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CDKL2 cyclin dependent kinase like 2 [ Homo sapiens (human) ]

Gene ID: 8999, updated on 14-Nov-2024

Summary

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Official Symbol
CDKL2provided by HGNC
Official Full Name
cyclin dependent kinase like 2provided by HGNC
Primary source
HGNC:HGNC:1782
See related
Ensembl:ENSG00000138769 MIM:603442; AllianceGenome:HGNC:1782
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
P56; KKIAMRE
Summary
This gene product is a member of a large family of CDC2-related serine/threonine protein kinases. It accumulates primarily in the cytoplasm, with lower levels in the nucleus. [provided by RefSeq, Jul 2008]
Expression
Biased expression in testis (RPKM 7.0), brain (RPKM 3.3) and 6 other tissues See more
Orthologs
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Genomic context

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See CDKL2 in Genome Data Viewer
Location:
4q21.1
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (75576496..75630528, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (78916642..78970655, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (76501706..76555712, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900717 Neighboring gene THAP domain containing 6 Neighboring gene Sharpr-MPRA regulatory region 12890 Neighboring gene odontogenesis associated phosphoprotein Neighboring gene cytochrome c oxidase subunit 6C pseudogene 9 Neighboring gene G3BP stress granule assembly factor 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:76597475-76598452 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21620 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:76599431-76600408 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:76600409-76601385 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15481 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21621 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:76627962-76628708 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:76630201-76630946 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:76641306-76641821 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:76648951-76649871 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:76649872-76650791 Neighboring gene USO1 vesicle transport factor

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Identification of a Set of Genes Improving Survival Prediction in Kidney Renal Clear Cell Carcinoma through Integrative Reanalysis of Transcriptomic Data.
    Title: Identification of a Set of Genes Improving Survival Prediction in Kidney Renal Clear Cell Carcinoma through Integrative Reanalysis of Transcriptomic Data.
  2. CDKL2 Is Associated with HER2 Status and Overall Survival in Gastric Cancer: Comparative Analysis of CDKL2 Protein Expression and Gene Copy Number.
    Title: CDKL2 Is Associated with HER2 Status and Overall Survival in Gastric Cancer: Comparative Analysis of CDKL2 Protein Expression and Gene Copy Number.
  3. Decreased CDKL2 expression is correlated with the progression and poor prognosis of glioma.
    Title: Decreased CDKL2 expression is correlated with the progression and poor prognosis of glioma.
  4. In HeLa cells infected with HSV-2, we detected significantly reduced expression of CDKN2A and CDKL2 and demonstrated the negative regulation effect of miRNA-H4-5p on these two target genes.
    Title: HSV-2-encoded miRNA-H4 Regulates Cell Cycle Progression and Act-D-induced Apoptosis in HeLa Cells by Targeting CDKL2 and CDKN2A.
  5. Results showed that the methylation levels of CDKL2 were higher in hepatocellular carcinoma (HCC) cell lines and tissues but the mRNA expression levels decreased both in HCC tissues and cell lines. CDKL2 status seems to correlate with tumor size and may play an important role in hepatocarcinogenesis.
    Title: Clinical significance of aberrant cyclin-dependent kinase-like 2 methylation in hepatocellular carcinoma.
  6. High CDKL2 promotes epithelial-mesenchymal transition and breast cancer progression.
    Title: CDKL2 promotes epithelial-mesenchymal transition and breast cancer progression.
  7. We hypothesized that LA might induce dissociation of p56(Lck) from CD4, thus leading to its downmodulation.
    Title: Lipoic acid downmodulates CD4 from human T lymphocytes by dissociation of p56(Lck).
Submit: New GeneRIF Correction

Phenotypes

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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)

Pathways from PubChem

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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

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 binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein kinase activity TAS
Traceable Author Statement
more info
 PubMed 
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 regulation of cell cycle IEA
Inferred from Electronic Annotation
more info
  
involved_in sex differentiation TAS
Traceable Author Statement
more info
 PubMed 
involved_in signal transduction TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in centrosome IDA
Inferred from Direct Assay
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
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 2
Names
CDC2-related kinase
p56 KKIAMRE protein kinase
protein kinase p56 KKIAMRE
serine/threonine protein kinase KKIAMRE
testicular tissue protein Li 35
NP_001317653.1
NP_003939.1
XP_006714469.1
XP_016864298.1
XP_016864299.1
XP_016864300.1
XP_047272338.1
XP_047272339.1
XP_047272340.1
XP_047272341.1
XP_047272342.1
XP_047272343.1
XP_054207161.1
XP_054207162.1
XP_054207163.1
XP_054207164.1
XP_054207165.1
XP_054207166.1
XP_054207167.1
XP_054207168.1

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_001330724.2 → NP_001317653.1  cyclin-dependent kinase-like 2 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains two consecutive alternate in-frame exons in the 3' coding region, compared to variant 1. The encoded isoform (2) is longer, but has the same N- and C-termini as isoform 1.
    Source sequence(s)
    AA813092, AC096759, AC104828, AK294866, BX095447, DA309702, DC400929, U35146
    Consensus CDS
    CCDS82933.1
    UniProtKB/TrEMBL
    B4DH08, J3KNE8
    Related
    ENSP00000306340.4, ENST00000307465.9
    Conserved Domains (2) summary
    smart00220
    Location:4 → 287
    S_TKc; Serine/Threonine protein kinases, catalytic domain
    cd07846
    Location:2 → 287
    STKc_CDKL2_3; Catalytic domain of the Serine/Threonine Kinases, Cyclin-Dependent protein Kinase Like 2 and 3

  2. NM_003948.5 → NP_003939.1  cyclin-dependent kinase-like 2 isoform 1

    See identical proteins and their annotated locations for NP_003939.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter isoform (1).
    Source sequence(s)
    AA813092, AC096759, AK294866, BX095447, DA309702, DC400929, U35146
    Consensus CDS
    CCDS3570.1
    UniProtKB/Swiss-Prot
    B2R695, Q92772
    UniProtKB/TrEMBL
    A0A140VJG1, B4DH08
    Related
    ENSP00000412365.2, ENST00000429927.6
    Conserved Domains (2) summary
    smart00220
    Location:4 → 287
    S_TKc; Serine/Threonine protein kinases, catalytic domain
    cd07846
    Location:2 → 287
    STKc_CDKL2_3; Catalytic domain of the Serine/Threonine Kinases, Cyclin-Dependent protein Kinase Like 2 and 3

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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    75576496..75630528 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017008811.2 → XP_016864300.1  cyclin-dependent kinase-like 2 isoform X5

    UniProtKB/TrEMBL
    B4DH08

  2. XM_017008810.2 → XP_016864299.1  cyclin-dependent kinase-like 2 isoform X4

    UniProtKB/Swiss-Prot
    B2R695, Q92772
    UniProtKB/TrEMBL
    A0A140VJG1, B4DH08
    Conserved Domains (2) summary
    smart00220
    Location:4 → 287
    S_TKc; Serine/Threonine protein kinases, catalytic domain
    cd07846
    Location:2 → 287
    STKc_CDKL2_3; Catalytic domain of the Serine/Threonine Kinases, Cyclin-Dependent protein Kinase Like 2 and 3

  3. XM_017008809.2 → XP_016864298.1  cyclin-dependent kinase-like 2 isoform X2

    UniProtKB/TrEMBL
    B4DH08, J3KNE8
    Conserved Domains (2) summary
    smart00220
    Location:4 → 287
    S_TKc; Serine/Threonine protein kinases, catalytic domain
    cd07846
    Location:2 → 287
    STKc_CDKL2_3; Catalytic domain of the Serine/Threonine Kinases, Cyclin-Dependent protein Kinase Like 2 and 3

  4. XM_047416384.1 → XP_047272340.1  cyclin-dependent kinase-like 2 isoform X4

    UniProtKB/Swiss-Prot
    B2R695, Q92772
    UniProtKB/TrEMBL
    A0A140VJG1

  5. XM_047416383.1 → XP_047272339.1  cyclin-dependent kinase-like 2 isoform X2

    UniProtKB/TrEMBL
    J3KNE8

  6. XM_006714406.3 → XP_006714469.1  cyclin-dependent kinase-like 2 isoform X3

    UniProtKB/TrEMBL
    B4DH08
    Conserved Domains (2) summary
    smart00220
    Location:4 → 287
    S_TKc; Serine/Threonine protein kinases, catalytic domain
    cd07846
    Location:2 → 287
    STKc_CDKL2_3; Catalytic domain of the Serine/Threonine Kinases, Cyclin-Dependent protein Kinase Like 2 and 3

  7. XM_047416386.1 → XP_047272342.1  cyclin-dependent kinase-like 2 isoform X7

  8. XM_047416382.1 → XP_047272338.1  cyclin-dependent kinase-like 2 isoform X1

  9. XM_047416385.1 → XP_047272341.1  cyclin-dependent kinase-like 2 isoform X6

  10. XM_047416387.1 → XP_047272343.1  cyclin-dependent kinase-like 2 isoform X8

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    78916642..78970655 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054351190.1 → XP_054207165.1  cyclin-dependent kinase-like 2 isoform X5

  2. XM_054351189.1 → XP_054207164.1  cyclin-dependent kinase-like 2 isoform X4

    UniProtKB/Swiss-Prot
    B2R695, Q92772
    UniProtKB/TrEMBL
    A0A140VJG1

  3. XM_054351187.1 → XP_054207162.1  cyclin-dependent kinase-like 2 isoform X2

    UniProtKB/TrEMBL
    J3KNE8

  4. XM_054351188.1 → XP_054207163.1  cyclin-dependent kinase-like 2 isoform X3

  5. XM_054351192.1 → XP_054207167.1  cyclin-dependent kinase-like 2 isoform X7

  6. XM_054351186.1 → XP_054207161.1  cyclin-dependent kinase-like 2 isoform X1

  7. XM_054351191.1 → XP_054207166.1  cyclin-dependent kinase-like 2 isoform X6

  8. XM_054351193.1 → XP_054207168.1  cyclin-dependent kinase-like 2 isoform X8

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92772.1 GenPept UniProtKB/Swiss-Prot:Q92772

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