACTGCAAGTGTGGATGAAGG
TGCTGGAGAAGGGCTCTGACCTCGTGGGCCGCTTCCGGGTGCTGGGCTGCTTGGTAACAGCTCA
CTCGGAGATGGGCCGCTACAAAGAGATGCTGAAGTTTGCCGTGGTCCAGATCGACACTGCTCGG
GAACTGGAGGATGCGGATTTCCTGCTCGAAAGCTACCTGAACCTGGCACGCAGCAATGAGAAGC
TATGTGAGTTTCACAAAACCATCTCCTACTGCAAGACCTGCCTCGGCCTGCCTGGCACCAGGGC
TGGTGCCCAGCTTGGGGGTCAGGTCAGCCTGAGCATGGGCAATGCTTTCCTGGGCCTCAGCCTC
TTCCAGAAGGCCCTAGAGAGCTTTGAGAAGGCCCTGCGCTATGCCCACAACAATGATGACACCA
TGCTGGAGTGCCGCGTCTGCTGCAGCCTGGGCAGTTTCTACGCCCAGGTCAAGGAGTCCATGAA
GATTGCCCTGCAGCATGGTGACCGCCCACTGCAAGCACTCTGTCTGCTCTGCTTTGCCGATATC
CACCGGAGCCGTGGGGACCTGGAGACAGCCTTCCCTAGGTACGATTCCGCTATGAGCATCATGA
CCGAGATCGGAAACCGCCTGGGGCAAGTGCATGTGCTGCTGGGTGTGGCCAAGTGCTGGATAGC
CAGGAAAGTGCTGGACAAGGCTTTGGATGCCATTGAGAAAGCCCAGGACCTGGCTGAAGAGGTT
GGAAATAAGCTGAGCCAGCTCAAGCTGCACTGCCTGAGTGAGGGCATCTGCCGCAGCAAGGGGC
TGCAGCGTGAGCTGCGCGCGCATGTAGTGAGGTTCCACGAGTGCGTGGAGGAGACTGAGCTCTA
CTGTGGCCTCTGTGGTGAGTCCATTGGGGAGAAGAACAGCCGGCTGCAGGCCCTGCCCTGCTCC
CACATCTTTCATCTCAGATGCCTGCAAAACAACGGCACTAGGAGTTGCCCCAACTGCCGCCGCT
CCTCCATGAAGCCAGGCTTTGTGTGACCTCAGTGGCCATCTTGGCACCTCCACCATCAAGCTGG
AGGCCCTGGTGAAATCCTAGGGTAGCAGCCAGGACCTCCACAGCCAACTCAGGGCCAGAGGCCT
GCCTGCTGCTCCTCTGGGCCTACCTCCCCTCCCTTGCCTCTTTGTACTTTGTTCTTTATAGAAA
AATAAAATGTTTCTACCTGGTG

hide sequence

RefSeq Acc Id:

XM_006234528 ⟹ XP_006234590

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	77,014,699 - 77,024,371 (+)	NCBI
Rnor_6.0	3	79,859,815 - 79,869,484 (+)	NCBI
Rnor_5.0	3	86,568,568 - 86,578,239 (+)	NCBI

Sequence:

show sequence

GAGAGAGAGAGAAGAAAAGAAAAACAGAAGAAAAGAAAAAGAAGCAAGGAGAATAAGCAGGCTG
GACATTCACCTCACCTCCCTGATGCCTGTATGCCCAGTGTTCTGCCTGCTGTTTTTCCTGCTGT
CAGAACCTCTGGCCTAAGGCTTGCCCACATCCTGGCAGACAGCCTTTGAGAGCTGAACCTGCTA
GGGCATCAAGGCCAGTGTCAAAGTGTCAAAAAGGCACCAAACAGGTTCTCAGGTGGCACAGTGC
CTGTATCCCCGGGGCAGCCACCTTTCAGCTTTGAGTGGGTGCAGCAGAAACCCTCGTGACCTTG
CTGCTGACATTCCTCAGAAGCCACGTGGCCCCAACTGGCAGGGACAGCTGCAGACAGGGGCTGA
ACCAGCCTTGTTCCCAGGGTGGCGCCCGTTGTCCATCCAGGCCCTGCTTAGCTTTTGCCTGGTG
TTGCTTTTCCCTCCCAGAGATCAGCTGGCACTGTGGGTCCAACACCATGAAGGTCTAAAGACAC
CTAGCCAACCACGGTCTTTCCGAGTGGCCAGACTGTGGGAGGATGGGGCAGGACCAGACAAAGC
AACAGATCGAAAAAGGACTGCAGCTGTACCAGTCCAACCAGACAGAGAAGGCACTGCAAGTGTG
GATGAAGGTGCTGGAGAAGGGCTCTGACCTCGTGGGCCGCTTCCGGGTGCTGGGCTGCTTGGTA
ACAGCTCACTCGGAGATGGGCCGCTACAAAGAGATGCTGAAGTTTGCCGTGGTCCAGATCGACA
CTGCTCGGGAACTGGAGGATGCGGATTTCCTGCTCGAAAGCTACCTGAACCTGGCACGCAGCAA
TGAGAAGCTATGTGAGTTTCACAAAACCATCTCCTACTGCAAGACCTGCCTCGGCCTGCCTGGC
ACCAGGGCTGGTGCCCAGCTTGGGGGTCAGGTCAGCCTGAGCATGGGCAATGCTTTCCTGGGCC
TCAGCCTCTTCCAGAAGGCCCTAGAGAGCTTTGAGAAGGCCCTGCGCTATGCCCACAACAATGA
TGACACCATGCTGGAGTGCCGCGTCTGCTGCAGCCTGGGCAGTTTCTACGCCCAGGTCAAGGAC
TATGAGAAAGCCCTGTTCTTTCCCTGCAAGGCTGCAGAGCTTGTCAACGACTATGGCAAAGGCT
GGAGCCTCAAATATCGGGCCATGAGCCAGTACCACATGGCTGTGGCCTACCGCCTGCTGGGCCA
CCTGGGCAGTGCCATGGAGTGTTGTGAGGAGTCCATGAAGATTGCCCTGCAGCATGGTGACCGC
CCACTGCAAGCACTCTGTCTGCTCTGCTTTGCCGATATCCACCGGAGCCGTGGGGACCTGGAGA
CAGCCTTCCCTAGGTACGATTCCGCTATGAGCATCATGACCGAGATCGGAAACCGCCTGGGGCA
AGTGCATGTGCTGCTGGGTGTGGCCAAGTGCTGGATAGCCAGGAAAGTGCTGGACAAGGCTTTG
GATGCCATTGAGAAAGCCCAGGACCTGGCTGAAGAGGTTGGAAATAAGCTGAGCCAGCTCAAGC
TGCACTGCCTGAGTGAGGGCATCTGCCGCAGCAAGGGGCTGCAGCGTGAGCTGCGCGCGCATGT
AGTGAGGTTCCACGAGTGCGTGGAGGAGACTGAGCTCTACTGTGGCCTCTGTGGTGAGTCCATT
GGGGAGAAGAACAGCCGGCTGCAGGCCCTGCCCTGCTCCCACATCTTTCATCTCAGATGCCTGC
AAAACAACGGCACTAGGAGTTGCCCCAACTGCCGCCGCTCCTCCATGAAGCCAGGCTTTGTGTG
ACCTCAGTGGCCATCTTGGCACCTCCACCATCAAGCTGGAGGCCCTGGTGAAATCCTAGGGTAG
CAGCCAGGACCTCCACAGCCAACTCAGGGCCAGAGGCCTGCCTGCTGCTCCTCTGGGCCTACCT
CCCCTCCCTTGCCTCTTTGTACTTTGTTCTTTATAGAAAAATAAAATGTTTCTACCTGG

hide sequence

RefSeq Acc Id:

XM_039105428 ⟹ XP_038961356

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	77,015,427 - 77,024,371 (+)	NCBI

RefSeq Acc Id:

XM_039105429 ⟹ XP_038961357

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	77,015,309 - 77,024,371 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001102054	(Get FASTA)	NCBI Sequence Viewer
	XP_006234590	(Get FASTA)	NCBI Sequence Viewer
	XP_038961356	(Get FASTA)	NCBI Sequence Viewer
	XP_038961357	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL79499	(Get FASTA)	NCBI Sequence Viewer
	EDL79500	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001102054 ⟸ NM_001108584

- UniProtKB:

D3ZPG2 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MGQDQTKQQIEKGLQLYQSNQTEKALQVWMKVLEKGSDLVGRFRVLGCLVTAHSEMGRYKEMLK
FAVVQIDTARELEDADFLLESYLNLARSNEKLCEFHKTISYCKTCLGLPGTRAGAQLGGQVSLS
MGNAFLGLSLFQKALESFEKALRYAHNNDDTMLECRVCCSLGSFYAQVKESMKIALQHGDRPLQ
ALCLLCFADIHRSRGDLETAFPRYDSAMSIMTEIGNRLGQVHVLLGVAKCWIARKVLDKALDAI
EKAQDLAEEVGNKLSQLKLHCLSEGICRSKGLQRELRAHVVRFHECVEETELYCGLCGESIGEK
NSRLQALPCSHIFHLRCLQNNGTRSCPNCRRSSMKPGFV

hide sequence

RefSeq Acc Id:	XP_006234590 ⟸ XM_006234528
- Peptide Label:	isoform X1
- UniProtKB:	A0A0G2K9X2 (UniProtKB/TrEMBL)
- Sequence:	show sequence MGQDQTKQQIEKGLQLYQSNQTEKALQVWMKVLEKGSDLVGRFRVLGCLVTAHSEMGRYKEMLK FAVVQIDTARELEDADFLLESYLNLARSNEKLCEFHKTISYCKTCLGLPGTRAGAQLGGQVSLS MGNAFLGLSLFQKALESFEKALRYAHNNDDTMLECRVCCSLGSFYAQVKDYEKALFFPCKAAEL VNDYGKGWSLKYRAMSQYHMAVAYRLLGHLGSAMECCEESMKIALQHGDRPLQALCLLCFADIH RSRGDLETAFPRYDSAMSIMTEIGNRLGQVHVLLGVAKCWIARKVLDKALDAIEKAQDLAEEVG NKLSQLKLHCLSEGICRSKGLQRELRAHVVRFHECVEETELYCGLCGESIGEKNSRLQALPCSH IFHLRCLQNNGTRSCPNCRRSSMKPGFV hide sequence

RefSeq Acc Id:

ENSRNOP00000060958 ⟸ ENSRNOT00000068444

RefSeq Acc Id:

ENSRNOP00000075166 ⟸ ENSRNOT00000081160

RefSeq Acc Id:	XP_038961357 ⟸ XM_039105429
- Peptide Label:	isoform X3

RefSeq Acc Id:	XP_038961356 ⟸ XM_039105428
- Peptide Label:	isoform X2

Protein Domains

RING-type TPR_REGION

Transcriptome

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

Promoters

RGD ID:

13692203

Promoter ID:

EPDNEW_R2728

Type:

single initiation site

Name:

Rapsn_1

Description:

receptor-associated protein of the synapse

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	3	79,860,208 - 79,860,268	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

Damaging Variants

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
3	75397933	75397934	G	A	snv	SS/JrHsdMcwi (MCW)
3	75397954	75397955	G	A	snv	SS/JrHsdMcwi (MCW)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1311592	AgrOrtholog
Ensembl Genes	ENSRNOG00000011208	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000060958	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOP00000075166	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000068444	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOT00000081160	UniProtKB/TrEMBL
Gene3D-CATH	1.25.40.10	UniProtKB/TrEMBL
	3.30.40.10	UniProtKB/TrEMBL
InterPro	Postsynaptic	UniProtKB/TrEMBL
	Postsynaptic_CS	UniProtKB/TrEMBL
	Rapsyn_myristoylation/link_N	UniProtKB/TrEMBL
	TPR-contain	UniProtKB/TrEMBL
	TPR-like_helical	UniProtKB/TrEMBL
	TPR_MalT	UniProtKB/TrEMBL
	TPR_repeat	UniProtKB/TrEMBL
	Znf_RING	UniProtKB/TrEMBL
	Znf_RING/FYVE/PHD	UniProtKB/TrEMBL
KEGG Report	rno:362161	UniProtKB/TrEMBL
NCBI Gene	362161	ENTREZGENE
Pfam	Rapsyn_N	UniProtKB/TrEMBL
	TPR_MalT	UniProtKB/TrEMBL
	zf-RING_2	UniProtKB/TrEMBL
PhenoGen	Rapsn	PhenoGen
PRINTS	POSTSYNAPTIC	UniProtKB/TrEMBL
PROSITE	43_KD_POSTSYNAPTIC	UniProtKB/TrEMBL
	TPR	UniProtKB/TrEMBL
	TPR_REGION	UniProtKB/TrEMBL
	ZF_RING_2	UniProtKB/TrEMBL
SMART	RING	UniProtKB/TrEMBL
	TPR	UniProtKB/TrEMBL
Superfamily-SCOP	SSF48452	UniProtKB/TrEMBL
UniProt	A0A0G2K9X2	ENTREZGENE, UniProtKB/TrEMBL
	D3ZPG2	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-04-30	Rapsn	receptor-associated protein of the synapse	Rapsn_predicted	receptor-associated protein of the synapse (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Rapsn_predicted	receptor-associated protein of the synapse (predicted)			Symbol and Name status set to approved	70820	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

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

RGD Manual Annotations

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

RGD Manual Annotations