Ncstn (nicastrin) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Ncstn (nicastrin) Rattus norvegicus
Analyze
Symbol: Ncstn
Name: nicastrin
RGD ID: 631418
Description: Enables peptidase activity. Involved in cerebellum development and protein processing. Located in several cellular components, including cytoplasmic vesicle; lysosomal membrane; and sarcolemma. Is integral component of presynaptic membrane. Part of protein-containing complex. Human ortholog(s) of this gene implicated in Alzheimer's disease; hidradenitis suppurativa; and schizophrenia. Orthologous to human NCSTN (nicastrin); PARTICIPATES IN Notch signaling pathway; syndecan signaling pathway; Alzheimer's disease pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21384,530,442 - 84,546,454 (-)NCBI
Rnor_6.0 Ensembl1390,451,044 - 90,467,256 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01390,451,046 - 90,467,256 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01394,974,010 - 94,990,220 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41388,060,484 - 88,076,493 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11388,249,971 - 88,265,285 (-)NCBI
Celera1384,142,219 - 84,158,230 (-)NCBICelera
Cytogenetic Map13q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Confaloni A, etal., Neurosci Lett. 2003 Dec 15;353(1):61-5.
2. Dermaut B, etal., Am J Hum Genet. 2002 Jun;70(6):1568-74. Epub 2002 Apr 24.
3. Dries DR, etal., J Biol Chem. 2016 May 27;291(22):11647-56. doi: 10.1074/jbc.M116.715078. Epub 2016 Mar 23.
4. Fiuza UM and Arias AM, J Endocrinol. 2007 Sep;194(3):459-74.
5. Frykman S, etal., PLoS One. 2010 Jan 28;5(1):e8948. doi: 10.1371/journal.pone.0008948.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. GOA data from the GO Consortium
8. Goo JS, etal., Mol Neurobiol. 2013 Aug;48(1):232-43. doi: 10.1007/s12035-013-8453-3. Epub 2013 Apr 18.
9. Gwon AR, etal., Aging Cell. 2012 Aug;11(4):559-68. doi: 10.1111/j.1474-9726.2012.00817.x. Epub 2012 Apr 9.
10. Hansson CA, etal., J Biol Chem 2004 Dec 3;279(49):51654-60. Epub 2004 Sep 28.
11. Leong DW, etal., J Biol Chem. 2012 Jun 8;287(24):20652-63. Epub 2012 Apr 25.
12. Lupton MK, etal., PLoS One. 2011 Feb 25;6(2):e17298. doi: 10.1371/journal.pone.0017298.
13. Ma Z, etal., Neurosci Lett. 2009 Jul 24;458(3):136-9. doi: 10.1016/j.neulet.2009.04.048. Epub 2009 Apr 24.
14. MGD data from the GO Consortium
15. Nadler Y, etal., Glia. 2008 Apr;56(5):552-67. doi: 10.1002/glia.20638.
16. OMIM Disease Annotation Pipeline
17. Orlacchio A, etal., Neurosci Lett. 2004 Jun 3;363(1):49-53. doi: 10.1016/j.neulet.2004.03.044.
18. Pasternak SH, etal., J Biol Chem 2003 Jul 18;278(29):26687-94.
19. Pipeline to import KEGG annotations from KEGG into RGD
20. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
21. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
22. RGD automated import pipeline for gene-chemical interactions
23. Sakuma K, etal., Biochim Biophys Acta. 2006 Jun;1760(6):980-7. Epub 2006 Mar 7.
24. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
25. Uchihara T, etal., Neurobiol Aging. 2006 Jan;27(1):88-97. doi: 10.1016/j.neurobiolaging.2004.12.011. Epub 2005 Mar 31.
26. Vetrivel KS, etal., J Biol Chem 2004 Oct 22;279(43):44945-54. Epub 2004 Aug 17.
27. Zhong L, etal., Eur J Neurosci. 2009 Nov;30(9):1831-6. doi: 10.1111/j.1460-9568.2009.06942.x. Epub 2009 Oct 14.
Additional References at PubMed
PMID:11943765   PMID:12297508   PMID:12646573   PMID:15274632   PMID:15634781   PMID:15886206   PMID:15893582   PMID:17222950   PMID:17897319   PMID:17913918   PMID:18201567   PMID:19056867  
PMID:19457123   PMID:19494151   PMID:19946888   PMID:20458337   PMID:21187406   PMID:21423176   PMID:21597003   PMID:22086926   PMID:22771797   PMID:23376485   PMID:23826707   PMID:24889619  
PMID:25043039   PMID:25438880   PMID:25592972   PMID:26094765   PMID:26280335   PMID:29176823  


Genomics

Comparative Map Data
Ncstn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21384,530,442 - 84,546,454 (-)NCBI
Rnor_6.0 Ensembl1390,451,044 - 90,467,256 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01390,451,046 - 90,467,256 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01394,974,010 - 94,990,220 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41388,060,484 - 88,076,493 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11388,249,971 - 88,265,285 (-)NCBI
Celera1384,142,219 - 84,158,230 (-)NCBICelera
Cytogenetic Map13q24NCBI
NCSTN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1160,343,316 - 160,358,952 (+)EnsemblGRCh38hg38GRCh38
GRCh381160,343,328 - 160,358,949 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371160,313,173 - 160,328,739 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361158,579,687 - 158,595,366 (+)NCBINCBI36hg18NCBI36
Build 341157,126,134 - 157,141,811NCBI
Celera1133,381,822 - 133,397,500 (+)NCBI
Cytogenetic Map1q23.2NCBI
HuRef1131,669,200 - 131,684,875 (+)NCBIHuRef
CHM1_11161,708,406 - 161,724,081 (+)NCBICHM1_1
Ncstn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391171,893,580 - 171,910,356 (-)NCBIGRCm39mm39
GRCm39 Ensembl1171,893,580 - 171,910,362 (-)Ensembl
GRCm381172,066,013 - 172,082,789 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1172,066,013 - 172,082,795 (-)EnsemblGRCm38mm10GRCm38
MGSCv371173,996,144 - 174,012,880 (-)NCBIGRCm37mm9NCBIm37
MGSCv361173,902,773 - 173,919,369 (-)NCBImm8
Celera1174,920,243 - 174,937,040 (-)NCBICelera
Cytogenetic Map1H3NCBI
cM Map179.54NCBI
Ncstn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546812,111,078 - 12,127,033 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495546812,111,078 - 12,126,404 (+)NCBIChiLan1.0ChiLan1.0
NCSTN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11139,618,229 - 139,633,911 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1139,618,229 - 139,633,911 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01135,697,592 - 135,713,293 (+)NCBIMhudiblu_PPA_v0panPan3
NCSTN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13821,878,071 - 21,891,362 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3821,685,868 - 21,892,097 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3821,951,865 - 21,966,592 (-)NCBI
ROS_Cfam_1.03821,994,646 - 22,009,338 (-)NCBI
UMICH_Zoey_3.13821,899,466 - 21,914,196 (-)NCBI
UNSW_CanFamBas_1.03822,295,995 - 22,310,753 (-)NCBI
UU_Cfam_GSD_1.03822,705,808 - 22,720,574 (-)NCBI
Ncstn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244050586,452,618 - 6,468,725 (+)NCBI
SpeTri2.0NW_004936740285,789 - 301,918 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NCSTN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl490,118,998 - 90,142,890 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1490,121,209 - 90,142,934 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2498,011,639 - 98,033,364 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NCSTN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1203,590,044 - 3,606,205 (-)NCBI
ChlSab1.1 Ensembl203,590,725 - 3,606,066 (-)Ensembl
Vero_WHO_p1.0NW_0236660382,647,801 - 2,663,966 (-)NCBI
Ncstn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624794908,227 - 923,474 (-)NCBI

Position Markers
RH127477  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21384,530,552 - 84,530,739 (+)MAPPER
Rnor_6.01390,451,157 - 90,451,343NCBIRnor6.0
Rnor_5.01394,974,121 - 94,974,307UniSTSRnor5.0
RGSC_v3.41388,060,595 - 88,060,781UniSTSRGSC3.4
Celera1384,142,330 - 84,142,516UniSTS
RH 3.4 Map13551.9UniSTS
Cytogenetic Map13q24UniSTS
RH140256  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21384,530,607 - 84,530,827 (+)MAPPER
Rnor_6.01390,451,212 - 90,451,431NCBIRnor6.0
Rnor_5.01394,974,176 - 94,974,395UniSTSRnor5.0
RGSC_v3.41388,060,650 - 88,060,869UniSTSRGSC3.4
Celera1384,142,385 - 84,142,604UniSTS
RH 3.4 Map13552.5UniSTS
Cytogenetic Map13q24UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131107975663Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1335301263107975663Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133614753399968921Rat
10755495Bp387Blood pressure QTL 3873.78arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133950130093652524Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134567662990676629Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)135108098996080989Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135156924896569248Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)135157782490675199Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1357903612102903612Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1362975663107975663Rat
738026Lnnr5Liver neoplastic nodule remodeling QTL 53.29liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)136500824591629354Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1366971778111971778Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1371230858114033958Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1371230858114033958Rat
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1372583716114033958Rat
1300166Kidm6Kidney mass QTL 63.93kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)137456837892916783Rat
1331783Bp221Blood pressure QTL 2213.72886arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)137456837892916783Rat
8655945Rf61Renal function QTL 613.6blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)137456837892916783Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)777694986114033958Rat
8655959Pur32Proteinuria QTL 328.4total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1379567081103613733Rat
738027Lnnr6Liver neoplastic nodule remodeling QTL 63.3liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)138040355991629354Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1380403559108770687Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1386833393114033958Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:403
Count of miRNA genes:205
Interacting mature miRNAs:242
Transcripts:ENSRNOT00000008150
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_174864 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006250283 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769733 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769734 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769735 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090515 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090516 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001840772 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005492222 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF510722 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY101378 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC074006 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC167747 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473985 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212793 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000245 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000008150   ⟹   ENSRNOP00000008150
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1390,451,053 - 90,467,256 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081534   ⟹   ENSRNOP00000075174
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1390,451,044 - 90,467,235 (-)Ensembl
RefSeq Acc Id: NM_174864   ⟹   NP_777353
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21384,530,442 - 84,546,454 (-)NCBI
Rnor_6.01390,451,046 - 90,467,256 (-)NCBI
Rnor_5.01394,974,010 - 94,990,220 (-)NCBI
RGSC_v3.41388,060,484 - 88,076,493 (-)RGD
Celera1384,142,219 - 84,158,230 (-)RGD
Sequence:
RefSeq Acc Id: XM_039090515   ⟹   XP_038946443
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21384,530,442 - 84,546,419 (-)NCBI
RefSeq Acc Id: XM_039090516   ⟹   XP_038946444
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21384,530,442 - 84,546,433 (-)NCBI
RefSeq Acc Id: XR_005492222
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21384,531,106 - 84,546,440 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_777353   ⟸   NM_174864
- Peptide Label: precursor
- UniProtKB: Q8CGU6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008150   ⟸   ENSRNOT00000008150
RefSeq Acc Id: ENSRNOP00000075174   ⟸   ENSRNOT00000081534
RefSeq Acc Id: XP_038946444   ⟸   XM_039090516
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038946443   ⟸   XM_039090515
- Peptide Label: isoform X1
Protein Domains
Ncstrn_small

Transcriptome

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

Promoters
RGD ID:13699033
Promoter ID:EPDNEW_R9542
Type:initiation region
Name:Ncstn_1
Description:nicastrin
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01390,467,172 - 90,467,232EPDNEW

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

Database Acc Id Source(s)
AGR Gene RGD:631418 AgrOrtholog
Ensembl Genes ENSRNOG00000005355 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000008150 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000075174 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008150 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000081534 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7103372 IMAGE-MGC_LOAD
  IMAGE:8365089 IMAGE-MGC_LOAD
InterPro Ncstrn_small UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nicastrin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:289231 UniProtKB/Swiss-Prot
MGC_CLONE MGC:187272 IMAGE-MGC_LOAD
  MGC:91413 IMAGE-MGC_LOAD
NCBI Gene 289231 ENTREZGENE
PANTHER PTHR21092 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Ncstrn_small UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ncstn PhenoGen
UniProt B3DM90_RAT UniProtKB/TrEMBL
  NICA_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q8CH12 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-11 Ncstn  nicastrin      Symbol and Name status set to approved 625702 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization co-localized with APP to the lysosomal membrane 724403