Syne1 (spectrin repeat containing nuclear envelope protein 1) - Rat Genome Database
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Gene: Syne1 (spectrin repeat containing nuclear envelope protein 1) Rattus norvegicus
Analyze
Symbol: Syne1
Name: spectrin repeat containing nuclear envelope protein 1
RGD ID: 620546
Description: Exhibits enzyme binding activity and signaling receptor binding activity. Involved in several processes, including negative regulation of mesenchymal cell apoptotic process; negative regulation of mini excitatory postsynaptic potential; and regulation of receptor-mediated endocytosis. Localizes to several cellular components, including dendritic spine head; midbody; and nuclear membrane. Human ortholog(s) of this gene implicated in autosomal dominant Emery-Dreifuss muscular dystrophy 4; autosomal recessive spinocerebellar ataxia 8; bipolar disorder; cerebellar ataxia; and muscular dystrophy. Orthologous to human SYNE1 (spectrin repeat containing nuclear envelope protein 1); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: MODEL
Also known as: CPG2; LOC102546492; Myne-1; nesprin 1 long isoform; nesprin 1 short isoform; nesprin-1; nesprin-1-like; spectrin repeat containing, nuclear envelope 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Syne1Tn(sb-T2/Bart3)2.68Mcwi  
Genetic Models: F344-Syne1Tn(sb-T2/Bart3)2.68Mcwi
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2141,512,146 - 41,983,382 (-)NCBI
Rnor_6.0 Ensembl141,608,418 - 42,077,535 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0141,844,840 - 42,086,662 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0141,608,287 - 41,763,591 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0142,947,742 - 43,158,478 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4135,803,552 - 36,269,628 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1135,805,545 - 35,961,017 (-)NCBI
Celera137,192,707 - 37,662,090 (-)NCBICelera
Cytogenetic Map1q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (EXP)
benzo[a]pyrene  (EXP,ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP,ISO)
C60 fullerene  (EXP)
carbon nanotube  (ISO)
cefaloridine  (EXP)
cisplatin  (ISO)
clobetasol  (ISO)
cobalt dichloride  (EXP)
cocaine  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
indometacin  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
mercury dibromide  (ISO)
methamphetamine  (ISO)
methapyrilene  (ISO)
methyl methanesulfonate  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
microcystin-LR  (ISO)
morphine  (ISO)
nickel atom  (ISO)
nickel dichloride  (EXP)
nicotine  (ISO)
oxaliplatin  (EXP)
p-chloromercuribenzoic acid  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (EXP,ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium dichromate  (EXP)
Soman  (EXP)
testosterone  (ISO)
tetraphene  (ISO)
thioacetamide  (EXP)
titanium dioxide  (EXP)
topotecan  (EXP)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
troglitazone  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
1. Attali R, etal., Hum Mol Genet. 2009 Sep 15;18(18):3462-9. doi: 10.1093/hmg/ddp290. Epub 2009 Jun 19.
2. Cottrell JR, etal., Neuron. 2004 Nov 18;44(4):677-90.
3. Dupré N, etal., Ann Neurol. 2007 Jul;62(1):93-8.
4. Fan J and Beck KA, J Cell Sci. 2004 Feb 1;117(Pt 4):619-29. Epub 2004 Jan 6.
5. Fanin M, etal., Muscle Nerve. 2015 Jan;51(1):145-7. doi: 10.1002/mus.24357. Epub 2014 Nov 24.
6. Kobayashi Y, etal., Exp Cell Res. 2006 Oct 1;312(16):3152-64. Epub 2006 Jun 27.
7. Loebrich S, etal., Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):E4548-56. doi: 10.1073/pnas.1318860110. Epub 2013 Nov 4.
8. NCBI rat LocusLink and RefSeq merged data July 26, 2002
9. Nedivi E, etal., Proc Natl Acad Sci U S A 1996 Mar 5;93(5):2048-53.
10. OMIM Disease Annotation Pipeline
11. Pare GC, etal., Exp Cell Res. 2005 Feb 15;303(2):388-99.
12. Puckelwartz MJ, etal., Hum Mol Genet. 2009 Feb 15;18(4):607-20. doi: 10.1093/hmg/ddn386. Epub 2008 Nov 13.
13. RGD automated data pipeline
14. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
15. RGD automated import pipeline for gene-chemical interactions
16. Sharp SI, etal., Psychiatr Genet. 2017 Jun;27(3):81-88. doi: 10.1097/YPG.0000000000000166.
17. Synofzik M, etal., Brain. 2016 May;139(Pt 5):1378-93. doi: 10.1093/brain/aww079. Epub 2016 Apr 17.
18. Yang W, etal., Int J Mol Med. 2013 Oct;32(4):805-12. doi: 10.3892/ijmm.2013.1445. Epub 2013 Jul 16.
19. Yang W, etal., Mol Med Rep. 2015 Jan;11(1):133-42. doi: 10.3892/mmr.2014.2754. Epub 2014 Oct 23.
20. Zhang Q, etal., J Cell Sci 2001 Dec;114(Pt 24):4485-98.
Additional References at PubMed
PMID:10878022   PMID:11801724   PMID:12163176   PMID:12408964   PMID:12808039   PMID:15276322   PMID:17267447   PMID:18396275   PMID:19596800   PMID:21630459   PMID:22518138   PMID:22658674  
PMID:22681889   PMID:24862572   PMID:26776730   PMID:31428857   PMID:31904090  


Genomics

Comparative Map Data
Syne1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2141,512,146 - 41,983,382 (-)NCBI
Rnor_6.0 Ensembl141,608,418 - 42,077,535 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0141,844,840 - 42,086,662 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0141,608,287 - 41,763,591 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0142,947,742 - 43,158,478 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4135,803,552 - 36,269,628 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1135,805,545 - 35,961,017 (-)NCBI
Celera137,192,707 - 37,662,090 (-)NCBICelera
Cytogenetic Map1q11NCBI
SYNE1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6152,121,684 - 152,637,801 (-)EnsemblGRCh38hg38GRCh38
GRCh386152,121,684 - 152,637,395 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh376152,442,819 - 152,958,497 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366152,484,515 - 153,000,227 (-)NCBINCBI36hg18NCBI36
Build 346152,535,028 - 153,050,648NCBI
Celera6153,176,558 - 153,692,233 (-)NCBI
Cytogenetic Map6q25.2NCBI
HuRef6150,004,601 - 150,521,666 (-)NCBIHuRef
CHM1_16152,706,924 - 153,222,498 (-)NCBICHM1_1
Syne1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39104,970,192 - 5,501,013 (-)NCBIGRCm39mm39
GRCm39 Ensembl104,970,917 - 5,501,482 (-)Ensembl
GRCm38105,020,192 - 5,550,692 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl105,020,917 - 5,551,482 (-)EnsemblGRCm38mm10GRCm38
MGSCv37104,795,849 - 5,326,349 (+)NCBIGRCm37mm9NCBIm37
MGSCv36104,795,849 - 5,324,786 (+)NCBImm8
Celera104,962,310 - 5,494,074 (-)NCBICelera
Cytogenetic Map10A1NCBI
Syne1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554399,131,227 - 9,574,112 (+)NCBIChiLan1.0ChiLan1.0
SYNE1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16154,627,898 - 155,144,076 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6154,627,904 - 155,144,076 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06149,936,306 - 150,454,822 (-)NCBIMhudiblu_PPA_v0panPan3
SYNE1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl142,384,038 - 42,823,388 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1142,384,136 - 42,831,229 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Syne1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364894,903,176 - 5,177,987 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYNE1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1113,715,644 - 14,201,711 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2116,016,262 - 16,243,210 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SYNE1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11379,572,233 - 80,104,951 (-)NCBI
ChlSab1.1 Ensembl1379,572,936 - 79,988,893 (-)Ensembl
Syne1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247855,647,041 - 6,144,065 (+)NCBI

Position Markers
D1Got40  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0141,645,414 - 41,645,553NCBIRnor6.0
Rnor_5.0142,984,990 - 42,985,129UniSTSRnor5.0
RGSC_v3.4135,839,843 - 35,839,983RGDRGSC3.4
RGSC_v3.4135,839,844 - 35,839,983UniSTSRGSC3.4
RGSC_v3.1135,842,788 - 35,842,928RGD
Celera137,229,279 - 37,229,428UniSTS
Cytogenetic Map1p11UniSTS
D1Got41  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0142,010,590 - 42,010,770NCBIRnor6.0
Rnor_5.0143,341,278 - 43,341,458UniSTSRnor5.0
RGSC_v3.4136,202,770 - 36,202,948RGDRGSC3.4
RGSC_v3.4136,202,770 - 36,202,950UniSTSRGSC3.4
RGSC_v3.1136,205,715 - 36,205,893RGD
Celera137,591,338 - 37,591,515UniSTS
RH 3.4 Map1456.5UniSTS
RH 3.4 Map1456.5RGD
Cytogenetic Map1p11UniSTS
RH134376  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0141,905,527 - 41,905,706NCBIRnor6.0
Rnor_5.0143,236,732 - 43,236,911UniSTSRnor5.0
RGSC_v3.4136,093,249 - 36,093,428UniSTSRGSC3.4
Celera137,485,388 - 37,485,567UniSTS
Cytogenetic Map1p11UniSTS
RH139857  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0141,683,911 - 41,684,126NCBIRnor6.0
Rnor_5.0143,023,487 - 43,023,702UniSTSRnor5.0
RGSC_v3.4135,878,343 - 35,878,558UniSTSRGSC3.4
Celera137,270,306 - 37,270,521UniSTS
Cytogenetic Map1p11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1164407321Rat
1578650Bmd6Bone mineral density QTL 612.2femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)125439343579402Rat
1578651Bmd7Bone mineral density QTL 714.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)125439343579402Rat
1578669Bss9Bone structure and strength QTL 96.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)125439343579402Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)125439386904217Rat
1600360Mcs16Mammary carcinoma susceptibility QTL 162.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1186804543724576Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1457869349578693Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15655769122614963Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1565577285706974Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11131448975844121Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)11131448983657083Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11131448983657083Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11131448983657083Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11131448983657083Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
631508Sald1Serum aldosterone level QTL 13.7blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)11249343957493439Rat
2302038Pia31Pristane induced arthritis QTL 315.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)11362925158629251Rat
5684998Bss101Bone structure and strength QTL 1013.6tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)11614314349547474Rat
5684999Bss102Bone structure and strength QTL 1025.50.00000072tibia strength trait (VT:1000284)tibia stiffness (CMO:0001735)11614314349547474Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)12034156058000154Rat
724520Bp145Blood pressure QTL 1452.10.0024arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12107930566079305Rat
631494Bp95Blood pressure QTL 95400.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12130082249454378Rat
1558642Prcr2Prostate cancer resistance QTL 24.3prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)12181262344409802Rat
1357397Bw41Body weight QTL 414.190.0001body mass (VT:0001259)body weight (CMO:0000012)12340642849547474Rat
1357401Bw43Body weight QTL 433.75body mass (VT:0001259)body weight (CMO:0000012)12340642849547474Rat
1357400Bw62Body weight QTL624.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)12340642868406428Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123406428108057505Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)12429779978748000Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)125951907130917265Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)13148945479689689Rat
1354643Foco2Food consumption QTL 27.170.0001eating behavior trait (VT:0001431)food intake rate (CMO:0000427)13444911279449112Rat
1354599Bw29Body weight QTL 293.460.001body mass (VT:0001259)body weight (CMO:0000012)13444911279449112Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134993530173445086Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13537750894364229Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135377692217372257Rat
9589820Insglur3Insulin/glucose ratio QTL 310.750.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)13585416780854167Rat
8552900Pigfal1Plasma insulin-like growth factor 1 level QTL 17.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13585416780854167Rat
8552948Pigfal11Plasma insulin-like growth factor 1 level QTL 114.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13585416780854167Rat
1331732Srn4Serum renin concentration QTL 44.467renin activity (VT:0005581)plasma renin activity level (CMO:0000116)13603316579689689Rat
1331792Rf29Renal function QTL 294.589urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)13603316579689689Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14190724986907249Rat


Genetic Models
This gene Syne1 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:308
Count of miRNA genes:189
Interacting mature miRNAs:216
Transcripts:ENSRNOT00000047472
Prediction methods:Microtar, Miranda
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 40 16 4 12 4 8 8 42 10 7 11 8
Low 3 3 41 37 7 37 3 32 25 33
Below cutoff 1

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_006227851 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006227852 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006227853 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008758713 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590500 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101492 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101493 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101494 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101495 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101496 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101497 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101498 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101499 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101500 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101501 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101502 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101503 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101504 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101505 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101506 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101507 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101509 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101510 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101511 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF452647 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY597251 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474052 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000016 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MK681777 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MK681778 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X95466 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000025795
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl141,905,436 - 41,938,439 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000047472
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl141,609,128 - 41,754,652 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081637
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl141,832,830 - 42,077,535 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000084571
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl141,608,418 - 41,821,544 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000084712
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl141,905,435 - 41,937,822 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000090638
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl141,635,315 - 41,761,735 (-)Ensembl
RefSeq Acc Id: XM_006227851   ⟹   XP_006227913
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,512,146 - 41,667,067 (-)NCBI
Rnor_6.0141,609,125 - 41,763,231 (-)NCBI
Rnor_5.0142,947,742 - 43,158,478 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006227852   ⟹   XP_006227914
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,512,273 - 41,558,038 (-)NCBI
Rnor_6.0141,608,287 - 41,655,449 (-)NCBI
Rnor_5.0142,947,742 - 43,158,478 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006227853   ⟹   XP_006227915
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,800,975 - 41,983,382 (-)NCBI
Rnor_6.0141,905,441 - 42,086,657 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008758713   ⟹   XP_008756935
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,512,146 - 41,717,733 (-)NCBI
Rnor_6.0141,608,287 - 41,763,591 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008774326   ⟹   XP_008772548
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera137,192,707 - 37,662,090 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017590500   ⟹   XP_017445989
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,513,038 - 41,983,375 (-)NCBI
Rnor_6.0141,844,840 - 42,086,662 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039101492   ⟹   XP_038957420
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,512,981 - 41,983,374 (-)NCBI
RefSeq Acc Id: XM_039101493   ⟹   XP_038957421
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,512,146 - 41,983,374 (-)NCBI
RefSeq Acc Id: XM_039101494   ⟹   XP_038957422
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,512,146 - 41,983,374 (-)NCBI
RefSeq Acc Id: XM_039101495   ⟹   XP_038957423
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,512,146 - 41,983,374 (-)NCBI
RefSeq Acc Id: XM_039101496   ⟹   XP_038957424
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,512,146 - 41,983,374 (-)NCBI
RefSeq Acc Id: XM_039101497   ⟹   XP_038957425
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,512,146 - 41,983,322 (-)NCBI
RefSeq Acc Id: XM_039101498   ⟹   XP_038957426
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,512,981 - 41,918,181 (-)NCBI
RefSeq Acc Id: XM_039101499   ⟹   XP_038957427
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,512,437 - 41,983,322 (-)NCBI
RefSeq Acc Id: XM_039101500   ⟹   XP_038957428
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,512,146 - 41,983,374 (-)NCBI
RefSeq Acc Id: XM_039101501   ⟹   XP_038957429
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,512,981 - 41,974,211 (-)NCBI
RefSeq Acc Id: XM_039101502   ⟹   XP_038957430
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,512,146 - 41,983,374 (-)NCBI
RefSeq Acc Id: XM_039101503   ⟹   XP_038957431
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,512,981 - 41,983,322 (-)NCBI
RefSeq Acc Id: XM_039101504   ⟹   XP_038957432
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,512,146 - 41,983,374 (-)NCBI
RefSeq Acc Id: XM_039101505   ⟹   XP_038957433
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,512,146 - 41,983,374 (-)NCBI
RefSeq Acc Id: XM_039101506   ⟹   XP_038957434
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,512,146 - 41,983,374 (-)NCBI
RefSeq Acc Id: XM_039101507   ⟹   XP_038957435
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,512,146 - 41,983,374 (-)NCBI
RefSeq Acc Id: XM_039101509   ⟹   XP_038957437
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,513,038 - 41,983,375 (-)NCBI
RefSeq Acc Id: XM_039101510   ⟹   XP_038957438
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,512,146 - 41,983,374 (-)NCBI
RefSeq Acc Id: XM_039101511   ⟹   XP_038957439
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,512,146 - 41,983,374 (-)NCBI
Protein Sequences
Protein RefSeqs XP_006227913 (Get FASTA)   NCBI Sequence Viewer  
  XP_006227914 (Get FASTA)   NCBI Sequence Viewer  
  XP_006227915 (Get FASTA)   NCBI Sequence Viewer  
  XP_008756935 (Get FASTA)   NCBI Sequence Viewer  
  XP_017445989 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957420 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957421 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957422 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957423 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957424 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957425 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957426 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957427 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957428 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957429 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957430 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957431 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957432 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957433 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957434 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957435 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957437 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957438 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957439 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAL47053 (Get FASTA)   NCBI Sequence Viewer  
  AAT08489 (Get FASTA)   NCBI Sequence Viewer  
  CAA64740 (Get FASTA)   NCBI Sequence Viewer  
  EDL92843 (Get FASTA)   NCBI Sequence Viewer  
  QFP98436 (Get FASTA)   NCBI Sequence Viewer  
  QFP98437 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_006227913   ⟸   XM_006227851
- Peptide Label: isoform X20
- Sequence:
RefSeq Acc Id: XP_006227914   ⟸   XM_006227852
- Peptide Label: isoform X22
- Sequence:
RefSeq Acc Id: XP_008772548   ⟸   XM_008774326
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_008756935   ⟸   XM_008758713
- Peptide Label: isoform X19
- Sequence:
RefSeq Acc Id: XP_006227915   ⟸   XM_006227853
- Peptide Label: isoform X21
- Sequence:
RefSeq Acc Id: XP_017445989   ⟸   XM_017590500
- Peptide Label: isoform X18
- Sequence:
RefSeq Acc Id: XP_038957439   ⟸   XM_039101511
- Peptide Label: isoform X23
RefSeq Acc Id: XP_038957428   ⟸   XM_039101500
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038957434   ⟸   XM_039101506
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038957435   ⟸   XM_039101507
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038957438   ⟸   XM_039101510
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038957432   ⟸   XM_039101504
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038957424   ⟸   XM_039101496
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038957423   ⟸   XM_039101495
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038957422   ⟸   XM_039101494
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038957433   ⟸   XM_039101505
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038957430   ⟸   XM_039101502
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038957421   ⟸   XM_039101493
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038957425   ⟸   XM_039101497
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038957427   ⟸   XM_039101499
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038957420   ⟸   XM_039101492
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038957431   ⟸   XM_039101503
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038957429   ⟸   XM_039101501
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038957426   ⟸   XM_039101498
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038957437   ⟸   XM_039101509
- Peptide Label: isoform X16
Protein Domains
Calponin-homology (CH)   KASH

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 (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 42962971 42962972 G A snv GK/Ox (KNAW)
1 42976141 42976142 C G snv SR/JrHsd (MCW)
1 43029029 43029030 C G snv DOB/Oda (KyushuU)
1 43029572 43029573 C T snv BUF/MNa (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620546 AgrOrtholog
Ensembl Genes ENSRNOG00000018960 Ensembl, ENTREZGENE
Gene3D-CATH 1.10.418.10 UniProtKB/TrEMBL
InterPro Actinin_actin-bd_CS UniProtKB/TrEMBL
  CH-domain UniProtKB/TrEMBL
  CH_dom_sf UniProtKB/TrEMBL
  KASH UniProtKB/TrEMBL
  Spectrin/alpha-actinin UniProtKB/TrEMBL
  Spectrin_repeat UniProtKB/TrEMBL
NCBI Gene 499010 ENTREZGENE
Pfam KASH UniProtKB/TrEMBL
  PF00307 UniProtKB/TrEMBL
  Spectrin UniProtKB/TrEMBL
PhenoGen Syne1 PhenoGen
PROSITE ACTININ_1 UniProtKB/TrEMBL
  ACTININ_2 UniProtKB/TrEMBL
  KASH UniProtKB/TrEMBL
  PS50021 UniProtKB/TrEMBL
SMART KASH UniProtKB/TrEMBL
  SM00033 UniProtKB/TrEMBL
  SPEC UniProtKB/TrEMBL
Superfamily-SCOP SSF47576 UniProtKB/TrEMBL
Transposagen Syne1 Transposagen
UniProt A0A5P8DHK4_RAT UniProtKB/TrEMBL
  A0A5P8DHN0_RAT UniProtKB/TrEMBL
  Q63128_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-29 Syne1  spectrin repeat containing, nuclear envelope 1  LOC102546492  nesprin-1-like  Data Merged 737654 PROVISIONAL
2013-12-18 LOC102546492  nesprin-1-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-02-25 Syne1  spectrin repeat containing, nuclear envelope 1  CPG2  CPG2 protein  Data Merged 737654 APPROVED
2005-07-08 Syne1  spectrin repeat containing, nuclear envelope 1    nesprin-1  Name updated 1299863 APPROVED
2002-08-07 CPG2  CPG2 protein      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-08-07 Syne1  nesprin-1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains have multiple, clustered spectrin-repeats 634176
gene_expression colocalizes with LAP1, emerin and lamins at the nuclear envelope 634176
gene_process maintains structural integrity and nuclear organization 634176
gene_regulation induced in adult visual cortical areas in response to light 632616