Dclk1 (doublecortin-like kinase 1) - Rat Genome Database

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Gene: Dclk1 (doublecortin-like kinase 1) Rattus norvegicus
Analyze
Symbol: Dclk1
Name: doublecortin-like kinase 1
RGD ID: 68437
Description: Enables protein kinase activity. Involved in protein phosphorylation. Located in growth cone. Orthologous to human DCLK1 (doublecortin like kinase 1); INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: activity and neurotransmitter-induced early gene protein 4 (ania-4); Ania4; calcium/calmodulin-dependent protein kinase type I-like CPG16; Cpg16; Dcamkl1; double cortin and calcium/calmodulin-dependent protein kinase-like 1; doublecortin-like and CAM kinase-like 1; serine/threonine-protein kinase DCLK1
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
mRatBN7.22139,417,234 - 139,710,956 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2139,417,163 - 139,710,956 (+)Ensembl
Rnor_6.02144,646,255 - 144,939,389 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2144,646,308 - 144,936,927 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02164,062,498 - 164,355,201 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42144,678,222 - 144,754,237 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12144,628,184 - 144,704,200 (+)NCBI
Celera2134,114,211 - 134,191,878 (+)NCBICelera
Cytogenetic Map2q26NCBI
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)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2-methylcholine  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3-methylcholanthrene  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aflatoxin B1  (EXP,ISO)
aflatoxin B2  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (EXP,ISO)
beta-naphthoflavone  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bosentan  (ISO)
butanal  (ISO)
C60 fullerene  (EXP)
carbon nanotube  (ISO)
cerium trichloride  (ISO)
choline  (ISO)
clozapine  (EXP,ISO)
copper atom  (EXP)
copper(0)  (EXP)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dioxygen  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP,ISO)
Enterolactone  (ISO)
entinostat  (ISO)
ethanol  (ISO)
flavonoids  (EXP)
fluoxetine  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
furan  (EXP)
genistein  (ISO)
haloperidol  (EXP,ISO)
ivermectin  (ISO)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
methylmercury chloride  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
olanzapine  (ISO)
oxaliplatin  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
pentanal  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
propanal  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
Tesaglitazar  (EXP)
testosterone  (EXP,ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
tributylstannane  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
troglitazone  (EXP)
urethane  (ISO)
valproic acid  (EXP,ISO)
vorinostat  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:8889548   PMID:10550327   PMID:15277470   PMID:16387638   PMID:16387639   PMID:16548883   PMID:16684769   PMID:16869982   PMID:17114649   PMID:19844571   PMID:20236041   PMID:20418180  
PMID:22344266   PMID:23374535   PMID:26758546   PMID:27900578   PMID:29476059   PMID:30879761  


Genomics

Comparative Map Data
Dclk1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22139,417,234 - 139,710,956 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2139,417,163 - 139,710,956 (+)Ensembl
Rnor_6.02144,646,255 - 144,939,389 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2144,646,308 - 144,936,927 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02164,062,498 - 164,355,201 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42144,678,222 - 144,754,237 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12144,628,184 - 144,704,200 (+)NCBI
Celera2134,114,211 - 134,191,878 (+)NCBICelera
Cytogenetic Map2q26NCBI
DCLK1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1335,768,652 - 36,131,382 (-)EnsemblGRCh38hg38GRCh38
GRCh381335,768,652 - 36,131,939 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371336,342,789 - 36,706,076 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361335,243,478 - 35,603,443 (-)NCBINCBI36hg18NCBI36
Build 341335,243,477 - 35,603,443NCBI
Celera1317,410,025 - 17,772,331 (-)NCBI
Cytogenetic Map13q13.3NCBI
HuRef1317,156,100 - 17,334,637 (-)NCBIHuRef
HuRef1317,497,886 - 17,517,445 (-)NCBIHuRef
CHM1_11336,310,364 - 36,673,089 (-)NCBICHM1_1
Dclk1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39355,149,724 - 55,446,489 (+)NCBIGRCm39mm39
GRCm39 Ensembl355,149,785 - 55,446,489 (+)Ensembl
GRCm38355,242,303 - 55,539,068 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl355,242,364 - 55,539,068 (+)EnsemblGRCm38mm10GRCm38
MGSCv37355,046,448 - 55,342,990 (+)NCBIGRCm37mm9NCBIm37
MGSCv36355,330,557 - 55,624,607 (+)NCBImm8
Celera354,960,357 - 55,257,519 (+)NCBICelera
Cytogenetic Map3CNCBI
Dclk1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554319,975,262 - 10,297,010 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554319,975,629 - 10,302,605 (+)NCBIChiLan1.0ChiLan1.0
DCLK1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11335,419,835 - 35,768,949 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1335,425,382 - 35,768,935 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01316,988,340 - 17,342,911 (-)NCBIMhudiblu_PPA_v0panPan3
DCLK1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1254,441,945 - 4,783,542 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl254,345,771 - 4,778,047 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha254,474,081 - 4,820,850 (+)NCBI
ROS_Cfam_1.0254,543,814 - 4,885,237 (+)NCBI
UMICH_Zoey_3.1254,450,895 - 4,791,838 (+)NCBI
UNSW_CanFamBas_1.0254,446,133 - 4,787,610 (+)NCBI
UU_Cfam_GSD_1.0254,510,453 - 4,851,667 (+)NCBI
Dclk1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945165,664,364 - 165,993,443 (+)NCBI
SpeTri2.0NW_00493647229,958,716 - 30,287,798 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DCLK1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1111,815,803 - 12,198,630 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11111,815,258 - 12,159,085 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21111,847,739 - 12,121,589 (-)NCBISscrofa10.2Sscrofa10.2susScr3
DCLK1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1314,358,997 - 14,713,621 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl314,362,301 - 14,536,027 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605729,580,519 - 29,932,214 (+)NCBIVero_WHO_p1.0
Dclk1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247761,299,691 - 1,679,888 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
AA963194  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22139,638,475 - 139,638,694 (+)MAPPERmRatBN7.2
Rnor_6.02144,867,175 - 144,867,393NCBIRnor6.0
Rnor_5.02164,283,008 - 164,283,226UniSTSRnor5.0
RGSC_v3.42144,683,942 - 144,684,160UniSTSRGSC3.4
Celera2134,119,937 - 134,120,155UniSTS
RH 3.4 Map2861.4UniSTS
Cytogenetic Map2q26UniSTS
RH139488  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22139,710,646 - 139,710,851 (+)MAPPERmRatBN7.2
Rnor_6.02144,939,080 - 144,939,284NCBIRnor6.0
Rnor_5.02164,354,892 - 164,355,096UniSTSRnor5.0
RGSC_v3.42144,756,390 - 144,756,594UniSTSRGSC3.4
Celera2134,191,569 - 134,191,773UniSTS
RH 3.4 Map2861.5UniSTS
RH 3.4 Map2861.4UniSTS
Cytogenetic Map2q26UniSTS
BF387208  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22139,656,970 - 139,657,138 (+)MAPPERmRatBN7.2
Rnor_6.02144,885,440 - 144,885,607NCBIRnor6.0
Rnor_5.02164,301,252 - 164,301,419UniSTSRnor5.0
RGSC_v3.42144,702,544 - 144,702,711UniSTSRGSC3.4
Celera2134,137,859 - 134,138,026UniSTS
RH 3.4 Map2861.5UniSTS
Cytogenetic Map2q26UniSTS
BE106390  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22139,700,456 - 139,700,618 (+)MAPPERmRatBN7.2
Rnor_6.02144,928,890 - 144,929,051NCBIRnor6.0
Rnor_5.02164,344,702 - 164,344,863UniSTSRnor5.0
RGSC_v3.42144,746,200 - 144,746,361UniSTSRGSC3.4
Celera2134,181,379 - 134,181,540UniSTS
RH 3.4 Map2861.4UniSTS
Cytogenetic Map2q26UniSTS
AI836758  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22139,710,570 - 139,710,712 (+)MAPPERmRatBN7.2
Rnor_6.02144,939,004 - 144,939,145NCBIRnor6.0
Rnor_5.02164,354,816 - 164,354,957UniSTSRnor5.0
RGSC_v3.42144,756,314 - 144,756,455UniSTSRGSC3.4
Celera2134,191,493 - 134,191,634UniSTS
Cytogenetic Map2q26UniSTS
RH137977  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22139,695,387 - 139,695,572 (+)MAPPERmRatBN7.2
Rnor_6.02144,923,821 - 144,924,005NCBIRnor6.0
Rnor_5.02164,339,633 - 164,339,817UniSTSRnor5.0
RGSC_v3.42144,741,131 - 144,741,315UniSTSRGSC3.4
Celera2134,176,310 - 134,176,494UniSTS
RH 3.4 Map2861.5UniSTS
Cytogenetic Map2q26UniSTS
RH138275  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22139,672,956 - 139,673,108 (+)MAPPERmRatBN7.2
Rnor_6.02144,901,393 - 144,901,544NCBIRnor6.0
Rnor_5.02164,317,205 - 164,317,356UniSTSRnor5.0
RGSC_v3.42144,718,702 - 144,718,853UniSTSRGSC3.4
Celera2134,153,832 - 134,153,983UniSTS
RH 3.4 Map2860.3UniSTS
Cytogenetic Map2q26UniSTS
RH140320  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22139,710,677 - 139,710,852 (+)MAPPERmRatBN7.2
Rnor_6.02144,939,111 - 144,939,285NCBIRnor6.0
Rnor_5.02164,354,923 - 164,355,097UniSTSRnor5.0
RGSC_v3.42144,756,421 - 144,756,595UniSTSRGSC3.4
Celera2134,191,600 - 134,191,774UniSTS
Cytogenetic Map2q26UniSTS
RH141428  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22139,638,085 - 139,638,299 (+)MAPPERmRatBN7.2
Rnor_6.02144,866,785 - 144,866,998NCBIRnor6.0
Rnor_5.02164,282,618 - 164,282,831UniSTSRnor5.0
RGSC_v3.42144,683,552 - 144,683,765UniSTSRGSC3.4
Celera2134,119,547 - 134,119,760UniSTS
RH 3.4 Map2862.2UniSTS
Cytogenetic Map2q26UniSTS
ha2752  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera2134,147,669 - 134,148,365UniSTS
Cytogenetic Map2q26UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)225413423143657569Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
2293835Kiddil5Kidney dilation QTL 53.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607157142209Rat
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607182042367Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243154682202446871Rat
2293671Bss44Bone structure and strength QTL 4410.970.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)243162366148478373Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243171017184114403Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256043031202447032Rat
61438Cia7Collagen induced arthritis QTL 74.60.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)259324377141596857Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118275202447032Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
1558653Prcr1Prostate cancer resistance QTL 15prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)272532993157142209Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)274786664206665859Rat
631198Cm22Cardiac mass QTL 224.30.0008heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)276539322150540526Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)276539322202447032Rat
2299162Iddm32Insulin dependent diabetes mellitus QTL 322.36blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)278665616143657569Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)281689826221035911Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
631566Bp90Blood pressure QTL 900.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2102803808147803808Rat
8662836Vetf8Vascular elastic tissue fragility QTL 80.66thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2104559726149559726Rat
1581552Pur12Proteinuria QTL 125.190.0009total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)2112103657148076632Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2112456140212696837Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2112456140212696837Rat
1354594Despr10Despair related QTL 100.00000249locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)2114654253159654253Rat
1359035Bp276Blood pressure QTL 276arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2114837527143657569Rat
1359035Bp276Blood pressure QTL 276arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2114837527143657569Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2114837527185876470Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2114837527185876470Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2114837527211674221Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2114837675212549332Rat
5135226Leukc2Leukocyte quantity QTL 2eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)2118111229149559726Rat
1582257Gluco21Glucose level QTL 213.10.0035blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2118111229157142209Rat
738007Anxrr7Anxiety related response QTL 74.4exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2118189491163189491Rat
1581578Cm49Cardiac mass QTL 494.90.01heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)2127447387143657569Rat
1358360Sradr2Stress Responsive Adrenal Weight QTL 210.24adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)2129164097152195315Rat
6907363Bp357Blood pressure QTL 3574.10.002arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2129540907174540907Rat
1300165Rf9Renal function QTL 93.28kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)2133914684202447032Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2135552573202446871Rat
1298076Bp166Blood pressure QTL 1660.0009arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2136445150202447032Rat
1581502Esta3Estrogen-induced thymic atrophy QTL 3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2136916935189599348Rat
1359022Ppulsi1Prepulse inhibition QTL 13.63prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)2136916935213594495Rat
12879830Bw178Body weight QTL 1780.001body mass (VT:0001259)body weight (CMO:0000012)2137219876142323610Rat
12879831Cm82Cardiac mass QTL 820.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)2137219876142323610Rat
12879832Cm83Cardiac mass QTL 830.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)2137219876142323610Rat
12879833Cm84Cardiac mass QTL 840.001heart right ventricle mass (VT:0007033)heart weight to body weight ratio (CMO:0000074)2137219876142323610Rat
12879834Am1Aortic mass QTL 10.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)2137219876142323610Rat
12879835Kidm60Kidney mass QTL 600.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2137219876142323610Rat
1549841Bp256Blood pressure QTL 2560.03arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2137219876142323610Rat
7488931Bp367Blood pressure QTL 3670.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2139401804142323610Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:2037
Count of miRNA genes:380
Interacting mature miRNAs:585
Transcripts:ENSRNOT00000019748, ENSRNOT00000072110
Prediction methods:Microtar, Miranda, 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 2 74 18 20
Low 3 43 26 10 17 10 8 10 17 21 11 8
Below cutoff 27 27 27 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_021584 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_053343 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591138 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591139 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103247 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103248 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103249 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103250 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103252 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103253 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103254 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103255 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103256 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103257 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103258 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103260 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF030089 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF045469 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BF407055 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB586027 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CF978300 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211799 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000069 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LC438344 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U78857 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000019748   ⟹   ENSRNOP00000019748
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2139,632,744 - 139,710,956 (+)Ensembl
Rnor_6.0 Ensembl2144,861,455 - 144,936,927 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000072110   ⟹   ENSRNOP00000067781
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2139,417,163 - 139,641,880 (+)Ensembl
Rnor_6.0 Ensembl2144,861,459 - 144,870,582 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000078337   ⟹   ENSRNOP00000075702
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2139,417,423 - 139,647,677 (+)Ensembl
Rnor_6.0 Ensembl2144,646,308 - 144,934,025 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093284   ⟹   ENSRNOP00000076110
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2139,649,914 - 139,710,956 (+)Ensembl
Rnor_6.0 Ensembl2144,861,455 - 144,936,807 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093407   ⟹   ENSRNOP00000076341
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2139,417,163 - 139,708,357 (+)Ensembl
Rnor_6.0 Ensembl2144,646,429 - 144,936,803 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000099182   ⟹   ENSRNOP00000090378
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2139,417,163 - 139,710,956 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000107822   ⟹   ENSRNOP00000083313
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2139,417,163 - 139,710,956 (+)Ensembl
RefSeq Acc Id: NM_021584   ⟹   NP_067595
RefSeq Status: REVIEWED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22139,632,744 - 139,641,884 (+)NCBI
Rnor_6.02144,861,445 - 144,870,583 (+)NCBI
Rnor_5.02164,062,498 - 164,355,201 (+)NCBI
Celera2134,114,211 - 134,123,345 (+)NCBI
Sequence:
RefSeq Acc Id: NM_053343   ⟹   NP_445795
RefSeq Status: REVIEWED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22139,632,744 - 139,710,956 (+)NCBI
Rnor_6.02144,861,445 - 144,939,389 (+)NCBI
Rnor_5.02164,062,498 - 164,355,201 (+)NCBI
RGSC_v3.42144,678,222 - 144,754,237 (+)RGD
Celera2134,114,211 - 134,191,878 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008761005   ⟹   XP_008759227
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22139,632,574 - 139,710,956 (+)NCBI
Rnor_6.02144,860,554 - 144,933,928 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017591138   ⟹   XP_017446627
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22139,632,572 - 139,710,956 (+)NCBI
Rnor_6.02144,860,553 - 144,939,389 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017591139   ⟹   XP_017446628
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22139,417,245 - 139,710,956 (+)NCBI
Rnor_6.02144,646,255 - 144,933,928 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039103247   ⟹   XP_038959175
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22139,417,244 - 139,710,956 (+)NCBI
RefSeq Acc Id: XM_039103248   ⟹   XP_038959176
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22139,417,243 - 139,710,956 (+)NCBI
RefSeq Acc Id: XM_039103249   ⟹   XP_038959177
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22139,417,241 - 139,710,956 (+)NCBI
RefSeq Acc Id: XM_039103250   ⟹   XP_038959178
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22139,417,247 - 139,710,956 (+)NCBI
RefSeq Acc Id: XM_039103252   ⟹   XP_038959180
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22139,417,245 - 139,710,956 (+)NCBI
RefSeq Acc Id: XM_039103253   ⟹   XP_038959181
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22139,417,242 - 139,710,956 (+)NCBI
RefSeq Acc Id: XM_039103254   ⟹   XP_038959182
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22139,417,240 - 139,710,956 (+)NCBI
RefSeq Acc Id: XM_039103255   ⟹   XP_038959183
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22139,632,574 - 139,710,956 (+)NCBI
RefSeq Acc Id: XM_039103256   ⟹   XP_038959184
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22139,632,570 - 139,710,956 (+)NCBI
RefSeq Acc Id: XM_039103257   ⟹   XP_038959185
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22139,417,236 - 139,641,884 (+)NCBI
RefSeq Acc Id: XM_039103258   ⟹   XP_038959186
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22139,417,234 - 139,641,884 (+)NCBI
RefSeq Acc Id: XM_039103260   ⟹   XP_038959188
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22139,417,234 - 139,641,884 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_445795   ⟸   NM_053343
- Peptide Label: isoform 1
- UniProtKB: O08875 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_067595   ⟸   NM_021584
- Peptide Label: isoform 2
- UniProtKB: Q9WVP7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008759227   ⟸   XM_008761005
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_017446628   ⟸   XM_017591139
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017446627   ⟸   XM_017591138
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: ENSRNOP00000019748   ⟸   ENSRNOT00000019748
RefSeq Acc Id: ENSRNOP00000076341   ⟸   ENSRNOT00000093407
RefSeq Acc Id: ENSRNOP00000075702   ⟸   ENSRNOT00000078337
RefSeq Acc Id: ENSRNOP00000076110   ⟸   ENSRNOT00000093284
RefSeq Acc Id: ENSRNOP00000067781   ⟸   ENSRNOT00000072110
RefSeq Acc Id: XP_038959186   ⟸   XM_039103258
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038959188   ⟸   XM_039103260
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038959185   ⟸   XM_039103257
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038959182   ⟸   XM_039103254
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038959177   ⟸   XM_039103249
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038959181   ⟸   XM_039103253
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038959176   ⟸   XM_039103248
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038959175   ⟸   XM_039103247
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038959180   ⟸   XM_039103252
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038959178   ⟸   XM_039103250
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038959184   ⟸   XM_039103256
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038959183   ⟸   XM_039103255
- Peptide Label: isoform X10
RefSeq Acc Id: ENSRNOP00000090378   ⟸   ENSRNOT00000099182
RefSeq Acc Id: ENSRNOP00000083313   ⟸   ENSRNOT00000107822
Protein Domains
Doublecortin   Protein kinase

Transcriptome

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

Promoters
RGD ID:13691347
Promoter ID:EPDNEW_R1858
Type:initiation region
Name:Dclk1_1
Description:doublecortin-like kinase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R1859  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02144,646,429 - 144,646,489EPDNEW
RGD ID:13691334
Promoter ID:EPDNEW_R1859
Type:multiple initiation site
Name:Dclk1_2
Description:doublecortin-like kinase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R1858  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02144,861,450 - 144,861,510EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
ACI/N (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
F344/NRrrc (MCW)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
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)
Visual CSV TAB Printer
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)
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
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)
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
LEW/NCrlBR (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
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
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
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)
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
MNS/Gib (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
MR/N (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
SBN/Ygl (MCW)
Visual CSV TAB Printer
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)
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
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)
Visual CSV TAB Printer
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)
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
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)
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
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
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)
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/N (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
WN/N (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:68437 AgrOrtholog
Ensembl Genes ENSRNOG00000032922 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000019748 UniProtKB/Swiss-Prot
  ENSRNOP00000067781 UniProtKB/TrEMBL
  ENSRNOP00000075702 UniProtKB/TrEMBL
  ENSRNOP00000076110 UniProtKB/TrEMBL
  ENSRNOP00000076341 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000019748 UniProtKB/Swiss-Prot
  ENSRNOT00000072110 UniProtKB/TrEMBL
  ENSRNOT00000078337 UniProtKB/TrEMBL
  ENSRNOT00000093284 UniProtKB/TrEMBL
  ENSRNOT00000093407 UniProtKB/TrEMBL
Gene3D-CATH 3.10.20.230 UniProtKB/TrEMBL
InterPro Doublecortin_dom UniProtKB/TrEMBL
  Doublecortin_dom_sf UniProtKB/TrEMBL
  Kinase-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Prot_kinase_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Protein_kinase_ATP_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ser/Thr_kinase_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:83825 UniProtKB/Swiss-Prot
NCBI Gene 83825 ENTREZGENE
Pfam DCX UniProtKB/TrEMBL
  Pkinase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Dclk1 PhenoGen
PROSITE PROTEIN_KINASE_ATP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_DOM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_ST UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PS50309 UniProtKB/TrEMBL
SMART DCX UniProtKB/TrEMBL
  S_TKc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF56112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF89837 UniProtKB/TrEMBL
TIGR TC231457
UniProt A0A0G2KB92_RAT UniProtKB/TrEMBL
  A0A1W2Q632_RAT UniProtKB/TrEMBL
  A0A1W2Q6Q2_RAT UniProtKB/TrEMBL
  A0A3Q9WS43_RAT UniProtKB/TrEMBL
  DCLK1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q9WVP7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-04-17 Dclk1  doublecortin-like kinase 1  Ania4  activity and neurotransmitter-induced early gene protein 4 (ania-4)  Data Merged 737654 PROVISIONAL
2007-04-03 Dclk1  doublecortin-like kinase 1  Dcamkl1  double cortin and calcium/calmodulin-dependent protein kinase-like 1  Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2002-08-07 Ania4  activity and neurotransmitter-induced early gene protein 4 (ania-4)      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Dcamkl1  double cortin and calcium/calmodulin-dependent protein kinase-like 1      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function has protein kinase activity 727578
gene_homology has similarity to calmodulin dependent protein kinases and to doublecortin 727578
gene_regulation expression is induced by kainate-elicited seizures in some regions of the hippocampus 631963