Human Gene CDKN2D (ENST00000393599.3_7) from GENCODE V47lift37
  Description: cyclin dependent kinase inhibitor 2D, transcript variant 2 (from RefSeq NM_079421.3)
Gencode Transcript: ENST00000393599.3_7
Gencode Gene: ENSG00000129355.7_9
Transcript (Including UTRs)
   Position: hg19 chr19:10,677,136-10,679,655 Size: 2,520 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr19:10,677,734-10,679,329 Size: 1,596 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 (chr19:10,677,136-10,679,655)mRNA (may differ from genome)Protein (166 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CDN2D_HUMAN
DESCRIPTION: RecName: Full=Cyclin-dependent kinase 4 inhibitor D; AltName: Full=p19-INK4d;
FUNCTION: Interacts strongly with CDK4 and CDK6 and inhibits them.
SUBUNIT: Interacts with CDK6.
SUBCELLULAR LOCATION: Nucleus. Cytoplasm.
SIMILARITY: Belongs to the CDKN2 cyclin-dependent kinase inhibitor family.
SIMILARITY: Contains 4 ANK repeats.
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/cdkn2d/";

-  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: CDKN2D
Diseases sorted by gene-association score: malignant melanoma, somatic* (6), deafness, autosomal recessive 68 (3)
* = 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: 105.79 RPKM in Whole Blood
Total median expression: 909.70 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 -200.00326-0.613 Picture PostScript Text
3' UTR -208.30598-0.348 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
IPR002110 - Ankyrin_rpt
IPR020683 - Ankyrin_rpt-contain_dom

Pfam Domains:
PF12796 - Ankyrin repeats (3 copies)
PF13637 - Ankyrin repeats (many copies)
PF13857 - Ankyrin repeats (many copies)

SCOP Domains:
140860 - Pseudo ankyrin repeat-like
48403 - Ankyrin repeat

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1BD8 - X-ray MuPIT 1BI8 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P55273
FrontTopSide
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 Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004861 cyclin-dependent protein serine/threonine kinase inhibitor activity
GO:0005515 protein binding
GO:0019901 protein kinase binding

Biological Process:
GO:0000079 regulation of cyclin-dependent protein serine/threonine kinase activity
GO:0000082 G1/S transition of mitotic cell cycle
GO:0000731 DNA synthesis involved in DNA repair
GO:0007049 cell cycle
GO:0007050 cell cycle arrest
GO:0007605 sensory perception of sound
GO:0008285 negative regulation of cell proliferation
GO:0009411 response to UV
GO:0030308 negative regulation of cell growth
GO:0031658 negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle
GO:0032526 response to retinoic acid
GO:0033280 response to vitamin D
GO:0042326 negative regulation of phosphorylation
GO:0043154 negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0048102 autophagic cell death
GO:1902230 negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage
GO:1902807 negative regulation of cell cycle G1/S phase transition

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0097129 cyclin D2-CDK4 complex


-  Descriptions from all associated GenBank mRNAs
  BC001822 - Homo sapiens cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4), mRNA (cDNA clone MGC:3718 IMAGE:3529045), complete cds.
U40343 - Human CDK inhibitor p19INK4d mRNA, complete cds.
JD201953 - Sequence 182977 from Patent EP1572962.
JD248912 - Sequence 229936 from Patent EP1572962.
JD120640 - Sequence 101664 from Patent EP1572962.
JD466832 - Sequence 447856 from Patent EP1572962.
JD249403 - Sequence 230427 from Patent EP1572962.
JD180835 - Sequence 161859 from Patent EP1572962.
JD320616 - Sequence 301640 from Patent EP1572962.
JD474333 - Sequence 455357 from Patent EP1572962.
JD459859 - Sequence 440883 from Patent EP1572962.
JD489400 - Sequence 470424 from Patent EP1572962.
U20498 - Human p19 protein mRNA, complete cds.
JD494132 - Sequence 475156 from Patent EP1572962.
JD527144 - Sequence 508168 from Patent EP1572962.
JD216269 - Sequence 197293 from Patent EP1572962.
U49399 - Human inhibitor of cyclin-dependent kinase 4 d INK4d mRNA, complete cds.
KJ890890 - Synthetic construct Homo sapiens clone ccsbBroadEn_00284 CDKN2D gene, encodes complete protein.
DQ892872 - Synthetic construct clone IMAGE:100005502; FLH190480.01X; RZPDo839A1076D cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4) (CDKN2D) gene, encodes complete protein.
DQ892951 - Synthetic construct Homo sapiens clone IMAGE:100005581; FLH263501.01X; RZPDo839H0776D cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4) (CDKN2D) gene, encodes complete protein.
DQ896120 - Synthetic construct Homo sapiens clone IMAGE:100010580; FLH190476.01L; RZPDo839A1066D cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4) (CDKN2D) gene, encodes complete protein.
CR542158 - Homo sapiens full open reading frame cDNA clone RZPDo834A0224D for gene CDKN2D, cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4); complete cds, without stopcodon.
AB464505 - Synthetic construct DNA, clone: pF1KB8875, Homo sapiens CDKN2D gene for cyclin-dependent kinase inhibitor 2D, without stop codon, in Flexi system.
CU674892 - Synthetic construct Homo sapiens gateway clone IMAGE:100020205 5' read CDKN2D mRNA.
JD263929 - Sequence 244953 from Patent EP1572962.
JD480958 - Sequence 461982 from Patent EP1572962.
JD472837 - Sequence 453861 from Patent EP1572962.
JD329385 - Sequence 310409 from Patent EP1572962.
JD107751 - Sequence 88775 from Patent EP1572962.
JD462655 - Sequence 443679 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_g2Pathway - Cell Cycle: G2/M Checkpoint
h_cellcyclePathway - Cyclins and Cell Cycle Regulation

Reactome (by CSHL, EBI, and GO)

Protein P55273 (Reactome details) participates in the following event(s):

R-HSA-182594 Association of INK4 with CDK4/6
R-HSA-69231 Cyclin D associated events in G1
R-HSA-2559580 Oxidative Stress Induced Senescence
R-HSA-2559582 Senescence-Associated Secretory Phenotype (SASP)
R-HSA-2559585 Oncogene Induced Senescence
R-HSA-69236 G1 Phase
R-HSA-2559583 Cellular Senescence
R-HSA-453279 Mitotic G1-G1/S phases
R-HSA-2262752 Cellular responses to stress
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-8953897 Cellular responses to external stimuli
R-HSA-1640170 Cell Cycle

-  Other Names for This Gene
  Alternate Gene Symbols: CDN2D_HUMAN, ENST00000393599.1, ENST00000393599.2, NM_079421, P55273, Q13102, Q6FGE9, uc318vzo.1, uc318vzo.2
UCSC ID: ENST00000393599.3_7
RefSeq Accession: NM_001800.4
Protein: P55273 (aka CDN2D_HUMAN or CDN7_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.