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 enable neurexin family protein binding activity; phosphatase binding activity; and phospholipid binding activity. Predicted to be involved in positive regulation of mucus secretion and vesicle docking involved in exocytosis. Predicted to act upstream of or within protein localization to plasma membrane. Predicted to be located in melanosome and membrane. Predicted to be extrinsic component of plasma membrane. Predicted to be active in exocytic vesicle and plasma membrane. 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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21144,272,870 - 144,379,310 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1144,273,360 - 144,379,222 (+)Ensembl
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_6.0 Ensembl1156,335,279 - 156,354,353 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1154,579,949 - 154,599,430 (+)EnsemblRnor6.0rn6Rnor6.0
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 alpha  (ISO)
all-trans-retinoic acid  (ISO)
antirheumatic drug  (ISO)
aristolochic acid  (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  (EXP,ISO)
PCB138  (EXP)
perfluorohexanesulfonic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
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)
temozolomide  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trichloroethene  (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

Biological Process

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 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1144,273,360 - 144,379,222 (+)Ensembl
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_6.0 Ensembl1156,335,279 - 156,354,353 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1154,579,949 - 154,599,430 (+)EnsemblRnor6.0rn6Rnor6.0
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
GRCh381185,694,229 - 85,854,870 (-)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 - 85,406,976 (-)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
CanFam3.12113,639,054 - 13,756,332 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2113,688,338 - 13,755,414 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2113,505,757 - 13,623,017 (+)NCBI
ROS_Cfam_1.02113,819,767 - 13,937,016 (+)NCBI
UMICH_Zoey_3.12113,608,437 - 13,725,706 (+)NCBI
UNSW_CanFamBas_1.02113,680,690 - 13,797,966 (+)NCBI
UU_Cfam_GSD_1.02113,733,418 - 13,850,744 (+)NCBI
Sytl2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494771,978,205 - 72,082,188 (-)NCBI
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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1176,937,076 - 77,061,895 (-)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604348,660,500 - 48,785,835 (+)NCBIVero_WHO_p1.0
Sytl2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248454,092,206 - 4,220,599 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D1Mit21  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21144,314,913 - 144,315,053 (+)MAPPERmRatBN7.2
mRatBN7.21144,314,913 - 144,315,053 (-)MAPPERmRatBN7.2
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 Map11125.8RGD
RH 3.4 Map11125.8UniSTS
Cytogenetic Map1q32UniSTS
RH140314  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21144,378,823 - 144,378,964 (+)MAPPERmRatBN7.2
mRatBN7.21144,378,823 - 144,378,964 (-)MAPPERmRatBN7.2
Rnor_6.01156,334,640 - 156,334,780NCBIRnor6.0
Rnor_6.01154,599,033 - 154,599,173NCBIRnor6.0
Rnor_5.01160,863,008 - 160,863,148UniSTSRnor5.0
Rnor_5.01162,580,762 - 162,580,902UniSTSRnor5.0
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 (mRatBN7.2)
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)132356093162846471Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149393172159356837Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)157336763151090257Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)181591954219808434Rat
724529Cm16Cardiac mass QTL 162.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)187580395150700247Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)190508614173018436Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)190508614180359386Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)194494440172949803Rat
1331751Bp199Blood pressure QTL 1993.60022arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)194494440181830018Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)194494440198211706Rat
70209Niddm23Non-insulin dependent diabetes mellitus QTL 232.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)194494440198324465Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)194642722214537671Rat
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)1100357752183970443Rat
2317833Alcrsp19Alcohol response QTL 1912.40.001response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1100979852145979852Rat
1641897Alcrsp1Alcohol response QTL 1response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1100979852145979852Rat
2303591Gluco41Glucose level QTL 412blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1102168504147168504Rat
61370Mcs3Mammary carcinoma susceptibility QTL 32.15mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1102268556147268556Rat
1354623Rf46Renal function QTL 463.8blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)1102813953151162766Rat
1354591Cm36Cardiac mass QTL 364.1heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1102813953201278233Rat
1354615Cm32Cardiac mass QTL 325.2heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1102813953201278233Rat
1354606Bp246Blood pressure QTL 2463.6arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)1102813953218753816Rat
9590300Scort16Serum corticosterone level QTL 164.390.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1103111621148111621Rat
8694370Bw154Body weight QTL 1548.910.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)1103111621148111621Rat
631496Bp97Blood pressure QTL 973.08arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1106047847151047847Rat
1300158Bp173Blood pressure QTL 1733.48arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1115540693185145286Rat
7794788Mcs32Mammary carcinoma susceptibility QTL 322.61mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)1115540693238914717Rat
631199Cm23Cardiac mass QTL 234.60.0004heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1115585465172949803Rat
7421630Bp362Blood pressure QTL 3620.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1118608292241799120Rat
2313060Bss71Bone structure and strength QTL 712.60.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)1118944747163944747Rat
631205Bp196Blood pressure QTL 19640.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1118944897199050459Rat
1598850Bp297Blood pressure QTL 2972.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1121006655166006655Rat
1598866Bp287Blood pressure QTL 2875.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1121006655166006655Rat
61442Strs1Sensitivity to stroke QTL 17.4cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)1121767634166767634Rat
2293140Bp313Blood pressure QTL 313arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1121833674166833674Rat
631544Bp84Blood pressure QTL 845.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1123350408181759564Rat
1358189Cstrr1Cold stress response QTL 10.0001catecholamine amount (VT:0010543)urine norepinephrine level (CMO:0001629)1123350408182418476Rat
1641895Bp298Blood pressure QTL 298arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1123350408182418476Rat
1578770Stresp23Stress response QTL 23kidney sympathetic nerve activity (VT:0004050)stimulated renal sympathetic nerve activity to basal renal sympathetic nerve activity ratio (CMO:0001786)1123350408182418476Rat
631549Bp89Blood pressure QTL 895.7arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1123350581201284552Rat
634348Bp138Blood pressure QTL 138arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1125611501168883176Rat
9685799Bp375Blood pressure QTL 375arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1125611501170611501Rat
631654Bp107Blood pressure QTL 107arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1125611501170611501Rat
9685802Bp376Blood pressure QTL 376arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1126540680171540680Rat
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)1130636910175636910Rat
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)1130636910175636910Rat
631202Gluco13Glucose level QTL 130.0001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1131763437159756369Rat
6893347Bw98Body weight QTL 980.20.53body mass (VT:0001259)body weight (CMO:0000012)1133680936178680936Rat
6893361Bw104Body weight QTL 1040.590.27body mass (VT:0001259)body weight (CMO:0000012)1133680936178680936Rat
1558645Bw55Body weight QTL 553.20.004body mass (VT:0001259)body weight (CMO:0000012)1133680936178680936Rat
631206Niddm40Non-insulin dependent diabetes mellitus QTL 40blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1136745990163747690Rat
71118Thym1Thymus enlargement QTL 110.170.001thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1136829932181829932Rat
724550Thym3Thymus enlargement QTL 37.820.001thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1136829932181829932Rat
631519Pia11Pristane induced arthritis QTL 115.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1136830018181830018Rat
1598853Memor3Memory QTL 34.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)1143506580212458660Rat
61348Bp30Blood pressure QTL 302.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1144017057197814409Rat
70160Bw18Body weight QTL 185.7body mass (VT:0001259)body weight (CMO:0000012)1144267353196383635Rat
737828Hcas3Hepatocarcinoma susceptibility QTL 34.9liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)1144267353222987745Rat
2302378Insul11Insulin level QTL 113.25blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1144267353251128347Rat
634315Niddm45Non-insulin dependent diabetes mellitus QTL 457.16blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1144267916172949660Rat
61379Bp44Blood pressure QTL 4419.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1144267916174133260Rat

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_003753316 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_003753317 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_003753318 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006223409 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229687 (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_008759652 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008774621 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008774622 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008774624 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008774625 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008774626 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588095 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590515 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590516 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590517 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590518 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590519 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590520 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590521 (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
mRatBN7.2 Ensembl1144,362,125 - 144,379,222 (+)Ensembl
Rnor_6.0 Ensembl1154,579,949 - 154,599,430 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000103814   ⟹   ENSRNOP00000077270
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1144,273,360 - 144,379,221 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000114461   ⟹   ENSRNOP00000096638
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1144,273,360 - 144,379,221 (+)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_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_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_008757873   ⟸   XM_008759651
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006229759   ⟸   XM_006229697
- Peptide Label: isoform X11
- 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
RefSeq Acc Id: ENSRNOP00000096638   ⟸   ENSRNOT00000114461
RefSeq Acc Id: ENSRNOP00000077270   ⟸   ENSRNOT00000103814
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 (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: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 144343361 144343362 G A snv GK/FarMcwi (2019)
1 144347764 144347765 A G snv LEXF11/Stm (2020), FHH/EurMcwi (2019), LE/Stm (2019), LEXF4/Stm (2020), LEXF1C/Stm (2019)
1 144349536 144349537 G A snv LEXF2B/Stm (2019), LEXF3/Stm (2020), LH/MavRrrcAek (2020), M520/N (2020), MWF/Hsd (2019), SR/JrHsd (2020), SS/JrHsdMcwi (2019), WN/N (2020), M520/NRrrcMcwi (2019), FXLE18/Stm (2020), LEXF1A/Stm (2019), LEW/Crl (2019), F344/Stm (2019), F344/NCrl (2019), LEXF10A/StmMcwi (2020), BUF/N (2020), F344/DuCrl (2019), F344/N (2020), FXLE16/Stm (2020), LL/MavRrrcAek (2020), LN/MavRrrcAek (2020)
1 144349929 144349930 C T snv PVG/Seac (2019)
1 144350050 144350051 C T snv BUF/N (2020), F344/DuCrl (2019), F344/NCrl (2019), F344/Stm (2019), FHH/EurMcwi (2019), GK/FarMcwi (2019), LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LH/MavRrrcAek (2020), M520/N (2020), MR/N (2020), MWF/Hsd (2019), SHRSP/A3NCrl (2019), SR/JrHsd (2020), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), WKY/NCrl (2019), WKY/N (2020), WN/N (2020), FXLE18/Stm (2020), F344/N (2020), FXLE16/Stm (2020), LL/MavRrrcAek (2020), LN/MavRrrcAek (2020), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019)
1 144359743 144359744 C T snv PVG/Seac (2019)
1 144369954 144369955 C T snv BUF/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/Stm (2019), GK/FarMcwi (2019), LEW/Crl (2019), LEXF1A/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LH/MavRrrcAek (2020), M520/N (2020), MWF/Hsd (2019), SR/JrHsd (2020), SS/JrHsdMcwi (2019), WN/N (2020), F344/N (2020), FXLE16/Stm (2020), FXLE18/Stm (2020), HXB10/IpcvMcwi (2019), HXB2/IpcvMcwi (2019), HXB4/IpcvMcwi (2020), LL/MavRrrcAek (2020), LN/MavRrrcAek (2020), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), SHR/OlalpcvMcwi (2019), ACI/EurMcwi (2019), ACI/N (2020)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 156364582 156364583 C T snv BUF/N (2020), SS/JrHsdMcwi (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), LEW/Crl (2019), LEXF1A/Stm (2019), LEXF3/Stm (2020), LL/MavRrrcAek (2020), LN/MavRrrcAek (2020), M520/NRrrcMcwi (2019), MWF/Hsd (2019), SR/JrHsd (2020), F344/DuCrl (2019)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307647 AgrOrtholog
Ensembl Genes ENSRNOG00000030776 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000049878 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000039142 UniProtKB/TrEMBL
  ENSRNOP00000048585 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000077270 ENTREZGENE
  ENSRNOP00000096638 ENTREZGENE
Ensembl Transcript ENSRNOT00000042163 UniProtKB/TrEMBL
  ENSRNOT00000045048 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000103814 ENTREZGENE
  ENSRNOT00000114461 ENTREZGENE
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
Superfamily-SCOP SSF49562 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