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ADAT3 Gene

protein-coding   GIFtS: 41
GCID: GC19P001906

Adenosine Deaminase, TRNA-Specific 3

(Previous names: adenosine deaminase, tRNA-specific 3, TAD3 homolog (S. cerevisiae))
  See ADAT3-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Adenosine Deaminase, TRNA-Specific 31 2     MST1212
TAD32 3 5     MSTP1212
TRNA-Specific Adenosine-34 Deaminase Subunit ADAT32 3     S863-52
MRT362 5     Adenosine Deaminase, TRNA-Specific 3, TAD3 Homolog2
Adenosine Deaminase, TRNA-Specific 3, TAD3 Homolog (S. Cerevisiae)1     Probable Inactive TRNA-Specific Adenosine Deaminase-Like Protein 32
TRNA-Specific Adenosine Deaminase 3 Homolog (S. Cerevisiae)1     TRNA-Specific Adenosine Deaminase 3 Homolog2
FWP0052     TRNA-Specific Adenosine Deaminase-Like Protein 32

External Ids:    HGNC: 251511   Entrez Gene: 1131792   Ensembl: ENSG000002136387   OMIM: 6153025   UniProtKB: Q96EY93   

Export aliases for ADAT3 gene to outside databases

Previous GC identifers: GC19P001865 GC19P001677


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for ADAT3 Gene:
ADAT3 (adenosine deaminase, tRNA-specific 3) is a protein-coding gene. Diseases associated with ADAT3 include mental retardation, autosomal recessive 36, and breast and colorectal cancer. GO annotations related to this gene include hydrolase activity.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the ADAT3 gene promoter:
         Max1   Pax-5   Tal-1   Olf-1   E47   Max   ZID   c-Myc   ATF   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for ADAT3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ADAT3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19p13.3   Ensembl cytogenetic band:  19p13.3   HGNC cytogenetic band: 19p13.3

ADAT3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ADAT3 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P001906:  view genomic region     (about GC identifiers)

Start:
1,905,377 bp from pter      End:
1,913,446 bp from pter
Size:
8,070 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: ADAT3_HUMAN, Q96EY9 (See protein sequence)
Recommended Name: Probable inactive tRNA-specific adenosine deaminase-like protein 3  
Size: 351 amino acids; 38071 Da
Cofactor: Zinc (By similarity)
Caution: Val-225 is present instead of the conserved Glu which is an active site in the cytidine and
deoxycytidylate deaminase family of enzymes. It is suggested that this protein may act as a regulatory subunit

Explore the universe of human proteins at neXtProt for ADAT3: NX_Q96EY9

Explore proteomics data for ADAT3 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See ADAT3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_612431.2  
    ENSEMBL proteins: 
     ENSP00000332448   ENSP00000404502   ENSP00000473571  

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    antibodies-online peptides for ADAT3

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR002125 CMP_dCMP_Zn-bd
     IPR016193 Cytidine_deaminase-like

    Graphical View of Domain Structure for InterPro Entry Q96EY9

    ProtoNet protein and cluster: Q96EY9

    1 Blocks protein domain: IPB002125 Cytidine/deoxycytidylate deaminase

    UniProtKB/Swiss-Prot: ADAT3_HUMAN, Q96EY9
    Similarity: Belongs to the cytidine and deoxycytidylate deaminase family. ADAT3 subfamily


    Find genes that share domains with ADAT3           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003824catalytic activity ----
    GO:0008270zinc ion binding IEA--
    GO:0016787hydrolase activity IEA--
         
    Find genes that share ontologies with ADAT3           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for ADAT3:
     Increased gamma-H2AX phosphory  Wnt reporter downregulated 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for ADAT3

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    chloroplast2
    cytosol2
    extracellular2
    nucleus2

    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for ADAT3
    Interactions:

        Search GeneGlobe Interaction Network for ADAT3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 23)

    Selected Interacting proteins for ADAT3 (Q96EY93 ENSP000003324484) via UniProtKB, MINT, STRING, and/or I2D (see all 25)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    KAT2AQ928303, ENSP000002259164I2D: score=1 STRING: ENSP00000225916
    NDUFA9Q167953I2D: score=2 
    TMEM214Q6NUQ43I2D: score=2 
    NT5C1AENSP000002356284STRING: ENSP00000235628
    NT5C1BENSP000003529044STRING: ENSP00000352904
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008033tRNA processing IEA--

    Find genes that share ontologies with ADAT3           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for ADAT3



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for ADAT3 gene: 
    NM_138422.2  

    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000329478(uc002luh.3) ENST00000454697 ENST00000602400
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      QuantiTect SYBR Green Assays in human, mouse, rat ADAT3
      QuantiFast Probe-based Assays in human, mouse, rat ADAT3

    Selected AceView cDNA sequences (see all 362):

    BQ957785 BU541426 BX105110 BE782627 BQ070832 BM713797 BU845441 BP364510 
    BM044653 BM708430 BE781053 AL597181 CR607576 BM703621 BU626013 BI761802 
    CR610772 BI771011 CK823425 BU541753 BM832617 BX647235 BM694499 AA232686 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    ADAT3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    ADAT3 Expression
    About this image

    ADAT3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ADAT3 Protein Expression
        Custom PCR Arrays for ADAT3
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ADAT3

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for ADAT3 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Adat31 , 5 adenosine deaminase, tRNA-specific 3, TAD2 homolog more5
    adenosine deaminase, tRNA-specific 31
    79.79(n)1
    82.18(a)1
      10 (39.72 cM)5
    1001133981  NM_001100606.11  NP_001094076.11 
     806028805 
    lizard
    (Anolis carolinensis)
    Reptilia ADAT36
    adenosine deaminase, tRNA-specific 3
    54(a)
    1 ↔ 1
    GL343220.1(79800-80914)
    zebrafish
    (Danio rerio)
    Actinopterygii adat31 adenosine deaminase, tRNA-specific 3 55.34(n)
    55.45(a)
      368634  NM_001005300.2  NP_001005300.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG109271 CG10927 47.28(n)
    35.71(a)
      37135  NM_137501.2  NP_611345.1 
    worm
    (Caenorhabditis elegans)
    Secernentea Y47D3A.146
    Protein Y47D3A.14 (Y47D3A.14) mRNA, complete cds
    28(a)
    1 ↔ 1
    III(11235577-11236870) WBGene00012927
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes TAD3(YLR316C)4 Subunit of tRNA-specific adenosine-34 deaminase, forms more   --   12(766358-765266) 851027  NP_013420.2 


    ENSEMBL Gene Tree for ADAT3 (if available)
    TreeFam Gene Tree for ADAT3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    2 SNPs for ADAT3    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0697784
    Mental retardation, autosomal recessive 36 (MRT36)4--see VAR_0697782 V M mis40--------
    VAR_0358044
    A breast cancer sample4--see VAR_0358042 R C mis40--------

    HapMap Linkage Disequilibrium report for ADAT3 (1905377 - 1913446 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for ADAT3 (see all 18):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2717853CNV Deletion23290073
    nsv470107CNV Loss18288195
    dgv3614n71CNV Loss21882294
    nsv910499CNV Loss21882294
    nsv910588CNV Loss21882294
    dgv3609n71CNV Loss21882294
    dgv3613n71CNV Loss21882294
    dgv3617n71CNV Loss21882294
    dgv3618n71CNV Loss21882294
    dgv3612n71CNV Loss21882294

    Human Gene Mutation Database (HGMD): ADAT3
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing ADAT3
    DNA2.0 Custom Variant and Variant Library Synthesis for ADAT3

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 615302   
    OMIM disorders: 615286  
    UniProtKB/Swiss-Prot: ADAT3_HUMAN, Q96EY9
  • Mental retardation, autosomal recessive 36 (MRT36) [MIM:615286]: A disorder characterized by
    significantly below average general intellectual functioning associated with impairments in adaptive behavior and
    manifested during the developmental period. MRT36 is often associated with esotropia and failure to thrive. Other
    more variable features included microcephaly, hypotonia, and mild brain abnormalities on MRI, such as dilated
    ventricles or delayed myelination. Note=The disease is caused by mutations affecting the gene represented in this
    entry

  • 2 diseases for ADAT3:    
    About MalaCards
    mental retardation, autosomal recessive 36    breast and colorectal cancer

    1 disease from the University of Copenhagen DISEASES database for ADAT3:
    Atopic dermatitis

    Find genes that share disorders with ADAT3           About GenesLikeMe


    Export disorders for ADAT3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for ADAT3 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with ADAT3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Mutation in ADAT3, encoding adenosine deaminase acting on transfer RNA, causes intellectual disability and strabismus. (PubMed id 23620220)1, 2 Alazami A.M....Alkuraya F.S. (J. Med. Genet. 2013)
    2. RNA editing by adenosine deaminases generates RNA and protein diversity. (PubMed id 12457566)1, 3 Schaub M. and Keller W. (Biochimie 2002)
    3. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    4. Toward an understanding of the protein interaction network of the human liver. (PubMed id 21988832)1 Wang J....Yang X. (Mol. Syst. Biol. 2011)
    5. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    6. A Myc network accounts for similarities between embryonic stem and cancer cell transcription programs. (PubMed id 20946988)1 Kim J....Orkin S.H. (Cell 2010)
    7. Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach. (PubMed id 19413330)2 Gauci S....Mohammed S. (Anal. Chem. 2009)
    8. The consensus coding sequences of human breast and colorectal cancers. (PubMed id 16959974)2 Sjoeblom T.... Velculescu V.E. (Science 2006)
    9. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 113179 HGNC: 25151 AceView: C19orf24 Ensembl:ENSG00000213638 euGenes: HUgn113179
    ECgene: ADAT3 H-InvDB: ADAT3

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for ADAT3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for ADAT3 gene:
    Search GeneIP for patents involving ADAT3

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from genOway)
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