Sik1 (salt-inducible kinase 1) - Rat Genome Database

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Gene: Sik1 (salt-inducible kinase 1) Rattus norvegicus
Analyze
Symbol: Sik1
Name: salt-inducible kinase 1
RGD ID: 69407
Description: Exhibits protein kinase binding activity and protein serine/threonine kinase activity. Involved in negative regulation of transcription by RNA polymerase II; protein phosphorylation; and regulation of sodium ion transport. Localizes to cytosol and nucleus. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 30. Orthologous to several human genes including SIK1B (salt inducible kinase 1B (putative)); INTERACTS WITH 1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: protein kinase KID2; salt-inducible protein kinase; salt-inducible protein kinase 1; serine/threonine-protein kinase SIK1; serine/threonine-protein kinase SNF1-like kinase 1; serine/threonine-protein kinase SNF1LK; Sik; SIK-1; SNF1-like kinase; Snf1lk
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2209,949,407 - 9,959,036 (-)NCBI
Rnor_6.0 Ensembl2010,668,411 - 10,680,283 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02010,670,747 - 10,680,279 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02012,845,508 - 12,855,040 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42010,282,203 - 10,291,735 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12010,280,420 - 10,292,014 (-)NCBI
Celera2011,458,458 - 11,467,962 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane  (EXP)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,6-dinitrotoluene  (EXP)
2-ethoxyethanol  (EXP)
2-hydroxypropanoic acid  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (EXP)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (EXP,ISO)
ammonium chloride  (EXP)
antimony(0)  (ISO)
aristolochic acid  (ISO)
astemizole  (EXP)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
butan-1-ol  (ISO)
butanal  (ISO)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP)
carbamazepine  (ISO)
carbon nanotube  (ISO)
carboplatin  (ISO)
chloroacetaldehyde  (ISO)
chloroprene  (EXP,ISO)
chlorpromazine  (EXP)
chromium atom  (ISO)
cidofovir anhydrous  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (EXP,ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (ISO)
dieldrin  (ISO)
dioxygen  (ISO)
dipotassium bis[mu-tartrato(4-)]diantimonate(2-) trihydrate  (ISO)
disulfiram  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
fenofibrate  (EXP,ISO)
formaldehyde  (ISO)
furan  (EXP)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
ibuprofen  (EXP,ISO)
indole-3-methanol  (EXP)
lead diacetate  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (ISO)
lipopolysaccharide  (EXP)
melphalan  (ISO)
menadione  (ISO)
mercury dichloride  (EXP)
metformin  (EXP)
methamphetamine  (EXP)
methylmercury chloride  (ISO)
monosodium L-glutamate  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
N-nitrosodimethylamine  (ISO)
N1'-[2-[[5-[(dimethylamino)methyl]-2-furanyl]methylthio]ethyl]-N1-methyl-2-nitroethene-1,1-diamine  (EXP)
nickel atom  (EXP,ISO)
nickel dichloride  (ISO)
nickel sulfate  (EXP)
ozone  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
perfluorononanoic acid  (ISO)
phenformin  (EXP)
phenobarbital  (ISO)
phenol  (ISO)
phenylephrine  (EXP)
phenylmercury acetate  (ISO)
PhIP  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
rac-lactic acid  (ISO)
ranitidine  (EXP)
rotenone  (EXP)
SB 431542  (ISO)
SCH 23390  (EXP)
sevoflurane  (EXP)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
Soman  (EXP)
sulfasalazine  (ISO)
sunitinib  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (ISO)
torcetrapib  (ISO)
trichostatin A  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IBA,ISO,ISS)
cytosol  (IDA)
nucleus  (IBA,IDA,ISO,ISS)

References

Additional References at PubMed
PMID:12200423   PMID:12624099   PMID:14976552   PMID:15134808   PMID:15177563   PMID:15511237   PMID:16148943   PMID:16306228   PMID:16817901   PMID:17468767   PMID:18348280   PMID:19103603  
PMID:19244231   PMID:19470703   PMID:19622832   PMID:19657284   PMID:20140255   PMID:21549091   PMID:21954104   PMID:22109884   PMID:23349925   PMID:23993098   PMID:25384047   PMID:25918234  
PMID:26210066   PMID:26567857   PMID:31233505   PMID:32106109  


Genomics

Comparative Map Data
Sik1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2209,949,407 - 9,959,036 (-)NCBI
Rnor_6.0 Ensembl2010,668,411 - 10,680,283 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02010,670,747 - 10,680,279 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02012,845,508 - 12,855,040 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42010,282,203 - 10,291,735 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12010,280,420 - 10,292,014 (-)NCBI
Celera2011,458,458 - 11,467,962 (-)NCBICelera
Cytogenetic Map20p12NCBI
SIK1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2143,414,483 - 43,427,131 (-)EnsemblGRCh38hg38GRCh38
GRCh382143,414,483 - 43,427,131 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372144,834,363 - 44,847,011 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362143,658,823 - 43,671,430 (-)NCBINCBI36hg18NCBI36
Build 342143,658,826 - 43,671,436NCBI
Celera2129,940,650 - 29,953,256 (-)NCBI
Cytogenetic Map21q22.3NCBI
HuRef2130,202,979 - 30,223,345 (-)NCBIHuRef
CHM1_12144,394,974 - 44,407,557 (-)NCBICHM1_1
Sik1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391732,063,222 - 32,074,808 (-)NCBIGRCm39mm39
GRCm39 Ensembl1732,063,224 - 32,074,778 (-)Ensembl
GRCm381731,844,248 - 31,855,804 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1731,844,250 - 31,855,804 (-)EnsemblGRCm38mm10GRCm38
MGSCv371731,981,195 - 31,992,737 (-)NCBIGRCm37mm9NCBIm37
MGSCv361731,572,967 - 31,584,494 (-)NCBImm8
Celera1732,760,486 - 32,771,258 (-)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1717.25NCBI
Sik1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540738,739,062 - 38,749,293 (+)NCBIChiLan1.0ChiLan1.0
SIK1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12142,975,914 - 42,987,948 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v02129,675,040 - 29,689,408 (-)NCBIMhudiblu_PPA_v0panPan3
SIK1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13137,455,130 - 37,466,829 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3136,610,274 - 36,622,021 (-)NCBI
ROS_Cfam_1.03136,998,123 - 37,010,456 (-)NCBI
UMICH_Zoey_3.13136,867,482 - 36,879,155 (-)NCBI
UNSW_CanFamBas_1.03136,852,129 - 36,863,810 (-)NCBI
UU_Cfam_GSD_1.03137,344,622 - 37,356,464 (-)NCBI
Sik1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497136,683,495 - 36,693,046 (-)NCBI
SpeTri2.0NW_004936500774,749 - 784,326 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SIK1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.113206,454,695 - 206,465,802 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213216,759,862 - 216,764,885 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103219558
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1287,204,386 - 87,217,044 (-)NCBI
Vero_WHO_p1.0NW_02366605415,257,361 - 15,270,116 (-)NCBI
Sik1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474527,529,037 - 27,539,253 (+)NCBI

Position Markers
RH134693  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2209,947,586 - 9,947,792 (+)MAPPER
Rnor_6.02010,668,929 - 10,669,134NCBIRnor6.0
Rnor_5.02012,843,690 - 12,843,895UniSTSRnor5.0
RGSC_v3.42010,280,385 - 10,280,590UniSTSRGSC3.4
Celera2011,456,771 - 11,456,976UniSTS
RH 3.4 Map20137.1UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124652101Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125653396Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20340211127968216Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20403911318872273Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20403911318872273Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RChigh CD8 T cell count to CD45RClow CD8 T cell count ratio (CMO:0001990)20485546810800530Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20485547515050565Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20587544818739210Rat
1581577Pur15Proteinuria QTL 154.380.0002total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20865434118872273Rat
4889870Pur30Proteinuria QTL 30190.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20865434130991290Rat
631265Iresp1Immunoglobin response QTL18.3blood anti-double stranded DNA antibody amount (VT:0004762)serum anti-DNA antibody level (CMO:0001533)20965564214411641Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:30
Count of miRNA genes:27
Interacting mature miRNAs:29
Transcripts:ENSRNOT00000001579
Prediction methods: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 1 24 23 11 19 11 45 27 33 11
Low 2 19 34 30 30 8 11 29 8 8 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000001579   ⟹   ENSRNOP00000001579
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2010,668,411 - 10,680,283 (-)Ensembl
RefSeq Acc Id: NM_021693   ⟹   NP_067725
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2209,949,407 - 9,958,939 (-)NCBI
Rnor_6.02010,670,747 - 10,680,279 (-)NCBI
Rnor_5.02012,845,508 - 12,855,040 (-)NCBI
RGSC_v3.42010,282,203 - 10,291,735 (-)RGD
Celera2011,458,458 - 11,467,962 (-)RGD
Sequence:
RefSeq Acc Id: XM_039099047   ⟹   XP_038954975
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2209,949,415 - 9,959,036 (-)NCBI
RefSeq Acc Id: XM_039099048   ⟹   XP_038954976
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2209,949,415 - 9,959,036 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_067725   ⟸   NM_021693
- UniProtKB: Q9R1U5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000001579   ⟸   ENSRNOT00000001579
RefSeq Acc Id: XP_038954976   ⟸   XM_039099048
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038954975   ⟸   XM_039099047
- Peptide Label: isoform X1
Protein Domains
Protein kinase   UBA

Transcriptome

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

Promoters
RGD ID:13701481
Promoter ID:EPDNEW_R12004
Type:initiation region
Name:Sik1_1
Description:salt-inducible kinase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02010,680,348 - 10,680,408EPDNEW

Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69407 AgrOrtholog
Ensembl Genes ENSRNOG00000001189 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000001579 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000001579 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro Kinase-like_dom_sf UniProtKB/Swiss-Prot
  Prot_kinase_dom UniProtKB/Swiss-Prot
  Protein_kinase_ATP_BS UniProtKB/Swiss-Prot
  Ser/Thr_kinase_AS UniProtKB/Swiss-Prot
  Ser/Thr_kinase_SIK1/2 UniProtKB/Swiss-Prot
  SIK UniProtKB/Swiss-Prot
  UBA UniProtKB/Swiss-Prot
KEGG Report rno:59329 UniProtKB/Swiss-Prot
NCBI Gene 59329 ENTREZGENE
Pfam Pkinase UniProtKB/Swiss-Prot
PhenoGen Sik1 PhenoGen
PIRSF Ser/Thr_PK_SNF1-like UniProtKB/Swiss-Prot
PROSITE PROTEIN_KINASE_ATP UniProtKB/Swiss-Prot
  PROTEIN_KINASE_DOM UniProtKB/Swiss-Prot
  PROTEIN_KINASE_ST UniProtKB/Swiss-Prot
  UBA UniProtKB/Swiss-Prot
SMART S_TKc UniProtKB/Swiss-Prot
Superfamily-SCOP SSF56112 UniProtKB/Swiss-Prot
UniProt Q9R1U5 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q9R081 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-05-05 Sik1  salt-inducible kinase 1  Snf1lk  SNF1-like kinase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Snf1lk  SNF1-like kinase      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference