Csnk1d (casein kinase 1, delta) - Rat Genome Database
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Gene: Csnk1d (casein kinase 1, delta) Rattus norvegicus
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Symbol: Csnk1d
Name: casein kinase 1, delta
RGD ID: 71031
Description: Exhibits protein serine/threonine kinase activity. Involved in cellular response to nerve growth factor stimulus and protein phosphorylation. Localizes to several cellular components, including Golgi apparatus; centrosome; and perinuclear region of cytoplasm. Human ortholog(s) of this gene implicated in advanced sleep phase syndrome 2. Orthologous to human CSNK1D (casein kinase 1 delta); PARTICIPATES IN Hedgehog signaling pathway; p53 signaling pathway; ribosome biogenesis pathway; INTERACTS WITH 2,4-dinitrotoluene; 2-ethoxyethanol; 2-methoxyethanol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: casein kinase 1 delta; casein kinase I; casein kinase I isoform delta; CKI-delta; tau-protein kinase CSNK1D
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
mRatBN7.210106,221,992 - 106,256,620 (-)NCBI
Rnor_6.0 Ensembl10110,148,600 - 110,182,408 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.010110,147,786 - 110,182,413 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.010109,738,952 - 109,769,940 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410110,166,244 - 110,197,233 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.110110,177,115 - 110,211,716 (-)NCBI
Celera10104,764,644 - 104,795,629 (-)NCBICelera
Cytogenetic Map10q32.3NCBI
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
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:7665585   PMID:8648628   PMID:8889548   PMID:10826492   PMID:11165242   PMID:15557340   PMID:16027726   PMID:16618118   PMID:17027228   PMID:17244647   PMID:17562708   PMID:17594292  
PMID:19414593   PMID:20412773   PMID:21399614   PMID:21422228   PMID:21564097   PMID:21718540   PMID:21930935   PMID:22549116   PMID:23861943   PMID:24055157   PMID:24648492   PMID:25245819  
PMID:25468996   PMID:25500533  


Genomics

Comparative Map Data
Csnk1d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.210106,221,992 - 106,256,620 (-)NCBI
Rnor_6.0 Ensembl10110,148,600 - 110,182,408 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.010110,147,786 - 110,182,413 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.010109,738,952 - 109,769,940 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410110,166,244 - 110,197,233 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.110110,177,115 - 110,211,716 (-)NCBI
Celera10104,764,644 - 104,795,629 (-)NCBICelera
Cytogenetic Map10q32.3NCBI
CSNK1D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1782,239,023 - 82,273,731 (-)EnsemblGRCh38hg38GRCh38
GRCh381782,239,019 - 82,273,750 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371780,196,895 - 80,231,626 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361777,795,527 - 77,824,862 (-)NCBINCBI36hg18NCBI36
Build 341777,795,530 - 77,824,862NCBI
Celera1776,796,458 - 76,825,073 (-)NCBI
Cytogenetic Map17q25.3NCBI
HuRef1775,600,124 - 75,630,539 (-)NCBIHuRef
CHM1_11780,286,271 - 80,316,917 (-)NCBICHM1_1
Csnk1d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911120,848,535 - 120,882,180 (-)NCBIGRCm39mm39
GRCm39 Ensembl11120,849,816 - 120,882,156 (-)Ensembl
GRCm3811120,957,709 - 120,991,350 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11120,958,990 - 120,991,330 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711120,823,055 - 120,852,647 (-)NCBIGRCm37mm9NCBIm37
MGSCv3611120,777,831 - 120,807,423 (-)NCBImm8
Celera11132,698,912 - 132,728,516 (-)NCBICelera
Cytogenetic Map11E2NCBI
Csnk1d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955506904,660 - 935,330 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955506904,659 - 936,293 (+)NCBIChiLan1.0ChiLan1.0
CSNK1D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11782,461,764 - 82,494,348 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1782,462,467 - 82,494,348 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01776,648,677 - 76,683,054 (-)NCBIMhudiblu_PPA_v0panPan3
CSNK1D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl973,215 - 110,269 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1983,395 - 110,309 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Csnk1d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365945,720,887 - 5,743,206 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CSNK1D
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl12768,865 - 796,532 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.112768,856 - 794,495 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.212969,952 - 977,839 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CSNK1D
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11674,157,875 - 74,192,142 (-)NCBI
ChlSab1.1 Ensembl1674,160,648 - 74,192,108 (-)Ensembl
Csnk1d
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462480111,031,102 - 11,074,100 (-)NCBI

Position Markers
RH142791  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.010110,175,037 - 110,175,239NCBIRnor6.0
Rnor_5.010109,762,569 - 109,762,771UniSTSRnor5.0
RGSC_v3.410110,189,862 - 110,190,064UniSTSRGSC3.4
Celera10104,788,261 - 104,788,463UniSTS
Cytogenetic Map10q32.3UniSTS
RH137468  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.010110,173,660 - 110,173,847NCBIRnor6.0
Rnor_5.010109,761,192 - 109,761,379UniSTSRnor5.0
RGSC_v3.410110,188,485 - 110,188,672UniSTSRGSC3.4
Celera10104,786,884 - 104,787,071UniSTS
Cytogenetic Map10q32.3UniSTS
UniSTS:532270  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.010110,152,044 - 110,152,969NCBIRnor6.0
Rnor_5.010109,739,576 - 109,740,501UniSTSRnor5.0
Celera10104,765,268 - 104,766,193UniSTS
Cytogenetic Map10q32.3UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014827894110992275Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1023861015112626471Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1053621375112626471Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1053621375112626471Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1055678976112626471Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1065590122110590122Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1065992275110992275Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1065992275110992275Rat
7387312Bw125Body weight QTL 12530.0047retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight (CMO:0000356)1067880046112626471Rat
1581559Eae18Experimental allergic encephalomyelitis QTL 180.00002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1067988218110992091Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1069385595112626471Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1069385595112626471Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1070166960112626471Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1070800069112626471Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1071692298112626471Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1073008136112626471Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1073008136112626471Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1073008136112626471Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1073467158112626471Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1075544754112626471Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1075544754112626471Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1078970279112626471Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1079927661112626471Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1080239190112626471Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1085079943112626471Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1086566908112626471Rat
631538Oia5Oil induced arthritis QTL 5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1090041957112626471Rat
61363Oia3Oil induced arthritis QTL 30.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1090296897112626471Rat
634320Niddm49Non-insulin dependent diabetes mellitus QTL 494.41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1091689348112626471Rat
1579915Bp280Blood pressure QTL 2800.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1093662786112626471Rat
12880395Cm109Cardiac mass QTL 1090.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1093662786112626471Rat
12880396Am13Aortic mass QTL 130.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1093662786112626471Rat
12880398Kidm67Kidney mass QTL 670.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1093662786112626471Rat
12880384Cm107Cardiac mass QTL 1070.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)93662786112626471Rat
12880385Cm108Cardiac mass QTL 1080.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)93662786112626471Rat
1300137Bp186Blood pressure QTL 1863.57arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1093886117110992275Rat
724530Bp149Blood pressure QTL 1490.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1093886117112626471Rat
1558652Bw57Body weight QTL 574.20.0008body mass (VT:0001259)body weight (CMO:0000012)1094170766112626471Rat
1354641Bvd2Brain ventricular dilatation QTL 26.360.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)1096520816110992275Rat
2292436Bp310Blood pressure QTL 310arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1098079221112626471Rat
10450493Bp382Blood pressure QTL 3820.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1098079221112626471Rat
1578663Bss18Bone structure and strength QTL 183.6femur width (VT:1000666)femoral neck width (CMO:0001695)10100155035110992275Rat
1578672Bmd16Bone mineral density QTL 166.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)10100155035110992275Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:450
Count of miRNA genes:245
Interacting mature miRNAs:313
Transcripts:ENSRNOT00000015178, ENSRNOT00000054936
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 42 57 41 19 41 6 9 74 35 41 11 6
Low 1 2 2 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000015178   ⟹   ENSRNOP00000015178
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl10110,148,600 - 110,182,291 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000054936   ⟹   ENSRNOP00000051819
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl10110,151,420 - 110,182,408 (-)Ensembl
RefSeq Acc Id: NM_139060   ⟹   NP_620691
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.210106,225,624 - 106,256,614 (-)NCBI
Rnor_6.010110,151,420 - 110,182,408 (-)NCBI
Rnor_5.010109,738,952 - 109,769,940 (-)NCBI
RGSC_v3.410110,166,244 - 110,197,233 (-)RGD
Celera10104,764,644 - 104,795,629 (-)RGD
Sequence:
RefSeq Acc Id: XM_008768511   ⟹   XP_008766733
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.210106,225,624 - 106,256,601 (-)NCBI
Rnor_6.010110,151,421 - 110,182,413 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039086796   ⟹   XP_038942724
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.210106,221,992 - 106,256,620 (-)NCBI
RefSeq Acc Id: XM_039086797   ⟹   XP_038942725
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.210106,221,992 - 106,249,218 (-)NCBI
RefSeq Acc Id: XR_594964
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.010110,147,786 - 110,182,413 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_620691   ⟸   NM_139060
- UniProtKB: Q06486 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008766733   ⟸   XM_008768511
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000051819   ⟸   ENSRNOT00000054936
RefSeq Acc Id: ENSRNOP00000015178   ⟸   ENSRNOT00000015178
RefSeq Acc Id: XP_038942724   ⟸   XM_039086796
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038942725   ⟸   XM_039086797
- Peptide Label: isoform X3
Protein Domains
Protein kinase

Transcriptome

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

Promoters
RGD ID:13697983
Promoter ID:EPDNEW_R8507
Type:initiation region
Name:Csnk1d_2
Description:casein kinase 1, delta
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R8508  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.010110,182,143 - 110,182,203EPDNEW
RGD ID:13697984
Promoter ID:EPDNEW_R8508
Type:multiple initiation site
Name:Csnk1d_1
Description:casein kinase 1, delta
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R8507  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.010110,182,408 - 110,182,468EPDNEW

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:71031 AgrOrtholog
Ensembl Genes ENSRNOG00000036676 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000015178 UniProtKB/Swiss-Prot
  ENSRNOP00000051819 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000015178 UniProtKB/Swiss-Prot
  ENSRNOT00000054936 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
KEGG Report rno:64462 UniProtKB/Swiss-Prot
NCBI Gene 64462 ENTREZGENE
Pfam Pkinase UniProtKB/Swiss-Prot
PhenoGen Csnk1d PhenoGen
PROSITE PROTEIN_KINASE_ATP UniProtKB/Swiss-Prot
  PROTEIN_KINASE_DOM UniProtKB/Swiss-Prot
  PROTEIN_KINASE_ST UniProtKB/Swiss-Prot
SMART S_TKc UniProtKB/Swiss-Prot
Superfamily-SCOP SSF56112 UniProtKB/Swiss-Prot
UniProt KC1D_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q99KK4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-07-09 Csnk1d  casein kinase 1, delta      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localized to the centrosome of interphase cells and to the mitotic spindle 727437