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    CDKL4 cyclin dependent kinase like 4 [ Homo sapiens (human) ]

    Gene ID: 344387, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CDKL4provided by HGNC
    Official Full Name
    cyclin dependent kinase like 4provided by HGNC
    Primary source
    HGNC:HGNC:19287
    See related
    Ensembl:ENSG00000205111 AllianceGenome:HGNC:19287
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Predicted to enable protein serine/threonine kinase activity. Predicted to be involved in protein phosphorylation and regulation of cell cycle. Predicted to be located in cytoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    See CDKL4 in Genome Data Viewer
    Location:
    2p22.1
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (39168045..39247120, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (39176994..39255940, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (39395186..39471124, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene SOS Ras/Rac guanine nucleotide exchange factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11383 Neighboring gene RNA, U6 small nuclear 198, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:39337207-39337706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15612 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11384 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15613 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15614 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15615 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 13 Neighboring gene CRISPRi-validated cis-regulatory element chr2.1553 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:39376789-39377290 Neighboring gene CRISPRi-validated cis-regulatory element chr2.1554 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:39378016-39378184 Neighboring gene Sharpr-MPRA regulatory region 10874 Neighboring gene MPRA-validated peak3670 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr2:39446895-39447396 Neighboring gene mitogen-activated protein kinase kinase kinase kinase 3 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:39547717-39548636 Neighboring gene MPRA-validated peak3671 silencer Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:39591272-39591838 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:39591839-39592405 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:39592406-39592972 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:39596426-39596599 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15616 Neighboring gene RNA, U6 small nuclear 1341, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11387 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11386 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15617 Neighboring gene MAP4K3 divergent transcript Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:39696648-39697148 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11388 Neighboring gene Sharpr-MPRA regulatory region 10578 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:39742467-39742687 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:39742776-39743368 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:39743369-39743960 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:39743961-39744553 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15618

    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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    Related articles in PubMed

    1. Novel mutations in the CDKL5 gene, predicted effects and associated phenotypes. Russo S, et al. Neurogenetics, 2009 Jul. PMID 19241098
    2. PAK4 promotes kinase-independent stabilization of RhoU to modulate cell adhesion. Dart AE, et al. J Cell Biol, 2015 Nov 23. PMID 26598620, Free PMC Article
    3. The BioPlex Network: A Systematic Exploration of the Human Interactome. Huttlin EL, et al. Cell, 2015 Jul 16. PMID 26186194, Free PMC Article
    4. Architecture of the human interactome defines protein communities and disease networks. Huttlin EL, et al. Nature, 2017 May 25. PMID 28514442, Free PMC Article
    5. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Huttlin EL, et al. Cell, 2021 May 27. PMID 33961781, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: Novel mutations in the CDKL5 gene, predicted effects and associated phenotypes.
    Submit: New GeneRIF Correction

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cyclin-dependent protein serine/threonine kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    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
    		  
    Process Evidence Code Pubs
    involved_in protein phosphorylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of cell cycle IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    cyclin-dependent kinase-like 4
    NP_001009565.1
    NP_001333840.1
    NP_001384829.1
    XP_011531117.1
    XP_011531119.1
    XP_011531121.1
    XP_016859471.1
    XP_016859473.1
    XP_016859474.1
    XP_047300097.1
    XP_047300098.1
    XP_054197734.1
    XP_054197735.1
    XP_054197736.1
    XP_054197737.1
    XP_054197738.1
    XP_054197739.1
    XP_054197740.1

    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)

    1. NM_001009565.2 → NP_001009565.1  cyclin-dependent kinase-like 4 isoform 2

      See identical proteins and their annotated locations for NP_001009565.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate intron in the 3' end compared to variant 1, that causes a frameshift. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC079615, AY845084
      Consensus CDS
      CCDS33184.1
      UniProtKB/Swiss-Prot
      Q5MAI5
      Conserved Domains (2) summary
      cd07847
      Location:2 → 286
      STKc_CDKL1_4; Catalytic domain of the Serine/Threonine Kinases, Cyclin-Dependent protein Kinase Like 1 and 4
      pfam00069
      Location:4 → 286
      Pkinase; Protein kinase domain

    2. NM_001346911.1 → NP_001333840.1  cyclin-dependent kinase-like 4 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC079615, AY847283
      Consensus CDS
      CCDS86834.1
      UniProtKB/Swiss-Prot
      Q2NME9, Q5MAI5
      Related
      ENSP00000378476.3, ENST00000395035.4

    3. NM_001397900.1 → NP_001384829.1  cyclin-dependent kinase-like 4 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC079615, AC092672
      Consensus CDS
      CCDS92740.1
      UniProtKB/TrEMBL
      H7BZI6
      Related
      ENSP00000389833.2, ENST00000451199.7
      Conserved Domains (1) summary
      cd07847
      Location:2 → 286
      STKc_CDKL1_4; Catalytic domain of the Serine/Threonine Kinases, Cyclin-Dependent protein Kinase Like 1 and 4

    RNA

    1. NR_144520.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains an alternate exon and lacks an alternate intron in the 3' end compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AY845084, BC144460

    2. NR_144521.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' and 3' ends and contains an alternate internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC079615, AC092672
      Related
      ENST00000699628.1

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      39168045..39247120 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047444141.1 → XP_047300097.1  cyclin-dependent kinase-like 4 isoform X1

      UniProtKB/TrEMBL
      H7BZI6

    2. XM_011532817.3 → XP_011531119.1  cyclin-dependent kinase-like 4 isoform X3

      Conserved Domains (2) summary
      pfam00069
      Location:4 → 245
      Pkinase; Protein kinase domain
      cl21453
      Location:2 → 245
      PKc_like; Protein Kinases, catalytic domain

    3. XM_017003982.2 → XP_016859471.1  cyclin-dependent kinase-like 4 isoform X1

      UniProtKB/TrEMBL
      H7BZI6
      Conserved Domains (1) summary
      cd07847
      Location:2 → 286
      STKc_CDKL1_4; Catalytic domain of the Serine/Threonine Kinases, Cyclin-Dependent protein Kinase Like 1 and 4

    4. XM_011532815.4 → XP_011531117.1  cyclin-dependent kinase-like 4 isoform X7

      See identical proteins and their annotated locations for XP_011531117.1

      UniProtKB/Swiss-Prot
      Q2NME9, Q5MAI5
      Conserved Domains (2) summary
      cd07847
      Location:2 → 286
      STKc_CDKL1_4; Catalytic domain of the Serine/Threonine Kinases, Cyclin-Dependent protein Kinase Like 1 and 4
      pfam00069
      Location:4 → 286
      Pkinase; Protein kinase domain

    5. XM_047444142.1 → XP_047300098.1  cyclin-dependent kinase-like 4 isoform X2

      Related
      ENSP00000368080.1, ENST00000378803.6

    6. XM_011532819.3 → XP_011531121.1  cyclin-dependent kinase-like 4 isoform X4

      See identical proteins and their annotated locations for XP_011531121.1

      UniProtKB/TrEMBL
      A0A8V8TNQ4
      Conserved Domains (1) summary
      cl21453
      Location:2 → 152
      PKc_like; Protein Kinases, catalytic domain

    7. XM_017003984.2 → XP_016859473.1  cyclin-dependent kinase-like 4 isoform X5

      UniProtKB/TrEMBL
      A0A8V8TNQ4

    8. XM_017003985.2 → XP_016859474.1  cyclin-dependent kinase-like 4 isoform X6

    RNA

    1. XR_001738736.2 RNA Sequence

    2. XR_007073748.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      39176994..39255940 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054341759.1 → XP_054197734.1  cyclin-dependent kinase-like 4 isoform X1

      UniProtKB/TrEMBL
      H7BZI6

    2. XM_054341761.1 → XP_054197736.1  cyclin-dependent kinase-like 4 isoform X3

    3. XM_054341760.1 → XP_054197735.1  cyclin-dependent kinase-like 4 isoform X1

      UniProtKB/TrEMBL
      H7BZI6

    4. XM_054341765.1 → XP_054197740.1  cyclin-dependent kinase-like 4 isoform X7

      UniProtKB/Swiss-Prot
      Q2NME9, Q5MAI5

    5. XM_054341762.1 → XP_054197737.1  cyclin-dependent kinase-like 4 isoform X4

    6. XM_054341763.1 → XP_054197738.1  cyclin-dependent kinase-like 4 isoform X5

    7. XM_054341764.1 → XP_054197739.1  cyclin-dependent kinase-like 4 isoform X6

    RNA

    1. XR_008486357.1 RNA Sequence

    2. XR_008486358.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5MAI5.2 GenPept UniProtKB/Swiss-Prot:Q5MAI5

    Gene LinkOut

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

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