Ncam1 (neural cell adhesion molecule 1) - Rat Genome Database

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Gene: Ncam1 (neural cell adhesion molecule 1) Rattus norvegicus
Analyze
Symbol: Ncam1
Name: neural cell adhesion molecule 1
RGD ID: 67378
Description: Enables LRR domain binding activity and phosphatase binding activity. Involved in several processes, including axon development; positive regulation of cardiac muscle cell proliferation; and thalamus development. Located in glutamatergic synapse; neuronal cell body; and plasma membrane. Is integral component of postsynaptic membrane and integral component of presynaptic membrane. Is active in Schaffer collateral - CA1 synapse. Used to study middle cerebral artery infarction. Biomarker of Alzheimer's disease; congestive heart failure; hypothyroidism; mental depression; and myocardial infarction. Human ortholog(s) of this gene implicated in bipolar disorder; middle cerebral artery infarction; and pancreatic cancer. Orthologous to human NCAM1 (neural cell adhesion molecule 1); PARTICIPATES IN fibroblast growth factor signaling pathway; prion disease pathway; INTERACTS WITH 1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Cd56; Cell adhesion molecule neural (CD56); cell adhesion molecule, neural (CD56); MGC124601; N-CAM; N-CAM-1; Ncam; NCAM-1; NCAM-C; NCAMC; neural cell adhesion molecule
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2849,865,629 - 50,165,687 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl849,865,633 - 50,166,014 (-)Ensembl
Rnor_6.0853,836,797 - 54,134,881 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl853,839,098 - 53,901,358 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0852,456,154 - 52,755,707 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4852,822,350 - 53,120,572 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1852,841,403 - 53,139,626 (-)NCBI
Celera849,420,106 - 49,716,981 (-)NCBICelera
RH 3.4 Map8537.1RGD
Cytogenetic Map8q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine  (EXP)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-methylcholine  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-methylcholanthrene  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-azacytidine  (EXP)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antimycin A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (ISO)
azoxystrobin  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
camptothecin  (ISO)
chlorpyrifos  (EXP,ISO)
choline  (ISO)
cimetidine  (ISO)
curcumin  (EXP)
cyclosporin A  (ISO)
cypermethrin  (EXP)
dichloromethane  (EXP)
dioxygen  (ISO)
disodium selenite  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
ethylbenzene  (EXP)
fipronil  (EXP)
flavonoids  (EXP)
fluoxetine  (EXP)
folic acid  (ISO)
fonofos  (ISO)
furan  (EXP)
gamma-aminobutyric acid  (EXP)
genistein  (ISO)
kainic acid  (EXP,ISO)
L-methionine  (ISO)
lead nitrate  (EXP)
lead(0)  (EXP,ISO)
lead(2+)  (EXP,ISO)
lead(II) chloride  (EXP)
mercury dibromide  (ISO)
methapyrilene  (ISO)
methylmercury chloride  (ISO)
morphine  (EXP)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
nickel dichloride  (ISO)
nicotine  (ISO)
nitrofen  (EXP)
nitroglycerin  (EXP)
ozone  (ISO)
p-chloromercuribenzoic acid  (ISO)
paracetamol  (ISO)
parathion  (ISO)
PCB138  (EXP)
perfluorooctane-1-sulfonic acid  (EXP)
phenethyl caffeate  (EXP)
Phenoxybenzamine  (EXP)
picoxystrobin  (ISO)
pirinixic acid  (ISO)
Ptaquiloside  (ISO)
pyrimidifen  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
sodium arsenite  (EXP,ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
terbufos  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP)
tetrachloromethane  (ISO)
thimerosal  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
triptonide  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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16. GOA data from the GO Consortium
17. Gong J, etal., BMC Neurosci. 2010 Apr 23;11:50.
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19. Islamov RR, etal., Brain Res Bull. 2017 Jun;132:44-52. doi: 10.1016/j.brainresbull.2017.05.005. Epub 2017 May 18.
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27. Macias M, etal., Neuroreport. 2002 Dec 20;13(18):2527-30.
28. Mackowiak M, etal., Brain Res. 2005 Sep 7;1055(1-2):149-55.
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30. Mazzetti S, etal., Brain Res Bull. 2007 Mar 30;71(6):578-86. Epub 2006 Dec 22.
31. MGD data from the GO Consortium
32. Miñana R, etal., J Neurochem. 2000 Sep;75(3):954-64. doi: 10.1046/j.1471-4159.2000.0750954.x.
33. Murphy JA, etal., Invest Ophthalmol Vis Sci. 2009 Feb;50(2):861-9. Epub 2008 Aug 29.
34. Nagao K, etal., J Mol Cell Cardiol. 2010 Jun;48(6):1157-68. Epub 2009 Oct 22.
35. Nakatani K, etal., Arch Histol Cytol. 2006 Mar;69(1):61-72.
36. Pekcec A, etal., J Neurochem. 2008 Apr;105(2):389-400. Epub 2008 Jan 8.
37. Perl AK, etal., Nat Med. 1999 Mar;5(3):286-91.
38. Pipeline to import KEGG annotations from KEGG into RGD
39. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
40. RGD automated data pipeline
41. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
42. RGD automated import pipeline for gene-chemical interactions
43. Sakai A, etal., Pain. 2008 Jul 15;137(2):378-88. Epub 2007 Oct 29.
44. Seki H, etal., J Surg Oncol. 1993 Jun;53(2):78-83.
45. Simonneau L, etal., J Comp Neurol 2003 Apr 28;459(2):113-26.
46. Small SJ, etal., J Cell Biol 1987 Nov;105(5):2335-45.
47. Sokolov ME, etal., Front Pharmacol. 2018 Feb 15;9:111. doi: 10.3389/fphar.2018.00111. eCollection 2018.
48. Son H, etal., Biochem Biophys Res Commun 2002 Oct 25;298(2):262-8.
49. Stallcup WB and Beasley L, Proc Natl Acad Sci U S A. 1985 Feb;82(4):1276-80.
50. Tanaka J, etal., Surg Today. 1998;28(11):1217-20.
51. Ter Horst JP, etal., Eur J Neurosci. 2008 Aug;28(3):419-27.
52. Tezel E, etal., Pancreas. 2001 Mar;22(2):122-5.
53. Thornton MR, etal., J Anat. 2005 Jan;206(1):69-78.
54. Thoulouze MI, etal., J Virol. 1998 Sep;72(9):7181-90. doi: 10.1128/JVI.72.9.7181-7190.1998.
55. Tsoory M, etal., Neuropsychopharmacology. 2008 Jan;33(2):378-93. Epub 2007 Apr 11.
56. Tur MK, etal., Am J Pathol. 2013 Apr;182(4):1205-18. doi: 10.1016/j.ajpath.2012.12.027. Epub 2013 Feb 8.
57. Varea E, etal., Eur Neuropsychopharmacol. 2007 Jul;17(8):546-57. Epub 2007 Feb 20.
58. Varea E, etal., Neurobiol Aging. 2009 May;30(5):808-18. Epub 2007 Sep 29.
59. Varea E, etal., Neuroscience. 2005;136(2):435-43. Epub 2005 Oct 10.
60. Venero C, etal., Neuroscience 2002;115(4):1211-9.
61. Voronkov DN, etal., Bull Exp Biol Med. 2019 Apr;166(6):793-796. doi: 10.1007/s10517-019-04442-y. Epub 2019 Apr 26.
62. Wang J, etal., J Ethnopharmacol. 2018 Mar 25;214:13-21. doi: 10.1016/j.jep.2017.11.037. Epub 2017 Dec 5.
63. Zhang M, etal., Toxicology. 2007 Jul 17;236(3):208-16. Epub 2007 Apr 24.
Additional References at PubMed
PMID:1694009   PMID:1699951   PMID:1996115   PMID:2483093   PMID:7613634   PMID:10766765   PMID:11817895   PMID:11936192   PMID:12477932   PMID:12757368   PMID:12774308   PMID:12786978  
PMID:12791257   PMID:12837245   PMID:12937148   PMID:13129654   PMID:14527396   PMID:14550299   PMID:14648585   PMID:14663363   PMID:14741393   PMID:14752119   PMID:15065125   PMID:15169853  
PMID:15256054   PMID:15490465   PMID:15738425   PMID:15964824   PMID:16776666   PMID:17213291   PMID:17223582   PMID:17336079   PMID:17355876   PMID:17460068   PMID:17513116   PMID:17634366  
PMID:17971410   PMID:18307098   PMID:18588533   PMID:19110037   PMID:19251664   PMID:19429186   PMID:19440374   PMID:19546439   PMID:19741142   PMID:19788570   PMID:19946888   PMID:20131911  
PMID:20175207   PMID:20598904   PMID:20610389   PMID:20617137   PMID:20622691   PMID:20843898   PMID:21115007   PMID:21389209   PMID:21436126   PMID:21700703   PMID:21708977   PMID:21787839  
PMID:21876469   PMID:21887252   PMID:22007488   PMID:22363206   PMID:22419107   PMID:22814229   PMID:22871113   PMID:22998873   PMID:23284756   PMID:23376485   PMID:23963795   PMID:24582971  
PMID:25002582   PMID:27559042   PMID:29169663   PMID:29476059   PMID:30477252  


Genomics

Comparative Map Data
Ncam1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2849,865,629 - 50,165,687 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl849,865,633 - 50,166,014 (-)Ensembl
Rnor_6.0853,836,797 - 54,134,881 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl853,839,098 - 53,901,358 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0852,456,154 - 52,755,707 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4852,822,350 - 53,120,572 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1852,841,403 - 53,139,626 (-)NCBI
Celera849,420,106 - 49,716,981 (-)NCBICelera
RH 3.4 Map8537.1RGD
Cytogenetic Map8q23NCBI
NCAM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl11112,961,247 - 113,278,436 (+)EnsemblGRCh38hg38GRCh38
GRCh3811112,961,420 - 113,278,436 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3711112,832,142 - 113,149,158 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3611112,337,205 - 112,654,368 (+)NCBINCBI36hg18NCBI36
Build 3411112,337,367 - 112,652,530NCBI
Celera11109,984,979 - 110,302,094 (+)NCBI
Cytogenetic Map11q23.2NCBI
HuRef11108,759,657 - 109,076,750 (+)NCBIHuRef
CHM1_111112,714,961 - 113,032,145 (+)NCBICHM1_1
Ncam1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39949,413,429 - 49,710,909 (-)NCBIGRCm39mm39
GRCm39 Ensembl949,413,436 - 49,710,225 (-)Ensembl
GRCm38949,502,129 - 49,799,393 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl949,502,136 - 49,798,925 (-)EnsemblGRCm38mm10GRCm38
MGSCv37949,310,243 - 49,607,174 (-)NCBIGRCm37mm9NCBIm37
MGSCv36949,269,508 - 49,551,120 (-)NCBImm8
Celera946,800,549 - 47,099,090 (-)NCBICelera
Cytogenetic Map9A5.3NCBI
cM Map926.83NCBI
Ncam1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541214,630,443 - 14,923,926 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541214,630,109 - 14,923,847 (+)NCBIChiLan1.0ChiLan1.0
NCAM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.111111,688,524 - 112,003,435 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11111,925,677 - 112,000,401 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v011107,845,507 - 108,160,441 (+)NCBIMhudiblu_PPA_v0panPan3
NCAM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1519,895,587 - 20,192,334 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl519,895,613 - 20,191,995 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha519,817,368 - 20,113,554 (-)NCBI
ROS_Cfam_1.0519,916,497 - 20,213,111 (-)NCBI
UMICH_Zoey_3.1519,978,946 - 20,275,227 (-)NCBI
UNSW_CanFamBas_1.0519,880,186 - 20,176,568 (-)NCBI
UU_Cfam_GSD_1.0519,928,019 - 20,223,810 (-)NCBI
Ncam1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494795,149,341 - 95,443,034 (+)NCBI
SpeTri2.0NW_0049366121,262,557 - 1,556,281 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NCAM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl940,628,750 - 40,960,608 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1940,628,602 - 40,960,605 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2945,463,323 - 45,794,721 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NCAM1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11104,332,622 - 104,647,258 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604321,358,968 - 21,671,871 (-)NCBIVero_WHO_p1.0
Ncam1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247848,339,582 - 8,635,025 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D8Mit2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2850,095,249 - 50,095,447 (+)MAPPERmRatBN7.2
Rnor_6.0854,065,044 - 54,065,241NCBIRnor6.0
Rnor_5.0852,685,897 - 52,686,094UniSTSRnor5.0
RGSC_v3.4853,049,279 - 53,049,477RGDRGSC3.4
RGSC_v3.4853,049,280 - 53,049,477UniSTSRGSC3.4
RGSC_v3.1853,068,254 - 53,068,551RGD
Celera849,646,904 - 49,647,101UniSTS
RH 3.4 Map8537.5UniSTS
RH 3.4 Map8537.5RGD
RH 2.0 Map8403.3RGD
Cytogenetic Map8q23UniSTS
D8Rat44  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2850,151,901 - 50,152,080 (+)MAPPERmRatBN7.2
Rnor_6.0854,121,386 - 54,121,562NCBIRnor6.0
Rnor_5.0852,742,239 - 52,742,415UniSTSRnor5.0
RGSC_v3.4853,106,856 - 53,107,032UniSTSRGSC3.4
RGSC_v3.4853,106,706 - 53,107,102RGDRGSC3.4
RGSC_v3.1853,125,910 - 53,126,086RGD
Celera849,703,547 - 49,703,723UniSTS
RH 3.4 Map8540.6RGD
RH 3.4 Map8540.6UniSTS
RH 2.0 Map8402.4RGD
SHRSP x BN Map838.1RGD
FHH x ACI Map846.93RGD
Cytogenetic Map8q23UniSTS
D8Rat215  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2850,088,598 - 50,088,795 (+)MAPPERmRatBN7.2
Rnor_6.0854,058,413 - 54,058,607NCBIRnor6.0
Rnor_5.0852,679,217 - 52,679,411UniSTSRnor5.0
RGSC_v3.4853,042,394 - 53,042,586RGDRGSC3.4
RGSC_v3.4853,042,395 - 53,042,589UniSTSRGSC3.4
RGSC_v3.1853,061,448 - 53,061,640RGD
Celera849,640,301 - 49,640,493UniSTS
SHRSP x BN Map838.1RGD
SHRSP x BN Map838.1UniSTS
Cytogenetic Map8q23UniSTS
D8Arb10  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2849,868,652 - 49,868,967 (+)MAPPERmRatBN7.2
Rnor_6.0853,839,814 - 53,840,128NCBIRnor6.0
Rnor_5.0852,458,915 - 52,459,229UniSTSRnor5.0
RGSC_v3.4852,822,490 - 52,822,804UniSTSRGSC3.4
RGSC_v3.1852,841,543 - 52,841,858RGD
Celera849,420,246 - 49,420,560UniSTS
Cytogenetic Map8q23UniSTS
D8Arb23  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2849,868,652 - 49,868,959 (+)MAPPERmRatBN7.2
Rnor_6.0853,839,814 - 53,840,120NCBIRnor6.0
Rnor_5.0852,458,915 - 52,459,221UniSTSRnor5.0
RGSC_v3.4852,822,490 - 52,822,796UniSTSRGSC3.4
RGSC_v3.1852,841,543 - 52,841,850RGD
Celera849,420,246 - 49,420,552UniSTS
Cytogenetic Map8q23UniSTS
RH134243  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2849,878,616 - 49,878,808 (+)MAPPERmRatBN7.2
Rnor_6.0853,849,778 - 53,849,969NCBIRnor6.0
Rnor_5.0852,468,879 - 52,469,070UniSTSRnor5.0
RGSC_v3.4852,832,454 - 52,832,645UniSTSRGSC3.4
Celera849,430,210 - 49,430,401UniSTS
RH 3.4 Map8537.6UniSTS
Cytogenetic Map8q23UniSTS
RH142318  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map8537.1UniSTS
Cytogenetic Map8q23UniSTS
BF400138  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2850,062,111 - 50,062,283 (+)MAPPERmRatBN7.2
Rnor_6.0854,031,926 - 54,032,097NCBIRnor6.0
Rnor_5.0852,652,730 - 52,652,901UniSTSRnor5.0
RGSC_v3.4853,015,908 - 53,016,079UniSTSRGSC3.4
Celera849,613,812 - 49,613,983UniSTS
RH 3.4 Map8538.6UniSTS
Cytogenetic Map8q23UniSTS
RH132569  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2849,915,271 - 49,915,464 (+)MAPPERmRatBN7.2
Rnor_6.0853,884,906 - 53,885,098NCBIRnor6.0
Rnor_5.0852,505,859 - 52,506,051UniSTSRnor5.0
RGSC_v3.4852,869,161 - 52,869,353UniSTSRGSC3.4
Celera849,466,848 - 49,467,040UniSTS
RH 3.4 Map8536.6UniSTS
Cytogenetic Map8q23UniSTS
RH143130  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2850,069,622 - 50,069,851 (+)MAPPERmRatBN7.2
Rnor_6.0854,039,437 - 54,039,665NCBIRnor6.0
Rnor_5.0852,660,241 - 52,660,469UniSTSRnor5.0
RGSC_v3.4853,023,419 - 53,023,647UniSTSRGSC3.4
Celera849,621,323 - 49,621,551UniSTS
RH 3.4 Map8538.1UniSTS
Cytogenetic Map8q23UniSTS
BF402045  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2849,881,838 - 49,881,984 (+)MAPPERmRatBN7.2
Rnor_6.0853,853,000 - 53,853,145NCBIRnor6.0
Rnor_5.0852,472,101 - 52,472,246UniSTSRnor5.0
RGSC_v3.4852,835,676 - 52,835,821UniSTSRGSC3.4
Celera849,433,432 - 49,433,577UniSTS
RH 3.4 Map8538.7UniSTS
Cytogenetic Map8q23UniSTS
RH138949  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2849,876,924 - 49,877,090 (+)MAPPERmRatBN7.2
Rnor_6.0853,848,086 - 53,848,251NCBIRnor6.0
Rnor_5.0852,467,187 - 52,467,352UniSTSRnor5.0
RGSC_v3.4852,830,762 - 52,830,927UniSTSRGSC3.4
Celera849,428,518 - 49,428,683UniSTS
RH 3.4 Map8536.6UniSTS
Cytogenetic Map8q23UniSTS
BF388149  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2849,884,136 - 49,884,303 (+)MAPPERmRatBN7.2
Rnor_6.0853,855,719 - 53,855,885NCBIRnor6.0
Rnor_5.0852,474,820 - 52,474,986UniSTSRnor5.0
RGSC_v3.4852,837,973 - 52,838,139UniSTSRGSC3.4
Celera849,435,729 - 49,435,895UniSTS
RH 3.4 Map8537.6UniSTS
Cytogenetic Map8q23UniSTS
D1S2854  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27115,614,738 - 115,616,116 (+)MAPPERmRatBN7.2
mRatBN7.2849,898,118 - 49,898,532 (+)MAPPERmRatBN7.2
Rnor_6.0853,869,700 - 53,870,115NCBIRnor6.0
Rnor_6.07125,135,860 - 125,137,237NCBIRnor6.0
Rnor_5.0852,488,801 - 52,489,216UniSTSRnor5.0
Rnor_5.07125,123,467 - 125,124,844UniSTSRnor5.0
RGSC_v3.47122,494,085 - 122,495,462UniSTSRGSC3.4
RGSC_v3.4852,851,954 - 52,852,369UniSTSRGSC3.4
Celera849,449,710 - 49,450,125UniSTS
Celera7111,917,433 - 111,918,810UniSTS
Cytogenetic Map7q34UniSTS
Cytogenetic Map8q23UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8767057852670578Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)8768895552688955Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8768895552688955Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)8873663553736635Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)8873663553736635Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)8971222053356647Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1558646Swd5Spike wave discharge measurement QTL 53.450.00036brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)81490675159906751Rat
61373Mcs4Mammary carcinoma susceptibility QTL 41.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)81629044461290444Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)81898416884531599Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)81933115293965294Rat
631842Inf1Infertility severity QTL 14.10.001seminal gland mass (VT:0010524)seminal vesicle wet weight (CMO:0001603)82266233067662330Rat
2303564Gluco43Glucose level QTL 433blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)82613018771130187Rat
2303572Insul13Insulin level QTL 132blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)82613018771130187Rat
631648Stl5Serum triglyceride level QTL 540.0003blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)82720571554998217Rat
1358892Kidm26Kidney mass QTL 263.69kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)82720571599103503Rat
1358896Bp262Blood pressure QTL 2622.89arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)82720571599103503Rat
1358907Cm40Cardiac mass QTL 401.89heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)82720571599103503Rat
1331804Cm30Cardiac mass QTL 303.77443heart mass (VT:0007028)heart wet weight (CMO:0000069)82824291253961020Rat
1300146Rf17Renal function QTL 172.9renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)82824291273242912Rat
8662823Vetf5Vascular elastic tissue fragility QTL 51.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)82824291299525068Rat
2302278Gluco36Glucose level QTL 364.2blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)82950266550095447Rat
724514Uae15Urinary albumin excretion QTL 152.9urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)82950266570386295Rat
1549908Neudeg1Neurodegradation QTL 15.50nervous system integrity trait (VT:0010566)logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)83018886794457446Rat
1331744Bp217Blood pressure QTL 2173.398arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815458482492Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)83084815461290444Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)83084815461290444Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815461290444Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815461290444Rat
11556286Cm81Cardiac mass QTL 810.01heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)83084815461290444Rat
1359033Bp273Blood pressure QTL 273arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815461290444Rat
2313046Bss78Bone structure and strength QTL 783.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)83084815482460899Rat
2313057Bss76Bone structure and strength QTL 7630.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)83084815482460899Rat
2313067Bss77Bone structure and strength QTL 773.10.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)83084815482460899Rat
2313088Bss75Bone structure and strength QTL 753.10.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)83084815482460899Rat
1578755Pur5Proteinuria QTL 53.30.0001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)830848154101699754Rat
1578765Klgr1Kidney lesion grade QTL 13.30.0001kidney morphology trait (VT:0002135)organ lesion measurement (CMO:0000677)830848154101699754Rat
1578769Uae31Urinary albumin excretion QTL 313.30.001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)830848154101699754Rat
2316950Scl66Serum cholesterol level QTL 664.1blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)830848259105647037Rat
1298065Scl16Serum cholesterol level QTL 163.8blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)83085640475856404Rat
1582222Epfw2Epididymal fat weight QTL 23.20.0005epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)83173772976737729Rat
61358Bp39Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83555193880551938Rat
61464Niddm11Non-insulin dependent diabetes mellitus QTL 113.10.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83558203280582032Rat
1331838Niddm61Non-insulin dependent diabetes mellitus QTL 613.530.0004blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83646953599083736Rat
737824Hcar10Hepatocarcinoma resistance QTL 102.9liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)84071306682925667Rat
1358906Bp253Blood pressure QTL 25340.0004arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)84071306693965294Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
1331769Rf39Renal function QTL 393.871urine output (VT:0003620)timed urine volume (CMO:0000260)84186687675097878Rat
1298079Activ2Activity QTL 29.50.000001voluntary movement trait (VT:0003491)rearing measurement (CMO:0001515)84186687686866876Rat
631216Stl9Serum triglyceride level QTL 94.710.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)84186701070386132Rat
5684993Bmd84Bone mineral density QTL 844.1tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)84269268450095447Rat
70161Bp62Blood pressure QTL 622.90.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)84269268490165460Rat
12879882Am8Aortic mass QTL 80.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)84329616998968765Rat
12879878Bw183Body weight QTL 1830.001body mass (VT:0001259)body weight (CMO:0000012)84329616998968765Rat
12879879Cm99Cardiac mass QTL 990.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)84329616998968765Rat
12879880Cm100Cardiac mass QTL 1000.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)84329616998968765Rat
12879881Cm101Cardiac mass QTL 1010.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)84329616998968765Rat
12879883Kidm65Kidney mass QTL 650.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)84329616998968765Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)846531639119088624Rat
1331837Bw23Body weight QTL 234.190.00007body mass (VT:0001259)body weight (CMO:0000012)84653172299083736Rat
2303570Gluco48Glucose level QTL 482blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)84980583194805831Rat
2313086Bss60Bone structure and strength QTL 604.10.0001tibia length (VT:0004357)tibia length (CMO:0000450)85009524982460899Rat
4889938Bss89Bone structure and strength QTL 893.8tibia size trait (VT:0100001)tibia cortical bone volume (CMO:0001725)85009524982460899Rat
5684973Bss100Bone structure and strength QTL 1004.7tibia area (VT:1000281)tibia area measurement (CMO:0001382)85009524982460899Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:82
Count of miRNA genes:33
Interacting mature miRNAs:38
Transcripts:ENSRNOT00000042281, ENSRNOT00000047666
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 26 6 4 4 74 22 27
Low 3 17 36 22 19 22 8 11 13 14 11 8
Below cutoff 15 15 15

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001395707 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001395708 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001395709 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001395710 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_031521 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242986 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242988 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242994 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008766192 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008766193 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595460 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595461 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595462 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595463 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595464 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595465 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080805 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080807 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080808 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080809 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080810 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080811 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080812 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080813 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080814 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080815 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080816 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080817 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080818 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC101924 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473975 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000198 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M32611 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M32612 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M63970 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X06564 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000042281   ⟹   ENSRNOP00000048442
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl849,865,633 - 50,166,014 (-)Ensembl
Rnor_6.0 Ensembl853,839,685 - 53,901,358 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000047666   ⟹   ENSRNOP00000046828
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl849,868,524 - 49,932,303 (-)Ensembl
Rnor_6.0 Ensembl853,839,683 - 53,901,358 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000072184   ⟹   ENSRNOP00000064969
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl853,870,121 - 53,874,934 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000082257   ⟹   ENSRNOP00000071509
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl849,867,519 - 49,931,725 (-)Ensembl
Rnor_6.0 Ensembl853,839,098 - 53,899,669 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000099180   ⟹   ENSRNOP00000091588
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl849,867,519 - 49,931,745 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000099284   ⟹   ENSRNOP00000080203
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl849,878,384 - 50,166,014 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000113915   ⟹   ENSRNOP00000079021
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl849,867,519 - 50,166,014 (-)Ensembl
RefSeq Acc Id: NM_031521   ⟹   NP_113709
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,868,513 - 50,165,537 (-)NCBI
Rnor_6.0853,839,674 - 54,134,731 (-)NCBI
Rnor_5.0852,456,154 - 52,755,707 (-)NCBI
RGSC_v3.4852,822,350 - 53,120,572 (-)RGD
Celera849,420,106 - 49,716,981 (-)RGD
Sequence:
RefSeq Acc Id: XM_006242986   ⟹   XP_006243048
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,865,629 - 50,165,687 (-)NCBI
Rnor_6.0853,836,797 - 54,134,881 (-)NCBI
Rnor_5.0852,456,154 - 52,755,707 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242988   ⟹   XP_006243050
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,865,629 - 50,165,687 (-)NCBI
Rnor_6.0853,836,797 - 54,134,881 (-)NCBI
Rnor_5.0852,456,154 - 52,755,707 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242994   ⟹   XP_006243056
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,865,629 - 50,165,687 (-)NCBI
Rnor_6.0853,836,797 - 54,134,881 (-)NCBI
Rnor_5.0852,456,154 - 52,755,707 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595460   ⟹   XP_017450949
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,865,629 - 50,165,687 (-)NCBI
Rnor_6.0853,836,797 - 54,134,881 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595461   ⟹   XP_017450950
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,865,629 - 50,165,687 (-)NCBI
Rnor_6.0853,836,797 - 54,134,881 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595463   ⟹   XP_017450952
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,865,629 - 50,165,687 (-)NCBI
Rnor_6.0853,836,797 - 54,134,881 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595464   ⟹   XP_017450953
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,878,379 - 50,165,687 (-)NCBI
Rnor_6.0853,847,976 - 54,134,881 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595465   ⟹   XP_017450954
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,878,379 - 50,165,687 (-)NCBI
Rnor_6.0853,847,976 - 54,134,881 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039080805   ⟹   XP_038936733
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,865,629 - 50,165,687 (-)NCBI
RefSeq Acc Id: XM_039080807   ⟹   XP_038936735
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,865,629 - 50,165,687 (-)NCBI
RefSeq Acc Id: XM_039080808   ⟹   XP_038936736
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,865,629 - 50,165,687 (-)NCBI
RefSeq Acc Id: XM_039080809   ⟹   XP_038936737
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,865,629 - 50,165,687 (-)NCBI
RefSeq Acc Id: XM_039080810   ⟹   XP_038936738
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,865,629 - 50,165,687 (-)NCBI
RefSeq Acc Id: XM_039080811   ⟹   XP_038936739
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,865,629 - 50,165,687 (-)NCBI
RefSeq Acc Id: XM_039080812   ⟹   XP_038936740
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,865,629 - 50,165,687 (-)NCBI
RefSeq Acc Id: XM_039080813   ⟹   XP_038936741
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,878,379 - 50,165,687 (-)NCBI
RefSeq Acc Id: XM_039080814   ⟹   XP_038936742
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,878,379 - 50,165,687 (-)NCBI
RefSeq Acc Id: XM_039080815   ⟹   XP_038936743
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,878,379 - 50,165,687 (-)NCBI
RefSeq Acc Id: XM_039080816   ⟹   XP_038936744
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,878,379 - 50,165,687 (-)NCBI
RefSeq Acc Id: XM_039080817   ⟹   XP_038936745
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,878,379 - 50,165,687 (-)NCBI
RefSeq Acc Id: XM_039080818   ⟹   XP_038936746
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,878,379 - 50,165,687 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001382636 (Get FASTA)   NCBI Sequence Viewer  
  NP_001382637 (Get FASTA)   NCBI Sequence Viewer  
  NP_001382638 (Get FASTA)   NCBI Sequence Viewer  
  NP_001382639 (Get FASTA)   NCBI Sequence Viewer  
  NP_113709 (Get FASTA)   NCBI Sequence Viewer  
  XP_006243048 (Get FASTA)   NCBI Sequence Viewer  
  XP_006243050 (Get FASTA)   NCBI Sequence Viewer  
  XP_006243056 (Get FASTA)   NCBI Sequence Viewer  
  XP_017450949 (Get FASTA)   NCBI Sequence Viewer  
  XP_017450950 (Get FASTA)   NCBI Sequence Viewer  
  XP_017450952 (Get FASTA)   NCBI Sequence Viewer  
  XP_017450953 (Get FASTA)   NCBI Sequence Viewer  
  XP_017450954 (Get FASTA)   NCBI Sequence Viewer  
  XP_038936733 (Get FASTA)   NCBI Sequence Viewer  
  XP_038936735 (Get FASTA)   NCBI Sequence Viewer  
  XP_038936736 (Get FASTA)   NCBI Sequence Viewer  
  XP_038936737 (Get FASTA)   NCBI Sequence Viewer  
  XP_038936738 (Get FASTA)   NCBI Sequence Viewer  
  XP_038936739 (Get FASTA)   NCBI Sequence Viewer  
  XP_038936740 (Get FASTA)   NCBI Sequence Viewer  
  XP_038936741 (Get FASTA)   NCBI Sequence Viewer  
  XP_038936742 (Get FASTA)   NCBI Sequence Viewer  
  XP_038936743 (Get FASTA)   NCBI Sequence Viewer  
  XP_038936744 (Get FASTA)   NCBI Sequence Viewer  
  XP_038936745 (Get FASTA)   NCBI Sequence Viewer  
  XP_038936746 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA41679 (Get FASTA)   NCBI Sequence Viewer  
  AAA41680 (Get FASTA)   NCBI Sequence Viewer  
  AAA41681 (Get FASTA)   NCBI Sequence Viewer  
  AAI01925 (Get FASTA)   NCBI Sequence Viewer  
  CAA29809 (Get FASTA)   NCBI Sequence Viewer  
  EDL95446 (Get FASTA)   NCBI Sequence Viewer  
  EDL95447 (Get FASTA)   NCBI Sequence Viewer  
  EDL95448 (Get FASTA)   NCBI Sequence Viewer  
  EDL95449 (Get FASTA)   NCBI Sequence Viewer  
  P13596 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_113709   ⟸   NM_031521
- Peptide Label: precursor
- UniProtKB: P13596 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006243056   ⟸   XM_006242994
- Peptide Label: isoform X12
- UniProtKB: Q3T1H3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006243050   ⟸   XM_006242988
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_006243048   ⟸   XM_006242986
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017450952   ⟸   XM_017595463
- Peptide Label: isoform X13
- Sequence:
RefSeq Acc Id: XP_017450950   ⟸   XM_017595461
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017450949   ⟸   XM_017595460
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017450954   ⟸   XM_017595465
- Peptide Label: isoform X20
- Sequence:
RefSeq Acc Id: XP_017450953   ⟸   XM_017595464
- Peptide Label: isoform X15
- Sequence:
RefSeq Acc Id: ENSRNOP00000046828   ⟸   ENSRNOT00000047666
RefSeq Acc Id: ENSRNOP00000071509   ⟸   ENSRNOT00000082257
RefSeq Acc Id: ENSRNOP00000048442   ⟸   ENSRNOT00000042281
RefSeq Acc Id: ENSRNOP00000064969   ⟸   ENSRNOT00000072184
RefSeq Acc Id: XP_038936740   ⟸   XM_039080812
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038936739   ⟸   XM_039080811
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038936737   ⟸   XM_039080809
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038936736   ⟸   XM_039080808
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038936738   ⟸   XM_039080810
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038936735   ⟸   XM_039080807
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038936733   ⟸   XM_039080805
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038936745   ⟸   XM_039080817
- Peptide Label: isoform X19
RefSeq Acc Id: XP_038936744   ⟸   XM_039080816
- Peptide Label: isoform X18
RefSeq Acc Id: XP_038936746   ⟸   XM_039080818
- Peptide Label: isoform X21
RefSeq Acc Id: XP_038936743   ⟸   XM_039080815
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038936742   ⟸   XM_039080814
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038936741   ⟸   XM_039080813
- Peptide Label: isoform X14
RefSeq Acc Id: ENSRNOP00000091588   ⟸   ENSRNOT00000099180
RefSeq Acc Id: ENSRNOP00000079021   ⟸   ENSRNOT00000113915
RefSeq Acc Id: ENSRNOP00000080203   ⟸   ENSRNOT00000099284
Protein Domains
Fibronectin type-III   Ig-like   Ig-like C2-type

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 52460515 52460516 C T snv HWY/Slc (KyushuU)
8 52461295 52461296 T G snv SR/JrHsd (MCW), ACI/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:67378 AgrOrtholog
Ensembl Genes ENSRNOG00000031890 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000046828 UniProtKB/TrEMBL
  ENSRNOP00000048442 UniProtKB/TrEMBL
  ENSRNOP00000064969 UniProtKB/TrEMBL
  ENSRNOP00000071509 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000042281 UniProtKB/TrEMBL
  ENSRNOT00000047666 UniProtKB/TrEMBL
  ENSRNOT00000072184 UniProtKB/TrEMBL
  ENSRNOT00000082257 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7936825 IMAGE-MGC_LOAD
InterPro FN3_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_V-set UniProtKB/TrEMBL
  Ncam1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neural_cell_adh UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24586 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124601 IMAGE-MGC_LOAD
NCBI Gene 24586 ENTREZGENE
PANTHER PTHR12231:SF239 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam fn3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ncam1 PhenoGen
PRINTS NCAMFAMILY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IGc2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IGv UniProtKB/TrEMBL
  SM00409 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49265 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K0M8_RAT UniProtKB/TrEMBL
  F1LNY3_RAT UniProtKB/TrEMBL
  F1LUV9_RAT UniProtKB/TrEMBL
  M0R6C2_RAT UniProtKB/TrEMBL
  NCAM1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q04017_RAT UniProtKB/TrEMBL
  Q3T1H3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2003-04-09 Ncam1  neural cell adhesion molecule 1      Symbol and Name updated 629477 APPROVED
2003-03-06 Ncam1  neural cell adhesion molecule 1  Ncam  neural cell adhesion molecule  Data Merged 628472 PROVISIONAL
2002-06-10 Ncam1        Symbol and Name status set to approved 70586 APPROVED
2001-10-23 Ncam  neural cell adhesion molecule      Name updated to reflect Human and Mouse nomenclature 68913 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_protein three isoforms exist of of apparent molecular masses 180, 140, and 120 kD 728977