Aliases for CTU1 Gene

Aliases for CTU1 Gene

  • Cytosolic Thiouridylase Subunit 1 2 3 5
  • NCS6 2 3 4
  • Cytoplasmic TRNA 2-Thiolation Protein 1 3 4
  • ATP-Binding Domain-Containing Protein 3 3 4
  • Cytoplasmic TRNA Adenylyltransferase 1 3 4
  • Cancer-Associated Gene Protein 3 4
  • ATP Binding Domain 3 2 3
  • ATPBD3 3 4
  • Cytosolic Thiouridylase Subunit 1 Homolog (S. Pombe) 2
  • Cytosolic Thiouridylase Subunit 1 Homolog 3
  • Cancer-Associated Protein 3
  • EC 2.7.7.- 4
  • MGC17332 2
  • EC 2.7.7 51
  • CTU1 5

External Ids for CTU1 Gene

Previous HGNC Symbols for CTU1 Gene

  • ATPBD3

Previous GeneCards Identifiers for CTU1 Gene

  • GC19M056295
  • GC19M051601
  • GC19M047934

Summaries for CTU1 Gene

GeneCards Summary for CTU1 Gene

CTU1 (Cytosolic Thiouridylase Subunit 1) is a Protein Coding gene. Diseases associated with CTU1 include Spinal Cord Ependymoma and Myxopapillary Ependymoma. Among its related pathways are tRNA processing and Sulfur relay system. Gene Ontology (GO) annotations related to this gene include tRNA binding and nucleotidyltransferase activity.

UniProtKB/Swiss-Prot Summary for CTU1 Gene

  • Plays a central role in 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of tRNA(Lys), tRNA(Glu) and tRNA(Gln). Directly binds tRNAs and probably acts by catalyzing adenylation of tRNAs, an intermediate required for 2-thiolation. It is unclear whether it acts as a sulfurtransferase that transfers sulfur from thiocarboxylated URM1 onto the uridine of tRNAs at wobble position.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CTU1 Gene

Genomics for CTU1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CTU1 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
GH19J051106 Promoter/Enhancer 1.7 Ensembl ENCODE CraniofacialAtlas 280.6 +0.2 244 2.5 CHD2 TBP MXD4 FEZF1 SIX5 NR2C1 DEK MNT IKZF1 BRCA1 CTU1 HSALNG0127178 ZNF841 ZNF350 POLD1 ZNF175 SHANK1 ZNF613 SYT3 IGLON5
GH19J051109 Promoter 0.6 Ensembl 250.7 -1.8 -1792 1.2 ZBTB40 SCRT1 ZMYM3 ATF3 ZBTB33 CTU1 LINC01869 SNORD88C C19orf48 SIGLEC9 HSALNG0127179
GH19J051360 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 31.6 -260.2 -260152 15.8 ZSCAN16 CHD2 TBP ZBTB10 SP1 MXD4 CEBPA NR2C1 FOXA1 MNT ETFB CLDND2 ENSG00000269403 HSALNG0127209 NKG7 NONHSAG026361.2 ZNF841 ZNF175 ZNF616 ZNF577
GH19J050657 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 30.7 +449.5 449505 3 ZSCAN16 TBP ZBTB10 SP1 MNT SMAD5 ETS1 IRF2 MBD2 BHLHE40 SYT3 lnc-SHANK1-3 POLD1 NUP62 PTOV1-AS2 ZNF175 IRF3 PNKP CTU1 CPT1C
GH19J050375 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 26.9 +731.6 731607 2.1 CHD2 TBP ZBTB10 SP1 CEBPA SIX5 NR2C1 MNT DEK IKZF1 HSALNG0127093 NR1H2 NAPSB PRR12 PTOV1-AS2 NUP62 CTU1 PIH1D1 POLD1 ENSG00000268047
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CTU1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CTU1

Genomic Locations for CTU1 Gene

Latest Assembly
chr19:51,097,606-51,108,409
(GRCh38/hg38)
Size:
10,804 bases
Orientation:
Minus strand

Previous Assembly
chr19:51,600,863-51,611,666
(GRCh37/hg19 by Entrez Gene)
Size:
10,804 bases
Orientation:
Minus strand

chr19:51,600,863-51,611,627
(GRCh37/hg19 by Ensembl)
Size:
10,765 bases
Orientation:
Minus strand

Genomic View for CTU1 Gene

Genes around CTU1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CTU1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CTU1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CTU1 Gene

Proteins for CTU1 Gene

  • Protein details for CTU1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7Z7A3-CTU1_HUMAN
    Recommended name:
    Cytoplasmic tRNA 2-thiolation protein 1
    Protein Accession:
    Q7Z7A3
    Secondary Accessions:
    • A8K558
    • Q96GZ7

    Protein attributes for CTU1 Gene

    Size:
    348 amino acids
    Molecular mass:
    36450 Da
    Quaternary structure:
    • Component of a complex at least composed of URM1, CTU2/NCS2 and CTU1/ATPBD3. May form a heterodimer with CTU2/NCS2.

neXtProt entry for CTU1 Gene

Selected DME Specific Peptides for CTU1 Gene

Q7Z7A3:
  • TGHNADD
  • AETVLMN
  • ASGGKDSTVLAH
  • GASGGKDSTVLA
  • SGQALCG
  • DLFGGWTMDAVARSTAGSGRSR
  • CFCAAFEAEVL
  • LEAARPSA

Post-translational modifications for CTU1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CTU1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for CTU1 Gene

Gene Families for CTU1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for CTU1 Gene

InterPro:
Blocks:
  • Protein of unknown function UPF0021
  • PP-loop
ProtoNet:

Suggested Antigen Peptide Sequences for CTU1 Gene

GenScript: Design optimal peptide antigens:
  • Cytoplasmic tRNA adenylyltransferase 1 (CTU1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q7Z7A3

UniProtKB/Swiss-Prot:

CTU1_HUMAN :
  • Belongs to the TtcA family. CTU1/NCS6/ATPBD3 subfamily.
Family:
  • Belongs to the TtcA family. CTU1/NCS6/ATPBD3 subfamily.
genes like me logo Genes that share domains with CTU1: view

Function for CTU1 Gene

Molecular function for CTU1 Gene

UniProtKB/Swiss-Prot Function:
Plays a central role in 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of tRNA(Lys), tRNA(Glu) and tRNA(Gln). Directly binds tRNAs and probably acts by catalyzing adenylation of tRNAs, an intermediate required for 2-thiolation. It is unclear whether it acts as a sulfurtransferase that transfers sulfur from thiocarboxylated URM1 onto the uridine of tRNAs at wobble position.

Enzyme Numbers (IUBMB) for CTU1 Gene

Phenotypes From GWAS Catalog for CTU1 Gene

Gene Ontology (GO) - Molecular Function for CTU1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000049 tRNA binding IBA 21873635
GO:0003723 RNA binding IEA --
GO:0005515 protein binding IPI 19017811
GO:0016740 transferase activity IEA --
GO:0016779 nucleotidyltransferase activity IEA --
genes like me logo Genes that share ontologies with CTU1: view
genes like me logo Genes that share phenotypes with CTU1: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CTU1

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CTU1 Gene

Localization for CTU1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CTU1 Gene

Cytoplasm.

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 CTU1 gene
Compartment Confidence
cytosol 4
mitochondrion 3
nucleus 2
extracellular 1
cytoskeleton 1
peroxisome 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for CTU1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002144 cytosolic tRNA wobble base thiouridylase complex IBA 21873635
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with CTU1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CTU1 Gene

Pathways & Interactions for CTU1 Gene

genes like me logo Genes that share pathways with CTU1: view

Pathways by source for CTU1 Gene

1 KEGG pathway for CTU1 Gene

UniProtKB/Swiss-Prot Q7Z7A3-CTU1_HUMAN

  • Pathway: tRNA modification; 5-methoxycarbonylmethyl-2-thiouridine-tRNA biosynthesis.

Gene Ontology (GO) - Biological Process for CTU1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002098 tRNA wobble uridine modification NAS 19017811
GO:0002143 tRNA wobble position uridine thiolation IBA 21873635
GO:0006400 tRNA modification TAS --
GO:0008033 tRNA processing IEA --
GO:0032447 protein urmylation IEA --
genes like me logo Genes that share ontologies with CTU1: view

No data available for SIGNOR curated interactions for CTU1 Gene

Drugs & Compounds for CTU1 Gene

No Compound Related Data Available

Transcripts for CTU1 Gene

mRNA/cDNA for CTU1 Gene

1 REFSEQ mRNAs :
3 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CTU1

Alternative Splicing Database (ASD) splice patterns (SP) for CTU1 Gene

No ASD Table

Relevant External Links for CTU1 Gene

GeneLoc Exon Structure for
CTU1

Expression for CTU1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CTU1 Gene

Protein differential expression in normal tissues from HIPED for CTU1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (28.9), Heart (14.0), and Pancreas (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CTU1 Gene



Protein tissue co-expression partners for CTU1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CTU1

SOURCE GeneReport for Unigene cluster for CTU1 Gene:

Hs.148425

Evidence on tissue expression from TISSUES for CTU1 Gene

  • Nervous system(4.4)
genes like me logo Genes that share expression patterns with CTU1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CTU1 Gene

Orthologs for CTU1 Gene

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

Orthologs for CTU1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CTU1 31
  • 99 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia -- 31
  • 94 (a)
OneToMany
LOC484342 30
  • 90.81 (n)
-- 31
  • 61 (a)
OneToMany
Cow
(Bos Taurus)
Mammalia CTU1 31
  • 93 (a)
OneToMany
-- 31
  • 93 (a)
OneToMany
LOC100297056 30
  • 91.55 (n)
Oppossum
(Monodelphis domestica)
Mammalia CTU1 31
  • 83 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Ctu1 30 17 31
  • 82.99 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ctu1 30
  • 81.85 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia CTU1 31
  • 73 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii ctu1 31
  • 51 (a)
OneToOne
zgc55395 30
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7038 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG8078 31
  • 48 (a)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea tut-1 31
  • 40 (a)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NCS6 31
  • 44 (a)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 47 (a)
OneToOne
Species where no ortholog for CTU1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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)
  • 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)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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)

Evolution for CTU1 Gene

ENSEMBL:
Gene Tree for CTU1 (if available)
TreeFam:
Gene Tree for CTU1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CTU1: view image

Paralogs for CTU1 Gene

Pseudogenes.org Pseudogenes for CTU1 Gene

genes like me logo Genes that share paralogs with CTU1: view

No data available for Paralogs for CTU1 Gene

Variants for CTU1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CTU1 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
rs17855403 - p.Ala107Val

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CTU1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for CTU1 Gene

Variant ID Type Subtype PubMed ID
esv34104 CNV loss 18971310
nsv1140251 OTHER inversion 24896259
nsv953606 CNV deletion 24416366

Variation tolerance for CTU1 Gene

Gene Damage Index Score: 7.92; 83.85% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CTU1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CTU1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CTU1 Gene

Disorders for CTU1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for CTU1 Gene - From: COP

Disorder Aliases PubMed IDs
spinal cord ependymoma
  • ependymal neoplasm of the spinal cord
myxopapillary ependymoma
  • ependymoma myxopapillary
neuropathy, hereditary sensory and autonomic, type iii
  • hsan3
sulfite oxidase deficiency, isolated
  • isod
- elite association - COSMIC cancer census association via MalaCards
Search CTU1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CTU1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with CTU1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CTU1 Gene

Publications for CTU1 Gene

  1. A functional proteomics approach links the ubiquitin-related modifier Urm1 to a tRNA modification pathway. (PMID: 19017811) Schlieker CD … Ploegh HL (Proceedings of the National Academy of Sciences of the United States of America 2008) 2 3 4
  2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 41
  3. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PMID: 16964243) Beausoleil SA … Gygi SP (Nature biotechnology 2006) 3 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. PLEKHA4/kramer Attenuates Dishevelled Ubiquitination to Modulate Wnt and Planar Cell Polarity Signaling. (PMID: 31091453) Shami Shah A … Baskin JM (Cell reports 2019) 3

Products for CTU1 Gene

Sources for CTU1 Gene