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

Summary

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 Rac protein signal transduction; 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; and intellectual disability. Orthologous to human CDKL5 (cyclin dependent kinase like 5). [provided by Alliance of Genome Resources, Dec 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

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_086039.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
Characterization of Cdkl5 transcript isoforms in the rat has been described.
Title: Characterisation of Cdkl5 transcript isoforms in rat.
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.
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.

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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

DXGot31 (e-PCR)
- UniSTS:111876

dxrat87 (e-PCR)
- UniSTS:122629

AI577388 (e-PCR)
- UniSTS:248766

AU048188 (e-PCR)
- UniSTS:109784

RH136752 (e-PCR)
- UniSTS:218841

RH137814 (e-PCR)
- UniSTS:219901

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 Rac protein signal transduction	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
acts_upstream_of_or_within protein localization to nucleus	ISO Inferred from Sequence Orthology 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

EC 2.7.11.22

XP_017457779.1

EC 2.7.11.22

XP_038956382.1

EC 2.7.11.22

XP_038956383.1

EC 2.7.11.22

XP_063135763.1

EC 2.7.11.22

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

Status: VALIDATED

Source sequence(s)

JAXUCZ010000021

UniProtKB/TrEMBL

A0A8I6A725

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

NC_086039.1 Reference GRCr8

Range

37566320..37796766

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A8I6G3S6, D3ZG85, E1U7Q0

Related

ENSRNOP00000005061.6, ENSRNOT00000005061.8