Csnk1d (casein kinase 1, delta) - Rat Genome Database

Name: Csnk1d
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Csnk1d (casein kinase 1, delta) Rattus norvegicus

Analyze

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 ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	CSNK1D (casein kinase 1 delta)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Csnk1d (casein kinase 1, delta)	HGNC	Treefam, EggNOG, NCBI, OMA, HomoloGene, Inparanoid, Panther, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Csnk1d (casein kinase 1 delta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CSNK1D (casein kinase 1 delta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CSNK1D (casein kinase 1 delta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Csnk1d (casein kinase 1 delta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CSNK1D (casein kinase 1 delta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	CSNK1D (casein kinase 1 delta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Csnk1d (casein kinase 1 delta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	CSNK1E (casein kinase 1 epsilon)	HGNC	OrthoDB
Alliance orthologs ³
Homo sapiens (human):	CSNK1D (casein kinase 1 delta)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Mus musculus (house mouse):	Csnk1d (casein kinase 1, delta)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Danio rerio (zebrafish):	csnk1da (casein kinase 1, delta a)	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB)
Danio rerio (zebrafish):	csnk1db (casein kinase 1, delta b)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER)
Saccharomyces cerevisiae (baker's yeast):	HRR25	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	dco	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PhylomeDB)
Caenorhabditis elegans (roundworm):	kin-20	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PhylomeDB)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	10	106,221,992 - 106,256,620 (-)	NCBI
Rnor_6.0 Ensembl	10	110,148,600 - 110,182,408 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	10	110,147,786 - 110,182,413 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	10	109,738,952 - 109,769,940 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	110,166,244 - 110,197,233 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	10	110,177,115 - 110,211,716 (-)	NCBI
Celera	10	104,764,644 - 104,795,629 (-)	NCBI		Celera
Cytogenetic Map	10	q32.3	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

advanced sleep phase syndrome 1 (ISO)

advanced sleep phase syndrome 2 (ISO)

Alzheimer's disease (ISO)

attention deficit hyperactivity disorder (ISS)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

2,4-dinitrotoluene (EXP)

2-ethoxyethanol (EXP)

2-hydroxypropanoic acid (ISO)

2-methoxyethanol (EXP)

3,4-methylenedioxymethamphetamine (ISO)

aflatoxin B1 (ISO)

ammonium chloride (EXP)

anthra[1,9-cd]pyrazol-6(2H)-one (ISO)

antirheumatic drug (ISO)

Aroclor 1254 (ISO)

arsane (ISO)

arsenic atom (ISO)

arsenite(3-) (ISO)

arsenous acid (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

bisphenol A (EXP,ISO)

choline (ISO)

clofibrate (ISO)

cobalt dichloride (ISO)

cycloheximide (ISO)

cyclosporin A (ISO)

cytarabine (ISO)

diarsenic trioxide (ISO)

diazinon (EXP)

dieldrin (EXP)

dioxygen (ISO)

dorsomorphin (ISO)

folic acid (ISO)

furan (EXP)

gentamycin (EXP)

hydrogen peroxide (ISO)

L-methionine (ISO)

methylmercury chloride (ISO)

N-methyl-4-phenylpyridinium (ISO)

N-methylformamide (ISO)

N-Vinyl-2-pyrrolidone (EXP)

nickel atom (ISO)

nickel dichloride (EXP,ISO)

paracetamol (ISO)

phenobarbital (EXP)

pyrazoles (ISO)

pyrimidines (ISO)

rac-lactic acid (ISO)

SB 431542 (ISO)

sodium arsenite (ISO)

sunitinib (ISO)

tert-butyl hydroperoxide (ISO)

titanium dioxide (ISO)

trichostatin A (ISO)

trimellitic anhydride (ISO)

triphenyl phosphate (EXP)

tunicamycin (ISO)

urethane (ISO)

valdecoxib (EXP)

valproic acid (ISO)

vanadyl sulfate (ISO)

vinclozolin (EXP)

vitamin E (ISO)

zinc atom (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cellular response to nerve growth factor stimulus (IEP)

circadian regulation of gene expression (ISO,ISS)

Golgi organization (ISO)

microtubule nucleation (ISO)

non-motile cilium assembly (IBA,ISO)

peptidyl-serine phosphorylation (IBA,ISO)

positive regulation of canonical Wnt signaling pathway (IBA,ISO)

positive regulation of non-canonical Wnt signaling pathway (ISO)

positive regulation of proteasomal ubiquitin-dependent protein catabolic process (IBA,ISO,ISS)

positive regulation of protein phosphorylation (ISO)

positive regulation of Wnt signaling pathway (ISO)

protein localization to centrosome (ISO)

protein localization to cilium (ISO)

protein localization to Golgi apparatus (ISO)

protein phosphorylation (IDA,ISO,ISS)

regulation of circadian rhythm (IBA,ISO,ISS)

spindle assembly (IBA,ISO)

Wnt signaling pathway (IEA)

Cellular Component

centrosome (IDA,ISO)

ciliary basal body (ISO)

cytoplasm (IBA)

Golgi apparatus (IDA,ISO)

neuron projection (IDA)

nucleus (IBA,ISO,ISS)

perinuclear region of cytoplasm (IDA,ISO)

plasma membrane (IDA,ISO)

spindle (ISO)

spindle microtubule (IBA,ISO)

Molecular Function

ATP binding (IEA)

kinase activity (IDA)

protein binding (IPI,ISO)

protein kinase activity (ISO,ISS)

protein serine kinase activity (IEA)

protein serine/threonine kinase activity (IBA,IDA,ISO)

protein threonine kinase activity (IEA)

tau-protein kinase activity (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

Hedgehog signaling pathway (IEA,ISO)

p53 signaling pathway (ISO)

ribosome biogenesis pathway (ISO)

References

References - curated


1.	Bischof J, etal., PLoS One. 2011;6(6):e20857. doi: 10.1371/journal.pone.0020857. Epub 2011 Jun 16.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	Ghoshal N, etal., Am J Pathol. 1999 Oct;155(4):1163-72.
4.	GOA data from the GO Consortium
5.	Graves PR, etal., J Biol Chem 1993 Mar 25;268(9):6394-401.
6.	Inuzuka H, etal., Cancer Cell. 2010 Aug 9;18(2):147-59. doi: 10.1016/j.ccr.2010.06.015.
7.	MGD data from the GO Consortium
8.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
9.	OMIM Disease Annotation Pipeline
10.	Pipeline to import KEGG annotations from KEGG into RGD
11.	Pipeline to import Pathway Interaction Database annotations from NCI into RGD
12.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
13.	RGD automated import pipeline for gene-chemical interactions
14.	Sillibourne JE, etal., J Mol Biol 2002 Sep 27;322(4):785-97.
15.	Wolff S, etal., Biochim Biophys Acta. 2005 Sep 10;1745(2):196-206.
16.	Wolff S, etal., FEBS Lett. 2006 Nov 27;580(27):6477-84. Epub 2006 Nov 7.
17.	Yasojima K, etal., Brain Res. 2000 May 19;865(1):116-20.
18.	Zemp I, etal., J Cell Sci. 2014 Mar 15;127(Pt 6):1242-53. doi: 10.1242/jcs.138719. Epub 2014 Jan 14.

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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	10	106,221,992 - 106,256,620 (-)	NCBI
Rnor_6.0 Ensembl	10	110,148,600 - 110,182,408 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	10	110,147,786 - 110,182,413 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	10	109,738,952 - 109,769,940 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	110,166,244 - 110,197,233 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	10	110,177,115 - 110,211,716 (-)	NCBI
Celera	10	104,764,644 - 104,795,629 (-)	NCBI		Celera
Cytogenetic Map	10	q32.3	NCBI

CSNK1D
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	17	82,239,023 - 82,273,731 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	17	82,239,019 - 82,273,750 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	17	80,196,895 - 80,231,626 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	17	77,795,527 - 77,824,862 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	17	77,795,530 - 77,824,862	NCBI
Celera	17	76,796,458 - 76,825,073 (-)	NCBI
Cytogenetic Map	17	q25.3	NCBI
HuRef	17	75,600,124 - 75,630,539 (-)	NCBI		HuRef
CHM1_1	17	80,286,271 - 80,316,917 (-)	NCBI		CHM1_1

Csnk1d
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	11	120,848,535 - 120,882,180 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	11	120,849,816 - 120,882,156 (-)	Ensembl
GRCm38	11	120,957,709 - 120,991,350 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	11	120,958,990 - 120,991,330 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	11	120,823,055 - 120,852,647 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	11	120,777,831 - 120,807,423 (-)	NCBI			mm8
Celera	11	132,698,912 - 132,728,516 (-)	NCBI		Celera
Cytogenetic Map	11	E2	NCBI

Csnk1d
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955506	904,660 - 935,330 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955506	904,659 - 936,293 (+)	NCBI	ChiLan1.0	ChiLan1.0

CSNK1D
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	17	82,461,764 - 82,494,348 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	17	82,462,467 - 82,494,348 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	17	76,648,677 - 76,683,054 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

CSNK1D
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	9	73,215 - 110,269 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	9	83,395 - 110,309 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Csnk1d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936594	5,720,887 - 5,743,206 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CSNK1D
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	12	768,865 - 796,532 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	12	768,856 - 794,495 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	12	969,952 - 977,839 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CSNK1D
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	16	74,157,875 - 74,192,142 (-)	NCBI
ChlSab1.1 Ensembl	16	74,160,648 - 74,192,108 (-)	Ensembl

Csnk1d
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624801	11,031,102 - 11,074,100 (-)	NCBI

Position Markers

RH142791

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	10	110,175,037 - 110,175,239	NCBI	Rnor6.0
Rnor_5.0	10	109,762,569 - 109,762,771	UniSTS	Rnor5.0
RGSC_v3.4	10	110,189,862 - 110,190,064	UniSTS	RGSC3.4
Celera	10	104,788,261 - 104,788,463	UniSTS
Cytogenetic Map	10	q32.3	UniSTS

RH137468

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	10	110,173,660 - 110,173,847	NCBI	Rnor6.0
Rnor_5.0	10	109,761,192 - 109,761,379	UniSTS	Rnor5.0
RGSC_v3.4	10	110,188,485 - 110,188,672	UniSTS	RGSC3.4
Celera	10	104,786,884 - 104,787,071	UniSTS
Cytogenetic Map	10	q32.3	UniSTS

UniSTS:532270

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	10	110,152,044 - 110,152,969	NCBI	Rnor6.0
Rnor_5.0	10	109,739,576 - 109,740,501	UniSTS	Rnor5.0
Celera	10	104,765,268 - 104,766,193	UniSTS
Cytogenetic Map	10	q32.3	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2316949	Gluco60	Glucose level QTL 60	3.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	10	14827894	110992275	Rat
1331791	Cm31	Cardiac mass QTL 31	3.84606		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	10	23861015	112626471	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	10	53621375	112626471	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	53621375	112626471	Rat
70171	Cari1	Carrageenan-induced inflammation QTL 1	4.9	0.0005	hypodermis integrity trait (VT:0010550)	inflammatory exudate volume (CMO:0001429)	10	55678976	112626471	Rat
61449	Ciaa2	CIA Autoantibody QTL 2	7.1		blood autoantibody amount (VT:0003725)	calculated serum anti-type 2 collagen antibody titer (CMO:0001279)	10	65590122	110590122	Rat
2313103	Bss80	Bone structure and strength QTL 80	2	0.0001	tibia strength trait (VT:1000284)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	10	65992275	110992275	Rat
2313105	Bss79	Bone structure and strength QTL 79	1.8	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	10	65992275	110992275	Rat
7387312	Bw125	Body weight QTL 125	3	0.0047	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight (CMO:0000356)	10	67880046	112626471	Rat
1581559	Eae18	Experimental allergic encephalomyelitis QTL 18		0.00002	nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis severity score (CMO:0001419)	10	67988218	110992091	Rat
2317029	Aia19	Adjuvant induced arthritis QTL 19	2.98		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	10	69385595	112626471	Rat
2317039	Aia6	Adjuvant induced arthritis QTL 6	4.31		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	10	69385595	112626471	Rat
10450498	Bp384	Blood pressure QTL 384		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	70166960	112626471	Rat
1642980	Bp300	Blood pressure QTL 300			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	70800069	112626471	Rat
61396	Bp9	Blood pressure QTL 9	4.8	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	71692298	112626471	Rat
2300172	Bmd57	Bone mineral density QTL 57	9.8	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	10	73008136	112626471	Rat
2293646	Bss25	Bone structure and strength QTL 25	10.96	0.0001	femur morphology trait (VT:0000559)	femur cross-sectional area (CMO:0001661)	10	73008136	112626471	Rat
2293663	Bss33	Bone structure and strength QTL 33	9.34	0.0001	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	10	73008136	112626471	Rat
6893366	Bw106	Body weight QTL 106	0.3	0.47	body mass (VT:0001259)	body weight (CMO:0000012)	10	73467158	112626471	Rat
70193	Mcs7	Mammary carcinoma susceptibility QTL 7	2.38		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	10	75544754	112626471	Rat
2298548	Neuinf7	Neuroinflammation QTL 7	3.4		nervous system integrity trait (VT:0010566)	spinal cord RT1-B protein level (CMO:0002132)	10	75544754	112626471	Rat
2292438	Bp311	Blood pressure QTL 311			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	78970279	112626471	Rat
1302404	Cia27	Collagen induced arthritis QTL 27	2.6	0.0045	joint integrity trait (VT:0010548)	experimental arthritis severity measurement (CMO:0001459)	10	79927661	112626471	Rat
4889492	Pancm2	Pancreatic morphology QTL 2	3.2		pancreatic beta cell morphology trait (VT:0005217)	ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)	10	80239190	112626471	Rat
2303589	Bw87	Body weight QTL 87	2		body mass (VT:0001259)	body weight (CMO:0000012)	10	85079943	112626471	Rat
2317754	Glom25	Glomerulus QTL 25	3.5		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	10	86566908	112626471	Rat
631538	Oia5	Oil induced arthritis QTL 5			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	90041957	112626471	Rat
61363	Oia3	Oil induced arthritis QTL 3		0.001	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	90296897	112626471	Rat
634320	Niddm49	Non-insulin dependent diabetes mellitus QTL 49	4.41		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	10	91689348	112626471	Rat
1579915	Bp280	Blood pressure QTL 280		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	93662786	112626471	Rat
12880395	Cm109	Cardiac mass QTL 109		0.001	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	10	93662786	112626471	Rat
12880396	Am13	Aortic mass QTL 13		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	10	93662786	112626471	Rat
12880398	Kidm67	Kidney mass QTL 67		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	10	93662786	112626471	Rat
12880384	Cm107	Cardiac mass QTL 107		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)		93662786	112626471	Rat
12880385	Cm108	Cardiac mass QTL 108		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)		93662786	112626471	Rat
1300137	Bp186	Blood pressure QTL 186	3.57		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	10	93886117	110992275	Rat
724530	Bp149	Blood pressure QTL 149		0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	93886117	112626471	Rat
1558652	Bw57	Body weight QTL 57	4.2	0.0008	body mass (VT:0001259)	body weight (CMO:0000012)	10	94170766	112626471	Rat
1354641	Bvd2	Brain ventricular dilatation QTL 2	6.36	0.001	brain ventricle morphology trait (VT:0000822)	hydrocephalus severity score (CMO:0001881)	10	96520816	110992275	Rat
2292436	Bp310	Blood pressure QTL 310			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	98079221	112626471	Rat
10450493	Bp382	Blood pressure QTL 382		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	98079221	112626471	Rat
1578663	Bss18	Bone structure and strength QTL 18	3.6		femur width (VT:1000666)	femoral neck width (CMO:0001695)	10	100155035	110992275	Rat
1578672	Bmd16	Bone mineral density QTL 16	6.2		femur mineral mass (VT:0010011)	cortical volumetric bone mineral density (CMO:0001730)	10	100155035	110992275	Rat

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

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_139060	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008768511	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039086796	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039086797	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AB063114	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC128909	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BM392381	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CB615084	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473948	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CV112274	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	DY312461	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000220	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000015178 ⟹ ENSRNOP00000015178

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	10	110,148,600 - 110,182,291 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000054936 ⟹ ENSRNOP00000051819

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	10	110,151,420 - 110,182,408 (-)	Ensembl

RefSeq Acc Id:

NM_139060 ⟹ NP_620691

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	106,225,624 - 106,256,614 (-)	NCBI
Rnor_6.0	10	110,151,420 - 110,182,408 (-)	NCBI
Rnor_5.0	10	109,738,952 - 109,769,940 (-)	NCBI
RGSC_v3.4	10	110,166,244 - 110,197,233 (-)	RGD
Celera	10	104,764,644 - 104,795,629 (-)	RGD

Sequence:

show sequence

ACAGCGCGATGGCGGCGGCTCCTTTAGGCAGCTGAAGGGGGATTTAGGCCCGGAAGATCCGAGT
CCATCCGCGGCGGGGAGAGGGCGAGCGGGGCCGGCAGGGGCCGGAGCAGCGGCGGCGGCGCTCG
GACTGTCCCATCCGCCCCGTATTGAGGCGCTGAGAGCGACGGGGCGACCAGAAAGCGATGGTGA
AAGCGGGGCCGTGAGGGGGGCGGAGTCGGACCGGACCCGCAGTAGCGGCAGCAGCGGCGCCGCC
TCCCGGAGCGCAGACCCAGGAAGCGGCCGGGCGGGCAGTAGCGAGCCGCACCGCTGCCATGGAG
CTGAGGGTCGGGAACAGGTACCGACTGGGCCGCAAGATCGGCAGCGGCTCCTTCGGAGACATCT
ATCTCGGTACGGACATTGCTGCAGGAGAAGAAGTTGCCATCAAGCTTGAATGTGTCAAAACCAA
ACATCCTCAGCTCCACATTGAGAGCAAGATCTACAAAATGATGCAGGGAGGAGTGGGCATCCCT
ACCATCAGATGGTGTGGGGCTGAGGGGGACTACAATGTCATGGTGATGGAGCTACTGGGACCCA
GCCTGGAAGACCTATTCAACTTCTGTTCAAGGAAGTTTAGTCTCAAAACTGTTCTGTTGCTTGC
TGACCAAATGATAAGTCGTATTGAGTACATTCATTCGAAGAATTTTATCCACCGAGACGTGAAA
CCAGATAACTTCCTCATGGGGCTGGGAAAGAAAGGCAACCTGGTCTACATCATTGACTTTGGGC
TGGCCAAGAAGTATCGGGATGCCCGCACCCACCAGCATATCCCCTATCGAGAGAACAAGAACCT
CACAGGGACAGCACGCTATGCCTCCATCAACACACACCTTGGCATTGAACAATCTCGAAGGGAT
GACTTGGAGTCTCTGGGGTACGTGCTGATGTACTTCAACCTGGGCTCTCTCCCCTGGCAGGGGC
TGAAGGCCGCCACCAAGAGGCAGAAGTATGAGAGGATCAGTGAGAAGAAGATGTCCACTCCAAT
TGAAGTGCTGTGCAAGGGCTATCCTTCTGAATTTGCCACATACCTGAATTTCTGCCGTTCCTTA
CGTTTTGATGACAAACCTGACTACTCCTACCTGAGACAGCTCTTCAGAAATCTGTTCCATCGCC
AGGGCTTCTCCTACGACTATGTGTTCGACTGGAACATGCTCAAATTTGGTGCCAGCCGGGCTGC
AGATGATGCTGAGCGGGAACGCCGGGACCGAGAAGAACGATTAAGACACTCCCGGAATCCAGCC
ACTCGTGGCCTCCCTTCTACAGCTTCCGGCCGTCTGCGGGGAACCCAGGAAGTGGCTCCCCCAA
CGCCCCTTACCCCTACCTCACATACGGCCAACACCTCTCCTAGACCCGTCTCTGGCATGGAACG
AGAACGGAAAGTGAGTATGCGGCTGCACCGTGGGGCCCCAGTCAACGTCTCCTCATCTGATCTC
ACGGGCCGACAAGATACCTCTCGCATGTCCACCTCACAGATTCCCGGTCGGGTGGCTTCCAGTG
GTCTTCAGTCTGTCGTGCACCGATGAGAACTCTCCTTTTTGCTGTGAAGGGCAGACAATGCATG
GCTGATCTACTCTGTTACCAATGGCTTTACTAGTGACACGCCCCCCGGTCTAAACCCGAAATGT
TAACGCCGGGAGCTCTCCAGGCCACTCACCCAGCGATGCACATGGGGAATCAAAACACAAACTA
AATGGACAGGCTCCAAGAGCTGCCATCGCCAGGGGCTGCCACCATGGCCCCATGTGAGCTCAGT
TGTCATGGGGCTGGGACGAAGAGCAGAGGCTGGGAAACCATTGCAGAGAGAACCCGACTCCCTG
TGAAGAGCCTCTCAGCTCCCACCAGTGGTGGCGGACCTGCGCTCCCTGATGATCCCACCGCAGC
TACCAGTCTTCTACTTGGTTAAGACAGTTTTGTATCATTTTGCTAAAAATTACTGGCTTAAATC
TGTGTAAAGAAATCTGTCTTTTTATTGTTTCTTTCTTGTCTGTTTTTGCGGTCTTAAACAAAAA
AGATGTTGACCTTAAAGAATCCTAAGACACGCTGGCTTGGAGCTTCTGTGTAAAATGGAGGCAG
GCAAGAGAGGGGCACATGTGAGTGTCGAGGATGTGTGTTTTGTTTTGTTTTCTTGTGTTGTGCT
GTTCACTTTGGAAAGGAAATTCTCATCAGTTGTGTATGTGTGTGTGTGTCTTGTGGGCTCCCAT
CAGCCTAATTTGGGCATCTTGCTTACTCTTTCCCACTGTAAACGGATATGCCTGCAGCCATCAG
AGCAGGTAGGGTACAACATCATGGAGTAGTAGGGTTCAGCAGTTCTAGCCTCAGCTGAGCACCA
TGGCATGGCATTCTTCCCAAAGGAGGCAAGAAGGAAGCCAAGACTGAAGAACCCACGTGCAGAG
ACCTTGAGAGCCATATAGGCTGCTGGAGAATTCCAAGATTCAAAGCTGAGCTTGTGTTTGTGGT
TTCTAGGGAGAGGATTGATTTTTGGGTAGGATTGGTTGCCTCTATGCCTTTGCACTTGGGAAGT
TGTGGAACTGACTGCATAGTCCCATGCAGATGCCACTTGGGTTTGTCATTGCCTCTCAGAGCCA
GGGAGCAGGCTGTCCTAGACACCATGGTTTGCCCAGAGGGACCAGTGGCCAAAGGGAATCCACC
CTGAAGTGCCAAGAAGCAGGTGACTGCCTACCTGACTCTAGAACCTTCACCTCCAGAAAGGTGT
GGTGCCACACGCCTCATGATCTTCAGCTGGACACATCTGCGGGCTGGGCTGCTCTGCCGCTGGC
GGTTAGGATGCCAACATGCTCTTCCCTACCATGTGCACCGGATATGAAGAGACAGCAGGACCTG
AGCTCCCCATCTGAGAAATGGGGTGCAGTACATGGGTGTGGGTCCATCTCTTTATTTTTCCTGT
CAGCCTGTGGAGAGAGTTATGCTGGGTACCTTGTTCCCTGTGGAGGTTTGGGCTCTAATGGTGC
CACCATGGCTTCTCCCTTCTTCCCAGAGTTCCTTGGCTCTGAGCACTGGCCCAAGGTTGGGGGA
CACACTGCTGATGTGTGATAGCATCCCAGAATGTGGCTGTTAATTGTGCCTGCCAGCCACGTGA
GCCTGTGGGTGCTTTCTGAATCCTGAGCTGGTTACTCTGCAAGCATTTTAGGGTGGAGAGACTT
GACTCGGTGGGATTGTGTGTCGAGGAGTGCAGAGGGAGGTTGGGGGGGTTGGGCGAGTTTGAGA
TCTTTGTTGCAAATTCTTTATCAGAGTTGGCCCTTCCCTCTCCAGTGGCAGGCCTGCCTGGCAA
GTGTTCTTGTAGATACCTGTGGTGCTGGAGGGGTACAGGGTGGTCTTGAGACTAATCCAGGTTC
AGCCTGGCTTTGTTGGGTTGTGCTCAGATTAGGCCCATTGGAAGTCTCCAGGGTGTGGCCCTGA
CAGTTCTTGCCCAATATTTAATCCCACCATCCCTCGCAGGAAGCGTAGTTAGAATGTGTGTATC
AACCTGTGTCTTGGTGAGCAGTCTCTGAGCTGTGCGTTTGTACTACCACTGTGTTTGTGTACTT
TAACAATTGTGTAAATAATAAATTCATAATGACTTCTACCTTTCAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_008768511 ⟹ XP_008766733

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	106,225,624 - 106,256,601 (-)	NCBI
Rnor_6.0	10	110,151,421 - 110,182,413 (-)	NCBI

Sequence:

show sequence

ACGTCACAGCGCGATGGCGGCGGCTCCTTTAGGCAGCTGAAGGGGGATTTAGGCCCGGAAGATC
CGAGTCCATCCGCGGCGGGGAGAGGGCGAGCGGGGCCGGCAGGGGCCGGAGCAGCGGCGGCGGC
GCTCGGACTGTCCCATCCGCCCCGTATTGAGGCGCTGAGAGCGACGGGGCGACCAGAAAGCGAT
GGTGAAAGCGGGGCCGTGAGGGGGGCGGAGTCGGACCGGACCCGCAGTAGCGGCAGCAGCGGCG
CCGCCTCCCGGAGCGCAGACCCAGGAAGCGGCCGGGCGGGCAGTAGCGAGCCGCACCGCTGCCA
TGGAGCTGAGGGTCGGGAACAGGTACCGACTGGGCCGCAAGATCGGCAGCGGCTCCTTCGGAGA
CATCTATCTCGGTACGGACATTGCTGCAGGAGAAGAAGTTGCCATCAAGCTTGAATGTGTCAAA
ACCAAACATCCTCAGCTCCACATTGAGAGCAAGATCTACAAAATGATGCAGGGAGGAGTGGGCA
TCCCTACCATCAGATGGTGTGGGGCTGAGGGGGACTACAATGTCATGGTGATGGAGCTACTGGG
ACCCAGCCTGGAAGACCTATTCAACTTCTGTTCAAGGAAGTTTAGTCTCAAAACTGTTCTGTTG
CTTGCTGACCAAATGATAAGTCGTATTGAGTACATTCATTCGAAGAATTTTATCCACCGAGACG
TGAAACCAGATAACTTCCTCATGGGGCTGGGAAAGAAAGGCAACCTGGTCTACATCATTGACTT
TGGGCTGGCCAAGAAGTATCGGGATGCCCGCACCCACCAGCATATCCCCTATCGAGAGAACAAG
AACCTCACAGGGACAGCACGCTATGCCTCCATCAACACACACCTTGGCATTGAACAATCTCGAA
GGGATGACTTGGAGTCTCTGGGGTACGTGCTGATGTACTTCAACCTGGGCTCTCTCCCCTGGCA
GGGGCTGAAGGCCGCCACCAAGAGGCAGAAGTATGAGAGGATCAGTGAGAAGAAGATGTCCACT
CCAATTGAAGTGCTGTGCAAGGGCTATCCTTCTGAATTTGCCACATACCTGAATTTCTGCCGTT
CCTTACGTTTTGATGACAAACCTGACTACTCCTACCTGAGACAGCTCTTCAGAAATCTGTTCCA
TCGCCAGGGCTTCTCCTACGACTATGTGTTCGACTGGAACATGCTCAAATTTGGTGCCAGCCGG
GCTGCAGATGATGCTGAGCGGGAACGCCGGGACCGAGAAGAACGATTAAGACACTCCCGGAATC
CAGCCACTCGTGGCCTCCCTTCTACAGCTTCCGGCCGTCTGCGGGGAACCCAGGAAGTGGCTCC
CCCAACGCCCCTTACCCCTACCTCACATACGGCCAACACCTCTCCTAGACCCGTCTCTGGCATG
GAACGAGAACGGAAAGTGAGTATGCGGCTGCACCGTGGGGCCCCAGTCAACGTCTCCTCATCTG
ATCTCACGGGCCGACAAGATACCTCTCGCATGTCCACCTCACAGAATAGCATTCCTTTCGAACA
CCACGGCAAGTAGCTGCTCGTCTCCATCGGAAGGCAGCACTGGATTCCCGGTCGGGTGGCTTCC
AGTGGTCTTCAGTCTGTCGTGCACCGATGAGAACTCTCCTTTTTGCTGTGAAGGGCAGACAATG
CATGGCTGATCTACTCTGTTACCAATGGCTTTACTAGTGACACGCCCCCCGGTCTAAACCCGAA
ATGTTAACGCCGGGAGCTCTCCAGGCCACTCACCCAGCGATGCACATGGGGAATCAAAACACAA
ACTAAATGGACAGGCTCCAAGAGCTGCCATCGCCAGGGGCTGCCACCATGGCCCCATGTGAGCT
CAGTTGTCATGGGGCTGGGACGAAGAGCAGAGGCTGGGAAACCATTGCAGAGAGAACCCGACTC
CCTGTGAAGAGCCTCTCAGCTCCCACCAGTGGTGGCGGACCTGCGCTCCCTGATGATCCCACCG
CAGCTACCAGTCTTCTACTTGGTTAAGACAGTTTTGTATCATTTTGCTAAAAATTACTGGCTTA
AATCTGTGTAAAGAAATCTGTCTTTTTATTGTTTCTTTCTTGTCTGTTTTTGCGGTCTTAAACA
AAAAAGATGTTGACCTTAAAGAATCCTAAGACACGCTGGCTTGGAGCTTCTGTGTAAAATGGAG
GCAGGCAAGAGAGGGGCACATGTGAGTGTCGAGGATGTGTGTTTTGTTTTGTTTTCTTGTGTTG
TGCTGTTCACTTTGGAAAGGAAATTCTCATCAGTTGTGTATGTGTGTGTGTGTCTTGTGGGCTC
CCATCAGCCTAATTTGGGCATCTTGCTTACTCTTTCCCACTGTAAACGGATATGCCTGCAGCCA
TCAGAGCAGGTAGGGTACAACATCATGGAGTAGTAGGGTTCAGCAGTTCTAGCCTCAGCTGAGC
ACCATGGCATGGCATTCTTCCCAAAGGAGGCAAGAAGGAAGCCAAGACTGAAGAACCCACGTGC
AGAGACCTTGAGAGCCATATAGGCTGCTGGAGAATTCCAAGATTCAAAGCTGAGCTTGTGTTTG
TGGTTTCTAGGGAGAGGATTGATTTTTGGGTAGGATTGGTTGCCTCTATGCCTTTGCACTTGGG
AAGTTGTGGAACTGACTGCATAGTCCCATGCAGATGCCACTTGGGTTTGTCATTGCCTCTCAGA
GCCAGGGAGCAGGCTGTCCTAGACACCATGGTTTGCCCAGAGGGACCAGTGGCCAAAGGGAATC
CACCCTGAAGTGCCAAGAAGCAGGTGACTGCCTACCTGACTCTAGAACCTTCACCTCCAGAAAG
GTGTGGTGCCACACGCCTCATGATCTTCAGCTGGACACATCTGCGGGCTGGGCTGCTCTGCCGC
TGGCGGTTAGGATGCCAACATGCTCTTCCCTACCATGTGCACCGGATATGAAGAGACAGCAGGA
CCTGAGCTCCCCATCTGAGAAATGGGGTGCAGTACATGGGTGTGGGTCCATCTCTTTATTTTTC
CTGTCAGCCTGTGGAGAGAGTTATGCTGGGTACCTTGTTCCCTGTGGAGGTTTGGGCTCTAATG
GTGCCACCATGGCTTCTCCCTTCTTCCCAGAGTTCCTTGGCTCTGAGCACTGGCCCAAGGTTGG
GGGACACACTGCTGATGTGTGATAGCATCCCAGAATGTGGCTGTTAATTGTGCCTGCCAGCCAC
GTGAGCCTGTGGGTGCTTTCTGAATCCTGAGCTGGTTACTCTGCAAGCATTTTAGGGTGGAGAG
ACTTGACTCGGTGGGATTGTGTGTCGAGGAGTGCAGAGGGAGGTTGGGGGGGTTGGGCGAGTTT
GAGATCTTTGTTGCAAATTCTTTATCAGAGTTGGCCCTTCCCTCTCCAGTGGCAGGCCTGCCTG
GCAAGTGTTCTTGTAGATACCTGTGGTGCTGGAGGGGTACAGGGTGGTCTTGAGACTAATCCAG
GTTCAGCCTGGCTTTGTTGGGTTGTGCTCAGATTAGGCCCATTGGAAGTCTCCAGGGTGTGGCC
CTGACAGTTCTTGCCCAATATTTAATCCCACCATCCCTCGCAGGAAGCGTAGTTAGAATGTGTG
TATCAACCTGTGTCTTGGTGAGCAGTCTCTGAGCTGTGCGTTTGTACTACCACTGTGTTTGTGT
ACTTTAACAATTGTGTAAATAATAAATTCATAATGACTTCTACCTTT

hide sequence

RefSeq Acc Id:

XM_039086796 ⟹ XP_038942724

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	106,221,992 - 106,256,620 (-)	NCBI

RefSeq Acc Id:

XM_039086797 ⟹ XP_038942725

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	106,221,992 - 106,249,218 (-)	NCBI

RefSeq Acc Id:

XR_594964

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	10	110,147,786 - 110,182,413 (-)	NCBI

Sequence:

show sequence

ACGTCACAGCGCGATGGCGGCGGCTCCTTTAGGCAGCTGAAGGGGGATTTAGGCCCGGAAGATC
CGAGTCCATCCGCGGCGGGGAGAGGGCGAGCGGGGCCGGCAGGGGCCGGAGCAGCGGCGGCGGC
GCTCGGACTGTCCCATCCGCCCCGTATTGAGGCGCTGAGAGCGACGGGGCGACCAGAAAGCGAT
GGTGAAAGCGGGGCCGTGAGGGGGGCGGAGTCGGACCGGACCCGCAGTAGCGGCAGCAGCGGCG
CCGCCTCCCGGAGCGCAGACCCAGGAAGCGGCCGGGCGGGCAGTAGCGAGCCGCACCGCTGCCA
TGGAGCTGAGGGTCGGGAACAGGTACCGACTGGGCCGCAAGATCGGCAGCGGCTCCTTCGGAGA
CATCTATCTCGGTACGGACATTGCTGCAGGAGAAGAAGTTGCCATCAAGCTTGAATGTGTCAAA
ACCAAACATCCTCAGCTCCACATTGAGAGCAAGATCTACAAAATGATGCAGGGAGGAGTGGGCA
TCCCTACCATCAGATGGTGTGGGGCTGAGGGGGACTACAATGTCATGGTGATGGAGCTACTGGG
ACCCAGCCTGGAAGACCTATTCAACTTCTGTTCAAGGAAGTTTAGTCTCAAAACTGTTCTGTTG
CTTGCTGACCAAATGATAAGTCGTATTGAGTACATTCATTCGAAGAATTTTATCCACCGAGACG
TGAAACCAGATAACTTCCTCATGGGGCTGGGAAAGAAAGGCAACCTGGTCTACATCATTGACTT
TGGGCTGGCCAAGAAGTATCGGGATGCCCGCACCCACCAGCATATCCCCTATCGAGAGAACAAG
AACCTCACAGGGACAGCACGCTATGCCTCCATCAACACACACCTTGGCATTGAACAATCTCGAA
GGGATGACTTGGAGTCTCTGGGGTACGTGCTGATGTACTTCAACCTGGGCTCTCTCCCCTGGCA
GGGGCTGAAGGCCGCCACCAAGAGGCAGAAGTATGAGAGGATCAGTGAGAAGAAGATGTCCACT
CCAATTGAAGTGCTGTGCAAGGGCTATCCTTCTGAATTTGCCACATACCTGAATTTCTGCCGTT
CCTTACGTTTTGATGACAAACCTGACTACTCCTACCTGAGACAGCTCTTCAGAAATCTGTTCCA
TCGCCAGGGCTTCTCCTACGACTATGTGTTCGACTGGAACATGCTCAAATTTGGTGCCAGCCGG
GCTGCAGATGATGCTGAGCGGGAACGCCGGGACCGAGAAGAACGATTAAGACACTCCCGGAATC
CAGCCACTCGTGGCCTCCCTTCTACAGCTTCCGGCCGTCTGCGGGGAACCCAGGAAGTGGCTCC
CCCAACGCCCCTTACCCCTACCTCACATACGGCCAACACCTCTCCTAGACCCGTCTCTGGCATG
GAACGAGAACGGAAAGTGAGTATGCGGCTGCACCGTGGGGCCCCAGTCAACGTCTCCTCATCTG
ATCTCACGGGCCGACAAGATACCTCTCGCATGTCCACCTCACAGAGGAGCAGGGACATGGCATC
TCTCCGGCTGCACGCGGCCCGCCAAGGTGCCCGCTGCCGTCCCCAGCGCCCACGACGTACCACC
TACTGAGGCGGCCCCAGCGGCCTCTGACCGGGCTTCCAGCCACGCAGGCCGCCACCGGCCACAG
GGCAGATCCACTTTGGAATGACGCGGTTCCCACCCCGCCACCTCTCCCCGCAAAACACTGACCC
GCTGACCAGGCAGCCAAGAGCTGAGCCGATGGCCCCGCCTCAGCTGGTCCTGTTTGTGAAATAA
ATATGAGCGTTGCCAGTCTC

hide sequence

Protein Sequences


Protein RefSeqs	NP_620691	(Get FASTA)	NCBI Sequence Viewer
	XP_008766733	(Get FASTA)	NCBI Sequence Viewer
	XP_038942724	(Get FASTA)	NCBI Sequence Viewer
	XP_038942725	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	BAB60852	(Get FASTA)	NCBI Sequence Viewer
	EDM06917	(Get FASTA)	NCBI Sequence Viewer
	EDM06918	(Get FASTA)	NCBI Sequence Viewer
	EDM06919	(Get FASTA)	NCBI Sequence Viewer
	EDM06920	(Get FASTA)	NCBI Sequence Viewer
	EDM06921	(Get FASTA)	NCBI Sequence Viewer
	EDM06922	(Get FASTA)	NCBI Sequence Viewer
	EDM06923	(Get FASTA)	NCBI Sequence Viewer
	EDM06924	(Get FASTA)	NCBI Sequence Viewer
	Q06486	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_620691 ⟸ NM_139060

- UniProtKB:

Q06486 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVG
IPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRD
VKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSR
RDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCR
SLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLKFGASRAADDAERERRDREERLRHSRN
PATRGLPSTASGRLRGTQEVAPPTPLTPTSHTANTSPRPVSGMERERKVSMRLHRGAPVNVSSS
DLTGRQDTSRMSTSQIPGRVASSGLQSVVHR

hide sequence

RefSeq Acc Id:

XP_008766733 ⟸ XM_008768511

- Peptide Label:

isoform X2

- Sequence:

show sequence

MELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVG
IPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRD
VKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSR
RDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCR
SLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLKFGASRAADDAERERRDREERLRHSRN
PATRGLPSTASGRLRGTQEVAPPTPLTPTSHTANTSPRPVSGMERERKVSMRLHRGAPVNVSSS
DLTGRQDTSRMSTSQNSIPFEHHGK

hide 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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	10	110,182,143 - 110,182,203	EPDNEW

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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	10	110,182,408 - 110,182,468	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN/SsN (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Buf/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

F344/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

FHH/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

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

External Database Links

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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - KEGG (archival)

Imported Annotations - PID (archival)