Csnk1d casein kinase 1, delta [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Csnk1dprovided by MGI
Official Full Name: casein kinase 1, deltaprovided by MGI
Primary source: MGI:MGI:1355272
See related: Ensembl:ENSMUSG00000025162
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: AA409348; 1200006A05Rik; D930010H05Rik
Summary: This gene encodes a member of the casein kinase I (CKI) family of serine/threonine protein kinases. A highly similar human protein regulates an array of cellular processes by influencing the Wnt and hedgehog signaling pathways. The encoded protein may also be involved in the regulation of apoptosis, circadian rhythm, microtubule dynamics, chromosome segregation, and p53-mediated effects on growth. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in CNS E14 (RPKM 50.8), whole brain E14.5 (RPKM 50.5) and 28 other tissues See more
Orthologs: human all

Genomic context

Location:: 11; 11 E2

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
106	current	GRCm38.p4 (GCF_000001635.24)	11	NC_000077.6 (120958009..120991333, complement)
Build 37.2	previous assembly	MGSCv37 (GCF_000001635.18)	11	NC_000077.5 (120823055..120852647, complement)

Chromosome 11 - NC_000077.6 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

CK1delta/epsilon disruption mouse had a long (27.4 h) behavioral period to which peripheral clocks entrained in vivo, albeit with an advanced phase ( approximately 6 h).
Title: Desynchrony between brain and peripheral clocks caused by CK1δ/ε disruption in GABA neurons does not lead to adverse metabolic outcomes.
Studied roles of CK1delta and CK1e in regulation of PER2 in circadian rhythm.
Title: CK1δ/ε protein kinase primes the PER2 circadian phosphoswitch.
the impact of obesity on the circadian system in mice at a behavioural and molecular level was assessed, and determined whether pharmacological targeting of casein kinase 1delta and epsilon (CK1delta/epsilon), key regulators of the circadian clock, can confer metabolic benefit.
Title: Targeting of the circadian clock via CK1δ/ε to improve glucose homeostasis in obesity.
Here, the authors identify another Wnt signaling amplifier, CKIepsilon, which is specifically upregulated in intestinal stem cells and is essential for intestinal stem cell maintenance, especially in the absence of its close isoform CKIdelta.
Title: Casein kinase 1-epsilon or 1-delta required for Wnt-mediated intestinal stem cell maintenance.
Report temperature-compensated CKIdelta-dependent multi-site phosphorylation in mammals underlies temperature compensated phosphorylation in circadian clocks.
Title: Temperature-Sensitive Substrate and Product Binding Underlie Temperature-Compensated Phosphorylation in the Clock.
Together, these findings suggest that CK1delta contributes to the efficient repair of DNA damage and the proper functioning of mitotic checkpoints by maintaining appropriate levels of Chk1.
Title: Lack of Casein Kinase 1 Delta Promotes Genomic Instability - The Accumulation of DNA Damage and Down-Regulation of Checkpoint Kinase 1.
we conclude that APC/C(Cdh1) controls CK1 delta levels to balance proliferation and cell-cycle exit in the developing CNS
Title: Casein kinase 1δ is an APC/C(Cdh1) substrate that regulates cerebellar granule cell neurogenesis.
CK1delta mediates primary ciliogenesis by multiple mechanisms, one involving its centrosomal function and another dependent on its interaction with AKAP450 at the Golgi.
Title: Casein kinase 1δ functions at the centrosome and Golgi to promote ciliogenesis.
this article reports the crystallization and structure determination of a new crystal form of casein kinase I delta belonging to space group P21.
Title: A monoclinic crystal form of casein kinase 1 δ.
decreases in CKIdelta activity can contribute to the pathogenesis of migraine.
Title: Casein kinase iδ mutations in familial migraine and advanced sleep phase.

Submit: New GeneRIF Correction See all GeneRIFs (22)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (1) 1 citation
Targeted (2) 1 citation
Endonuclease-mediated (1) 1 citation

Pathways from BioSystems

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AURKA Activation by TPX2, organism-specific biosystem (from REACTOME)
AURKA Activation by TPX2, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Anchoring of the basal body to the plasma membrane, organism-specific biosystem (from REACTOME)
Anchoring of the basal body to the plasma membrane, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Asparagine N-linked glycosylation, organism-specific biosystem (from REACTOME)
Asparagine N-linked glycosylation, organism-specific biosystemcomputationally inferred pathway (not manually curated)
COPII (Coat Protein 2) Mediated Vesicle Transport, organism-specific biosystem (from REACTOME)
COPII (Coat Protein 2) Mediated Vesicle Transport, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Cell Cycle, organism-specific biosystem (from REACTOME)
Cell Cycle, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Cell Cycle, Mitotic, organism-specific biosystem (from REACTOME)
Cell Cycle, Mitotic, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Centrosome maturation, organism-specific biosystem (from REACTOME)
Centrosome maturation, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Cilium Assembly, organism-specific biosystem (from REACTOME)
Cilium Assembly, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Circadian Clock, organism-specific biosystem (from REACTOME)
Circadian Clock, organism-specific biosystemAt the center of the mouse circadian clock is a negative transcription/translation-based feedback loop: The Bmal1:Clock/Npas2 (Arntl:Clock/Npas2) heterodimer transactivates Cryptochrome (Cry) and Per...
Circadian Clock, organism-specific biosystem (from REACTOME)
Circadian Clock, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Circadian rhythm, organism-specific biosystem (from KEGG)
Circadian rhythm, organism-specific biosystemCircadian rhythm is an internal biological clock, which enables to sustain an approximately 24-hour rhythm in the absence of environmental cues. In mammals, the circadian clock mechanism consists of ...
Circadian rhythm, conserved biosystem (from KEGG)
Circadian rhythm, conserved biosystemCircadian rhythm is an internal biological clock, which enables to sustain an approximately 24-hour rhythm in the absence of environmental cues. In mammals, the circadian clock mechanism consists of ...
ER to Golgi Anterograde Transport, organism-specific biosystem (from REACTOME)
ER to Golgi Anterograde Transport, organism-specific biosystemcomputationally inferred pathway (not manually curated)
G2/M Transition, organism-specific biosystem (from REACTOME)
G2/M Transition, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Gap junction, organism-specific biosystem (from KEGG)
Gap junction, organism-specific biosystemGap junctions contain intercellular channels that allow direct communication between the cytosolic compartments of adjacent cells. Each gap junction channel is formed by docking of two 'hemichannels'...
Gap junction, conserved biosystem (from KEGG)
Gap junction, conserved biosystemGap junctions contain intercellular channels that allow direct communication between the cytosolic compartments of adjacent cells. Each gap junction channel is formed by docking of two 'hemichannels'...
Hedgehog signaling pathway, organism-specific biosystem (from KEGG)
Hedgehog signaling pathway, organism-specific biosystemThe Hedgehog (Hh) signaling pathway has numerous roles in the control of cell proliferation, tissue patterning, stem cell maintenance and development. The primary cilium is an important center for tr...
Hedgehog signaling pathway, conserved biosystem (from KEGG)
Hedgehog signaling pathway, conserved biosystemThe Hedgehog (Hh) signaling pathway has numerous roles in the control of cell proliferation, tissue patterning, stem cell maintenance and development. The primary cilium is an important center for tr...
Hippo signaling pathway, organism-specific biosystem (from KEGG)
Hippo signaling pathway, organism-specific biosystemHippo signaling is an evolutionarily conserved signaling pathway that controls organ size from flies to humans. In humans and mice, the pathway consists of the MST1 and MST2 kinases, their cofactor S...
Hippo signaling pathway, conserved biosystem (from KEGG)
Hippo signaling pathway, conserved biosystemHippo signaling is an evolutionarily conserved signaling pathway that controls organ size from flies to humans. In humans and mice, the pathway consists of the MST1 and MST2 kinases, their cofactor S...
Loss of Nlp from mitotic centrosomes, organism-specific biosystem (from REACTOME)
Loss of Nlp from mitotic centrosomes, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Loss of proteins required for interphase microtubule organization from the centrosome, organism-specific biosystem (from REACTOME)
Loss of proteins required for interphase microtubule organization from the centrosome, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Membrane Trafficking, organism-specific biosystem (from REACTOME)
Membrane Trafficking, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Metabolism of proteins, organism-specific biosystem (from REACTOME)
Metabolism of proteins, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Mitotic G2-G2/M phases, organism-specific biosystem (from REACTOME)
Mitotic G2-G2/M phases, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Mus musculus biological processes, organism-specific biosystem (from REACTOME)
Mus musculus biological processes, organism-specific biosystemCertain mouse pathways have been fully manually curated in Reactome in order to support the manual inference of well-conserved but less well-studied human pathways. These pathways include Circadian...
Organelle biogenesis and maintenance, organism-specific biosystem (from REACTOME)
Organelle biogenesis and maintenance, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Post-translational protein modification, organism-specific biosystem (from REACTOME)
Post-translational protein modification, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Recruitment of mitotic centrosome proteins and complexes, organism-specific biosystem (from REACTOME)
Recruitment of mitotic centrosome proteins and complexes, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Regulation of PLK1 Activity at G2/M Transition, organism-specific biosystem (from REACTOME)
Regulation of PLK1 Activity at G2/M Transition, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Transport to the Golgi and subsequent modification, organism-specific biosystem (from REACTOME)
Transport to the Golgi and subsequent modification, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
Vesicle-mediated transport, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Wnt Signaling Pathway NetPath, organism-specific biosystem (from WikiPathways)
Wnt Signaling Pathway NetPath, organism-specific biosystemWnt family of proteins are a large family of cysteine-rich secreted glycoproteins that regulate cell-cell interactions. They bind to members of the Frizzled family of 7 transmembrane receptors. Bindi...

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:532270

Csnk1d (e-PCR), detects polymorphism
- UniSTS:532270

D11Bhm20 (e-PCR), detects polymorphism
- UniSTS:141619

D9Mit34.1 (e-PCR), detects polymorphism
- UniSTS:131903

RH124850 (e-PCR)
- UniSTS:161672

Homology

Homologs of the Csnk1d gene: The Csnk1d gene is conserved in human, chimpanzee, dog, rat, chicken, zebrafish, C.elegans, S.cerevisiae, K.lactis, E.gossypii, S.pombe, M.oryzae, N.crassa, A.thaliana, and frog.
Orthologs from Annotation Pipeline: 252 organisms have orthologs with human gene Csnk1d
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
ATP binding	IEA Inferred from Electronic Annotation more info
kinase activity	ISO Inferred from Sequence Orthology more info
nucleotide binding	IEA Inferred from Electronic Annotation more info
protein binding	IPI Inferred from Physical Interaction more info	PubMed
protein kinase activity	IDA Inferred from Direct Assay more info	PubMed
protein kinase activity	IGI Inferred from Genetic Interaction more info	PubMed
protein kinase activity	ISO Inferred from Sequence Orthology more info
protein serine/threonine kinase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
protein serine/threonine kinase activity	ISO Inferred from Sequence Orthology more info
tau-protein kinase activity	IEA Inferred from Electronic Annotation more info
transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
Golgi organization	ISO Inferred from Sequence Orthology more info
Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
circadian regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
microtubule nucleation	ISO Inferred from Sequence Orthology more info
non-motile cilium assembly	IBA Inferred from Biological aspect of Ancestor more info	PubMed
non-motile cilium assembly	IMP Inferred from Mutant Phenotype more info	PubMed
non-motile cilium assembly	ISO Inferred from Sequence Orthology more info
peptidyl-serine phosphorylation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
peptidyl-serine phosphorylation	ISO Inferred from Sequence Orthology more info
peptidyl-threonine phosphorylation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
phosphorylation	IEA Inferred from Electronic Annotation more info
positive regulation of Wnt signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
positive regulation of Wnt-mediated midbrain dopaminergic neuron differentiation	IC Inferred by Curator more info	PubMed
positive regulation of canonical Wnt signaling pathway	IBA Inferred from Biological aspect of Ancestor more info	PubMed
positive regulation of canonical Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
positive regulation of non-canonical Wnt signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
positive regulation of proteasomal ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info	PubMed
positive regulation of proteasomal ubiquitin-dependent protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of protein phosphorylation	ISO Inferred from Sequence Orthology more info
protein localization to Golgi apparatus	ISO Inferred from Sequence Orthology more info
protein localization to centrosome	ISO Inferred from Sequence Orthology more info
protein localization to cilium	ISO Inferred from Sequence Orthology more info
protein phosphorylation	IDA Inferred from Direct Assay more info	PubMed
protein phosphorylation	IGI Inferred from Genetic Interaction more info	PubMed
protein phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
protein phosphorylation	ISO Inferred from Sequence Orthology more info
regulation of circadian rhythm	IBA Inferred from Biological aspect of Ancestor more info	PubMed
regulation of circadian rhythm	IMP Inferred from Mutant Phenotype more info	PubMed
rhythmic process	IEA Inferred from Electronic Annotation more info
spindle assembly	IBA Inferred from Biological aspect of Ancestor more info	PubMed
spindle assembly	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
Golgi apparatus	ISO Inferred from Sequence Orthology more info
centrosome	ISO Inferred from Sequence Orthology more info
cytoplasm	IBA Inferred from Biological aspect of Ancestor more info	PubMed
cytoskeleton	IEA Inferred from Electronic Annotation more info
membrane	IEA Inferred from Electronic Annotation more info
neuron projection	ISO Inferred from Sequence Orthology more info
nucleus	IBA Inferred from Biological aspect of Ancestor more info	PubMed
nucleus	IDA Inferred from Direct Assay more info	PubMed
perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info
plasma membrane	ISO Inferred from Sequence Orthology more info
spindle	ISO Inferred from Sequence Orthology more info
spindle microtubule	IBA Inferred from Biological aspect of Ancestor more info	PubMed
spindle microtubule	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: casein kinase I isoform delta; casein kinase I

Names: CKI-delta; CKId; tau-protein kinase CSNK1D

NP_082150.1

EC 2.7.11.1

EC 2.7.11.26

NP_620690.1

EC 2.7.11.1

EC 2.7.11.26

XP_011246964.1

EC 2.7.11.1

EC 2.7.11.26

XP_011246965.1

EC 2.7.11.1

EC 2.7.11.26

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_027874.2 → NP_082150.1 casein kinase I isoform delta isoform 2

See identical proteins and their annotated locations for NP_082150.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) has an additional exon in the 3' coding region compared to variant 1. It encodes isoform 2 which has a shorter, distinct C-terminus compared to isoform 1.

Source sequence(s)

AK146600, BY009834, BY420266

Consensus CDS

CCDS25763.1

UniProtKB/TrEMBL

Q3UBT6

Related

ENSMUSP00000070721.7, ENSMUST00000070575.13

Conserved Domains (1) summary

cd14125
Location:8 → 282

STKc_CK1_delta_epsilon; Catalytic domain of the Serine/Threonine protein kinases, Casein Kinase 1 delta and epsilon
NM_139059.2 → NP_620690.1 casein kinase I isoform delta isoform 1

See identical proteins and their annotated locations for NP_620690.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AK152721, BY009834, BY420266

Consensus CDS

CCDS25762.1

UniProtKB/Swiss-Prot

Q9DC28

Related

ENSMUSP00000018274.3, ENSMUST00000018274.9

Conserved Domains (1) summary

cd14125
Location:8 → 282

STKc_CK1_delta_epsilon; Catalytic domain of the Serine/Threonine protein kinases, Casein Kinase 1 delta and epsilon

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm38.p4 C57BL/6J

Genomic

NC_000077.6 Reference GRCm38.p4 C57BL/6J

Range

120958009..120991333 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011248663.2 → XP_011246965.1 casein kinase I isoform X1

See identical proteins and their annotated locations for XP_011246965.1

UniProtKB/TrEMBL

Q3USK2

Conserved Domains (1) summary

cd14125
Location:8 → 282

STKc_CK1_delta_epsilon; Catalytic domain of the Serine/Threonine protein kinases, Casein Kinase 1 delta and epsilon
XM_011248662.1 → XP_011246964.1 casein kinase I isoform X1

See identical proteins and their annotated locations for XP_011246964.1

UniProtKB/TrEMBL

Q3USK2

Conserved Domains (1) summary

cd14125
Location:8 → 282

STKc_CK1_delta_epsilon; Catalytic domain of the Serine/Threonine protein kinases, Casein Kinase 1 delta and epsilon