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Aliases for PDE12 Gene

Aliases for PDE12 Gene

  • Phosphodiesterase 12 2 3 5
  • Mitochondrial Deadenylase 3 4
  • 2-Phosphodiesterase 2 3
  • 2-PDE 3 4
  • 2,5-Phosphodiesterase 12 3
  • EC 3.1.13.4 4
  • EC 3.1.4.- 4
  • EC 3.1.4 58

External Ids for PDE12 Gene

Previous GeneCards Identifiers for PDE12 Gene

  • GC03P057520
  • GC03P057521
  • GC03P057541

Summaries for PDE12 Gene

GeneCards Summary for PDE12 Gene

PDE12 (Phosphodiesterase 12) is a Protein Coding gene. Diseases associated with PDE12 include Microphthalmia With Limb Anomalies. GO annotations related to this gene include poly(A)-specific ribonuclease activity. An important paralog of this gene is CNOT6L.

UniProtKB/Swiss-Prot for PDE12 Gene

  • Enzyme that cleaves 2,5-phosphodiester bond linking adenosines of the 5-triphosphorylated oligoadenylates, triphosphorylated oligoadenylates referred as 2-5A modulates the 2-5A system. This enzyme degraded triphosphorylated 2-5A to produce AMP and ATP. Also cleaves 3,5-phosphodiester bond of oligoadenylates. Plays a role as a negative regulator of the The 2-5A system that is one of the major pathways for antiviral and antitumor functions induced by interferons (IFNs). Suppression of this enzyme induces reduction of viral replication in Hela cells, thus counteracting the antiviral pathway probably by inhibiting the 2-5A system.

Additional gene information for PDE12 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDE12 Gene

Genomics for PDE12 Gene

Regulatory Elements for PDE12 Gene

Enhancers for PDE12 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03H058332 1.4 ENCODE dbSUPER 22.5 +778.2 778208 4 FOXA2 ARNT ARID4B SIN3A FEZF1 ZNF2 ZNF766 CBX5 ZNF416 ZNF207 DENND6A FLNB-AS1 FLNB KCTD6 RPP14 PDE12 LOC105377110 HTD2 FAM107A PXK
GH03H057016 1.6 FANTOM5 Ensembl ENCODE dbSUPER 11.8 -539.0 -538966 1 PKNOX1 NFRKB ZSCAN4 TCF12 FOS RCOR1 ETV6 RUNX3 CREM ZBTB2 FLNB APPL1 PDE12 SPATA12 ARHGEF3 CCDC66 ARHGEF3-AS1
GH03H056921 1.6 FANTOM5 Ensembl ENCODE dbSUPER 10.9 -631.9 -631888 6 MAX PYGO2 ZNF7 POLR2A RUNX3 ZBTB20 ZNF639 RFX1 CAVIN1 ZNF740 CCDC66 FAM208A DENND6A APPL1 ARHGEF3 PDE12 GC03M056906 ARHGEF3-AS1
GH03H057594 1.4 ENCODE dbSUPER 11.3 +41.3 41320 6 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF207 ZNF143 DENND6A FAM208A ARF4 DENND6A-AS1 PDE12 DENND6A-DT APPL1 HESX1 FLNB DNAH12
GH03H057555 1.2 ENCODE 11.6 +0.5 508 3 PKNOX1 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 DENND6A APPL1 CCDC66 FAM208A FLNB-AS1 FLNB PDE12 DENND6A-DT HESX1 ARF4
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PDE12 on UCSC Golden Path with GeneCards custom track

Promoters for PDE12 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000153086 448 3001 PKNOX1 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9

Genomic Location for PDE12 Gene

Chromosome:
3
Start:
57,556,252 bp from pter
End:
57,654,979 bp from pter
Size:
98,728 bases
Orientation:
Plus strand

Genomic View for PDE12 Gene

Genes around PDE12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDE12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDE12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDE12 Gene

Proteins for PDE12 Gene

  • Protein details for PDE12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6L8Q7-PDE12_HUMAN
    Recommended name:
    2,5-phosphodiesterase 12
    Protein Accession:
    Q6L8Q7
    Secondary Accessions:
    • B4DTU8
    • Q8IYU3
    • Q8NDU2
    • Q8TE78

    Protein attributes for PDE12 Gene

    Size:
    609 amino acids
    Molecular mass:
    67352 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for PDE12 Gene

    Alternative splice isoforms for PDE12 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PDE12 Gene

Selected DME Specific Peptides for PDE12 Gene

Q6L8Q7:
  • AAAKKSRK
  • VLQRSSV
  • DLYPGIPVIFCGDFNSTPSTGMYHFVI
  • LSRIATNALKGHAK
  • SDPLHKELLEKL

Post-translational modifications for PDE12 Gene

  • Ubiquitination at posLast=6161, Lys84, and posLast=9797
  • Modification sites at PhosphoSitePlus

Other Protein References for PDE12 Gene

Domains & Families for PDE12 Gene

Gene Families for PDE12 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for PDE12 Gene

Suggested Antigen Peptide Sequences for PDE12 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q6L8Q7

UniProtKB/Swiss-Prot:

PDE12_HUMAN :
  • Belongs to the CCR4/nocturin family.
Family:
  • Belongs to the CCR4/nocturin family.
genes like me logo Genes that share domains with PDE12: view

Function for PDE12 Gene

Molecular function for PDE12 Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
pH dependence: Optimum pH is 8.0 for 2-5 oligoadenylate exonuclease activity. {ECO:0000269 PubMed:22285541};
UniProtKB/Swiss-Prot CatalyticActivity:
Exonucleolytic cleavage of poly(A) to 5-AMP.
UniProtKB/Swiss-Prot Function:
Enzyme that cleaves 2,5-phosphodiester bond linking adenosines of the 5-triphosphorylated oligoadenylates, triphosphorylated oligoadenylates referred as 2-5A modulates the 2-5A system. This enzyme degraded triphosphorylated 2-5A to produce AMP and ATP. Also cleaves 3,5-phosphodiester bond of oligoadenylates. Plays a role as a negative regulator of the The 2-5A system that is one of the major pathways for antiviral and antitumor functions induced by interferons (IFNs). Suppression of this enzyme induces reduction of viral replication in Hela cells, thus counteracting the antiviral pathway probably by inhibiting the 2-5A system.

Enzyme Numbers (IUBMB) for PDE12 Gene

Gene Ontology (GO) - Molecular Function for PDE12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000175 3-5-exoribonuclease activity IMP 21245038
GO:0004527 exonuclease activity IEA,IMP 15231837
GO:0004535 poly(A)-specific ribonuclease activity IEA --
GO:0016787 hydrolase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PDE12: view
genes like me logo Genes that share phenotypes with PDE12: view

Animal Models for PDE12 Gene

MGI Knock Outs for PDE12:

Animal Model Products

CRISPR Products

miRNA for PDE12 Gene

miRTarBase miRNAs that target PDE12

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for PDE12
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PDE12 Gene

Localization for PDE12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDE12 Gene

Mitochondrion matrix.

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 PDE12 gene
Compartment Confidence
mitochondrion 4
cytoskeleton 2
cytosol 2
nucleus 1

Gene Ontology (GO) - Cellular Components for PDE12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
GO:0005759 mitochondrial matrix IEA,IMP 21245038
genes like me logo Genes that share ontologies with PDE12: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PDE12 Gene

Pathways & Interactions for PDE12 Gene

SuperPathways for PDE12 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PDE12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay IMP 21245038
GO:0000958 mitochondrial mRNA catabolic process IMP 21245038
GO:0006397 mRNA processing IEA --
GO:0035457 cellular response to interferon-alpha IMP 15231837
GO:0044528 regulation of mitochondrial mRNA stability IMP 21666256
genes like me logo Genes that share ontologies with PDE12: view

No data available for Pathways by source and SIGNOR curated interactions for PDE12 Gene

Drugs & Compounds for PDE12 Gene

No Compound Related Data Available

Transcripts for PDE12 Gene

mRNA/cDNA for PDE12 Gene

Unigene Clusters for PDE12 Gene

Phosphodiesterase 12:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for PDE12
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for PDE12 Gene

No ASD Table

Relevant External Links for PDE12 Gene

GeneLoc Exon Structure for
PDE12
ECgene alternative splicing isoforms for
PDE12

Expression for PDE12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PDE12 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PDE12 Gene



Protein tissue co-expression partners for PDE12 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PDE12 Gene:

PDE12

SOURCE GeneReport for Unigene cluster for PDE12 Gene:

Hs.572993

mRNA Expression by UniProt/SwissProt for PDE12 Gene:

Q6L8Q7-PDE12_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for PDE12 Gene

  • Lymph node(4.2)
  • Nervous system(3.4)
genes like me logo Genes that share expression patterns with PDE12: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PDE12 Gene

Orthologs for PDE12 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PDE12 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PDE12 33 34
  • 99.34 (n)
cow
(Bos Taurus)
Mammalia PDE12 33 34
  • 88.45 (n)
dog
(Canis familiaris)
Mammalia PDE12 33 34
  • 88.12 (n)
mouse
(Mus musculus)
Mammalia Pde12 33 16 34
  • 86.57 (n)
rat
(Rattus norvegicus)
Mammalia Pde12 33
  • 86.47 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PDE12 34
  • 78 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PDE12 34
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDE12 34
  • 71 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PDE12 34
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.2468 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.25679 33
zebrafish
(Danio rerio)
Actinopterygii pde12 33 34
  • 57.74 (n)
-- 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009079 33
  • 48.29 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG31759 33 34
  • 45.26 (n)
worm
(Caenorhabditis elegans)
Secernentea pde-12 34
  • 20 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CCR4 34
  • 13 (a)
OneToMany
NGL3 36
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9594 34
  • 40 (a)
OneToOne
Species where no ortholog for PDE12 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • wheat (Triticum aestivum)

Evolution for PDE12 Gene

ENSEMBL:
Gene Tree for PDE12 (if available)
TreeFam:
Gene Tree for PDE12 (if available)

Paralogs for PDE12 Gene

Paralogs for PDE12 Gene

genes like me logo Genes that share paralogs with PDE12: view

Variants for PDE12 Gene

Sequence variations from dbSNP and Humsavar for PDE12 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs1000012709 -- 57,590,290(+) GACCA(A/G)CCTGG intron-variant
rs1000042127 -- 57,578,636(+) CACCA(C/T)ACCTA intron-variant
rs1000101374 -- 57,572,123(+) ATACT(A/G)TTTAA intron-variant, utr-variant-3-prime
rs1000132113 -- 57,591,927(+) CTAAT(G/T)GGTAT intron-variant
rs1000153260 -- 57,609,311(+) TAACA(C/T)CACAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PDE12 Gene

Variant ID Type Subtype PubMed ID
nsv1008684 CNV gain 25217958
nsv590368 CNV gain 21841781

Variation tolerance for PDE12 Gene

Residual Variation Intolerance Score: 26.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.31; 88.29% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PDE12 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDE12

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDE12 Gene

Disorders for PDE12 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PDE12 Gene - From: DISEASES

Disorder Aliases PubMed IDs
microphthalmia with limb anomalies
  • anophthalmia-syndactyly syndrome
- elite association - COSMIC cancer census association via MalaCards
Search PDE12 in MalaCards View complete list of genes associated with diseases

Relevant External Links for PDE12

Genetic Association Database (GAD)
PDE12
Human Genome Epidemiology (HuGE) Navigator
PDE12
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PDE12
genes like me logo Genes that share disorders with PDE12: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PDE12 Gene

Publications for PDE12 Gene

  1. Identification of 2'-phosphodiesterase, which plays a role in the 2-5A system regulated by interferon. (PMID: 15231837) Kubota K … Iijima Y (The Journal of biological chemistry 2004) 2 3 4 60
  2. Characterization of human phosphodiesterase 12 and identification of a novel 2'-5' oligoadenylate nuclease - The ectonucleotide pyrophosphatase/phosphodiesterase 1. (PMID: 22285541) Poulsen JB … Martensen PM (Biochimie 2012) 3 4 60
  3. PDE12 removes mitochondrial RNA poly(A) tails and controls translation in human mitochondria. (PMID: 21666256) Rorbach J … Minczuk M (Nucleic acids research 2011) 3 4 60
  4. Human 2'-phosphodiesterase localizes to the mitochondrial matrix with a putative function in mitochondrial RNA turnover. (PMID: 21245038) Poulsen JB … Martensen PM (Nucleic acids research 2011) 3 4 60
  5. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 45 60

Products for PDE12 Gene

Sources for PDE12 Gene

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