Nptn (neuroplastin) - Rat Genome Database

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

	Submit Data \| Help \| Video Tutorials \| News \| Publications \| Download \| REST API \| Citing RGD \| Contact
	Search RGD Grant Resources Citing RGD About Us Contact Us Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) RatMine GViewer (Genome Viewer) Overgo Probe Designer ACP Haplotyper Genome Scanner VCMap Aging & Age-Related Disease Cancer Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease Find Models new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive Pathways Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
	Advanced Search (OLGA)

Gene: Nptn (neuroplastin) Rattus norvegicus

Analyze

Symbol:

Nptn

Name:

neuroplastin

RGD ID:

620296

Description:

Exhibits cell adhesion molecule binding activity; ion channel binding activity; and type 1 fibroblast growth factor receptor binding activity. Involved in several processes, including homophilic cell adhesion via plasma membrane adhesion molecules; positive regulation of signal transduction; and regulation of synaptic plasticity. Localizes to several cellular components, including GABA-ergic synapse; Schaffer collateral - CA1 synapse; and integral component of synaptic membrane. Orthologous to human NPTN (neuroplastin); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,4-dinitrotoluene; 2,6-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

glycoprotein 55; glycoprotein 55/65; glycoprotein 65; gp55/65; Sdfr1; SDR-1; stromal cell derived factor receptor 1; stromal cell-derived receptor 1

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):	NPTN (neuroplastin)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Nptn (neuroplastin)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Nptn (neuroplastin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	NPTN (neuroplastin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	NPTN (neuroplastin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Nptn (neuroplastin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	NPTN (neuroplastin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	NPTN (neuroplastin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Nptn (neuroplastin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	NPTN (neuroplastin)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Nptn (neuroplastin)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	nptna (neuroplastin a)	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	Bsg	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|OrthoInspector\|PhylomeDB\|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	8	58,996,876 - 59,063,402 (+)	NCBI
Rnor_6.0 Ensembl	8	63,379,087 - 63,445,686 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	8	63,379,062 - 63,445,694 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	8	63,149,031 - 63,215,298 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	8	62,389,893 - 62,466,128 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	8	62,408,946 - 62,485,178 (+)	NCBI
Celera	8	58,456,063 - 58,522,680 (+)	NCBI		Celera
Cytogenetic Map	8	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

Bloom syndrome (ISO)

colon cancer (ISO)

hypertension (ISO)

Myocardial Ischemia (ISO)

schizophrenia (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

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

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

2,4-dinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

2-methylcholine (ISO)

3-isobutyl-1-methyl-7H-xanthine (ISO)

4-hydroxyphenyl retinamide (ISO)

acrylamide (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

arsenous acid (ISO)

asbestos (ISO)

benzo[a]pyrene (EXP,ISO)

bis(2-chloroethyl) sulfide (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

clozapine (ISO)

copper(II) sulfate (ISO)

crocidolite asbestos (ISO)

cyclosporin A (ISO)

Deoxycorticosterone acetate (EXP)

dexamethasone (ISO)

diarsenic trioxide (ISO)

disodium selenite (ISO)

doxorubicin (ISO)

enzyme inhibitor (ISO)

ethanol (ISO)

flavonoids (EXP)

folic acid (ISO)

gentamycin (EXP)

hydrogen peroxide (ISO)

indometacin (ISO)

methotrexate (ISO)

olanzapine (ISO)

pirinixic acid (ISO)

potassium chloride (EXP)

potassium chromate (ISO)

potassium dichromate (ISO)

pregnenolone 16alpha-carbonitrile (EXP)

rotenone (EXP)

tetrachloromethane (ISO)

triclosan (ISO)

triptonide (ISO)

urethane (ISO)

valproic acid (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

axon guidance (IBA)

cellular calcium ion homeostasis (ISO)

dendrite self-avoidance (IBA)

excitatory synapse assembly (ISO)

homophilic cell adhesion via plasma membrane adhesion molecules (IBA,IDA)

long-term synaptic potentiation (IDA)

modulation of chemical synaptic transmission (ISO)

negative regulation of cytokine production (ISO,ISS)

positive regulation of cellular protein localization (IMP)

positive regulation of cytosolic calcium ion concentration (IDA)

positive regulation of ERK1 and ERK2 cascade (IDA)

positive regulation of fibroblast growth factor receptor signaling pathway (IDA)

positive regulation of long-term neuronal synaptic plasticity (IMP)

positive regulation of long-term synaptic potentiation (IMP)

positive regulation of neuron projection development (IDA)

positive regulation of protein phosphorylation (IDA)

regulation of cell adhesion (TAS)

regulation of receptor localization to synapse (IEA,ISO)

synapse organization (ISO)

trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission (IDA)

visual learning (IDA)

Cellular Component

axon (IBA)

cell surface (IDA)

dendrite (IDA,ISO)

GABA-ergic synapse (EXP,IDA)

glutamatergic synapse (EXP,IDA)

immunological synapse (ISO,ISS)

inhibitory synapse (IDA)

integral component of membrane (TAS)

integral component of postsynaptic density membrane (IDA)

integral component of presynaptic active zone membrane (EXP,IDA)

plasma membrane (IBA,TAS)

postsynaptic density (IDA)

postsynaptic membrane (TAS)

presynaptic membrane (IDA)

Schaffer collateral - CA1 synapse (IDA)

synaptic membrane (IDA)

Molecular Function

cell adhesion molecule binding (IDA)

cell-cell adhesion mediator activity (IBA)

ion channel binding (IPI)

protein binding (ISO)

type 1 fibroblast growth factor receptor binding (IDA)

References

References - curated


1.	Boyken J, etal., Neuron. 2013 Apr 24;78(2):285-97. doi: 10.1016/j.neuron.2013.02.027.
2.	Empson RM, etal., J Neurochem. 2006 Nov;99(3):850-60.
3.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4.	Hill IE, etal., Brain Res. 1988 Sep 27;461(1):27-43.
5.	Kreutz MR, etal., Invest Ophthalmol Vis Sci. 2001 Jul;42(8):1907-14.
6.	Langnaese K, etal., J Biol Chem 1997 Jan 10;272(2):821-7.
7.	MGD data from the GO Consortium
8.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
9.	Owczarek S, etal., FASEB J. 2010 Apr;24(4):1139-50. Epub 2009 Dec 1.
10.	Owczarek S, etal., J Neurochem. 2011 Jun;117(6):984-94. doi: 10.1111/j.1471-4159.2011.07269.x. Epub 2011 May 13.
11.	RGD automated import pipeline for gene-chemical interactions
12.	Sarto-Jackson I, etal., J Biol Chem. 2012 Apr 20;287(17):14201-14. doi: 10.1074/jbc.M111.293175. Epub 2012 Mar 2.
13.	Smalla KH, etal., Proc Natl Acad Sci U S A. 2000 Apr 11;97(8):4327-32.
14.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
15.	Willmott T, etal., J Neurochem. 1992 Jun;58(6):2037-43.

Additional References at PubMed

PMID:15489334	PMID:19581412	PMID:24260123	PMID:24554721	PMID:28827723	PMID:29476059

Genomics

Comparative Map Data

Nptn
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	8	58,996,876 - 59,063,402 (+)	NCBI
Rnor_6.0 Ensembl	8	63,379,087 - 63,445,686 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	8	63,379,062 - 63,445,694 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	8	63,149,031 - 63,215,298 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	8	62,389,893 - 62,466,128 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	8	62,408,946 - 62,485,178 (+)	NCBI
Celera	8	58,456,063 - 58,522,680 (+)	NCBI		Celera
Cytogenetic Map	8	q24	NCBI

NPTN
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	15	73,560,014 - 73,634,134 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	15	73,560,014 - 73,633,389 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	15	73,852,355 - 73,925,730 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	15	71,639,410 - 71,712,806 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	15	71,639,415 - 71,712,747	NCBI
Celera	15	50,730,984 - 50,804,846 (-)	NCBI
Cytogenetic Map	15	q24.1	NCBI
HuRef	15	50,683,637 - 50,757,046 (-)	NCBI		HuRef
CHM1_1	15	73,970,294 - 74,043,707 (-)	NCBI		CHM1_1

Nptn
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	9	58,489,504 - 58,560,162 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	9	58,489,523 - 58,565,238 (+)	Ensembl
GRCm38	9	58,582,240 - 58,652,879 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	9	58,582,240 - 58,657,955 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	9	58,430,047 - 58,500,686 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	9	58,380,546 - 58,451,008 (+)	NCBI			mm8
Celera	9	55,815,258 - 55,885,738 (+)	NCBI		Celera
Cytogenetic Map	9	B	NCBI

Nptn
(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_004955450	3,938,403 - 4,004,059 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955450	3,938,403 - 4,002,694 (+)	NCBI	ChiLan1.0	ChiLan1.0

NPTN
(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	15	71,228,099 - 71,301,545 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	15	71,229,992 - 71,269,579 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	15	52,470,545 - 52,544,046 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

NPTN
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	30	36,846,475 - 36,880,096 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	30	36,847,022 - 36,880,097 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	30	36,782,851 - 36,853,036 (-)	NCBI
ROS_Cfam_1.0	30	37,053,693 - 37,123,723 (-)	NCBI
UMICH_Zoey_3.1	30	37,005,919 - 37,076,149 (-)	NCBI
UNSW_CanFamBas_1.0	30	37,031,794 - 37,101,280 (-)	NCBI
UU_Cfam_GSD_1.0	30	37,288,062 - 37,358,082 (-)	NCBI

Nptn
(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_024408640	114,880,040 - 114,965,377 (-)	NCBI
SpeTri2.0	NW_004936471	32,726,953 - 32,813,429 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

NPTN
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	7	59,713,204 - 59,840,594 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	7	59,768,414 - 59,840,594 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	7	64,428,151 - 64,461,654 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

NPTN
(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	26	9,852,592 - 9,924,952 (+)	NCBI
ChlSab1.1 Ensembl	26	9,852,658 - 9,926,109 (+)	Ensembl
Vero_WHO_p1.0	NW_023666048	131,687,452 - 131,759,755 (-)	NCBI

Nptn
(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_004624781	752,048 - 818,250 (+)	NCBI

Position Markers

47.MMHAP30FLH5.seq

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	8	63,381,112 - 63,381,232	NCBI	Rnor6.0
Rnor_5.0	8	63,151,080 - 63,151,200	UniSTS	Rnor5.0
RGSC_v3.4	8	62,391,918 - 62,392,038	UniSTS	RGSC3.4
Celera	8	58,458,088 - 58,458,208	UniSTS
Cytogenetic Map	8	q24	UniSTS

RH137991

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	8	63,402,893 - 63,403,076	NCBI	Rnor6.0
Rnor_5.0	8	63,172,456 - 63,172,639	UniSTS	Rnor5.0
RGSC_v3.4	8	62,422,755 - 62,422,938	UniSTS	RGSC3.4
Celera	8	58,479,926 - 58,480,109	UniSTS
RH 3.4 Map	8	693.6	UniSTS
Cytogenetic Map	8	q24	UniSTS

AW554172

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	8	63,445,091 - 63,445,193	NCBI	Rnor6.0
Rnor_5.0	8	63,214,695 - 63,214,797	UniSTS	Rnor5.0
RGSC_v3.4	8	62,465,529 - 62,465,631	UniSTS	RGSC3.4
Celera	8	58,522,081 - 58,522,183	UniSTS
Cytogenetic Map	8	q24	UniSTS

UniSTS:236151

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	8	63,389,898 - 63,390,199	NCBI	Rnor6.0
Rnor_5.0	8	63,159,584 - 63,159,885	UniSTS	Rnor5.0
RGSC_v3.4	8	62,402,736 - 62,403,037	UniSTS	RGSC3.4
Celera	8	58,466,934 - 58,467,235	UniSTS
Cytogenetic Map	8	q24	UniSTS

MARC_21804-21805:1025095690:1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	8	63,444,108 - 63,444,746	NCBI	Rnor6.0
Rnor_5.0	8	63,213,712 - 63,214,350	UniSTS	Rnor5.0
RGSC_v3.4	8	62,464,546 - 62,465,184	UniSTS	RGSC3.4
Celera	8	58,521,098 - 58,521,736	UniSTS
Cytogenetic Map	8	q24	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
1581557	Eae16	Experimental allergic encephalomyelitis QTL 16	3.8		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	8	9531047	119211942	Rat
631650	Stl6	Serum triglyceride level QTL 6	4	0.0019	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	8	10938911	120496129	Rat
61373	Mcs4	Mammary carcinoma susceptibility QTL 4	1.1		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	8	20717592	65717592	Rat
631271	Lecl1	Lens clarity QTL 1		0.001	lens clarity trait (VT:0001304)	age of onset/diagnosis of cataract (CMO:0001584)	8	21464919	91140553	Rat
731182	Uae24	Urinary albumin excretion QTL 24	6.4		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	8	21813070	100873963	Rat
631842	Inf1	Infertility severity QTL 1	4.1	0.001	seminal gland mass (VT:0010524)	seminal vesicle wet weight (CMO:0001603)	8	27841496	72841496	Rat
1358892	Kidm26	Kidney mass QTL 26	3.69		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	8	29867983	106526740	Rat
1358896	Bp262	Blood pressure QTL 262	2.89		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	29867983	106526740	Rat
1358907	Cm40	Cardiac mass QTL 40	1.89		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	8	29867983	106526740	Rat
2303564	Gluco43	Glucose level QTL 43	3		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	8	30144800	75144800	Rat
2303572	Insul13	Insulin level QTL 13	2		blood insulin amount (VT:0001560)	blood insulin level (CMO:0000349)	8	30144800	75144800	Rat
1300146	Rf17	Renal function QTL 17	2.9		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	8	30918112	75918112	Rat
8662823	Vetf5	Vascular elastic tissue fragility QTL 5	1.9		artery integrity trait (VT:0010639)	patent ductus arteriosus score (CMO:0002566)	8	30918112	107206309	Rat
724514	Uae15	Urinary albumin excretion QTL 15	2.9		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	8	32201981	75971421	Rat
1549908	Neudeg1	Neurodegradation QTL 1	5.5	0	nervous system integrity trait (VT:0010566)	logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)	8	32888352	101374135	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	33558660	65717592	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	33558660	65717592	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	8	33558660	65717592	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	8	33558660	65717592	Rat
1359033	Bp273	Blood pressure QTL 273			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	33558660	65717592	Rat
11556286	Cm81	Cardiac mass QTL 81		0.01	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	8	33558660	65717592	Rat
2313046	Bss78	Bone structure and strength QTL 78	3.5	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	8	33558660	89058369	Rat
2313057	Bss76	Bone structure and strength QTL 76	3	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	8	33558660	89058369	Rat
2313067	Bss77	Bone structure and strength QTL 77	3.1	0.0001	tibia size trait (VT:0100001)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	8	33558660	89058369	Rat
2313088	Bss75	Bone structure and strength QTL 75	3.1	0.0001	body length (VT:0001256)	body length, nose to rump (CMO:0000079)	8	33558660	89058369	Rat
1578765	Klgr1	Kidney lesion grade QTL 1	3.3	0.0001	kidney morphology trait (VT:0002135)	organ lesion measurement (CMO:0000677)	8	33558660	109028082	Rat
1578769	Uae31	Urinary albumin excretion QTL 31	3.3	0.001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	8	33558660	109028082	Rat
1578755	Pur5	Proteinuria QTL 5	3.3	0.0001	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	8	33558660	109028082	Rat
2316950	Scl66	Serum cholesterol level QTL 66	4.1		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	8	33558764	113580387	Rat
1298065	Scl16	Serum cholesterol level QTL 16	3.8		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	8	35041414	80041414	Rat
1582222	Epfw2	Epididymal fat weight QTL 2	3.2	0.0005	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	8	35925594	80925594	Rat
1331838	Niddm61	Non-insulin dependent diabetes mellitus QTL 61	3.53	0.0004	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	8	39230130	106506973	Rat
61358	Bp39	Blood pressure QTL 39	2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	39927901	84927901	Rat
61464	Niddm11	Non-insulin dependent diabetes mellitus QTL 11	3.1	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	8	39958022	84958022	Rat
737824	Hcar10	Hepatocarcinoma resistance QTL 10	2.9		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	8	44219197	89542960	Rat
1358906	Bp253	Blood pressure QTL 253	4	0.0004	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	44219197	100873963	Rat
1554321	Bmd3	Bone mineral density QTL 3	7.9	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	8	44458129	118087517	Rat
1331769	Rf39	Renal function QTL 39	3.871		urine output (VT:0003620)	timed urine volume (CMO:0000260)	8	45712344	80003418	Rat
1298079	Activ2	Activity QTL 2	9.5	0.000001	voluntary movement trait (VT:0003491)	rearing measurement (CMO:0001515)	8	45712344	90712344	Rat
631216	Stl9	Serum triglyceride level QTL 9	4.71	0.0001	blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	8	45712475	75971259	Rat
70161	Bp62	Blood pressure QTL 62	2.9	0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	46588437	96998640	Rat
12879882	Am8	Aortic mass QTL 8		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	8	47200750	106394378	Rat
12879878	Bw183	Body weight QTL 183		0.001	body mass (VT:0001259)	body weight (CMO:0000012)	8	47200750	106394378	Rat
12879879	Cm99	Cardiac mass QTL 99		0.001	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	8	47200750	106394378	Rat
12879880	Cm100	Cardiac mass QTL 100		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	8	47200750	106394378	Rat
12879881	Cm101	Cardiac mass QTL 101		0.001	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	8	47200750	106394378	Rat
12879883	Kidm65	Kidney mass QTL 65		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	8	47200750	106394378	Rat
70197	BpQTLcluster8	Blood pressure QTL cluster 8	3.482		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	50529480	128036471	Rat
70197	BpQTLcluster8	Blood pressure QTL cluster 8	3.482		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	8	50529480	128036471	Rat
70197	BpQTLcluster8	Blood pressure QTL cluster 8	3.482		arterial blood pressure trait (VT:2000000)	absolute change in systolic blood pressure (CMO:0000607)	8	50529480	128036471	Rat
70197	BpQTLcluster8	Blood pressure QTL cluster 8	3.482		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	50529480	128036471	Rat
1331837	Bw23	Body weight QTL 23	4.19	0.00007	body mass (VT:0001259)	body weight (CMO:0000012)	8	50529563	106506973	Rat
2313086	Bss60	Bone structure and strength QTL 60	4.1	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	8	54065044	89058369	Rat
4889938	Bss89	Bone structure and strength QTL 89	3.8		tibia size trait (VT:0100001)	tibia cortical bone volume (CMO:0001725)	8	54065044	89058369	Rat
5684973	Bss100	Bone structure and strength QTL 100	4.7		tibia area (VT:1000281)	tibia area measurement (CMO:0001382)	8	54065044	89058369	Rat
1358912	Bw51	Body weight QTL 51	2.95		body mass (VT:0001259)	body weight (CMO:0000012)	8	55435004	115812386	Rat
2303570	Gluco48	Glucose level QTL 48	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	8	55659105	100659105	Rat
2293697	Bmd39	Bone mineral density QTL 39			femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	8	58230766	106394378	Rat
1582243	Bw66	Body weight QTL 66	3.4	0.0048	body mass (VT:0001259)	body weight (CMO:0000012)	8	58425510	91990535	Rat
1582254	Kidm31	Kidney mass QTL 31	3		kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	8	58425510	91990535	Rat
631664	Hcar3	Hepatocarcinoma resistance QTL 3	2.9	0.0005	liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	8	58425510	106526740	Rat
1300177	Cm2	Cardiac mass QTL 2	3.65		heart mass (VT:0007028)	heart weight (CMO:0000017)	8	59234112	108068306	Rat
2301402	Bp316	Blood pressure QTL 316		0.005	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	61394378	106394378	Rat
10402857	Bp380	Blood pressure QTL 380		0.95	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	61394378	106394378	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	129
Count of miRNA genes:	108
Interacting mature miRNAs:	111
Transcripts:	ENSRNOT00000012091, ENSRNOT00000012295
Prediction methods:	Microtar, Miranda, Rnahybrid
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	43	57	41	19	41	8	11	74	35	39	11	8
Low											2
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_019380	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006243172	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006243174	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008766330	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039082020	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_001839232	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005487908	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005487909	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005487910	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC070947	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473975	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ211615	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ226464	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000198	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	X99337	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	X99338	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000012091 ⟹ ENSRNOP00000012091

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	8	63,379,087 - 63,445,686 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000012295 ⟹ ENSRNOP00000012295

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	8	63,379,190 - 63,445,642 (+)	Ensembl

RefSeq Acc Id:

NM_019380 ⟹ NP_062253

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	8	58,996,902 - 59,063,398 (+)	NCBI
Rnor_6.0	8	63,379,087 - 63,445,690 (+)	NCBI
Rnor_5.0	8	63,149,031 - 63,215,298 (+)	NCBI
RGSC_v3.4	8	62,389,893 - 62,466,128 (+)	RGD
Celera	8	58,456,063 - 58,522,680 (+)	RGD

Sequence:

show sequence

GGGACGGGGGAAGGACGGAGCTCGGCCGCTGCTGCCTCCCTCGTTCACTCCCTCGCGCTCTCGC
CCGCCCCCTCCCTCCCTCCCCTCCCTTCCCCGGGCCCGGGCCCGGACCATTCGCTGCTCGCTCT
CCGGCTAGGGAGGATGTCGGGCTCGTCGCTCCCCGGCGCCCTGGCCCTCTCGCTCTTGCTGGTC
TCTGGCTCGCTCCTCCCAGGGCCAGGCGCTGCTCAGAACGCTGGGTTTGTCAAGTCGCCCATGT
CAGAAACTAAGCTCACAGGGGACGCCTTTGAGCTGTACTGTGATGTGGTCGGGAGTCCCACGCC
AGAGATCCAGTGGTGGTACGCAGAAGTCAACCGGGCAGAGTCTTTCAGACAGCTGTGGGACGGT
GCTCGGAAGCGCCGTGTCACCGTAAACACCGCCTACGGGTCAAACGGCGTGAGTGTGCTGAGAA
TAACCCGGCTCACCTTGGAGGACTCTGGGACTTACGAGTGCAGGGCAAGCAACGACCCCAAACG
GAATGACTTGAGGCAAAACCCTTCCATAACATGGATTCGAGCCCAGGCCACCATAAGCGTCCTT
CAGAAACCAAGAATTGTCACCAGCGAAGAGGTCATTATTCGAGACAGCCTCCTTCCTGTCACCC
TGCAGTGTAACCTCACTTCCAGCTCTCACACCCTTATGTACAGCTACTGGACAAAGAATGGGGT
AGAACTCACTGCCACCCGTAAGAATGCCAGCAACATGGAATACAGGATCAATAAGCCAAGAGCT
GAGGATTCAGGCGAATACCACTGTGTATATCATTTTGTCAGCGCTCCTAAAGCAAATGCCACCA
TTGAAGTGAAAGCTGCTCCTGACATCACTGGCCATAAACGCAGTGAAAACAAAAATGAAGGGCA
GGATGCTATGATGTATTGCAAGTCTGTTGGCTACCCCCACCCGGAATGGATGTGGCGCAAGAAG
GAGAATGGTGTGTTTGAGGAGATTTCCAATAGCTCTGGTCGCTTCTTCATCATCAACAAGGAGA
ATTACACTGAATTGAATATTGTGAATCTCCAAATCACAGAAGATCCTGGAGAGTATGAATGTAA
TGCCACCAACTCCATTGGCTCTGCCTCCGTTTCCACAGTCCTCAGGGTACGGAGCCACCTTGCC
CCACTTTGGCCTTTCTTGGGAATTCTGGCTGAAATCATCATCCTTGTGGTGATCATTGTTGTGT
ATGAGAAGAGGAAGAGGCCAGATGAGGTTCCTGATGCCGGGCCAATGAAAACCAACTCTACCAA
CAATCACAAAGATAAAAACTTGCGCCAGAGAAACACAAATTAAGTACTGCTTTTAATCTCTTTA
GGTTCCTGAAAAATGATGGCAACATGACCTGCTAAGTTTTCTGCTTGGACCTCTTTGGTCTCTC
CCTTTCAAGTGAGCAACACCACAATGACCGTCTAAAGCATGCCTTATTTAGCCTCTCCTATAAG
GGTGACCTAGCCAGGTACATTTTAAACAATGCTTCAGTGTAGAAGGTGTAAACTATTTTGGGGC
TTGATGTGCTGTGAATGTTGCTTTCCCTCCCTTTGTTAAAATATTTAAATAGAAGCGAAAGGTC
CTTTGAGGATCAGATCATGCATGCGCCATTTTTTTACTTATACAGCTGTTAAATTGGCAAAGCT
CTAAATGCACTGCTGCCATCTAGTGATCATTTTGNAAAGTACAGCAAAACCTACAGATATATAC
AGTATATAAATATATATATATTCATATCNCNGGGGGTGGGAGAAATCCAAAATAAAGTCAAAGC
TTGTTTCATTTTTAAGCTGCTGATACTCATTCCTTATTATTTGTTGTCAGATGAGGAAGCTGCA
GTTCTGGTACAAAAAGATGAGAGTATAAACTTAAGTCTGTCATTCTAAGGGCTTACTTACCCTA
TAACTTTAAGAACCTGGAACAGTCCACTGAACGGCTAGAATGAATTGCAGTATATATGTATGAT
TGCTTTTTAAGTGACTATTTTTCCTTTTGTCAAATCATGTAAATTCTGAAATCTTTTGCACTGA
TGTGTCGAACCTTATTCTTGTATATTCAATCAAGGCAACTTTTATAATTTCCCATTTGTTTTCA
ATGACCCTGAAATGTTAATAGCATGGTGATATTCTATGCAACTCTAGTTATACCTTTTGGTTTG
ACACTGTATTTTCACATTGATTTCATGACTGATGATAGATTTTATAACCTGACTGGGTTCTCAT
GCGGTACTAACTGTAGATGCATGTACTTGTGTTCTGTGTAATTATTGAAGTGCAATGGTGTACA
AAAAAAGTGAATTCACCTGTTTTTAACAATAAAACATTGATAAAAAAAAAAAAAAAAAAAAAAA
A

hide sequence

RefSeq Acc Id:

XM_006243172 ⟹ XP_006243234

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	8	58,996,878 - 59,063,402 (+)	NCBI
Rnor_6.0	8	63,379,063 - 63,445,694 (+)	NCBI
Rnor_5.0	8	63,149,031 - 63,215,298 (+)	NCBI

Sequence:

show sequence

TTGGACGCTGCGGCGGTAGGAGGAGGACGGGGAAGGACGGAGCTCGGCCGCTGCTGCCTCCCTC
GTTCACTCCCTCGCGCTCTCGCCCGCCCCCTCCCTCCCTCCCCTCCCTTCCCCGGCCCCGGCCC
CGGCCCATTCGCTGCTCGCTCTCCGGCTAGGGAGGATGTCGGGCTCGTCGCTCCCCGGCGCCCT
GGCCCTCTCGCTCTTGCTGGTCTCTGGCTCGCTCCTCCCAGGGCCAGGCGCTGCTCAGAACGCT
GGGTTTGTCAAGTCGCCCATGTCAGAAACTAAGCTCACAGGGGACGCCTTTGAGCTGTACTGTG
ATGTGGTCGGGAGTCCCACGCCAGAGATCCAGTGGTGGTACGCAGAAGTCAACCGGGCAGAGTC
TTTCAGACAGCTGTGGGACGGTGCTCGGAAGCGCCGTGTCACCGTAAACACCGCCTACGGGTCA
AACGGCGTGAGTGTGCTGAGAATAACCCGGCTCACCTTGGAGGACTCTGGGACTTACGAGTGCA
GGGCAAGCAACGACCCCAAACGGAATGACTTGAGGCAAAACCCTTCCATAACATGGATTCGAGC
CCAGGCCACCATAAGCGTCCTTCAGAAACCAAGAATTGTCACCAGCGAAGAGGTCATTATTCGA
GACAGCCTCCTTCCTGTCACCCTGCAGTGTAACCTCACTTCCAGCTCTCACACCCTTATGTACA
GCTACTGGACAAAGAATGGGGTAGAACTCACTGCCACCCGTAAGAATGCCAGCAACATGGAATA
CAGGATCAATAAGCCAAGAGCTGAGGATTCAGGCGAATACCACTGTGTATATCATTTTGTCAGC
GCTCCTAAAGCAAATGCCACCATTGAAGTGAAAGCTGCTCCTGACATCACTGGCCATAAACGCA
GTGAAAACAAAAATGAAGGGCAGGATGCTATGATGTATTGCAAGTCTGTTGGCTACCCCCACCC
GGAATGGATGTGGCGCAAGAAGGAGAATGGTGTGTTTGAGGAGATTTCCAATAGCTCTGGTCGC
TTCTTCATCATCAACAAGGAGAATTACACTGAATTGAATATTGTGAATCTCCAAATCACAGAAG
ATCCTGGAGAGTATGAATGTAATGCCACCAACTCCATTGGCTCTGCCTCCGTTTCCACAGTCCT
CAGGGTACGGAGCCACCTTGCCCCACTTTGGCCTTTCTTGGGAATTCTGGCTGAAATCATCATC
CTTGTGGTGATCATTGTTGTGTATGAGAAGAGGAAGAGGCCAGATGAGGTTCCTGATGATGATG
AACCAGCCGGGCCAATGAAAACCAACTCTACCAACAATCACAAAGATAAAAACTTGCGCCAGAG
AAACACAAATTAAGTACTGCTTTTAATCTCTTTAGGTTCCTGAAAAATGATGGCAACATGACCT
GCTAAGTTTTCTGCTTGGACCTCTTTGGTCTCTCCCTTTCAAGTGAGCAACACCACAATGACCG
TCTAAAGCATGCCTTATTTAGCCTCTCCTATAAGGGTGACCTAGCCAGGTACATTTTAAACAAT
GCTTCAGTGTAGAAGGTGTAAACTATTTTGGGCTTGATGTGCTGTGAATGTTGCTTTCCCTCCC
TTTGTTAAAATATTTAAATAGAAGCGAAAGGTCCTTTGAGGATCAGATCATGCATGCGCCATTT
TTTACTTATACAGCTGTTAAATTGGCAAAGCTCTAAATGCACTGCTGCCATCTAGTGATCATTT
TGTAAAGTACAGCAAAACCTACAGATATATACAGTATATAAATATATATATATTTATATTTTTG
GGGGTGGGAGAAATCCAAAATAAAGTCAAAGCTTGTTTCATTTTTAAGCTGCTGATACTCATTC
CTTATTATTTGTTGTCAGATGAGGAAGCTGCAGTTCTGGTACAAAAAGATGAGAGTATAAACTT
AAGTCTGTCATTCTAAGGGCTTACTTACCCTATAACTTTAAGAACCTGGAACAGTCCACTGAAC
GGCTAGAATGAATTGCAGTATATATGTATGATTGCTTTTTAAGTGACTATTTTTCCTTTTGTCA
AATCATGTAAATTCTGAAATCTTTTGCACTGATGTGTCGAACCTTATTCTTGTATATTCAATCA
AGGCAACTTTTATAATTTCCCATTTGTTTTCAATGACCCTGAAATGTTAATAGCATGGTGATAT
TCTATGCAACTCTAGTTATACCTTTTGGTTTGACACTGTATTTTCACATTGATTTCATGACTGA
TGATAGATTTTATAACCTGACTGGGTTCTCATGCGGTACTAACTGTAGATGCATGTACTTGTGT
TCTGTGTAATTATTGAAGTGCAATGGTGTACAAAAAAAGTGAATTCACCTGTTTTTAACAATAA
AACATTGATAAAAGGTG

hide sequence

RefSeq Acc Id:

XM_006243174 ⟹ XP_006243236

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	8	58,996,878 - 59,063,390 (+)	NCBI
Rnor_6.0	8	63,379,063 - 63,445,694 (+)	NCBI
Rnor_5.0	8	63,149,031 - 63,215,298 (+)	NCBI

Sequence:

show sequence

TTGGACGCTGCGGCGGTAGGAGGAGGACGGGGAAGGACGGAGCTCGGCCGCTGCTGCCTCCCTC
GTTCACTCCCTCGCGCTCTCGCCCGCCCCCTCCCTCCCTCCCCTCCCTTCCCCGGCCCCGGCCC
CGGCCCATTCGCTGCTCGCTCTCCGGCTAGGGAGGATGTCGGGCTCGTCGCTCCCCGGCGCCCT
GGCCCTCTCGCTCTTGCTGGTCTCTGGCTCGCTCCTCCCAGGGCCAGGCGCTGCTCAGAACGAA
CCAAGAATTGTCACCAGCGAAGAGGTCATTATTCGAGACAGCCTCCTTCCTGTCACCCTGCAGT
GTAACCTCACTTCCAGCTCTCACACCCTTATGTACAGCTACTGGACAAAGAATGGGGTAGAACT
CACTGCCACCCGTAAGAATGCCAGCAACATGGAATACAGGATCAATAAGCCAAGAGCTGAGGAT
TCAGGCGAATACCACTGTGTATATCATTTTGTCAGCGCTCCTAAAGCAAATGCCACCATTGAAG
TGAAAGCTGCTCCTGACATCACTGGCCATAAACGCAGTGAAAACAAAAATGAAGGGCAGGATGC
TATGATGTATTGCAAGTCTGTTGGCTACCCCCACCCGGAATGGATGTGGCGCAAGAAGGAGAAT
GGTGTGTTTGAGGAGATTTCCAATAGCTCTGGTCGCTTCTTCATCATCAACAAGGAGAATTACA
CTGAATTGAATATTGTGAATCTCCAAATCACAGAAGATCCTGGAGAGTATGAATGTAATGCCAC
CAACTCCATTGGCTCTGCCTCCGTTTCCACAGTCCTCAGGGTACGGAGCCACCTTGCCCCACTT
TGGCCTTTCTTGGGAATTCTGGCTGAAATCATCATCCTTGTGGTGATCATTGTTGTGTATGAGA
AGAGGAAGAGGCCAGATGAGGTTCCTGATGATGATGAACCAGCCGGGCCAATGAAAACCAACTC
TACCAACAATCACAAAGATAAAAACTTGCGCCAGAGAAACACAAATTAAGTACTGCTTTTAATC
TCTTTAGGTTCCTGAAAAATGATGGCAACATGACCTGCTAAGTTTTCTGCTTGGACCTCTTTGG
TCTCTCCCTTTCAAGTGAGCAACACCACAATGACCGTCTAAAGCATGCCTTATTTAGCCTCTCC
TATAAGGGTGACCTAGCCAGGTACATTTTAAACAATGCTTCAGTGTAGAAGGTGTAAACTATTT
TGGGCTTGATGTGCTGTGAATGTTGCTTTCCCTCCCTTTGTTAAAATATTTAAATAGAAGCGAA
AGGTCCTTTGAGGATCAGATCATGCATGCGCCATTTTTTACTTATACAGCTGTTAAATTGGCAA
AGCTCTAAATGCACTGCTGCCATCTAGTGATCATTTTGTAAAGTACAGCAAAACCTACAGATAT
ATACAGTATATAAATATATATATATTTATATTTTTGGGGGTGGGAGAAATCCAAAATAAAGTCA
AAGCTTGTTTCATTTTTAAGCTGCTGATACTCATTCCTTATTATTTGTTGTCAGATGAGGAAGC
TGCAGTTCTGGTACAAAAAGATGAGAGTATAAACTTAAGTCTGTCATTCTAAGGGCTTACTTAC
CCTATAACTTTAAGAACCTGGAACAGTCCACTGAACGGCTAGAATGAATTGCAGTATATATGTA
TGATTGCTTTTTAAGTGACTATTTTTCCTTTTGTCAAATCATGTAAATTCTGAAATCTTTTGCA
CTGATGTGTCGAACCTTATTCTTGTATATTCAATCAAGGCAACTTTTATAATTTCCCATTTGTT
TTCAATGACCCTGAAATGTTAATAGCATGGTGATATTCTATGCAACTCTAGTTATACCTTTTGG
TTTGACACTGTATTTTCACATTGATTTCATGACTGATGATAGATTTTATAACCTGACTGGGTTC
TCATGCGGTACTAACTGTAGATGCATGTACTTGTGTTCTGTGTAATTATTGAAGTGCAATGGTG
TACAAAAAAAGTGAATTCACCTGTTTTTAACAATAAAACATTGATAAAAGGTG

hide sequence

RefSeq Acc Id:

XM_008766330 ⟹ XP_008764552

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	8	58,996,915 - 59,063,398 (+)	NCBI
Rnor_6.0	8	63,379,063 - 63,445,694 (+)	NCBI

Sequence:

show sequence

TTGGACGCTGCGGCGGTAGGAGGAGGACGGGGAAGGACGGAGCTCGGCCGCTGCTGCCTCCCTC
GTTCACTCCCTCGCGCTCTCGCCCGCCCCCTCCCTCCCTCCCCTCCCTTCCCCGGCCCCGGCCC
CGGCCCATTCGCTGCTCGCTCTCCGGCTAGGGAGGATGTCGGGCTCGTCGCTCCCCGGCGCCCT
GGCCCTCTCGCTCTTGCTGGTCTCTGGCTCGCTCCTCCCAGGGCCAGGCGCTGCTCAGAACGAA
CCAAGAATTGTCACCAGCGAAGAGGTCATTATTCGAGACAGCCTCCTTCCTGTCACCCTGCAGT
GTAACCTCACTTCCAGCTCTCACACCCTTATGTACAGCTACTGGACAAAGAATGGGGTAGAACT
CACTGCCACCCGTAAGAATGCCAGCAACATGGAATACAGGATCAATAAGCCAAGAGCTGAGGAT
TCAGGCGAATACCACTGTGTATATCATTTTGTCAGCGCTCCTAAAGCAAATGCCACCATTGAAG
TGAAAGCTGCTCCTGACATCACTGGCCATAAACGCAGTGAAAACAAAAATGAAGGGCAGGATGC
TATGATGTATTGCAAGTCTGTTGGCTACCCCCACCCGGAATGGATGTGGCGCAAGAAGGAGAAT
GGTGTGTTTGAGGAGATTTCCAATAGCTCTGGTCGCTTCTTCATCATCAACAAGGAGAATTACA
CTGAATTGAATATTGTGAATCTCCAAATCACAGAAGATCCTGGAGAGTATGAATGTAATGCCAC
CAACTCCATTGGCTCTGCCTCCGTTTCCACAGTCCTCAGGGTACGGAGCCACCTTGCCCCACTT
TGGCCTTTCTTGGGAATTCTGGCTGAAATCATCATCCTTGTGGTGATCATTGTTGTGTATGAGA
AGAGGAAGAGGCCAGATGAGGTTCCTGATGCCGGGCCAATGAAAACCAACTCTACCAACAATCA
CAAAGATAAAAACTTGCGCCAGAGAAACACAAATTAAGTACTGCTTTTAATCTCTTTAGGTTCC
TGAAAAATGATGGCAACATGACCTGCTAAGTTTTCTGCTTGGACCTCTTTGGTCTCTCCCTTTC
AAGTGAGCAACACCACAATGACCGTCTAAAGCATGCCTTATTTAGCCTCTCCTATAAGGGTGAC
CTAGCCAGGTACATTTTAAACAATGCTTCAGTGTAGAAGGTGTAAACTATTTTGGGCTTGATGT
GCTGTGAATGTTGCTTTCCCTCCCTTTGTTAAAATATTTAAATAGAAGCGAAAGGTCCTTTGAG
GATCAGATCATGCATGCGCCATTTTTTACTTATACAGCTGTTAAATTGGCAAAGCTCTAAATGC
ACTGCTGCCATCTAGTGATCATTTTGTAAAGTACAGCAAAACCTACAGATATATACAGTATATA
AATATATATATATTTATATTTTTGGGGGTGGGAGAAATCCAAAATAAAGTCAAAGCTTGTTTCA
TTTTTAAGCTGCTGATACTCATTCCTTATTATTTGTTGTCAGATGAGGAAGCTGCAGTTCTGGT
ACAAAAAGATGAGAGTATAAACTTAAGTCTGTCATTCTAAGGGCTTACTTACCCTATAACTTTA
AGAACCTGGAACAGTCCACTGAACGGCTAGAATGAATTGCAGTATATATGTATGATTGCTTTTT
AAGTGACTATTTTTCCTTTTGTCAAATCATGTAAATTCTGAAATCTTTTGCACTGATGTGTCGA
ACCTTATTCTTGTATATTCAATCAAGGCAACTTTTATAATTTCCCATTTGTTTTCAATGACCCT
GAAATGTTAATAGCATGGTGATATTCTATGCAACTCTAGTTATACCTTTTGGTTTGACACTGTA
TTTTCACATTGATTTCATGACTGATGATAGATTTTATAACCTGACTGGGTTCTCATGCGGTACT
AACTGTAGATGCATGTACTTGTGTTCTGTGTAATTATTGAAGTGCAATGGTGTACAAAAAAAGT
GAATTCACCTGTTTTTAACAATAAAACATTGATAAAAGGTG

hide sequence

RefSeq Acc Id:

XM_039082020 ⟹ XP_038937948

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	8	58,996,876 - 59,054,621 (+)	NCBI

RefSeq Acc Id:

XR_001839232

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	8	63,379,062 - 63,443,349 (+)	NCBI

Sequence:

show sequence

CTTGGACGCTGCGGCGGTAGGAGGAGGACGGGGAAGGACGGAGCTCGGCCGCTGCTGCCTCCCT
CGTTCACTCCCTCGCGCTCTCGCCCGCCCCCTCCCTCCCTCCCCTCCCTTCCCCGGCCCCGGCC
CCGGCCCATTCGCTGCTCGCTCTCCGGCTAGGGAGGATGTCGGGCTCGTCGCTCCCCGGCGCCC
TGGCCCTCTCGCTCTTGCTGGTCTCTGGCTCGCTCCTCCCAGGGCCAGGCGCTGCTCAGAACGC
TGGGTTTGTCAAGTCGCCCATGTCAGAAACTAAGCTCACAGGGGACGCCTTTGAGCTGTACTGT
GATGTGGTCGGGAGTCCCACGCCAGAGATCCAGTGGTGGTACGCAGAAGTCAACCGGGCAGAGT
CTTTCAGACAGCTGTGGGACGGTGCTCGGAAGCGCCGTGTCACCGTAAACACCGCCTACGGGTC
AAACGGCGTGAGTGTGCTGAGAATAACCCGGCTCACCTTGGAGGACTCTGGGACTTACGAGTGC
AGGGCAAGCAACGACCCCAAACGGAATGACTTGAGGCAAAACCCTTCCATAACATGGATTCGAG
CCCAGGCCACCATAAGCGTCCTTCAGAAACCAAGAATTGTCACCAGCGAAGAGGTCATTATTCG
AGACAGCCTCCTTCCTGTCACCCTGCAGTGTAACCTCACTTCCAGCTCTCACACCCTTATGTAC
AGCTACTGGACAAAGAATGGGGTAGAACTCACTGCCACCCGTAAGAATGCCAGCAACATGGAAT
ACAGGATCAATAAGCCAAGAGCTGAGGATTCAGGCGAATACCACTGTGTATATCATTTTGTCAG
CGCTCCTAAAGCAAATGCCACCATTGAAGTGAAAGCTGCTCCTGACATCACTGGCCATAAACGC
AGTGAAAACAAAAATGAAGGGCAGGATGCTATGATGTATTGCAAGTCTGTTGGCTACCCCCACC
CGGAATGGATGTGGCGCAAGAAGGAGAATGGTGTGTTTGAGGAGATTTCCAATAGCTCTGGTCG
CTTCTTCATCATCAACAAGGAGAATTACACTGAATTGAATATTGTGAATCTCCAAATCACAGAA
GATCCTGGAGAGTATGAATGTAATGCCACCAACTCCATTGGCTCTGCCTCCGTTTCCACAGTCC
TCAGGGTACGGAGCCACCTTGCCCCACTTTGGCCTTTCTTGGGAATTCTGGCTGAAATCATCAT
CCTTGTGGTGATCATTGTTGTGTATGAGAAGAGGAAGAGGCCAGATGAGGTTCCTGATGATCAT
CAGGCAGATTGAGCTTGAGGAGAATCCAAGTCAAGCCTAGAAGCCACCCCAAGATCACAGGCCA
CCTGTTCTTTCAGGCAGATTTAAGATGATGAACCAGCCGGGCCAAT

hide sequence

RefSeq Acc Id:

XR_005487908

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	8	58,996,876 - 59,063,402 (+)	NCBI

RefSeq Acc Id:

XR_005487909

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	8	58,996,876 - 59,063,390 (+)	NCBI

RefSeq Acc Id:

XR_005487910

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	8	58,996,876 - 59,063,402 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_062253	(Get FASTA)	NCBI Sequence Viewer
	XP_006243234	(Get FASTA)	NCBI Sequence Viewer
	XP_006243236	(Get FASTA)	NCBI Sequence Viewer
	XP_008764552	(Get FASTA)	NCBI Sequence Viewer
	XP_038937948	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH70947	(Get FASTA)	NCBI Sequence Viewer
	CAA67711	(Get FASTA)	NCBI Sequence Viewer
	CAA67712	(Get FASTA)	NCBI Sequence Viewer
	EDL95683	(Get FASTA)	NCBI Sequence Viewer
	EDL95684	(Get FASTA)	NCBI Sequence Viewer
	EDL95685	(Get FASTA)	NCBI Sequence Viewer
	P97546	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_062253 ⟸ NM_019380
- Peptide Label:	precursor
- UniProtKB:	P97546 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MSGSSLPGALALSLLLVSGSLLPGPGAAQNAGFVKSPMSETKLTGDAFELYCDVVGSPTPEIQW WYAEVNRAESFRQLWDGARKRRVTVNTAYGSNGVSVLRITRLTLEDSGTYECRASNDPKRNDLR QNPSITWIRAQATISVLQKPRIVTSEEVIIRDSLLPVTLQCNLTSSSHTLMYSYWTKNGVELTA TRKNASNMEYRINKPRAEDSGEYHCVYHFVSAPKANATIEVKAAPDITGHKRSENKNEGQDAMM YCKSVGYPHPEWMWRKKENGVFEEISNSSGRFFIINKENYTELNIVNLQITEDPGEYECNATNS IGSASVSTVLRVRSHLAPLWPFLGILAEIIILVVIIVVYEKRKRPDEVPDAGPMKTNSTNNHKD KNLRQRNTN hide sequence

RefSeq Acc Id:	XP_006243236 ⟸ XM_006243174
- Peptide Label:	isoform X3
- UniProtKB:	P97546 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MSGSSLPGALALSLLLVSGSLLPGPGAAQNEPRIVTSEEVIIRDSLLPVTLQCNLTSSSHTLMY SYWTKNGVELTATRKNASNMEYRINKPRAEDSGEYHCVYHFVSAPKANATIEVKAAPDITGHKR SENKNEGQDAMMYCKSVGYPHPEWMWRKKENGVFEEISNSSGRFFIINKENYTELNIVNLQITE DPGEYECNATNSIGSASVSTVLRVRSHLAPLWPFLGILAEIIILVVIIVVYEKRKRPDEVPDDD EPAGPMKTNSTNNHKDKNLRQRNTN hide sequence

RefSeq Acc Id:

XP_006243234 ⟸ XM_006243172

- Peptide Label:

isoform X1

- Sequence:

show sequence

MSGSSLPGALALSLLLVSGSLLPGPGAAQNAGFVKSPMSETKLTGDAFELYCDVVGSPTPEIQW
WYAEVNRAESFRQLWDGARKRRVTVNTAYGSNGVSVLRITRLTLEDSGTYECRASNDPKRNDLR
QNPSITWIRAQATISVLQKPRIVTSEEVIIRDSLLPVTLQCNLTSSSHTLMYSYWTKNGVELTA
TRKNASNMEYRINKPRAEDSGEYHCVYHFVSAPKANATIEVKAAPDITGHKRSENKNEGQDAMM
YCKSVGYPHPEWMWRKKENGVFEEISNSSGRFFIINKENYTELNIVNLQITEDPGEYECNATNS
IGSASVSTVLRVRSHLAPLWPFLGILAEIIILVVIIVVYEKRKRPDEVPDDDEPAGPMKTNSTN
NHKDKNLRQRNTN

hide sequence

RefSeq Acc Id:	XP_008764552 ⟸ XM_008766330
- Peptide Label:	isoform X4
- UniProtKB:	P97546 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MSGSSLPGALALSLLLVSGSLLPGPGAAQNEPRIVTSEEVIIRDSLLPVTLQCNLTSSSHTLMY SYWTKNGVELTATRKNASNMEYRINKPRAEDSGEYHCVYHFVSAPKANATIEVKAAPDITGHKR SENKNEGQDAMMYCKSVGYPHPEWMWRKKENGVFEEISNSSGRFFIINKENYTELNIVNLQITE DPGEYECNATNSIGSASVSTVLRVRSHLAPLWPFLGILAEIIILVVIIVVYEKRKRPDEVPDAG PMKTNSTNNHKDKNLRQRNTN hide sequence

RefSeq Acc Id:

ENSRNOP00000012295 ⟸ ENSRNOT00000012295

RefSeq Acc Id:

ENSRNOP00000012091 ⟸ ENSRNOT00000012091

RefSeq Acc Id:	XP_038937948 ⟸ XM_039082020
- Peptide Label:	isoform X2

Protein Domains

Ig-like

Transcriptome

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

Promoters

RGD ID:

13696044

Promoter ID:

EPDNEW_R6559

Type:

multiple initiation site

Name:

Nptn_1

Description:

neuroplastin

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	8	63,379,197 - 63,379,257	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

FHL/EurMcwi (RGD)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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:620296	AgrOrtholog
Ensembl Genes	ENSRNOG00000009029	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000012091	ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOP00000012295	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000012091	ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOT00000012295	UniProtKB/Swiss-Prot
Gene3D-CATH	2.60.40.10	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7103647	IMAGE-MGC_LOAD
InterPro	Basigin-like	UniProtKB/Swiss-Prot
	Ig-like_dom	UniProtKB/Swiss-Prot
	Ig-like_dom_sf	UniProtKB/Swiss-Prot
	Ig-like_fold	UniProtKB/Swiss-Prot
	Ig_sub	UniProtKB/Swiss-Prot
	Ig_sub2	UniProtKB/Swiss-Prot
	Neuroplastin/Basigin	UniProtKB/Swiss-Prot
KEGG Report	rno:56064	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:91715	IMAGE-MGC_LOAD
NCBI Gene	56064	ENTREZGENE
PANTHER	PTHR10075	UniProtKB/Swiss-Prot
	PTHR10075:SF5	UniProtKB/Swiss-Prot
PhenoGen	Nptn	PhenoGen
PROSITE	IG_LIKE	UniProtKB/Swiss-Prot
SMART	IGc2	UniProtKB/Swiss-Prot
	SM00409	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF48726	UniProtKB/Swiss-Prot
UniProt	NPTN_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary	P97547	UniProtKB/Swiss-Prot
	Q6IRE8	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-02-22	Nptn	neuroplastin	Sdfr1	stromal cell derived factor receptor 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2004-02-26	Sdfr1	stromal cell derived factor receptor 1			Symbol and Name status set to approved	625702	APPROVED
2002-08-07	Sdfr1	stromal cell derived factor receptor 1			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_domains	contains Ig domains	634005
gene_expression	expressed specifically in brain	634005

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

Send us a Message

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD