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    CILK1 ciliogenesis associated kinase 1 [ Homo sapiens (human) ]

    Gene ID: 22858, updated on 14-Nov-2024

    Summary

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    Official Symbol
    CILK1provided by HGNC
    Official Full Name
    ciliogenesis associated kinase 1provided by HGNC
    Primary source
    HGNC:HGNC:21219
    See related
    Ensembl:ENSG00000112144 MIM:612325; AllianceGenome:HGNC:21219
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ECO; ICK; MRK; LCK2; hICK; EJM10
    Summary
    Eukaryotic protein kinases are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases. This gene encodes an intestinal serine/threonine kinase harboring a dual phosphorylation site found in mitogen-activating protein (MAP) kinases. The protein localizes to the intestinal crypt region and is thought to be important in intestinal epithelial cell proliferation and differentiation. Alternative splicing has been observed at this locus and two variants, encoding the same isoform, have been identified. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in adrenal (RPKM 9.9), placenta (RPKM 5.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CILK1 in Genome Data Viewer
    Location:
    6p12.1
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (53001303..53061824, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (52840881..52901428, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (52866101..52926622, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92160 Neighboring gene glutathione S-transferase alpha 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:52860003-52860234 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24693 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17287 Neighboring gene RNA component of 7SK nuclear ribonucleoprotein Neighboring gene uncharacterized LOC128092246 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:52908870-52909424 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17288 Neighboring gene uncharacterized LOC128031835 Neighboring gene F-box protein 9 Neighboring gene RNA, 7SL, cytoplasmic 244, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Ciliogenesis-associated Kinase 1 Promotes Breast Cancer Cell Proliferation and Chemoresistance via Phosphorylating ERK1.
      Title: Ciliogenesis-associated Kinase 1 Promotes Breast Cancer Cell Proliferation and Chemoresistance via Phosphorylating ERK1.
    2. The Scaffold Protein KATNIP Enhances CILK1 Control of Primary Cilia.
      Title: The Scaffold Protein KATNIP Enhances CILK1 Control of Primary Cilia.
    3. BROMI/TBC1D32 together with CCRK/CDK20 and FAM149B1/JBTS36 contributes to intraflagellar transport turnaround involving ICK/CILK1.
      Title: BROMI/TBC1D32 together with CCRK/CDK20 and FAM149B1/JBTS36 contributes to intraflagellar transport turnaround involving ICK/CILK1.
    4. Functional Alterations in Ciliogenesis-Associated Kinase 1 (CILK1) that Result from Mutations Linked to Juvenile Myoclonic Epilepsy.
      Title: Functional Alterations in Ciliogenesis-Associated Kinase 1 (CILK1) that Result from Mutations Linked to Juvenile Myoclonic Epilepsy.
    5. Anterograde trafficking of ciliary MAP kinase-like ICK/CILK1 by the intraflagellar transport machinery is required for intraciliary retrograde protein trafficking.
      Title: Anterograde trafficking of ciliary MAP kinase-like ICK/CILK1 by the intraflagellar transport machinery is required for intraciliary retrograde protein trafficking.
    6. Previously known as intestinal cell kinase because it was cloned from that origin, CILK1 is now recognized as a widely expressed and highly conserved. Mutations in the human CILK1 gene have been associated with ciliopathies. Thus, CILK1 has a fundamental role in the function of the cilium. Several candidate substrates have been proposed for CILK1. [review]
      Title: Ciliogenesis associated kinase 1: targets and functions in various organ systems.
    7. Study demonstrates that human ICK (intestinal cell kinase) that authors herein call CAPK (ciliopathy-associated protein kinase) interacts with human KIF3A and phosphorylates a conserved site Thr672 both in vitro and in vivo. Long, unstructured, non-catalytic carboxyl-terminal domain (CTD) of CAPK is required for this interaction with and phosphorylation of KIF3A.
      Title: Ciliopathy-Associated Protein Kinase ICK Requires Its Non-Catalytic Carboxyl-Terminal Domain for Regulation of Ciliogenesis.
    8. Our data provide evidence that heterozygous variants in ICK caused juvenile myoclonic epilepsy in 7% of the patients included in our analysis. Variant ICK affects cell processes that help explain microdysgenesis and polyspike networks observed on EEG in juvenile myoclonic epilepsy.
      Title: Variant Intestinal-Cell Kinase in Juvenile Myoclonic Epilepsy.
    9. These data identify ICK as an short rib polydactyly syndromes (SRPS)-associated gene and reveal that abnormalities in signalling pathways contribute to defective skeletogenesis
      Title: An inactivating mutation in intestinal cell kinase, ICK, impairs hedgehog signalling and causes short rib-polydactyly syndrome.
    10. findings suggest that increased ICK expression/activity in response to protein deprivation likely provides a novel protective mechanism to limit apoptosis and support compensatory mucosal growth under nutritional stress.
      Title: Intestinal cell kinase is a novel participant in intestinal cell signaling responses to protein malnutrition.
    Submit: New GeneRIF Correction See all GeneRIFs (21)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Endocrine-cerebro-osteodysplasia syndrome
    MedGen: C2675227 OMIM: 612651 GeneReviews: Not available
    		not available
    Epilepsy, juvenile myoclonic, susceptibility to, 10
    MedGen: C4693613 OMIM: 617924 GeneReviews: Not available
    		not available

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0936, MGC46090

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 3-phosphoinositide-dependent protein kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables AMP-activated protein kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-dependent protein kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables Rho-dependent protein serine/threonine kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables eukaryotic translation initiation factor 2alpha kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H2AS1 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H2AS121 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H2AT120 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H2AXS139 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H2BS14 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H2BS36 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3S10 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3S28 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3S57 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3T11 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3T3 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3T45 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3T6 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H4S1 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables magnesium ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein kinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein serine kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein serine/threonine kinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein serine/threonine kinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ribosomal protein S6 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cilium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in intracellular signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intracellular signal transduction IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in intraciliary anterograde transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in intraciliary retrograde transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in intraciliary transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intraciliary transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein phosphorylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in signal transduction TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in ciliary basal body ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in ciliary base ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in ciliary tip IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    is_active_in cilium IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cilium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in fibrillar center IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    serine/threonine-protein kinase ICK
    Names
    MAK-related kinase
    iciliogenesis associated kinase 1
    intestinal cell (MAK-like) kinase
    intestinal cell kinase
    laryngeal cancer kinase 2
    serine/threonine protein kinase
    NP_001362326.1
    NP_001362327.1
    NP_001362328.1
    NP_001362329.1
    NP_001362330.1
    NP_001362331.1
    NP_055735.1
    NP_057597.2

    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.

    Genomic

    1. NG_012159.2 RefSeqGene

      Range
      4979..65500
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001375397.1 → NP_001362326.1  serine/threonine-protein kinase ICK isoform 2

      Status: REVIEWED

      Source sequence(s)
      AL031178, AL162581
      Consensus CDS
      CCDS93933.1
      UniProtKB/TrEMBL
      A0A7I2PIU1, B3KQG4
      Related
      ENSP00000263043.8, ENST00000350082.10
      Conserved Domains (1) summary
      cd07830
      Location:4 → 284
      STKc_MAK_like; Catalytic domain of Male germ cell-Associated Kinase-like Serine/Threonine Kinases

    2. NM_001375398.1 → NP_001362327.1  serine/threonine-protein kinase ICK isoform 1

      Status: REVIEWED

      Source sequence(s)
      AL031178, AL162581
      Consensus CDS
      CCDS4949.1
      UniProtKB/Swiss-Prot
      A7MD41, O75985, Q5THL2, Q8IYH8, Q9BX17, Q9NYX3, Q9UPZ9
      UniProtKB/TrEMBL
      B3KQG4
      Conserved Domains (1) summary
      cd07830
      Location:4 → 284
      STKc_MAK_like; Catalytic domain of Male germ cell-Associated Kinase-like Serine/Threonine Kinases

    3. NM_001375399.1 → NP_001362328.1  serine/threonine-protein kinase ICK isoform 1

      Status: REVIEWED

      Source sequence(s)
      AL031178, AL162581
      Consensus CDS
      CCDS4949.1
      UniProtKB/Swiss-Prot
      A7MD41, O75985, Q5THL2, Q8IYH8, Q9BX17, Q9NYX3, Q9UPZ9
      UniProtKB/TrEMBL
      B3KQG4
      Conserved Domains (1) summary
      cd07830
      Location:4 → 284
      STKc_MAK_like; Catalytic domain of Male germ cell-Associated Kinase-like Serine/Threonine Kinases

    4. NM_001375400.1 → NP_001362329.1  serine/threonine-protein kinase ICK isoform 1

      Status: REVIEWED

      Source sequence(s)
      AL031178, AL162581
      Consensus CDS
      CCDS4949.1
      UniProtKB/Swiss-Prot
      A7MD41, O75985, Q5THL2, Q8IYH8, Q9BX17, Q9NYX3, Q9UPZ9
      UniProtKB/TrEMBL
      B3KQG4
      Conserved Domains (1) summary
      cd07830
      Location:4 → 284
      STKc_MAK_like; Catalytic domain of Male germ cell-Associated Kinase-like Serine/Threonine Kinases

    5. NM_001375401.1 → NP_001362330.1  serine/threonine-protein kinase ICK isoform 1

      Status: REVIEWED

      Source sequence(s)
      AL031178, AL162581
      Consensus CDS
      CCDS4949.1
      UniProtKB/Swiss-Prot
      A7MD41, O75985, Q5THL2, Q8IYH8, Q9BX17, Q9NYX3, Q9UPZ9
      UniProtKB/TrEMBL
      B3KQG4
      Conserved Domains (1) summary
      cd07830
      Location:4 → 284
      STKc_MAK_like; Catalytic domain of Male germ cell-Associated Kinase-like Serine/Threonine Kinases

    6. NM_001375402.1 → NP_001362331.1  serine/threonine-protein kinase ICK isoform 1

      Status: REVIEWED

      Source sequence(s)
      AL031178, AL162581
      Consensus CDS
      CCDS4949.1
      UniProtKB/Swiss-Prot
      A7MD41, O75985, Q5THL2, Q8IYH8, Q9BX17, Q9NYX3, Q9UPZ9
      UniProtKB/TrEMBL
      B3KQG4
      Conserved Domains (1) summary
      cd07830
      Location:4 → 284
      STKc_MAK_like; Catalytic domain of Male germ cell-Associated Kinase-like Serine/Threonine Kinases

    7. NM_014920.5 → NP_055735.1  serine/threonine-protein kinase ICK isoform 1

      See identical proteins and their annotated locations for NP_055735.1

      Status: REVIEWED

      Source sequence(s)
      AL031178, AL162581
      Consensus CDS
      CCDS4949.1
      UniProtKB/Swiss-Prot
      A7MD41, O75985, Q5THL2, Q8IYH8, Q9BX17, Q9NYX3, Q9UPZ9
      UniProtKB/TrEMBL
      B3KQG4
      Related
      ENSP00000501692.1, ENST00000676107.1
      Conserved Domains (1) summary
      cd07830
      Location:4 → 284
      STKc_MAK_like; Catalytic domain of Male germ cell-Associated Kinase-like Serine/Threonine Kinases

    8. NM_016513.5 → NP_057597.2  serine/threonine-protein kinase ICK isoform 1

      See identical proteins and their annotated locations for NP_057597.2

      Status: REVIEWED

      Source sequence(s)
      AL031178, AL162581
      Consensus CDS
      CCDS4949.1
      UniProtKB/Swiss-Prot
      A7MD41, O75985, Q5THL2, Q8IYH8, Q9BX17, Q9NYX3, Q9UPZ9
      UniProtKB/TrEMBL
      B3KQG4
      Related
      ENSP00000349458.3, ENST00000356971.3
      Conserved Domains (1) summary
      cd07830
      Location:4 → 284
      STKc_MAK_like; Catalytic domain of Male germ cell-Associated Kinase-like Serine/Threonine Kinases

    RNA

    1. NR_164684.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL031178, AL162581

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      53001303..53061824 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      52840881..52901428 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_173041.1: Suppressed sequence

      Description
      NM_173041.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UPZ9.1 GenPept UniProtKB/Swiss-Prot:Q9UPZ9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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