Human Gene CDKN2A (ENST00000579755.2_12) from GENCODE V47lift37
  Description: cyclin dependent kinase inhibitor 2A, transcript variant 4 (from RefSeq NM_058195.4)
Gencode Transcript: ENST00000579755.2_12
Gencode Gene: ENSG00000147889.18_16
Transcript (Including UTRs)
   Position: hg19 chr9:21,967,751-21,994,391 Size: 26,641 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr9:21,971,002-21,994,330 Size: 23,329 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:21,967,751-21,994,391)mRNA (may differ from genome)Protein (132 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CD2A2_HUMAN
DESCRIPTION: RecName: Full=Cyclin-dependent kinase inhibitor 2A, isoform 4; AltName: Full=p14ARF; AltName: Full=p19ARF;
FUNCTION: Capable of inducing cell cycle arrest in G1 and G2 phases. Acts as a tumor suppressor. Binds to MDM2 and blocks its nucleocytoplasmic shuttling by sequestering it in the nucleolus. This inhibits the oncogenic action of MDM2 by blocking MDM2- induced degradation of p53 and enhancing p53-dependent transactivation and apoptosis. Also induces G2 arrest and apoptosis in a p53-independent manner by preventing the activation of cyclin B1/CDC2 complexes. Binds to BCL6 and down-regulates BCL6-induced transcriptional repression. Binds to E2F1 and MYC and blocks their transcriptional activator activity but has no effect on MYC transcriptional repression. Binds to TOP1/TOPOI and stimulates its activity. This complex binds to rRNA gene promoters and may play a role in rRNA transcription and/or maturation. Interacts with NPM1/B23 and promotes its polyubiquitination and degradation, thus inhibiting rRNA processing. Interacts with COMMD1 and promotes its 'Lys63'-linked polyubiquitination. Interacts with UBE2I/UBC9 and enhances sumoylation of a number of its binding partners including MDM2 and E2F1. Binds to HUWE1 and represses its ubiquitin ligase activity. May play a role in controlling cell proliferation and apoptosis during mammary gland development.
SUBUNIT: Does not interact with cyclins, CDK1, CDK2, CDK4, CDK5 or CDK6. Binds to BCL6, E2F1, HUWE1, MDM2, MYC, NPM1/B23, TOP1/TOPOI and UBE2I/UBC9. Interacts with TBRG1 and COMMD1. Interacts with CDKN2AIP and E4F1.
INTERACTION: Q9UER7:DAXX; NbExp=8; IntAct=EBI-625922, EBI-77321; Q8AZK7:EBNA-LP (xeno); NbExp=5; IntAct=EBI-625922, EBI-1185167; Q7Z6Z7:HUWE1; NbExp=4; IntAct=EBI-625922, EBI-625934; Q00987:MDM2; NbExp=3; IntAct=EBI-625922, EBI-389668;
SUBCELLULAR LOCATION: Nucleus, nucleolus. Nucleus, nucleoplasm.
PTM: Ubiquitinated in normal cells by TRIP12 via the ubiquitin fusion degradation (UFD) pathway, a process that mediates ubiquitination at the N-terminus, regardeless of the absence of lysine residues. Ubiquitination leads to its degradation. In cancer cells, however, TRIP12 is located in a different cell compartment, preventing ubiquitination and degradation.
SEQUENCE CAUTION: Sequence=AAB01737.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=AAC60649.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=AAH15960.3; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=AAH21998.3; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=AAM77919.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=CAH70601.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=EAW58600.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=EAW58601.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/cdkn2a/";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: CDKN2A
Diseases sorted by gene-association score: pancreatic cancer/melanoma syndrome* (1325), melanoma and neural system tumor syndrome* (1025), melanoma, cutaneous malignant, 2* (906), dysplastic nevus syndrome* (818), malignant melanoma, somatic* (402), leukemia, acute lymphoblastic 3* (164), cdkn2a-related cutaneous malignant melanoma* (125), precursor t-cell acute lymphoblastic leukemia* (90), skin melanoma (49), pancreatic cancer* (32), cervical squamous cell carcinoma (31), cervical adenocarcinoma (31), cervical intraepithelial neoplasia (28), melanoma (27), oropharynx cancer (26), astrocytoma (25), endocervical adenocarcinoma (25), papilloma (24), adenocarcinoma in situ (23), anal squamous cell carcinoma (23), gallbladder adenoma (22), bowenoid papulosis (18), lung cancer (18), localized osteosarcoma (17), uveal melanoma (17), cervical cancer, somatic (17), squamous cell carcinoma (16), endocervical carcinoma (16), vulva squamous cell carcinoma (16), vulva cancer (16), oligodendroglioma (16), endometrial mucinous adenocarcinoma (15), conjunctival intraepithelial neoplasm (15), pleomorphic liposarcoma (15), endometrial transitional cell carcinoma (15), fallopian tube squamous cell carcinoma (15), penile cancer (14), lung carcinoma in situ (14), early invasive cervical adenocarcinoma (14), verrucous carcinoma (14), actinic keratosis (13), primary cutaneous diffuse large b-cell lymphoma, leg type (13), peritoneal mesothelioma (13), glioblastoma multiforme (12), li-fraumeni syndrome (12), megaesophagus (12), malignant peripheral nerve sheath tumor (12), anus cancer (12), atypical lipomatous tumor (12), malignant glioma (11), oral cancer (11), acral lentiginous melanoma (11), adenocarcinoma (11), tonsil cancer (11), pancreatic ductal adenocarcinoma (11), sarcomatoid mesothelioma (11), squamous cell carcinoma, head and neck (11), endometrial cancer (11), keratinizing squamous cell carcinoma (11), fibrosarcoma of bone (11), endometrial adenocarcinoma (10), biliary tract neoplasm (10), malignant peritoneal mesothelioma (10), basaloid squamous cell carcinoma (10), urinary bladder cancer (10), ameloblastic carcinoma (10), brain stem astrocytic neoplasm (10), barrett's adenocarcinoma (10), scrotal carcinoma (10), esophageal cancer (10), persistent hyperplastic primary vitreous (10), ocular melanoma (10), breast papillomatosis (10), oral squamous cell carcinoma (10), larynx cancer (10), inverted papilloma (10), fallopian tube endometrioid adenocarcinoma (10), cholangiolocellular carcinoma (10), small cell neuroendocrine carcinoma (10), bladder cancer, somatic (10), vulvar seborrheic keratosis (9), mesothelioma, somatic (9), nasopharyngeal carcinoma (9), cervix uteri carcinoma in situ (9), anal canal carcinoma (9), gallbladder cancer (9), pharynx cancer (9), bladder squamous cell carcinoma (9), cd3epsilon deficiency (9), barrett esophagus/esophageal adenocarcinoma (9), central nervous system lymphoma (8), bladder carcinoma in situ (8), dedifferentiated liposarcoma (8), acute lymphoblastic leukemia, childhood (8), vulval paget's disease (8), grade iii astrocytoma (8), blastic plasmacytoid dendritic cell (8), inverted transitional papilloma (8), spitz nevus (8), mucinous bronchioloalveolar adenocarcinoma (8), tonsil squamous cell carcinoma (8), cell type cancer (8), tongue squamous cell carcinoma (8), vulvar dystrophy (8), cervix disease (8), neurofibroma (8), leukemia (8), retinoblastoma (7), nasal cavity cancer (7), anaplastic oligodendroglioma (7), mucinous adenocarcinoma (7), atypical neurofibroma (7), vulva adenocarcinoma (7), retinal cancer (7), tongue cancer (7), sensory system cancer (7), primary central nervous system lymphoma (7), acute lymphocytic leukemia (7), oral leukoplakia (7), bizarre leiomyoma (7), pancreatic ductal carcinoma (7), adenoid basal cell carcinoma (7), adult t-cell leukemia (7), pilocytic astrocytoma (7), thyroid lymphoma (6), malignant pleural mesothelioma (6), liposarcoma (6), nasal cavity adenocarcinoma (6), infiltrating angiolipoma (6), integumentary system cancer (6), melanomatosis (6), gastric adenosquamous carcinoma (6), retroperitoneum carcinoma (6), retinitis pigmentosa 22 (6), skin carcinoma in situ (6), cholecystitis (6), plasmablastic lymphoma (6), pleural cancer (6), pre-malignant neoplasm (6), balanitis xerotica obliterans (6), balanoposthitis (6), bone squamous cell carcinoma (6), leukemia, acute lymphoblastic (6), anogenital venereal wart (6), chordoma (6), chronic cervicitis (6), ductal carcinoma in situ (6), epstein-barr virus-associated gastric carcinoma (5), cervicitis (5), lymphoblastic leukemia (5), glioblastoma (5), glioma (5), histiocytic sarcoma (5), esophagus adenocarcinoma (5), lynch syndrome (5), keratosis (5), vulvar intraepithelial neoplasia (5), ewing's family of tumors (5), ocular cancer (5), female reproductive organ cancer (5), chromosome 2p16.1-p15 deletion syndrome (5), optic nerve sheath meningioma (5), blackwater fever (5), endometrial squamous cell carcinoma (5), conventional leiomyosarcoma (5), chondromyxoid fibroma (5), cervix small cell carcinoma (5), pancreas adenocarcinoma (5), ischemic fasciitis (5), colorectal cancer (5), cervical adenosquamous carcinoma (5), nervous system cancer (5), bone cancer (5), anal canal squamous cell carcinoma (5), glycogen-rich clear cell breast carcinoma (5), acute kidney tubular necrosis (5), colon lymphoma (4), periosteal chondrosarcoma (4), central nervous system melanocytic neoplasm (4), in situ carcinoma (4), vulvar melanoma (4), meningeal melanocytoma (4), breast giant fibroadenoma (4), nasal cavity squamous cell carcinoma (4), meningeal melanomatosis (4), cellular schwannoma (4), juvenile pilocytic astrocytoma (4), necrotizing sialometaplasia (4), optic nerve neoplasm (4), b-cell lymphomas (4), nodular malignant melanoma (3), hepatocellular carcinoma (3), mantle cell lymphoma (3), kidney cancer (3), gastrointestinal stromal tumor (3), stomach cancer (3), lung cancer susceptibility 3 (2), multiple myeloma (2), osteosarcoma, somatic (2), adamantinoma of long bones (2), ovarian cancer, somatic (2), gastrointestinal system cancer (2), reproductive organ cancer (2), cell type benign neoplasm (1), endocrine gland cancer (1), gastrointestinal system benign neoplasm (1), tetralogy of fallot (1), gastric cancer, somatic (1), leukemia, acute myeloid (0)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 6.71 RPKM in Pituitary
Total median expression: 27.50 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -27.0061-0.443 Picture PostScript Text
3' UTR -168.40592-0.284 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR010868 - Cyclin_kinase-Inhib_2A

Pfam Domains:
PF07392 - Cyclin-dependent kinase inhibitor 2a p19Arf N-terminus

ModBase Predicted Comparative 3D Structure on Q8N726
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0002039 p53 binding
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0008134 transcription factor binding
GO:0019789 SUMO transferase activity
GO:0055105 ubiquitin-protein transferase inhibitor activity
GO:0097371 MDM2/MDM4 family protein binding
GO:0097718 disordered domain specific binding
GO:1990948 ubiquitin ligase inhibitor activity

Biological Process:
GO:0000209 protein polyubiquitination
GO:0000422 mitophagy
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006364 rRNA processing
GO:0006469 negative regulation of protein kinase activity
GO:0006915 apoptotic process
GO:0006919 activation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0007049 cell cycle
GO:0007050 cell cycle arrest
GO:0008285 negative regulation of cell proliferation
GO:0008637 apoptotic mitochondrial changes
GO:0010389 regulation of G2/M transition of mitotic cell cycle
GO:0010628 positive regulation of gene expression
GO:0016925 protein sumoylation
GO:0030889 negative regulation of B cell proliferation
GO:0031647 regulation of protein stability
GO:0031648 protein destabilization
GO:0033088 negative regulation of immature T cell proliferation in thymus
GO:0033235 positive regulation of protein sumoylation
GO:0043065 positive regulation of apoptotic process
GO:0043517 positive regulation of DNA damage response, signal transduction by p53 class mediator
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0046825 regulation of protein export from nucleus
GO:0048103 somatic stem cell division
GO:0050821 protein stabilization
GO:0051444 negative regulation of ubiquitin-protein transferase activity
GO:0051882 mitochondrial depolarization
GO:0070534 protein K63-linked ubiquitination
GO:0071158 positive regulation of cell cycle arrest
GO:0090398 cellular senescence
GO:1900182 positive regulation of protein localization to nucleus
GO:1901798 positive regulation of signal transduction by p53 class mediator
GO:1902510 regulation of apoptotic DNA fragmentation
GO:1903051 negative regulation of proteolysis involved in cellular protein catabolic process
GO:1903214 regulation of protein targeting to mitochondrion
GO:1904667 negative regulation of ubiquitin protein ligase activity
GO:1990000 amyloid fibril formation
GO:2000059 negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process
GO:2000435 negative regulation of protein neddylation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005739 mitochondrion
GO:0032991 macromolecular complex
GO:0016604 nuclear body


-  Descriptions from all associated GenBank mRNAs
  KC806059 - Homo sapiens p14ARF/p16INK4a fusion protein (p14ARF/p16INK4a fusion) mRNA, complete cds.
KC814157 - Homo sapiens p16-ACT fusion protein (p16ink4a) mRNA, complete cds.
L27211 - Human CDK4-inhibitor (p16-INK4) mRNA, complete cds.
U26727 - Human p16INK4/MTS1 mRNA, complete cds.
JD507893 - Sequence 488917 from Patent EP1572962.
BC015960 - Homo sapiens cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4), mRNA (cDNA clone IMAGE:3954155), partial cds.
BC021998 - Homo sapiens cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4), mRNA (cDNA clone IMAGE:2988668), partial cds.
U38945 - Human hypothetical 18.1 kDa protein (CDKN2A) mRNA, complete cds.
KF311101 - Homo sapiens CAI2 lncRNA (CDKN2A), partial sequence.
JQ694043 - Homo sapiens isolate iPCH460_Col5 cyclin-dependent kinase inhibitor 2A (CDKN2A) mRNA, complete cds.
JQ694044 - Homo sapiens isolate iPCH460_Col9 cyclin-dependent kinase inhibitor 2A (CDKN2A) mRNA, complete cds.
JQ694045 - Homo sapiens isolate iPCH460_Col12 cyclin-dependent kinase inhibitor 2A (CDKN2A) mRNA, complete cds.
DQ318021 - Homo sapiens cyclin-dependent kinase inhibitor (CDKN2A) mRNA, complete cds, alternatively spliced.
JD189027 - Sequence 170051 from Patent EP1572962.
AF115544 - Homo sapiens cyclin-dependent kinase inhibitor p12 (p16INK4a) mRNA, alternatively spliced form, complete cds.
JD435944 - Sequence 416968 from Patent EP1572962.
JD037742 - Sequence 18766 from Patent EP1572962.
JD391771 - Sequence 372795 from Patent EP1572962.
S78535 - tumor suppressor gene, P16/MTS1/CDKN2=cell cycle negative regulator beta form [human, mRNA Partial, 660 nt].
KJ901333 - Synthetic construct Homo sapiens clone ccsbBroadEn_10727 CDKN2A gene, encodes complete protein.
JD484377 - Sequence 465401 from Patent EP1572962.
JD322858 - Sequence 303882 from Patent EP1572962.
BT007020 - Homo sapiens cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) mRNA, complete cds.
AB464504 - Synthetic construct DNA, clone: pF1KB8879, Homo sapiens CDKN2A gene for cyclin-dependent kinase inhibitor 2A, without stop codon, in Flexi system.
JD157669 - Sequence 138693 from Patent EP1572962.
JD400426 - Sequence 381450 from Patent EP1572962.
JD200275 - Sequence 181299 from Patent EP1572962.
AJ844636 - Homo sapiens partial pre-mRNA for cyclin-dependent kinase inhibitor 2A (CDKN2A gene).
DI434958 - KR 1020140128524-A/4: Use of treatment of gastric tumorigenesis or suppression of senescence through MKRN1-mediated post-translational regulation of P14ARG.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_arfPathway - Tumor Suppressor Arf Inhibits Ribosomal Biogenesis
h_cellcyclePathway - Cyclins and Cell Cycle Regulation
h_ctcfPathway - CTCF: First Multivalent Nuclear Factor
h_g1Pathway - Cell Cycle: G1/S Check Point

Reactome (by CSHL, EBI, and GO)

Protein Q8N726 (Reactome details) participates in the following event(s):

R-HSA-6804998 p14-ARF forms a ternary complex with MDM2 and TP53
R-HSA-6804996 p14-ARF sequesters MDM2
R-HSA-4568846 CDKN2A (p14-ARF) SUMOylates WRN with SUMO1
R-HSA-2997706 MDM2 SUMOylates TP53 with SUMO2,3
R-HSA-2559580 Oxidative Stress Induced Senescence
R-HSA-2559585 Oncogene Induced Senescence
R-HSA-6804757 Regulation of TP53 Degradation
R-HSA-2559583 Cellular Senescence
R-HSA-6806003 Regulation of TP53 Expression and Degradation
R-HSA-3108214 SUMOylation of DNA damage response and repair proteins
R-HSA-3232118 SUMOylation of transcription factors
R-HSA-2262752 Cellular responses to stress
R-HSA-5633007 Regulation of TP53 Activity
R-HSA-3108232 SUMO E3 ligases SUMOylate target proteins
R-HSA-8953897 Cellular responses to external stimuli
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-2990846 SUMOylation
R-HSA-212436 Generic Transcription Pathway
R-HSA-597592 Post-translational protein modification
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-392499 Metabolism of proteins
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: ARF_HUMAN, CDKN2 , CDKN2A , D3DRK2, ENST00000579755.1, MLM, NM_058195, Q13195, Q13399, Q16360, Q7KZR9, Q8N726, uc326hza.1, uc326hza.2
UCSC ID: ENST00000579755.2_12
RefSeq Accession: NM_058195.4
Protein: Q8N726 (aka CD2A2_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.