Cadps2 (calcium dependent secretion activator 2) - Rat Genome Database

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Gene: Cadps2 (calcium dependent secretion activator 2) Rattus norvegicus
Analyze
Symbol: Cadps2
Name: calcium dependent secretion activator 2
RGD ID: 1559440
Description: Predicted to enable metal ion binding activity. Predicted to be involved in exocytosis and positive regulation of exocytosis. Predicted to act upstream of or within cellular response to starvation; hematopoietic stem cell homeostasis; and synaptic vesicle priming. Predicted to be located in cytoplasmic vesicle; nucleoplasm; and synaptic membrane. Predicted to be active in glutamatergic synapse; parallel fiber to Purkinje cell synapse; and presynapse. Orthologous to human CADPS2 (calcium dependent secretion activator 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl; 3H-1,2-dithiole-3-thione.
Type: protein-coding
RefSeq Status: MODEL
Also known as: Ca++-dependent secretion activator 2; Ca2+ dependent secretion activator 2; Ca2+-dependent activator protein for secretion 2; calcium-dependent secretion activator 2; LOC312166; RGD1559440; similar to Ca2+-dependent activator for secretion 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
mRatBN7.2451,780,415 - 52,309,641 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl451,781,053 - 52,309,829 (-)Ensembl
Rnor_6.0450,326,447 - 50,861,161 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl450,326,442 - 50,860,756 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0450,109,220 - 50,640,613 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4449,658,535 - 50,206,014 (-)NCBIRGSC3.4rn4RGSC3.4
Celera446,974,764 - 47,500,739 (-)NCBICelera
Cytogenetic Map4q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP)
6-propyl-2-thiouracil  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
amiodarone  (EXP)
aristolochic acid  (EXP,ISO)
benzbromarone  (EXP)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP)
bisphenol F  (ISO)
cadmium atom  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
cisplatin  (EXP,ISO)
clofibrate  (EXP)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
dicrotophos  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
etoposide  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
GW 4064  (ISO)
L-ethionine  (EXP)
L-methionine  (ISO)
lipopolysaccharide  (ISO)
methylmercury chloride  (ISO)
mitomycin C  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-nitrosodiethylamine  (ISO)
O-methyleugenol  (ISO)
omeprazole  (EXP)
perfluorooctanoic acid  (EXP)
permethrin  (EXP)
phenobarbital  (ISO)
pirinixic acid  (EXP,ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
quercetin  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sulforaphane  (ISO)
sunitinib  (ISO)
testosterone  (ISO)
thioacetamide  (EXP)
tributylstannane  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:14715936   PMID:15932944   PMID:21040848   PMID:23260145   PMID:25374362   PMID:25437547  


Genomics

Comparative Map Data
Cadps2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2451,780,415 - 52,309,641 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl451,781,053 - 52,309,829 (-)Ensembl
Rnor_6.0450,326,447 - 50,861,161 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl450,326,442 - 50,860,756 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0450,109,220 - 50,640,613 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4449,658,535 - 50,206,014 (-)NCBIRGSC3.4rn4RGSC3.4
Celera446,974,764 - 47,500,739 (-)NCBICelera
Cytogenetic Map4q22NCBI
CADPS2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl7122,318,411 - 122,886,759 (-)EnsemblGRCh38hg38GRCh38
GRCh387122,318,411 - 122,886,500 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh377121,958,465 - 122,526,514 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 367121,745,714 - 122,313,790 (-)NCBINCBI36hg18NCBI36
Build 347121,553,403 - 122,120,465NCBI
Celera7116,762,799 - 117,331,572 (-)NCBI
Cytogenetic Map7q31.32NCBI
HuRef7116,321,864 - 116,889,045 (-)NCBIHuRef
CHM1_17121,891,856 - 122,459,852 (-)NCBICHM1_1
CRA_TCAGchr7v27121,353,164 - 121,915,693 (-)NCBI
Cadps2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39623,262,772 - 23,840,662 (-)NCBIGRCm39mm39
GRCm39 Ensembl623,262,772 - 23,839,420 (-)Ensembl
GRCm38623,262,773 - 23,841,175 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl623,262,773 - 23,839,421 (-)EnsemblGRCm38mm10GRCm38
MGSCv37623,212,838 - 23,789,300 (-)NCBIGRCm37mm9NCBIm37
MGSCv36623,212,839 - 23,789,139 (-)NCBImm8
Celera623,306,392 - 23,862,052 (-)NCBICelera
Cytogenetic Map6A3.1NCBI
Cadps2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554793,961,731 - 4,485,710 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554793,961,877 - 4,485,710 (-)NCBIChiLan1.0ChiLan1.0
CADPS2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17127,013,043 - 127,579,665 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7127,014,772 - 127,579,249 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v07114,328,933 - 114,896,388 (-)NCBIMhudiblu_PPA_v0panPan3
CADPS2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11460,109,253 - 60,465,982 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1460,107,538 - 60,556,817 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1459,530,071 - 59,982,436 (-)NCBI
ROS_Cfam_1.01460,148,277 - 60,601,897 (-)NCBI
UMICH_Zoey_3.11460,238,319 - 60,691,363 (-)NCBI
UNSW_CanFamBas_1.01459,866,769 - 60,319,711 (-)NCBI
UU_Cfam_GSD_1.01460,244,197 - 60,696,999 (-)NCBI
Cadps2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511849,191,231 - 49,699,089 (-)NCBI
SpeTri2.0NW_0049366052,505,064 - 3,012,322 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CADPS2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1824,372,544 - 24,867,284 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11824,372,547 - 24,867,287 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21825,969,731 - 26,464,337 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CADPS2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12191,117,749 - 91,669,284 (-)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604211,821,174 - 12,425,811 (+)NCBIVero_WHO_p1.0
Cadps2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462478313,142,036 - 13,701,430 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
AW550108  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2451,780,690 - 51,780,826 (+)MAPPERmRatBN7.2
Rnor_6.0450,326,719 - 50,326,854NCBIRnor6.0
Rnor_5.0450,109,487 - 50,109,622UniSTSRnor5.0
RGSC_v3.4449,658,806 - 49,658,941UniSTSRGSC3.4
Celera446,975,036 - 46,975,171UniSTS
Cytogenetic Map4q22UniSTS
GDB:1317954  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2451,955,795 - 51,955,941 (+)MAPPERmRatBN7.2
Rnor_6.0450,503,086 - 50,503,231NCBIRnor6.0
Rnor_5.0450,283,907 - 50,284,052UniSTSRnor5.0
RGSC_v3.4449,835,751 - 49,835,896UniSTSRGSC3.4
Celera447,150,413 - 47,150,558UniSTS
Cytogenetic Map4q22UniSTS
RH137681  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2451,943,397 - 51,943,518 (+)MAPPERmRatBN7.2
Rnor_6.0450,490,204 - 50,490,324NCBIRnor6.0
Rnor_5.0450,271,025 - 50,271,145UniSTSRnor5.0
RGSC_v3.4449,823,353 - 49,823,473UniSTSRGSC3.4
Celera447,138,016 - 47,138,136UniSTS
RH 3.4 Map4297.1UniSTS
Cytogenetic Map4q22UniSTS
PMC126259P3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2451,780,477 - 51,780,600 (+)MAPPERmRatBN7.2
Rnor_6.0450,326,506 - 50,326,628NCBIRnor6.0
Rnor_5.0450,109,274 - 50,109,396UniSTSRnor5.0
RGSC_v3.4449,658,593 - 49,658,715UniSTSRGSC3.4
Celera446,974,823 - 46,974,945UniSTS
Cytogenetic Map4q22UniSTS
BE119864  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2451,798,315 - 51,798,508 (+)MAPPERmRatBN7.2
Rnor_6.0450,344,342 - 50,344,534NCBIRnor6.0
Rnor_5.0450,127,110 - 50,127,302UniSTSRnor5.0
RGSC_v3.4449,676,430 - 49,676,622UniSTSRGSC3.4
Celera446,992,657 - 46,992,849UniSTS
RH 3.4 Map4297.3UniSTS
Cytogenetic Map4q22UniSTS
AU049560  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2452,262,878 - 52,263,163 (+)MAPPERmRatBN7.2
Rnor_6.0450,804,890 - 50,805,174NCBIRnor6.0
Rnor_5.0450,584,618 - 50,584,902UniSTSRnor5.0
RGSC_v3.4450,159,492 - 50,159,776UniSTSRGSC3.4
Celera447,454,133 - 47,454,417UniSTS
Cytogenetic Map4q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829457114705Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521917856647776Rat
6478724Anxrr35Anxiety related response QTL 350.00449defecation behavior trait (VT:0010462)defecation measurement (CMO:0000997)41008408955084089Rat
6478766Anxrr47Anxiety related response QTL 470.09637locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)41008408955084089Rat
6478769Anxrr48Anxiety related response QTL 480.02514locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)41008408955084089Rat
8694374Bw155Body weight QTL 1553.390.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)41008408955084089Rat
9590304Scort17Serum corticosterone level QTL 174.960.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)41008408955084089Rat
8552906Pigfal3Plasma insulin-like growth factor 1 level QTL 3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)41008408955084089Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2303585Bw86Body weight QTL 864body mass (VT:0001259)body weight (CMO:0000012)41467806559678065Rat
2313401Anxrr27Anxiety related response QTL 27aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)41793350862933508Rat
61412Pia2Pristane induced arthritis QTL 23.9joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)42133334362278020Rat
6909122Insul22Insulin level QTL 224.63blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)42690728575585128Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)42690728575585128Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)42949419581006281Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)432583980114627242Rat
11530004Niddm71Non-insulin dependent diabetes mellitus QTL 710.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)43258419952754138Rat
8552782Vie1Viral induced encephalitis QTL 126.4brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8552801Bw143Body weight QTL 1437.3body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)43443048482490359Rat
8552809Vie5Viral induced encephalitis QTL 525.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8655961Kidm43Kidney mass QTL 4318kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)436303261103194984Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)438465774146803430Rat
61475Aia2Adjuvant induced arthritis QTL 25.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)43950527573892441Rat
1331807Rf31Renal function QTL 312.988urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)43952426474726312Rat
1300139Hrtrt6Heart rate QTL 62.85heart pumping trait (VT:2000009)heart rate (CMO:0000002)439524264116179656Rat
61445Strs3Sensitivity to stroke QTL 33cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)44043338885433388Rat
8694439Bw168Body weight QTL 1689.570.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)44043341485433414Rat
6893678Bw108Body weight QTL 1082.60.006body mass (VT:0001259)body weight (CMO:0000012)44345797688457976Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)444463908148090542Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)444463908148090542Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)445456990146803430Rat
10450818Scl76Serum cholesterol level QTL 763.60.01blood VLDL cholesterol amount (VT:0005144)blood high density lipoprotein cholesterol level (CMO:0000052)44917811657114705Rat
10450821Scl77Serum cholesterol level QTL 774.10.01blood VLDL cholesterol amount (VT:0005144)blood high density lipoprotein cholesterol level (CMO:0000052)44917811657114705Rat
10450825Scl78Serum cholesterol level QTL 783.70.01blood VLDL cholesterol amount (VT:0005144)blood low density lipoprotein cholesterol level (CMO:0000053)44917811657114705Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)450119848146803430Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:448
Count of miRNA genes:177
Interacting mature miRNAs:196
Transcripts:ENSRNOT00000010537, ENSRNOT00000064206, ENSRNOT00000065088, ENSRNOT00000067030, ENSRNOT00000068404, ENSRNOT00000072896, ENSRNOT00000074651
Prediction methods:Microtar, Miranda, Rnahybrid
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 2 11 9 9 42 10 14 11
Low 1 43 46 32 19 32 8 10 32 25 27 8
Below cutoff 1

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_001060172 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_002726331 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_002729291 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_003749705 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_003753870 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224832 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224837 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224838 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224839 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236147 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236152 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236153 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236154 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592957 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592958 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592959 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592961 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592962 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592964 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602758 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602759 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602760 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602762 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602763 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602764 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602765 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108609 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108610 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108611 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108612 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108613 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108614 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_231528 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473959 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000141 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000068404   ⟹   ENSRNOP00000060154
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl451,781,053 - 52,309,264 (-)Ensembl
Rnor_6.0 Ensembl450,326,442 - 50,860,756 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000108432   ⟹   ENSRNOP00000097144
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl451,781,053 - 52,309,829 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000114656   ⟹   ENSRNOP00000077369
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl451,781,053 - 52,309,829 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000114880   ⟹   ENSRNOP00000092324
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl451,781,053 - 52,309,829 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000117045   ⟹   ENSRNOP00000085438
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl451,781,053 - 52,309,829 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000119022   ⟹   ENSRNOP00000080739
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl451,781,053 - 52,309,652 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000119282   ⟹   ENSRNOP00000077855
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl451,781,053 - 52,309,829 (-)Ensembl
RefSeq Acc Id: XM_002729291   ⟹   XP_002729337
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,780,415 - 52,309,641 (-)NCBI
Rnor_6.0450,326,447 - 50,861,161 (-)NCBI
Rnor_5.0450,109,220 - 50,640,613 (-)NCBI
RGSC_v3.4449,658,535 - 50,206,014 (-)RGD
Sequence:
RefSeq Acc Id: XM_003749705   ⟹   XP_003749753
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,781,174 - 52,309,264 (-)NCBI
Rnor_6.0450,327,202 - 50,860,930 (-)NCBI
Rnor_5.0450,109,220 - 50,640,613 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006236147   ⟹   XP_006236209
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,780,415 - 52,309,639 (-)NCBI
Rnor_6.0450,326,447 - 50,861,161 (-)NCBI
Rnor_5.0450,109,220 - 50,640,613 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006236152   ⟹   XP_006236214
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,781,174 - 52,309,264 (-)NCBI
Rnor_6.0450,327,202 - 50,860,930 (-)NCBI
Rnor_5.0450,109,220 - 50,640,613 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006236153   ⟹   XP_006236215
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,781,174 - 52,309,264 (-)NCBI
Rnor_6.0450,327,202 - 50,860,930 (-)NCBI
Rnor_5.0450,109,220 - 50,640,613 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006236154   ⟹   XP_006236216
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,781,174 - 52,309,264 (-)NCBI
Rnor_6.0450,327,202 - 50,860,930 (-)NCBI
Rnor_5.0450,109,220 - 50,640,613 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592957   ⟹   XP_017448446
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,780,415 - 52,309,640 (-)NCBI
Rnor_6.0450,326,447 - 50,861,161 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592958   ⟹   XP_017448447
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,780,415 - 52,309,640 (-)NCBI
Rnor_6.0450,326,447 - 50,861,161 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592959   ⟹   XP_017448448
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,781,174 - 52,309,264 (-)NCBI
Rnor_6.0450,326,447 - 50,861,161 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592960   ⟹   XP_017448449
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,780,415 - 52,309,640 (-)NCBI
Rnor_6.0450,326,447 - 50,861,161 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592961   ⟹   XP_017448450
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,780,415 - 52,309,639 (-)NCBI
Rnor_6.0450,326,447 - 50,861,161 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592962   ⟹   XP_017448451
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,781,174 - 52,309,264 (-)NCBI
Rnor_6.0450,326,447 - 50,861,161 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592963   ⟹   XP_017448452
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,781,174 - 52,309,264 (-)NCBI
Rnor_6.0450,326,447 - 50,861,161 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039108609   ⟹   XP_038964537
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,780,415 - 52,309,640 (-)NCBI
RefSeq Acc Id: XM_039108610   ⟹   XP_038964538
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,780,415 - 52,309,640 (-)NCBI
RefSeq Acc Id: XM_039108611   ⟹   XP_038964539
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,781,174 - 52,309,264 (-)NCBI
RefSeq Acc Id: XM_039108612   ⟹   XP_038964540
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,781,174 - 52,309,264 (-)NCBI
RefSeq Acc Id: XM_039108613   ⟹   XP_038964541
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,781,174 - 52,309,264 (-)NCBI
RefSeq Acc Id: XM_039108614   ⟹   XP_038964542
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,781,174 - 52,309,264 (-)NCBI
RefSeq Acc Id: XM_231528   ⟹   XP_231528
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,781,174 - 52,309,264 (-)NCBI
Rnor_6.0450,327,202 - 50,860,930 (-)NCBI
Rnor_5.0450,109,220 - 50,640,613 (-)NCBI
RGSC_v3.4449,658,535 - 50,206,014 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: XP_231528   ⟸   XM_231528
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_002729337   ⟸   XM_002729291
- Peptide Label: isoform X18
- Sequence:
RefSeq Acc Id: XP_003749753   ⟸   XM_003749705
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: XP_006236216   ⟸   XM_006236154
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_006236215   ⟸   XM_006236153
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_006236214   ⟸   XM_006236152
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_006236209   ⟸   XM_006236147
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017448446   ⟸   XM_017592957
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017448452   ⟸   XM_017592963
- Peptide Label: isoform X19
- Sequence:
RefSeq Acc Id: XP_017448449   ⟸   XM_017592960
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017448451   ⟸   XM_017592962
- Peptide Label: isoform X15
- Sequence:
RefSeq Acc Id: XP_017448447   ⟸   XM_017592958
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017448450   ⟸   XM_017592961
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: XP_017448448   ⟸   XM_017592959
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000060154   ⟸   ENSRNOT00000068404
RefSeq Acc Id: XP_038964538   ⟸   XM_039108610
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038964537   ⟸   XM_039108609
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038964542   ⟸   XM_039108614
- Peptide Label: isoform X20
RefSeq Acc Id: XP_038964540   ⟸   XM_039108612
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038964541   ⟸   XM_039108613
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038964539   ⟸   XM_039108611
- Peptide Label: isoform X13
RefSeq Acc Id: ENSRNOP00000077855   ⟸   ENSRNOT00000119282
RefSeq Acc Id: ENSRNOP00000080739   ⟸   ENSRNOT00000119022
RefSeq Acc Id: ENSRNOP00000097144   ⟸   ENSRNOT00000108432
RefSeq Acc Id: ENSRNOP00000092324   ⟸   ENSRNOT00000114880
RefSeq Acc Id: ENSRNOP00000085438   ⟸   ENSRNOT00000117045
RefSeq Acc Id: ENSRNOP00000077369   ⟸   ENSRNOT00000114656
Protein Domains
C2   MHD1   PH

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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 50134947 50134948 T C snv RCS/Kyo (KyushuU)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 49792406 49792407 A G snv SR/JrHsd (MCW)
4 50205912 50205913 C T snv SHRSP/Gcrc (ICL), SHRSP/Gcrc (MDC)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1559440 AgrOrtholog
Ensembl Genes ENSRNOG00000007636 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000060154 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000077369 ENTREZGENE
  ENSRNOP00000077855 ENTREZGENE
  ENSRNOP00000080739 ENTREZGENE
  ENSRNOP00000085438 ENTREZGENE
  ENSRNOP00000092324 ENTREZGENE
Ensembl Transcript ENSRNOT00000068404 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000114656 ENTREZGENE
  ENSRNOT00000114880 ENTREZGENE
  ENSRNOT00000117045 ENTREZGENE
  ENSRNOT00000119022 ENTREZGENE
  ENSRNOT00000119282 ENTREZGENE
Gene3D-CATH 2.30.29.30 UniProtKB/TrEMBL
InterPro C2_dom UniProtKB/TrEMBL
  Ca-dep_secretion_activator UniProtKB/TrEMBL
  CAPS UniProtKB/TrEMBL
  Munc13_1 UniProtKB/TrEMBL
  PH_like_dom UniProtKB/TrEMBL
  Pleckstrin_homology UniProtKB/TrEMBL
NCBI Gene 312166 ENTREZGENE
PANTHER PTHR12166 UniProtKB/TrEMBL
Pfam DUF1041 UniProtKB/TrEMBL
  PF00169 UniProtKB/TrEMBL
PhenoGen Cadps2 PhenoGen
PROSITE MHD1 UniProtKB/TrEMBL
  PH_DOMAIN UniProtKB/TrEMBL
  PS50004 UniProtKB/TrEMBL
SMART DUF1041 UniProtKB/TrEMBL
  SM00233 UniProtKB/TrEMBL
UniProt F1LWT1_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-22 Cadps2  calcium dependent secretion activator 2  Cadps2  Ca2+ dependent secretion activator 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-11 Cadps2  Ca2+ dependent secretion activator 2  Cadps2  Ca++-dependent secretion activator 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-29 Cadps2  Ca++-dependent secretion activator 2  Cadps2  Ca2+-dependent activator protein for secretion 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Cadps2  Ca2+-dependent activator protein for secretion 2  RGD1559440_predicted  similar to Ca2+-dependent activator for secretion protein 2 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1559440_predicted  similar to Ca2+-dependent activator for secretion protein 2 (predicted)  LOC312166  similar to Ca2+-dependent activator for secretion protein 2  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC312166  similar to Ca2+-dependent activator for secretion protein 2      Symbol and Name status set to provisional 70820 PROVISIONAL