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Aliases for CDKN2A-DT Gene

Subcategory (RNA class) for CDKN2A-DT Gene

non-coding RNA

Quality Score for this RNA gene is

13

Aliases for CDKN2A-DT Gene

  • CDKN2A Divergent Transcript 2 3
  • CDKN2A Antisense RNA 1 (Head To Head) 2 3 5
  • CDKN2A-AS1 3 5
  • Chromosome 9 Open Reading Frame 53 2
  • Susceptibility Protein NSG-X 3
  • BA149I2.3 3
  • C9orf53 3

External Ids for CDKN2A-DT Gene

Previous HGNC Symbols for CDKN2A-DT Gene

  • C9orf53
  • CDKN2A-AS1

Summaries for CDKN2A-DT Gene

GeneCards Summary for CDKN2A-DT Gene

CDKN2A-DT (CDKN2A Divergent Transcript) is an RNA Gene, and is affiliated with the non-coding RNA class. Diseases associated with CDKN2A-DT include Lung Squamous Cell Carcinoma.

Additional gene information for CDKN2A-DT Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CDKN2A-DT Gene

Genomics for CDKN2A-DT Gene

GeneHancer (GH) Regulatory Elements for CDKN2A-DT Gene

Promoters and enhancers for CDKN2A-DT Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J021964 Enhancer 1.2 FANTOM5 Ensembl ENCODE 650.7 -1.5 -1502 1.2 CTCF SUZ12 CBFB ARID4B RAD21 RELA TEAD3 TGIF2 SP1 XRCC5 CDKN2A-DT PIR35648 ENSG00000264545
GH09J021967 Enhancer 0.3 ENCODE 650.7 +0.8 798 0 EZH2 CDKN2A-DT GC09M021977 PIR47863 ENSG00000264545
GH09J021809 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 11.6 -154.8 -154834 4.8 PKNOX1 FOXA2 ARID4B SIN3A ZNF2 IRF4 YY1 ZNF143 FOS RUNX3 PIR60166 TUBB8P1 MTAP CDKN2A CDKN2B-AS1 CDKN2A-DT CDKN2B UBA52P6 ENSG00000264545
GH09J021989 Enhancer 1.2 Ensembl ENCODE dbSUPER 13.1 +23.3 23252 1.2 ZBTB21 SUZ12 ZNF335 ZFHX2 GLIS2 ZNF366 PATZ1 ZSCAN5C ZNF600 KLF8 KLHL9 CDKN2A-DT UBA52P6 ENSG00000265194 MTAP CDKN2B CDKN2B-AS1 CDKN2A GC09M021977 PIR47863
GH09J021986 Enhancer 1.1 Ensembl ENCODE dbSUPER 13.1 +20.8 20776 2.6 PKNOX1 ZSCAN4 NFRKB BACH1 RFX5 YY1 POLR2A ZSCAN5C MAFK EZH2 CDKN2B CDKN2A-DT UBA52P6 CDKN2A CDKN2B-AS1 GC09M021977 PIR47863 ENSG00000264545
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CDKN2A-DT on UCSC Golden Path with GeneCards custom track

Genomic Locations for CDKN2A-DT Gene

Genomic Locations for CDKN2A-DT Gene
chr9:21,966,929-21,967,754
(GRCh38/hg38)
Size:
826 bases
Orientation:
Plus strand
chr9:21,967,137-21,967,753
(GRCh37/hg19)
Size:
617 bases
Orientation:
Plus strand

Genomic View for CDKN2A-DT Gene

Genes around CDKN2A-DT on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CDKN2A-DT Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CDKN2A-DT Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CDKN2A-DT Gene

Proteins for CDKN2A-DT Gene

Post-translational modifications for CDKN2A-DT Gene

No Post-translational modifications

No data available for DME Specific Peptides for CDKN2A-DT Gene

Domains & Families for CDKN2A-DT Gene

Suggested Antigen Peptide Sequences for CDKN2A-DT Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

No data available for Gene Families , Protein Domains and UniProtKB/Swiss-Prot for CDKN2A-DT Gene

Function for CDKN2A-DT Gene

Phenotypes From GWAS Catalog for CDKN2A-DT Gene

Phenotypes for CDKN2A-DT Gene

genes like me logo Genes that share phenotypes with CDKN2A-DT: view

Animal Model Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CDKN2A-DT Gene

Localization for CDKN2A-DT Gene

Subcellular locations from

COMPARTMENTS
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 CDKN2A-DT gene
Compartment Confidence
nucleus 2
cytosol 2
extracellular 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for CDKN2A-DT Gene

Pathways & Interactions for CDKN2A-DT Gene

SuperPathways for CDKN2A-DT Gene

No Data Available

Interacting Proteins for CDKN2A-DT Gene

Gene Ontology (GO) - Biological Process for CDKN2A-DT Gene

None

No data available for Pathways by source and SIGNOR curated interactions for CDKN2A-DT Gene

Drugs & Compounds for CDKN2A-DT Gene

No Compound Related Data Available

Transcripts for CDKN2A-DT Gene

mRNA/cDNA for CDKN2A-DT Gene

(1) REFSEQ mRNAs :
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :
(2) RNA Central transcripts :

Alternative Splicing Database (ASD) splice patterns (SP) for CDKN2A-DT Gene

No ASD Table

Relevant External Links for CDKN2A-DT Gene

GeneLoc Exon Structure for
CDKN2A-DT
ECgene alternative splicing isoforms for
CDKN2A-DT

Expression for CDKN2A-DT Gene

No Expression Related Data Available

Primer Products

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for CDKN2A-DT Gene

Orthologs for CDKN2A-DT Gene

This gene was present in the common ancestor of human and chimp.

Orthologs for CDKN2A-DT Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia C9orf53 34
  • 99 (a)
OneToOne
Species where no ortholog for CDKN2A-DT 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)
  • cow (Bos Taurus)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • mouse (Mus musculus)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for CDKN2A-DT Gene

ENSEMBL:
Gene Tree for CDKN2A-DT (if available)
TreeFam:
Gene Tree for CDKN2A-DT (if available)

Paralogs for CDKN2A-DT Gene

No data available for Paralogs for CDKN2A-DT Gene

Variants for CDKN2A-DT Gene

Sequence variations from dbSNP and Humsavar for CDKN2A-DT Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs1060501271 uncertain-significance, Hereditary cutaneous melanoma 21,968,237(+) G/C downstream_transcript_variant
rs1060501272 uncertain-significance, Hereditary cutaneous melanoma 21,968,242(+) T/A downstream_transcript_variant
rs375628411 likely-benign, benign, not specified, Hereditary cancer-predisposing syndrome 21,968,223(+) G/A/C/T downstream_transcript_variant
rs749753811 likely-benign, Hereditary cutaneous melanoma, not specified, Hereditary cancer-predisposing syndrome 21,968,232(+) A/G downstream_transcript_variant
rs778871932 likely-benign, Hereditary cutaneous melanoma, Hereditary cancer-predisposing syndrome 21,968,241(+) G/A downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for CDKN2A-DT Gene

Variant ID Type Subtype PubMed ID
esv2764150 CNV gain+loss 21179565
nsv1018514 CNV gain 25217958
nsv8426 CNV loss 18304495

Variation tolerance for CDKN2A-DT Gene

Gene Damage Index Score: 0.05; 1.25% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CDKN2A-DT Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CDKN2A-DT

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CDKN2A-DT Gene

Disorders for CDKN2A-DT Gene

MalaCards: The human disease database

(1) MalaCards diseases for CDKN2A-DT Gene - From: LncRNADisease

Disorder Aliases PubMed IDs
lung squamous cell carcinoma
  • epidermoid cell carcinoma of the lung
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CDKN2A-DT

genes like me logo Genes that share disorders with CDKN2A-DT: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CDKN2A-DT Gene

Publications for CDKN2A-DT Gene

  1. Chromosome 9p21.3 genotype is associated with vascular dementia and Alzheimer's disease. (PMID: 19664850) Emanuele E … Politi P (Neurobiology of aging 2011) 3 58
  2. Single nucleotide polymorphisms of matrix metalloproteinase 9 (MMP9) and tumor protein 73 (TP73) interact with Epstein-Barr virus in chronic lymphocytic leukemia: results from the European case-control study EpiLymph. (PMID: 21048031) Casabonne D … de Sanjose S (Haematologica 2011) 3 58
  3. Six sequence variants on chromosome 9p21.3 are associated with a positive family history of myocardial infarction: a multicenter registry. (PMID: 21385355) Scheffold T … Forschungsverbund Herz-Kreislauf in NRW (Research Consortium Heart and Circulation in North Rhine-Westphalia) (BMC cardiovascular disorders 2011) 3 58
  4. The contribution of a 9p21.3 variant, a KIF6 variant, and C-reactive protein to predicting risk of myocardial infarction in a prospective study. (PMID: 21406102) Shiffman D … Psaty BM (BMC cardiovascular disorders 2011) 3 58
  5. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 58

Products for CDKN2A-DT Gene

Sources for CDKN2A-DT Gene

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