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    CDKN3 cyclin dependent kinase inhibitor 3 [ Homo sapiens (human) ]

    Gene ID: 1033, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CDKN3provided by HGNC
    Official Full Name
    cyclin dependent kinase inhibitor 3provided by HGNC
    Primary source
    HGNC:HGNC:1791
    See related
    Ensembl:ENSG00000100526 MIM:123832; AllianceGenome:HGNC:1791
    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
    KAP; CDI1; CIP2; KAP1
    Summary
    The protein encoded by this gene belongs to the dual specificity protein phosphatase family. It was identified as a cyclin-dependent kinase inhibitor, and has been shown to interact with, and dephosphorylate CDK2 kinase, thus prevent the activation of CDK2 kinase. This gene was reported to be deleted, mutated, or overexpressed in several kinds of cancers. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]
    Expression
    Biased expression in testis (RPKM 79.3), bone marrow (RPKM 10.8) and 5 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CDKN3 in Genome Data Viewer
    Location:
    14q22.2
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (54397007..54420218)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (48602154..48625376)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (54863725..54886936)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene ATP synthase F1 subunit gamma pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8409 Neighboring gene uncharacterized LOC105370507 Neighboring gene NANOG hESC enhancer GRCh37_chr14:54551221-54551722 Neighboring gene uncharacterized LOC105370505 Neighboring gene Sharpr-MPRA regulatory region 2316 Neighboring gene HNF4 motif-containing MPRA enhancer 145 Neighboring gene Sharpr-MPRA regulatory region 14732 Neighboring gene VISTA enhancer hs1414 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:54718298-54719497 Neighboring gene NANOG hESC enhancer GRCh37_chr14:54806435-54806956 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:54828631-54829198 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:54829199-54829766 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:54836737-54837238 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:54860347-54860846 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5761 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:54907701-54908499 Neighboring gene cornichon family member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8411 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5764 Neighboring gene glia maturation factor beta

    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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    Related articles in PubMed

    1. Human pan-cancer analysis of the predictive biomarker for the CDKN3. Chen Y, et al. Eur J Med Res, 2024 May 8. PMID 38720365, Free PMC Article
    2. Aberrant transcripts of the cyclin-dependent kinase-associated protein phosphatase in hepatocellular carcinoma. Yeh CT, et al. Cancer Res, 2000 Sep 1. PMID 10987270
    3. Choline availability modulates human neuroblastoma cell proliferation and alters the methylation of the promoter region of the cyclin-dependent kinase inhibitor 3 gene. Niculescu MD, et al. J Neurochem, 2004 Jun. PMID 15147518, Free PMC Article
    4. Overexpression of cyclin-dependent kinase-associated protein phosphatase enhances cell proliferation in renal cancer cells. Lai MW, et al. Urol Oncol, 2012 Nov-Dec. PMID 21396835
    5. Cyclin-dependent kinase inhibitor 3 (CDKN3) novel cell cycle computational network between human non-malignancy associated hepatitis/cirrhosis and hepatocellular carcinoma (HCC) transformation. Wang L, et al. Cell Prolif, 2011 Jun. PMID 21535270, Free PMC Article

    See all (69) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. N6-Methyladenosine modified circ-NAB1 modulates cell cycle and epithelial-mesenchymal transition via CDKN3 in endometrial cancer.
      Title: N6-Methyladenosine modified circ-NAB1 modulates cell cycle and epithelial-mesenchymal transition via CDKN3 in endometrial cancer.
    2. Human pan-cancer analysis of the predictive biomarker for the CDKN3.
      Title: Human pan-cancer analysis of the predictive biomarker for the CDKN3.
    3. MicroRNA-127-3p Inhibits Cardiomyocyte Inflammation and Apoptosis after Acute Myocardial Infarction via Targeting CDKN3.
      Title: MicroRNA-127-3p Inhibits Cardiomyocyte Inflammation and Apoptosis after Acute Myocardial Infarction via Targeting CDKN3.
    4. PSMD12 interacts with CDKN3 and facilitates pancreatic cancer progression.
      Title: PSMD12 interacts with CDKN3 and facilitates pancreatic cancer progression.
    5. Cyclin dependent kinase inhibitor 3 (CDKN3) upregulation is associated with unfavorable prognosis in clear cell renal cell carcinoma and shapes tumor immune microenvironment: A bioinformatics analysis.
      Title: Cyclin dependent kinase inhibitor 3 (CDKN3) upregulation is associated with unfavorable prognosis in clear cell renal cell carcinoma and shapes tumor immune microenvironment: A bioinformatics analysis.
    6. GID2 Interacts With CDKN3 and Regulates Pancreatic Cancer Growth and Apoptosis.
      Title: GID2 Interacts With CDKN3 and Regulates Pancreatic Cancer Growth and Apoptosis.
    7. Identifying key genes related to inflammasome in severe COVID-19 patients based on a joint model with random forest and artificial neural network.
      Title: Identifying key genes related to inflammasome in severe COVID-19 patients based on a joint model with random forest and artificial neural network.
    8. Identification of cell cycle-associated and -unassociated regulators for expression of a hepatocellular carcinoma oncogene cyclin-dependent kinase inhibitor 3.
      Title: Identification of cell cycle-associated and -unassociated regulators for expression of a hepatocellular carcinoma oncogene cyclin-dependent kinase inhibitor 3.
    9. CDKN3 expression predicates poor prognosis and regulates adriamycin sensitivity in hepatocellular carcinoma in vitro.
      Title: CDKN3 expression predicates poor prognosis and regulates adriamycin sensitivity in hepatocellular carcinoma in vitro.
    10. Integrated transcriptomics explored the cancer-promoting genes CDKN3 in esophageal squamous cell cancer.
      Title: Integrated transcriptomics explored the cancer-promoting genes CDKN3 in esophageal squamous cell cancer.
    Submit: New GeneRIF Correction See all GeneRIFs (39)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association scan of dental caries in the permanent dentition.
    EBI GWAS Catalog
    Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study.
    EBI GWAS Catalog
    Genome-wide pharmacogenomic study of neurocognition as an indicator of antipsychotic treatment response in schizophrenia.
    EBI GWAS Catalog

    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

    Clone Names

    • FLJ25787, MGC70625

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables myosin phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein serine/threonine phosphatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein tyrosine phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein tyrosine phosphatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein tyrosine/serine/threonine phosphatase activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in G1/S transition of mitotic cell cycle TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of cell population proliferation TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in protein dephosphorylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of cell cycle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of cyclin-dependent protein serine/threonine kinase activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    cyclin-dependent kinase inhibitor 3
    Names
    CDK2-associated dual specificity phosphatase
    Cdk-associated protein phosphatase
    cyclin-dependent kinase inhibitor
    cyclin-dependent kinase interacting protein 2
    cyclin-dependent kinase interactor 1
    kinase-associated phosphatase
    NP_001124323.1
    NP_001317102.1
    NP_005183.2

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_023235.1 RefSeqGene

      Range
      5053..28264
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001130851.2 → NP_001124323.1  cyclin-dependent kinase inhibitor 3 isoform 2

      See identical proteins and their annotated locations for NP_001124323.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame segment in the CDS, as compared to variant 1. The resulting isoform (2) lacks an internal segment, as compared to isoform 1.
      Source sequence(s)
      BC064965
      Consensus CDS
      CCDS45109.1
      UniProtKB/TrEMBL
      Q9BPV5
      Related
      ENSP00000415333.2, ENST00000442975.6
      Conserved Domains (1) summary
      cl21483
      Location:11 → 128
      PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...

    2. NM_001330173.2 → NP_001317102.1  cyclin-dependent kinase inhibitor 3 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate exon in the 3' coding region, resulting in a frameshift compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AL049778, AL359792
      Consensus CDS
      CCDS81804.1
      UniProtKB/TrEMBL
      G3V2J7, Q9C043
      Related
      ENSP00000450711.1, ENST00000556102.6
      Conserved Domains (1) summary
      pfam05706
      Location:1 → 168
      CDKN3; Cyclin-dependent kinase inhibitor 3 (CDKN3)

    3. NM_005192.4 → NP_005183.2  cyclin-dependent kinase inhibitor 3 isoform 1

      See identical proteins and their annotated locations for NP_005183.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AK098653, BC064965
      Consensus CDS
      CCDS9716.1
      UniProtKB/Swiss-Prot
      Q16667, Q53ZU6, Q5U0M4, Q6P1N8, Q99585, Q9BPW7, Q9BY36, Q9C042, Q9C046, Q9C047, Q9C049, Q9C051, Q9C053
      UniProtKB/TrEMBL
      H7C0S3
      Related
      ENSP00000335357.6, ENST00000335183.11
      Conserved Domains (1) summary
      pfam05706
      Location:1 → 168
      CDKN3; Cyclin-dependent kinase inhibitor 3 (CDKN3)

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      54397007..54420218
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      48602154..48625376
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q16667.1 GenPept UniProtKB/Swiss-Prot:Q16667

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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