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Cdkl5 cyclin-dependent kinase-like 5 [ Rattus norvegicus (Norway rat) ]

Gene ID: 100362725, updated on 2-Nov-2024

Summary

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Official Symbol
Cdkl5provided by RGD
Official Full Name
cyclin-dependent kinase-like 5provided by RGD
Primary source
RGD:2324133
See related
EnsemblRapid:ENSRNOG00000003742 AllianceGenome:RGD:2324133
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Enables small GTPase binding activity. Involved in several processes, including positive regulation of GTPase activity; positive regulation of dendritic spine development; and positive regulation of neurogenesis. Located in dendrite; perinuclear region of cytoplasm; and ruffle membrane. Is active in glutamatergic synapse and postsynaptic density, intracellular component. Human ortholog(s) of this gene implicated in Rett syndrome; developmental and epileptic encephalopathy 2; intellectual disability; and visual epilepsy. Orthologous to human CDKL5 (cyclin dependent kinase like 5). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Brain (RPKM 192.7), Lung (RPKM 78.5) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Cdkl5 in Genome Data Viewer
Location:
Xq14
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) X NC_086039.1 (37566320..37796766)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) X NC_051356.1 (33757605..33988075)
106 previous assembly Rnor_6.0 (GCF_000001895.5) X NC_005120.4 (35536396..35773204)

Chromosome X - NC_086039.1Genomic Context describing neighboring genes Neighboring gene BEN domain containing 2 Neighboring gene Scm polycomb group protein like 2 Neighboring gene gap junction protein, alpha 6 Neighboring gene transfer RNA valine (anticodon UAC) Neighboring gene retinoschisin 1 Neighboring gene protein phosphatase with EF-hand domain 1 Neighboring gene metallothionein 1F

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Epilepsy-Related CDKL5 Deficiency Slows Synaptic Vesicle Endocytosis in Central Nerve Terminals. Kontaxi C, et al. J Neurosci, 2023 Mar 15. PMID 36759195, Free PMC Article
  2. Characterisation of Cdkl5 transcript isoforms in rat. Hector RD, et al. Gene, 2017 Mar 1. PMID 27940108
  3. Enhanced hippocampal LTP but normal NMDA receptor and AMPA receptor function in a rat model of CDKL5 deficiency disorder. Simões de Oliveira L, et al. Mol Autism, 2024 Jun 14. PMID 38877552, Free PMC Article
  4. Novel mutations in cyclin-dependent kinase-like 5 (CDKL5) gene in Indian cases of Rett syndrome. Das DK, et al. Neuromolecular Med, 2013 Mar. PMID 23242510
  5. CDKL5 is a brain MeCP2 target gene regulated by DNA methylation. Carouge D, et al. Neurobiol Dis, 2010 Jun. PMID 20211261

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Enhanced hippocampal LTP but normal NMDA receptor and AMPA receptor function in a rat model of CDKL5 deficiency disorder.
    Title: Enhanced hippocampal LTP but normal NMDA receptor and AMPA receptor function in a rat model of CDKL5 deficiency disorder.
  2. Cdkl5 is a MeCP2-repressed target gene providing a link between genes the mutation of which generates overlapping symptoms: DNA methylation changes are a potential mechanism participating in the long-term plasticity triggered by pharmacological agents
    Title: CDKL5 is a brain MeCP2 target gene regulated by DNA methylation.
  3. Epilepsy-Related CDKL5 Deficiency Slows Synaptic Vesicle Endocytosis in Central Nerve Terminals.
    Title: Epilepsy-Related CDKL5 Deficiency Slows Synaptic Vesicle Endocytosis in Central Nerve Terminals.
  4. the molecular pathology in CDKL5 disorder may have distinct neuron-type specific origins and effects.
    Title: Neuron-Type Specific Loss of CDKL5 Leads to Alterations in mTOR Signaling and Synaptic Markers.
  5. Characterization of Cdkl5 transcript isoforms in the rat has been described.
    Title: Characterisation of Cdkl5 transcript isoforms in rat.
  6. Palmitoylation-dependent CDKL5-PSD-95 interaction regulates synaptic targeting of CDKL5 and dendritic spine development.
    Title: Palmitoylation-dependent CDKL5-PSD-95 interaction regulates synaptic targeting of CDKL5 and dendritic spine development.
  7. these results demonstrate a critical role of CDKL5 in neuronal morphogenesis and identify a Rho GTPase signaling pathway which may contribute to CDKL5-related disorders.
    Title: CDKL5, a protein associated with rett syndrome, regulates neuronal morphogenesis via Rac1 signaling.
Submit: New GeneRIF Correction

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 RGD

Function Evidence Code Pubs
enables ATP binding ISO
Inferred from Sequence Orthology
more info
  
enables kinase activity ISO
Inferred from Sequence Orthology
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein kinase activity ISO
Inferred from Sequence Orthology
more info
  
enables protein serine/threonine kinase activity IEA
Inferred from Electronic Annotation
more info
  
enables small GTPase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in modulation of chemical synaptic transmission ISO
Inferred from Sequence Orthology
more info
  
involved_in neuron migration IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of GTPase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of axon extension IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of axon extension IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of dendrite morphogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of dendritic spine development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein autophosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in protein autophosphorylation ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within protein localization to nucleus ISO
Inferred from Sequence Orthology
more info
  
involved_in protein phosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of cilium assembly ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of dendrite development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of dendrite development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of postsynapse organization ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in centrosome ISO
Inferred from Sequence Orthology
more info
  
located_in ciliary basal body ISO
Inferred from Sequence Orthology
more info
  
located_in ciliary tip ISO
Inferred from Sequence Orthology
more info
  
is_active_in dendrite cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in dendrite cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in dendritic growth cone IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in glutamatergic synapse IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in glutamatergic synapse ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in postsynaptic density, intracellular component IDA
Inferred from Direct Assay
more info
 PubMed 
located_in ruffle membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
cyclin-dependent kinase-like 5
NP_001408462.1
XP_017457779.1
XP_038956382.1
XP_038956383.1
XP_063135763.1

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_001421533.1 → NP_001408462.1  cyclin-dependent kinase-like 5

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000021
    Related
    ENSRNOP00000098998.1, ENSRNOT00000174042.1

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086039.1 Reference GRCr8

    Range
    37566320..37796766
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039100455.1 → XP_038956383.1  cyclin-dependent kinase-like 5 isoform X2

    UniProtKB/TrEMBL
    A0A8I5ZVL4
    Conserved Domains (1) summary
    cd07848
    Location:11 → 297
    STKc_CDKL5; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase Like 5

  2. XM_017602290.2 → XP_017457779.1  cyclin-dependent kinase-like 5 isoform X1

    UniProtKB/TrEMBL
    A0A8I5ZVL4
    Related
    ENSRNOP00000107456.1, ENSRNOT00000150186.1
    Conserved Domains (1) summary
    cd07848
    Location:11 → 297
    STKc_CDKL5; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase Like 5

  3. XM_039100454.2 → XP_038956382.1  cyclin-dependent kinase-like 5 isoform X1

    UniProtKB/TrEMBL
    A0A8I5ZVL4
    Conserved Domains (1) summary
    cd07848
    Location:11 → 297
    STKc_CDKL5; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase Like 5

  4. XM_063279693.1 → XP_063135763.1  cyclin-dependent kinase-like 5 isoform X3

    UniProtKB/TrEMBL
    D3ZG85, E1U7Q0
    Related
    ENSRNOP00000005061.6, ENSRNOT00000005061.8
Nucleotide Protein Strain
Heading Accession and Version

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