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

Gene ID: 344387, updated on 2-May-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 cyclin-dependent protein serine/threonine kinase activity. Predicted to be involved in protein phosphorylation. Predicted to be located in cytoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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Location:
2p22.1
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (39168045..39247120, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (39176994..39255940, complement)
105.20220307 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
  • 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 IBA
Inferred from Biological aspect of Ancestor
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_2023_10

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

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