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Aliases for CDKL3 Gene

Aliases for CDKL3 Gene

  • Cyclin Dependent Kinase Like 3 2 3 5
  • Serine-Threonine Protein Kinase NKIAMRE 2 3
  • Cyclin-Dependent Kinase-Like 3 2 3
  • NKIAMRE 3 4
  • Serine/Threonine-Protein Kinase NKIAMRE 4
  • EC 4

External Ids for CDKL3 Gene

Previous GeneCards Identifiers for CDKL3 Gene

  • GC05M133292
  • GC05M134158
  • GC05M133664
  • GC05M133710
  • GC05M133662
  • GC05M128818
  • GC05M133541

Summaries for CDKL3 Gene

Entrez Gene Summary for CDKL3 Gene

  • The protein encoded by this gene is a member of cyclin-dependent protein kinase (CDK) family. CDK family members are highly similar to the gene products of Saccharomyces cerevisiae cdc28, and Schizosaccharomyces pombe cdc2, and are known to be important regulators of cell cycle progression. This gene was identified as a gene absent in leukemic patients with chromosome 5q deletion. This loss may be an important determinant of dysmyelopoiesis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

GeneCards Summary for CDKL3 Gene

CDKL3 (Cyclin Dependent Kinase Like 3) is a Protein Coding gene. Diseases associated with CDKL3 include Orofaciodigital Syndrome Vi and Joubert Syndrome 1. Gene Ontology (GO) annotations related to this gene include transferase activity, transferring phosphorus-containing groups and protein tyrosine kinase activity. An important paralog of this gene is CDKL2.

Additional gene information for CDKL3 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CDKL3 Gene

Genomics for CDKL3 Gene

GeneHancer (GH) Regulatory Elements for CDKL3 Gene

Promoters and enhancers for CDKL3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J134369 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 650.7 -0.1 -115 3.6 CLOCK MLX DMAP1 YY1 ZNF213 E2F8 ZNF143 ZNF548 SP3 NFYC ENSG00000273345 UBE2B CDKL3 C5orf15 DDX46 SKP1 JADE2 SEC24A ENSG00000248559 C5orf66
GH05J134366 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.7 +4.3 4295 1.6 PKNOX1 ARID4B SIN3A DMAP1 YY1 POLR2B ZNF766 CBX5 E2F8 ZNF143 CDKL3 SKP1 ENSG00000273345 GC05P134270 GC05P134014
GH05J134410 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 10.5 -43.3 -43322 8.5 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 NFYC ZNF610 RCOR2 NBN KDM1A CDKN2AIPNL DDX46 RNU6-456P JADE2 CATSPER3 CDKL3 C5orf66 C5orf24 SKP1 RPS10P11
GH05J134094 Enhancer 0.8 dbSUPER 10.3 +276.5 276500 0.8 ZNF493 MZF1 RAD21 ZEB1 YY1 ZNF121 ZNF213 ZNF138 KLF7 ZNF548 DDX46 SKP1 CDKL3 C5orf24 TCF7 LOC105379185 LOC101060024 GC05P134014
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CDKL3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CDKL3 gene promoter:
  • Sp1
  • GR-alpha
  • GR
  • HNF-4alpha2
  • HNF-4alpha1
  • COUP-TF1
  • COUP
  • ARP-1

Genomic Locations for CDKL3 Gene

Genomic Locations for CDKL3 Gene
135,350 bases
Minus strand
165,434 bases
Minus strand

Genomic View for CDKL3 Gene

Genes around CDKL3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CDKL3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CDKL3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CDKL3 Gene

Proteins for CDKL3 Gene

  • Protein details for CDKL3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Cyclin-dependent kinase-like 3
    Protein Accession:
    Secondary Accessions:
    • D3DQA0
    • D3DQA1
    • Q9P114

    Protein attributes for CDKL3 Gene

    592 amino acids
    Molecular mass:
    67514 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for CDKL3 Gene

    Alternative splice isoforms for CDKL3 Gene


neXtProt entry for CDKL3 Gene

Post-translational modifications for CDKL3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CDKL3 Gene

Domains & Families for CDKL3 Gene

Gene Families for CDKL3 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for CDKL3 Gene

Graphical View of Domain Structure for InterPro Entry



  • The [NKR]KIAxRE motif seems to be a cyclin-binding region.
  • Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily.
  • The [NKR]KIAxRE motif seems to be a cyclin-binding region.
  • Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily.
genes like me logo Genes that share domains with CDKL3: view

Function for CDKL3 Gene

Molecular function for CDKL3 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
ATP + a protein = ADP + a phosphoprotein.

Enzyme Numbers (IUBMB) for CDKL3 Gene

Phenotypes From GWAS Catalog for CDKL3 Gene

Gene Ontology (GO) - Molecular Function for CDKL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004672 protein kinase activity TAS 10463609
GO:0004674 protein serine/threonine kinase activity IEA --
GO:0004693 cyclin-dependent protein serine/threonine kinase activity IBA --
GO:0005515 protein binding IPI 25416956
GO:0005524 ATP binding IEA --
genes like me logo Genes that share ontologies with CDKL3: view
genes like me logo Genes that share phenotypes with CDKL3: view

Animal Model Products

  • Taconic Biosciences Mouse Models for CDKL3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CDKL3

Clone Products

  • Addgene plasmids for CDKL3

No data available for Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CDKL3 Gene

Localization for CDKL3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CDKL3 Gene


Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CDKL3 gene
Compartment Confidence
nucleus 5
cytosol 3
golgi apparatus 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (1)
  • Vesicles (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CDKL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with CDKL3: view

Pathways & Interactions for CDKL3 Gene

SuperPathways for CDKL3 Gene

No Data Available

Pathways by source for CDKL3 Gene

1 GeneTex pathway for CDKL3 Gene

Gene Ontology (GO) - Biological Process for CDKL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006464 cellular protein modification process TAS 10463609
GO:0006468 protein phosphorylation IEA --
GO:0016310 phosphorylation IEA --
GO:0030517 negative regulation of axon extension IBA --
GO:0050775 positive regulation of dendrite morphogenesis IBA --
genes like me logo Genes that share ontologies with CDKL3: view

No data available for SIGNOR curated interactions for CDKL3 Gene

Drugs & Compounds for CDKL3 Gene

(1) Drugs for CDKL3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
ATP Investigational Nutra Agonist, Activator, Full agonist, Antagonist, Potentiation, Pore Blocker 0

(1) Additional Compounds for CDKL3 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
Full agonist, Agonist, Partial agonist, Antagonist, Gating inhibitor 58-64-0
genes like me logo Genes that share compounds with CDKL3: view

Transcripts for CDKL3 Gene

mRNA/cDNA for CDKL3 Gene

(36) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(3) Selected AceView cDNA sequences:
(10) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CDKL3 Gene

Cyclin-dependent kinase-like 3:
Representative Sequences:

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CDKL3

Clone Products

  • Addgene plasmids for CDKL3

Alternative Splicing Database (ASD) splice patterns (SP) for CDKL3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13
SP1: -
SP2: - - - -
SP4: - -

Relevant External Links for CDKL3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CDKL3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CDKL3 Gene

mRNA differential expression in normal tissues according to GTEx for CDKL3 Gene

This gene is overexpressed in Testis (x6.1).

Protein differential expression in normal tissues from HIPED for CDKL3 Gene

This gene is overexpressed in Plasma (31.3), Bone marrow mesenchymal stem cell (19.7), Liver, secretome (10.7), and Pancreatic juice (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CDKL3 Gene

NURSA nuclear receptor signaling pathways regulating expression of CDKL3 Gene:


SOURCE GeneReport for Unigene cluster for CDKL3 Gene:


Evidence on tissue expression from TISSUES for CDKL3 Gene

  • Heart(4.2)
genes like me logo Genes that share expression patterns with CDKL3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CDKL3 Gene

Orthologs for CDKL3 Gene

This gene was present in the common ancestor of animals.

Orthologs for CDKL3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CDKL3 34 33
  • 99.83 (n)
(Canis familiaris)
Mammalia CDKL3 33
  • 91.54 (n)
  • 87 (a)
(Bos Taurus)
Mammalia CDKL3 34 33
  • 90.41 (n)
(Mus musculus)
Mammalia Cdkl3 16 34 33
  • 83.14 (n)
(Rattus norvegicus)
Mammalia Cdkl3 33
  • 82.78 (n)
(Monodelphis domestica)
Mammalia CDKL3 34
  • 76 (a)
(Ornithorhynchus anatinus)
Mammalia CDKL3 34
  • 73 (a)
(Anolis carolinensis)
Reptilia CDKL3 34
  • 67 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG7236 34
  • 29 (a)
(Caenorhabditis elegans)
Secernentea Y42A5A.4 34
  • 30 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 58 (a)
Species where no ortholog for CDKL3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • zebrafish (Danio rerio)

Evolution for CDKL3 Gene

Gene Tree for CDKL3 (if available)
Gene Tree for CDKL3 (if available)
Evolutionary constrained regions (ECRs) for CDKL3: view image

Paralogs for CDKL3 Gene

Paralogs for CDKL3 Gene

(69) SIMAP similar genes for CDKL3 Gene using alignment to 12 proteins:

  • B4DX41_HUMAN
  • B7Z2C5_HUMAN
  • E5RI54_HUMAN
  • E7ET86_HUMAN
  • H0YB17_HUMAN
genes like me logo Genes that share paralogs with CDKL3: view

Variants for CDKL3 Gene

Sequence variations from dbSNP and Humsavar for CDKL3 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs367537996 not-provided, not provided 134,371,618(-) G/C upstream_transcript_variant
rs1000025626 -- 134,324,074(-) G/T intron_variant
rs1000047754 -- 134,365,872(-) A/G genic_upstream_transcript_variant, intron_variant
rs1000050217 -- 134,325,240(-) C/G intron_variant
rs1000090740 -- 134,370,530(-) C/A genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CDKL3 Gene

Variant ID Type Subtype PubMed ID
esv3606845 CNV loss 21293372
esv3606846 CNV loss 21293372

Variation tolerance for CDKL3 Gene

Residual Variation Intolerance Score: 86% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.16; 39.14% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CDKL3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CDKL3 Gene

Disorders for CDKL3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for CDKL3 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
orofaciodigital syndrome vi
  • ofd6
joubert syndrome 1
  • jbts1
- elite association - COSMIC cancer census association via MalaCards
Search CDKL3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CDKL3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CDKL3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CDKL3 Gene

Publications for CDKL3 Gene

  1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  2. Enhancement of cell proliferation in various mammalian cell lines by gene insertion of a cyclin-dependent kinase homolog. (PMID: 17945021) Jaluria P … Shiloach J (BMC biotechnology 2007) 3 22 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. NKIAMRE, a novel conserved CDC2-related kinase with features of both mitogen-activated protein kinases and cyclin-dependent kinases. (PMID: 12927787) Yee KW … Minden MD (Biochemical and biophysical research communications 2003) 3 22 58
  5. Identification of NKIAMRE, the human homologue to the mitogen-activated protein kinase-/cyclin-dependent kinase-related protein kinase NKIATRE, and its loss in leukemic blasts with chromosome arm 5q deletion. (PMID: 10463609) Midmer M … Zanke BW (Cancer research 1999) 2 3 58

Products for CDKL3 Gene

  • Addgene plasmids for CDKL3

Sources for CDKL3 Gene

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