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DTD1 Gene(Protein Coding)

D-Tyrosyl-TRNA Deacylase 1

GCID:
GC20P018587
GIFtS:
40
Genes Participants
UDN Logo

Aliases for DTD1 Gene

Aliases for DTD1 Gene

  • D-Tyrosyl-TRNA Deacylase 1 2 3 5
  • DNA-Unwinding Element-Binding Protein B 3 4
  • Histidyl-TRNA Synthase-Related 3 4
  • Gly-TRNA(Ala) Deacylase 3 4
  • C20orf88 3 4
  • HARS2 3 4
  • DUE-B 3 4
  • DUEB 3 4
  • DTD 3 4
  • D-Tyrosyl-TRNA Deacylase 1 Homolog (S. Cerevisiae) 2
  • Chromosome 20 Open Reading Frame 88 2
  • D-Tyrosyl-TRNA Deacylase 1 Homolog 3
  • D-Tyrosyl-TRNA(Tyr) Deacylase 1 3
  • D-Aminoacyl-TRNA Deacylase 1 3
  • Histidyl-TRNA Synthetase 2 3
  • EC 3.1.1.96 4
  • EC 3.1.1.- 4
  • Pqn-68 3

External Ids for DTD1 Gene

Previous HGNC Symbols for DTD1 Gene

  • C20orf88
  • HARS2

Previous GeneCards Identifiers for DTD1 Gene

  • GC20P018517
  • GC20P018530
  • GC20P018568

Summaries for DTD1 Gene

Entrez Gene Summary for DTD1 Gene

  • The protein encoded by this gene is similar in sequence to histidyl-tRNA synthetase, which hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr). The encoded protein binds the DNA unwinding element and plays a role in the initiation of DNA replication. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

GeneCards Summary for DTD1 Gene

DTD1 (D-Tyrosyl-TRNA Deacylase 1) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include hydrolase activity, acting on ester bonds and D-tyrosyl-tRNA(Tyr) deacylase activity. An important paralog of this gene is ENSG00000284776.

UniProtKB/Swiss-Prot for DTD1 Gene

  • Possible ATPase (PubMed:15653697) involved in DNA replication, may facilitate loading of CDC45 onto pre-replication complexes (PubMed:20065034).

  • An aminoacyl-tRNA editing enzyme that deacylates mischarged D-aminoacyl-tRNAs. Also deacylates mischarged glycyl-tRNA(Ala), protecting cells against glycine mischarging by AlaRS. Acts via tRNA-based rather than protein-based catalysis; rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo and helps enforce protein L-homochirality.

Additional gene information for DTD1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DTD1 Gene

Genomics for DTD1 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for DTD1 Gene

Promoters and enhancers for DTD1 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
GH20J018587 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 661.7 +0.4 380 1.9 HDGF PKNOX1 ARID4B SIN3A DMAP1 ZBTB7B YY1 ZNF207 ZNF143 KLF13 DTD1 LOC100270804 ZNF133 SMIM26 LOC100286962 SEC23B RN7SL638P ENSG00000284776
GH20J018593 Promoter 0.6 EPDnew 650.4 +5.9 5852 0.1 POLR2A RN7SL638P DTD1 RNU6ATAC34P ENSG00000284776
GH20J018627 Promoter 0.5 EPDnew 650.3 +40.0 40031 0.1 DTD1 PIR61674 DUXAP7 ENSG00000284776
GH20J018566 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 23.7 -20.3 -20333 2.1 HDGF PKNOX1 MLX ZFP64 ARID4B NEUROD1 SIN3A DMAP1 ZNF2 IRF4 SMIM26 ENSG00000284776 DTD1 SEC23B RBBP9 DZANK1 POLR3F
GH20J018465 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 7 -120.8 -120811 3 PKNOX1 CLOCK ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF213 DZANK1 POLR3F SNX5 GCNT1P1 DTD1 RNA5SP476
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around DTD1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the DTD1 gene promoter:
  • FOXL1
  • Pax-5
  • Cart-1
  • PPAR-alpha
  • SRY
  • TGIF
  • GATA-1
  • Gfi-1
  • RelA

Genomic Locations for DTD1 Gene

Genomic Locations for DTD1 Gene
chr20:18,587,893-18,766,644
(GRCh38/hg38)
Size:
178,752 bases
Orientation:
Plus strand
chr20:18,568,537-18,744,561
(GRCh37/hg19)
Size:
176,025 bases
Orientation:
Plus strand

Genomic View for DTD1 Gene

Genes around DTD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DTD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DTD1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for DTD1 Gene

Proteins for DTD1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for DTD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TEA8-DTD1_HUMAN
    Recommended name:
    D-aminoacyl-tRNA deacylase 1
    Protein Accession:
    Q8TEA8
    Secondary Accessions:
    • A8K5X5
    • D3DW37
    • Q496D1
    • Q5W184
    • Q8WXU8
    • Q9BW67
    • Q9H464
    • Q9H474

    Protein attributes for DTD1 Gene

    Size:
    209 amino acids
    Molecular mass:
    23424 Da
    Quaternary structure:
    • Homodimer (PubMed15653697). Interacts with CDC45 and TOPBP1 (PubMed:20065034).
    SequenceCaution:
    • Sequence=BAB85044.1; Type=Miscellaneous discrepancy; Note=Presence of Alu-repeat DNA.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for DTD1 Gene

neXtProt entry for DTD1 Gene

Protein Expression for DTD1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for DTD1 Gene

  • Preferentially phosphorylated in cells arrested early in S phase (PubMed:15653697). Phosphorylation in the C-terminus weakens the interaction with CDC45 (PubMed:20065034).
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for DTD1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for DTD1 Gene

Domains & Families for DTD1 Gene

Gene Families for DTD1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for DTD1 Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for DTD1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8TEA8

UniProtKB/Swiss-Prot:

DTD1_HUMAN :
  • A Gly-cisPro motif from one monomer fits into the active site of the other monomer to allow specific chiral rejection of L-amino acids.
  • Belongs to the DTD family.
Domain:
  • A Gly-cisPro motif from one monomer fits into the active site of the other monomer to allow specific chiral rejection of L-amino acids.
Family:
  • Belongs to the DTD family.
genes like me logo Genes that share domains with DTD1: view

Function for DTD1 Gene

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  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for DTD1 Gene

UniProtKB/Swiss-Prot Function:
Possible ATPase (PubMed:15653697) involved in DNA replication, may facilitate loading of CDC45 onto pre-replication complexes (PubMed:20065034).
UniProtKB/Swiss-Prot Function:
An aminoacyl-tRNA editing enzyme that deacylates mischarged D-aminoacyl-tRNAs. Also deacylates mischarged glycyl-tRNA(Ala), protecting cells against glycine mischarging by AlaRS. Acts via tRNA-based rather than protein-based catalysis; rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo and helps enforce protein L-homochirality.
UniProtKB/Swiss-Prot CatalyticActivity:
Glycyl-tRNA(Ala) + H(2)O = glycine + tRNA(Ala).
UniProtKB/Swiss-Prot CatalyticActivity:
A D-aminoacyl-tRNA + H(2)O = a D-amino acid + tRNA.

Enzyme Numbers (IUBMB) for DTD1 Gene

Gene Ontology (GO) - Molecular Function for DTD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000049 tRNA binding IEA --
GO:0002161 aminoacyl-tRNA editing activity IBA,IEA --
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding IEA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with DTD1: view
genes like me logo Genes that share phenotypes with DTD1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for DTD1

CRISPR Products

miRNA for DTD1 Gene

miRTarBase miRNAs that target DTD1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for DTD1

Clone Products

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for DTD1 Gene

Localization for DTD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DTD1 Gene

Nucleus. Cytoplasm. Note=Associated with chromatin at some replication origins containing functional DNA-unwinding elements (PubMed:20065034).

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 DTD1 gene
Compartment Confidence
nucleus 5
cytosol 5
mitochondrion 3
peroxisome 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (1)
  • Nucleoli (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for DTD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm IEA,IBA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with DTD1: view

Pathways & Interactions for DTD1 Gene

SuperPathways for DTD1 Gene

PathCards logo More details on SuperPathways for DTD1
No Data Available

Gene Ontology (GO) - Biological Process for DTD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006260 DNA replication IEA --
GO:0006399 tRNA metabolic process IBA --
GO:0106074 aminoacyl-tRNA metabolism involved in translational fidelity IEA --
genes like me logo Genes that share ontologies with DTD1: view

No data available for Pathways by source and SIGNOR curated interactions for DTD1 Gene

Drugs & Compounds for DTD1 Gene

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  1. Drug
No Compound Related Data Available

Transcripts for DTD1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for DTD1 Gene

(3) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(271) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for DTD1 Gene

D-tyrosyl-tRNA deacylase 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for DTD1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for DTD1 Gene

No ASD Table

Relevant External Links for DTD1 Gene

GeneLoc Exon Structure for
DTD1
ECgene alternative splicing isoforms for
DTD1

Expression for DTD1 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for DTD1 Gene

mRNA expression in normal human tissues for DTD1 Gene
mRNA expression by GTEx for DTD1 Gene

Protein differential expression in normal tissues from HIPED for DTD1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (8.6), Fetal Brain (6.6), and Frontal cortex (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for DTD1 Gene



Protein tissue co-expression partners for DTD1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of DTD1 Gene:

DTD1

SOURCE GeneReport for Unigene cluster for DTD1 Gene:

Hs.659442

mRNA Expression by UniProt/SwissProt for DTD1 Gene:

Q8TEA8-DTD1_HUMAN
Tissue specificity: Expressed in many adult and fetal tissues. Highest levels in testis, ovary, spleen and in adult and fetal brain.

Evidence on tissue expression from TISSUES for DTD1 Gene

  • Nervous system(4.7)
  • Blood(4.2)
  • Skin(4.2)
  • Liver(4.1)
genes like me logo Genes that share expression patterns with DTD1: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for DTD1 Gene

Orthologs for DTD1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for DTD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia DTD1 34 33
  • 99.68 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia DTD1 34 33
  • 91.07 (n)
 OneToOne
mouse
(Mus musculus)
 Mammalia Dtd1 16 34 33
  • 88.36 (n)
cow
(Bos Taurus)
 Mammalia DTD1 34 33
  • 88.04 (n)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia DTD1 34
  • 88 (a)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Dtd1 33
  • 87.63 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia DTD1 34
  • 80 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves DTD1 34 33
  • 79.77 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia DTD1 34
  • 86 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia dtd1 33
  • 74.76 (n)
Str.17396 33
African clawed frog
(Xenopus laevis)
 Amphibia Xl.4690 33
zebrafish
(Danio rerio)
 Actinopterygii dtd1 34 33
  • 71.52 (n)
 OneToOne
rainbow trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.9158 33
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP001371 33
  • 59.56 (n)
fruit fly
(Drosophila melanogaster)
 Insecta CG18643 34 33
  • 58.96 (n)
 OneToOne
worm
(Caenorhabditis elegans)
 Secernentea pqn-68 34 33
  • 54.65 (n)
 OneToOne
A. gosspyii yeast
(Ashbya gossypii)
 Saccharomycetes AGOS_ABL152W 33
  • 49.65 (n)
K. lactis yeast
(Kluyveromyces lactis)
 Saccharomycetes KLLA0D08690g 33
  • 48.55 (n)
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes DTD1 36 34 33
  • 46.94 (n)
thale cress
(Arabidopsis thaliana)
 eudicotyledons AT4G18460 33
  • 54.73 (n)
rice
(Oryza sativa)
 Liliopsida Os01g0242500 33
  • 58.5 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 67 (a)
 OneToOne
Cin.2652 33
bread mold
(Neurospora crassa)
 Ascomycetes NCU03854 33
  • 50.11 (n)
fission yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes SPAC8C9.05 33
  • 48.59 (n)
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.2652 33
Species where no ortholog for DTD1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for DTD1 Gene

ENSEMBL:
Gene Tree for DTD1 (if available)
TreeFam:
Gene Tree for DTD1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for DTD1: view image

Paralogs for DTD1 Gene

Paralogs for DTD1 Gene

genes like me logo Genes that share paralogs with DTD1: view

Variants for DTD1 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for DTD1 Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs1000014960 -- 18,628,389(+) C/T intron_variant
rs1000024230 -- 18,661,499(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000024954 -- 18,654,807(+) A/T genic_downstream_transcript_variant, intron_variant
rs1000078053 -- 18,722,191(+) C/G genic_downstream_transcript_variant, intron_variant
rs1000095428 -- 18,756,619(+) A/G genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for DTD1 Gene

Variant ID Type Subtype PubMed ID
nsv954259 CNV insertion 24416366
nsv473794 CNV novel sequence insertion 20440878
nsv178936 CNV deletion 16902084
nsv178568 CNV deletion 16902084
nsv1142306 CNV tandem duplication 24896259
nsv1123460 CNV deletion 24896259
nsv1078315 OTHER inversion 25765185
esv3645443 CNV gain 21293372
esv3645442 CNV loss 21293372
esv3556909 CNV deletion 23714750
esv2658051 CNV deletion 23128226
esv2468883 CNV insertion 19546169
esv1653693 CNV insertion 17803354
esv1522771 CNV deletion 17803354
esv1476050 CNV insertion 17803354
esv1401622 CNV insertion 17803354
dgv4283n100 CNV loss 25217958

Variation tolerance for DTD1 Gene

Residual Variation Intolerance Score: 51.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.41; 54.38% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for DTD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
DTD1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DTD1 Gene

Disorders for DTD1 Gene

Additional Disease Information for DTD1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for DTD1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for DTD1 Gene

Publications for DTD1 Gene

  1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  2. The DNA unwinding element binding protein DUE-B interacts with Cdc45 in preinitiation complex formation. (PMID: 20065034) Chowdhury A … Leffak M (Molecular and cellular biology 2010) 3 4 58
  3. Structure and function of the c-myc DNA-unwinding element-binding protein DUE-B. (PMID: 17264083) Kemp M … Nair SK (The Journal of biological chemistry 2007) 3 4 58
  4. The c-myc DNA-unwinding element-binding protein modulates the assembly of DNA replication complexes in vitro. (PMID: 15653697) Casper JM … Leffak M (The Journal of biological chemistry 2005) 3 4 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

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