Sytl2 (synaptotagmin-like 2) - Rat Genome Database
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Gene: Sytl2 (synaptotagmin-like 2) Rattus norvegicus
Analyze
Symbol: Sytl2
Name: synaptotagmin-like 2
RGD ID: 1307647
Description: Predicted to have neurexin family protein binding activity; phosphatase binding activity; and phospholipid binding activity. Predicted to be involved in several processes, including negative regulation of phosphatase activity; positive regulation of mucus secretion; and vesicle docking involved in exocytosis. Predicted to localize to exocytic vesicle; extrinsic component of plasma membrane; and melanosome. Orthologous to human SYTL2 (synaptotagmin like 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; acrylamide.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC361604; LOW QUALITY PROTEIN: synaptotagmin-like protein 2; MGC189337; synaptotagmin-like protein 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21144,272,870 - 144,379,310 (+)NCBI
Rnor_6.0 Ensembl1156,335,279 - 156,354,353 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1154,579,949 - 154,599,430 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01154,536,592 - 154,599,515 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.01156,334,298 - 156,440,327 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01160,800,567 - 160,863,654 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41146,977,959 - 147,084,664 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1142,493,600 - 142,599,739 (+)NCBICelera
Cytogenetic Map1q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
5-fluorouracil  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
choline  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (EXP,ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
entinostat  (ISO)
folic acid  (ISO)
genistein  (ISO)
hydrogen peroxide  (ISO)
indometacin  (ISO)
ketamine  (EXP)
L-methionine  (ISO)
leflunomide  (EXP)
methylmercury chloride  (ISO)
mitoxantrone  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
nickel sulfate  (ISO)
oxaliplatin  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
PCB138  (EXP)
propanal  (ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sunitinib  (ISO)
tamoxifen  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:8889548   PMID:11243866   PMID:11773082   PMID:12477932   PMID:16716193   PMID:17182843   PMID:18266782   PMID:18812475   PMID:19389623   PMID:24284068  


Genomics

Comparative Map Data
Sytl2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21144,272,870 - 144,379,310 (+)NCBI
Rnor_6.0 Ensembl1156,335,279 - 156,354,353 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1154,579,949 - 154,599,430 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01154,536,592 - 154,599,515 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.01156,334,298 - 156,440,327 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01160,800,567 - 160,863,654 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41146,977,959 - 147,084,664 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1142,493,600 - 142,599,739 (+)NCBICelera
Cytogenetic Map1q32NCBI
SYTL2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1185,694,224 - 85,811,159 (-)EnsemblGRCh38hg38GRCh38
GRCh381185,694,221 - 85,811,182 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371185,405,264 - 85,522,184 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361185,082,912 - 85,146,692 (-)NCBINCBI36hg18NCBI36
Build 341185,082,914 - 85,107,859NCBI
Celera1182,714,568 - 82,831,481 (-)NCBI
Cytogenetic Map11q14.1NCBI
HuRef1181,702,610 - 81,819,526 (-)NCBIHuRef
CHM1_11185,290,075 - 85,407,000 (-)NCBICHM1_1
Sytl2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39789,951,421 - 90,059,927 (+)NCBIGRCm39mm39
GRCm39 Ensembl789,951,460 - 90,059,927 (+)Ensembl
GRCm38790,302,211 - 90,410,719 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl790,302,252 - 90,410,719 (+)EnsemblGRCm38mm10GRCm38
MGSCv37797,497,209 - 97,558,949 (+)NCBIGRCm37mm9NCBIm37
MGSCv36790,223,891 - 90,285,897 (+)NCBImm8
Celera787,675,751 - 87,737,560 (+)NCBICelera
Cytogenetic Map7E1NCBI
Sytl2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554147,104,268 - 7,174,001 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554147,104,239 - 7,172,791 (+)NCBIChiLan1.0ChiLan1.0
SYTL2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11184,358,095 - 84,474,422 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1184,358,155 - 84,421,509 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01180,749,861 - 80,866,479 (-)NCBIMhudiblu_PPA_v0panPan3
SYTL2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2113,688,338 - 13,755,414 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12113,639,054 - 13,756,332 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Sytl2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493649813,577,839 - 13,681,782 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYTL2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl919,617,291 - 19,734,636 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1919,617,287 - 19,763,439 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2921,887,423 - 22,023,108 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SYTL2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1176,937,076 - 77,061,895 (-)NCBI
Sytl2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248454,092,206 - 4,220,599 (+)NCBI

Position Markers
D1Mit21  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01154,535,070 - 154,535,209NCBIRnor6.0
Rnor_6.01156,399,063 - 156,399,202NCBIRnor6.0
Rnor_5.01162,645,185 - 162,645,324UniSTSRnor5.0
Rnor_5.01160,799,045 - 160,799,184UniSTSRnor5.0
RGSC_v3.41147,020,341 - 147,020,480UniSTSRGSC3.4
RGSC_v3.41147,020,340 - 147,020,480RGDRGSC3.4
RGSC_v3.11147,098,747 - 147,098,886RGD
Celera1142,535,144 - 142,535,283UniSTS
RH 3.4 Map11125.8UniSTS
RH 3.4 Map11125.8RGD
Cytogenetic Map1q32UniSTS
RH140314  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01154,599,033 - 154,599,173NCBIRnor6.0
Rnor_6.01156,334,640 - 156,334,780NCBIRnor6.0
Rnor_5.01162,580,762 - 162,580,902UniSTSRnor5.0
Rnor_5.01160,863,008 - 160,863,148UniSTSRnor5.0
RGSC_v3.41147,084,260 - 147,084,400UniSTSRGSC3.4
Celera1142,599,257 - 142,599,397UniSTS
RH 3.4 Map11129.0UniSTS
Cytogenetic Map1q32UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134993530173445086Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135377692217372257Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)149147799156446783Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149578577169852184Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149578693217054291Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)158354072161711996Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)182788437239853971Rat
724529Cm16Cardiac mass QTL 162.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)190804143161321256Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)194201400184846632Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)194201400197187904Rat
724567Tcas6Tongue tumor susceptibility QTL 66.85tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)195304961156446783Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)199983293188289386Rat
1331751Bp199Blood pressure QTL 1993.60022arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)199983293198656062Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)199983293216213510Rat
70209Niddm23Non-insulin dependent diabetes mellitus QTL 232.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)199983293216325819Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1100131562236763528Rat
8655649Arrd1Age-related retinal degeneration QTL 14.89retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1106002252202571904Rat
61370Mcs3Mammary carcinoma susceptibility QTL 32.15mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1108057233167517487Rat
1354623Rf46Renal function QTL 463.8blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)1108986301161784422Rat
1354591Cm36Cardiac mass QTL 364.1heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1108986301219232156Rat
1354615Cm32Cardiac mass QTL 325.2heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1108986301219232156Rat
1354606Bp246Blood pressure QTL 2463.6arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)1108986301238830534Rat
2303591Gluco41Glucose level QTL 412blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1109634374154634374Rat
9590300Scort16Serum corticosterone level QTL 164.390.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1110620749155620749Rat
8694370Bw154Body weight QTL 1548.910.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)1110620749155620749Rat
61399Tcat1Tongue tumor resistance QTL 13.3tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 5 mm (CMO:0001879)1111446783156446783Rat
61346Rf2Renal disease susceptibility QTL 23.7urine protein amount (VT:0005160)urine protein level (CMO:0000591)1111446783156446783Rat
631496Bp97Blood pressure QTL 973.08arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1113593576158593576Rat
1300158Bp173Blood pressure QTL 1733.48arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1122614824201146953Rat
7794788Mcs32Mammary carcinoma susceptibility QTL 322.61mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)1122614824262664716Rat
2313060Bss71Bone structure and strength QTL 712.60.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)1124090312169090312Rat
631199Cm23Cardiac mass QTL 234.60.0004heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1124603592188289386Rat
7421630Bp362Blood pressure QTL 3620.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1125875758262433692Rat
631205Bp196Blood pressure QTL 19640.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1126240667217054291Rat
2293140Bp313Blood pressure QTL 313arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1129208943174208943Rat
631544Bp84Blood pressure QTL 845.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1130779148198585664Rat
1358189Cstrr1Cold stress response QTL 10.0001catecholamine amount (VT:0010543)urine norepinephrine level (CMO:0001629)1130779148199254774Rat
1578770Stresp23Stress response QTL 23kidney sympathetic nerve activity (VT:0004050)stimulated renal sympathetic nerve activity to basal renal sympathetic nerve activity ratio (CMO:0001786)1130779148199254774Rat
1641895Bp298Blood pressure QTL 298arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1130779148199254774Rat
631549Bp89Blood pressure QTL 895.7arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1130779320219238476Rat
1598850Bp297Blood pressure QTL 2972.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1131334152176334152Rat
1598866Bp287Blood pressure QTL 2875.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1131334152176334152Rat
631654Bp107Blood pressure QTL 107arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1133076978178076978Rat
9685799Bp375Blood pressure QTL 375arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1133076978178076978Rat
634348Bp138Blood pressure QTL 138arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1133076978184188922Rat
61442Strs1Sensitivity to stroke QTL 17.4cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)1133946489178946489Rat
9685802Bp376Blood pressure QTL 376arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1134089429179089429Rat
724562Rends1Renal damage susceptibility QTL 10.05kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)1137787261236763528Rat
61341Bp26Blood pressure QTL 26arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1137787261236763528Rat
631202Gluco13Glucose level QTL 130.0001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1139523928170246858Rat
738006Anxrr14Anxiety related response QTL 1440.00035locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1141296374186296374Rat
738028Anxrr12Anxiety related response QTL 124.90.00001locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1141296374186296374Rat
1558645Bw55Body weight QTL 553.20.004body mass (VT:0001259)body weight (CMO:0000012)1144395993189395993Rat
6893347Bw98Body weight QTL 980.20.53body mass (VT:0001259)body weight (CMO:0000012)1144395993189395993Rat
6893361Bw104Body weight QTL 1040.590.27body mass (VT:0001259)body weight (CMO:0000012)1144395993189395993Rat
7771612Cm80Cardiac mass QTL 808.4heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)1144634295241482368Rat
631206Niddm40Non-insulin dependent diabetes mellitus QTL 40blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1144723107174343537Rat
71118Thym1Thymus enlargement QTL 110.170.001thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1153655976198655976Rat
724550Thym3Thymus enlargement QTL 37.820.001thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1153655976198655976Rat
631519Pia11Pristane induced arthritis QTL 115.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1153656062198656062Rat
1598853Memor3Memory QTL 34.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)1153834077232297227Rat
61348Bp30Blood pressure QTL 302.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1154337847215828102Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:507
Count of miRNA genes:222
Interacting mature miRNAs:283
Transcripts:ENSRNOT00000042163, ENSRNOT00000045048
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 11 1 1 25 20 7 11 1
Low 30 53 37 19 37 7 9 48 15 34 7
Below cutoff 2 3 4 4 4 1 4 1 1 3

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001108492 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229697 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008759651 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082402 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082407 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082411 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082420 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082423 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082427 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082431 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082435 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082436 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082440 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC168993 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473956 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK842035 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000041 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000042163   ⟹   ENSRNOP00000039142
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1156,335,279 - 156,354,353 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000045048   ⟹   ENSRNOP00000048585
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1154,579,949 - 154,599,430 (+)Ensembl
RefSeq Acc Id: NM_001108492   ⟹   NP_001101962
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,273,360 - 144,379,224 (+)NCBI
RefSeq Acc Id: XM_003753316   ⟹   XP_003753364
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1142,493,608 - 142,599,739 (+)NCBI
Sequence:
RefSeq Acc Id: XM_003753317   ⟹   XP_003753365
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1142,493,608 - 142,599,739 (+)NCBI
Sequence:
RefSeq Acc Id: XM_003753318   ⟹   XP_003753366
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1142,493,608 - 142,599,739 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006223409   ⟹   XP_006223471
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1142,572,756 - 142,599,739 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006229687   ⟹   XP_006229749
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01154,536,592 - 154,599,515 (+)NCBI
Rnor_5.01160,800,567 - 160,863,654 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006229697   ⟹   XP_006229759
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,353,107 - 144,379,310 (+)NCBI
Rnor_6.01156,334,298 - 156,361,590 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008759651   ⟹   XP_008757873
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,272,872 - 144,379,310 (+)NCBI
Rnor_6.01156,334,298 - 156,440,326 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008759652   ⟹   XP_008757874
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01156,334,298 - 156,440,326 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008774621   ⟹   XP_008772843
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1142,493,601 - 142,599,739 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008774622   ⟹   XP_008772844
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1142,493,743 - 142,599,739 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008774624   ⟹   XP_008772846
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1142,493,601 - 142,599,739 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008774625   ⟹   XP_008772847
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1142,493,601 - 142,599,739 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008774626   ⟹   XP_008772848
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1142,493,600 - 142,599,739 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588095   ⟹   XP_017443584
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1142,576,364 - 142,599,739 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017590515   ⟹   XP_017446004
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01156,334,298 - 156,440,326 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017590516   ⟹   XP_017446005
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01156,334,298 - 156,440,326 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017590517   ⟹   XP_017446006
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01156,334,298 - 156,440,327 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017590518   ⟹   XP_017446007
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01156,334,298 - 156,440,315 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017590519   ⟹   XP_017446008
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01156,334,298 - 156,440,315 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017590520   ⟹   XP_017446009
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01156,334,298 - 156,440,316 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017590521   ⟹   XP_017446010
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01156,334,298 - 156,357,981 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039082402   ⟹   XP_038938330
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,272,872 - 144,379,310 (+)NCBI
RefSeq Acc Id: XM_039082407   ⟹   XP_038938335
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,272,870 - 144,379,310 (+)NCBI
RefSeq Acc Id: XM_039082411   ⟹   XP_038938339
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,272,870 - 144,379,310 (+)NCBI
RefSeq Acc Id: XM_039082420   ⟹   XP_038938348
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,272,873 - 144,379,310 (+)NCBI
RefSeq Acc Id: XM_039082423   ⟹   XP_038938351
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,273,342 - 144,379,310 (+)NCBI
RefSeq Acc Id: XM_039082427   ⟹   XP_038938355
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,273,342 - 144,379,310 (+)NCBI
RefSeq Acc Id: XM_039082431   ⟹   XP_038938359
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,273,337 - 144,379,310 (+)NCBI
RefSeq Acc Id: XM_039082435   ⟹   XP_038938363
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,273,336 - 144,379,310 (+)NCBI
RefSeq Acc Id: XM_039082436   ⟹   XP_038938364
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,353,108 - 144,379,310 (+)NCBI
RefSeq Acc Id: XM_039082440   ⟹   XP_038938368
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,353,106 - 144,379,310 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_003753364   ⟸   XM_003753316
- Peptide Label: isoform X15
- Sequence:
RefSeq Acc Id: XP_003753366   ⟸   XM_003753318
- Peptide Label: isoform X17
- Sequence:
RefSeq Acc Id: XP_003753365   ⟸   XM_003753317
- Peptide Label: isoform X16
- Sequence:
RefSeq Acc Id: XP_006223471   ⟸   XM_006223409
- Peptide Label: isoform X19
- Sequence:
RefSeq Acc Id: XP_006229749   ⟸   XM_006229687
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008772843   ⟸   XM_008774621
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_008772848   ⟸   XM_008774626
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: XP_008772846   ⟸   XM_008774624
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: XP_008772847   ⟸   XM_008774625
- Peptide Label: isoform X13
- Sequence:
RefSeq Acc Id: XP_008772844   ⟸   XM_008774622
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_008757873   ⟸   XM_008759651
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008757874   ⟸   XM_008759652
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006229759   ⟸   XM_006229697
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_017443584   ⟸   XM_017588095
- Peptide Label: isoform X18
- Sequence:
RefSeq Acc Id: XP_017446006   ⟸   XM_017590517
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017446005   ⟸   XM_017590516
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017446004   ⟸   XM_017590515
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017446009   ⟸   XM_017590520
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017446008   ⟸   XM_017590519
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017446007   ⟸   XM_017590518
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017446010   ⟸   XM_017590521
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: ENSRNOP00000048585   ⟸   ENSRNOT00000045048
RefSeq Acc Id: ENSRNOP00000039142   ⟸   ENSRNOT00000042163
RefSeq Acc Id: XP_038938335   ⟸   XM_039082407
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038938339   ⟸   XM_039082411
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038938330   ⟸   XM_039082402
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038938348   ⟸   XM_039082420
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038938363   ⟸   XM_039082435
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038938359   ⟸   XM_039082431
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038938351   ⟸   XM_039082423
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038938355   ⟸   XM_039082427
- Peptide Label: isoform X7
RefSeq Acc Id: NP_001101962   ⟸   NM_001108492
RefSeq Acc Id: XP_038938368   ⟸   XM_039082440
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038938364   ⟸   XM_039082436
- Peptide Label: isoform X10
Protein Domains
C2

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307647 AgrOrtholog
Ensembl Genes ENSRNOG00000030776 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000049878 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000039142 UniProtKB/TrEMBL
  ENSRNOP00000048585 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000042163 UniProtKB/TrEMBL
  ENSRNOT00000045048 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.150 UniProtKB/TrEMBL
InterPro C2_Ca-dep UniProtKB/TrEMBL
  C2_domain_sf UniProtKB/TrEMBL
  SYTL1-5_C2B UniProtKB/TrEMBL
  SYTL2 UniProtKB/TrEMBL
NCBI Gene 361604 ENTREZGENE
PANTHER PTHR45716:SF5 UniProtKB/TrEMBL
Pfam PF00168 UniProtKB/TrEMBL
PhenoGen Sytl2 PhenoGen
PRINTS C2DOMAIN UniProtKB/TrEMBL
PROSITE PS50004 UniProtKB/TrEMBL
SMART SM00239 UniProtKB/TrEMBL
UniProt B5DFB1_RAT UniProtKB/TrEMBL
UniProt Secondary F1LN23 UniProtKB/TrEMBL
  F1LNJ5 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Sytl2  synaptotagmin-like 2   Sytl2_predicted  synaptotagmin-like 2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Sytl2_predicted  synaptotagmin-like 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED