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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 61

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 Kabuki Syndrome 1 and Microphthalmia With Limb Anomalies. GO annotations related to this gene include poly(A)-specific ribonuclease activity. An important paralog of this gene is CNOT6.

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.

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
GH03G057594 1.4 ENCODE dbSUPER 11.3 +41.3 41320 6.0 CREB3L1 AGO1 DMAP1 YY1 ZNF143 ZNF263 SP3 NFYC MEF2D GLIS1 DENND6A ARF4 FAM208A DENND6A-AS1 PDE12 LOC101929159 APPL1 HESX1 FLNB DNAH12
GH03G057576 0.8 FANTOM5 dbSUPER 16.8 +20.2 20201 0.2 ZSCAN5C DENND6A PDE12 APPL1 LOC101929159 HESX1 SLMAP GC03P057599
GH03G057582 0.7 dbSUPER 11.7 +27.1 27121 1.6 CTCF RAD21 CTBP1 GATA3 ZFHX2 POLR2A SMC3 NFE2 EGR2 ZNF654 ARF4 PDE12 DENND6A-AS1 DENND6A LOC101929159 GC03P057599
GH03G057754 1.4 ENCODE dbSUPER 5.1 +200.4 200415 3.5 HDGF MLX ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF766 LOC101929159 DENND6A IL17RD PDE12 DNAH12 ARF4 ENSG00000272202 SLMAP PDHA1P1
GH03G057199 0.6 ENCODE 10.4 -356.1 -356060 0.8 TAL1 MAX ZNF384 CHD7 POLR2A BCL11A GLIS1 POU5F1 MLLT1 EZH2 APPL1 HESX1 IL17RD PDE12 ASB14 DNAH12 ARHGEF3 GC03P057200 GC03M057226
- 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 MLX CREB3L1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 TBX21 ZFP41

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, posLast=8484, and posLast=9797
  • Modification sites at PhosphoSitePlus

Other Protein References for PDE12 Gene

Domains & Families for PDE12 Gene

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

No data available for Gene Families for PDE12 Gene

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:0004527 exonuclease activity IEA --
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

No data available for 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 --
genes like me logo Genes that share ontologies with PDE12: view

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:0006397 mRNA processing IEA --
GO:0090305 nucleic acid phosphodiester bond hydrolysis IEA --
GO:0090503 RNA phosphodiester bond hydrolysis, exonucleolytic IEA --
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

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 34 35
  • 99.34 (n)
cow
(Bos Taurus)
Mammalia PDE12 34 35
  • 88.45 (n)
dog
(Canis familiaris)
Mammalia PDE12 34 35
  • 88.12 (n)
mouse
(Mus musculus)
Mammalia Pde12 34 16 35
  • 86.57 (n)
rat
(Rattus norvegicus)
Mammalia Pde12 34
  • 86.47 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PDE12 35
  • 78 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PDE12 35
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDE12 35
  • 71 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PDE12 35
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.2468 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.25679 34
zebrafish
(Danio rerio)
Actinopterygii pde12 34 35
  • 57.74 (n)
-- 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009079 34
  • 48.29 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG31759 34 35
  • 45.26 (n)
worm
(Caenorhabditis elegans)
Secernentea pde-12 35
  • 20 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CCR4 35
  • 13 (a)
OneToMany
NGL3 37
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9594 35
  • 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

(2) MalaCards diseases for PDE12 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
kabuki syndrome 1
  • kabuki syndrome
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. (J. Biol. Chem. 2004) 2 3 4 64
  2. PDE12 removes mitochondrial RNA poly(A) tails and controls translation in human mitochondria. (PMID: 21666256) Rorbach J. … Minczuk M. (Nucleic Acids Res. 2011) 3 4 64
  3. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson S.L. … O'Brien S.J. (PLoS ONE 2010) 3 46 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function. (PMID: 27499296) Floyd B.J. … Pagliarini D.J. (Mol. Cell 2016) 3 64

Products for PDE12 Gene

Sources for PDE12 Gene

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