CTU2 Gene (Protein Coding)

Cytosolic Thiouridylase Subunit 2

GC16P088706
GIFtS:
33
This gene encodes a protein which is involved in the post-transcriptional modification of transfer RNAs (tRNAs). The encoded protein plays a role in thiolation of uridine residue present at the wobble position in a subset of tRNAs, resulting in enhanced codon reading accuracy. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by... See more...

Aliases for CTU2 Gene

Aliases for CTU2 Gene

  • Cytosolic Thiouridylase Subunit 2 2 3 4 5
  • Cytoplasmic TRNA 2-Thiolation Protein 2 2 3 4
  • NCS2 2 3 4
  • C16orf84 3 4
  • Cytosolic Thiouridylase Subunit 2 Homolog (S. Pombe) 2
  • Cytosolic Thiouridylase Subunit 2 Homolog 3
  • Chromosome 16 Open Reading Frame 84 2
  • UPF0432 3
  • MFRG 3
  • CTU2 5

External Ids for CTU2 Gene

Previous HGNC Symbols for CTU2 Gene

  • C16orf84

Previous GeneCards Identifiers for CTU2 Gene

  • GC16P087301
  • GC16P088773
  • GC16P074467

Summaries for CTU2 Gene

Entrez Gene Summary for CTU2 Gene

  • This gene encodes a protein which is involved in the post-transcriptional modification of transfer RNAs (tRNAs). The encoded protein plays a role in thiolation of uridine residue present at the wobble position in a subset of tRNAs, resulting in enhanced codon reading accuracy. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]

GeneCards Summary for CTU2 Gene

CTU2 (Cytosolic Thiouridylase Subunit 2) is a Protein Coding gene. Diseases associated with CTU2 include Microcephaly, Facial Dysmorphism, Renal Agenesis, And Ambiguous Genitalia Syndrome and Peroneal Neuropathy. Among its related pathways are Gene Expression and tRNA processing. Gene Ontology (GO) annotations related to this gene include tRNA binding and nucleotidyltransferase activity.

UniProtKB/Swiss-Prot Summary for CTU2 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). May act by forming a heterodimer with CTU1/ATPBD3 that ligates sulfur from thiocarboxylated URM1 onto the uridine of tRNAs at wobble position.

Gene Wiki entry for CTU2 Gene

Additional gene information for CTU2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CTU2 Gene

Genomics for CTU2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for CTU2 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CTU2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CTU2

Genomic Locations for CTU2 Gene

Genomic Locations for CTU2 Gene
chr16:88,706,481-88,715,396
(GRCh38/hg38)
Size:
8,916 bases
Orientation:
Plus strand
chr16:88,772,871-88,781,794
(GRCh37/hg19)
Size:
8,924 bases
Orientation:
Plus strand

Genomic View for CTU2 Gene

Genes around CTU2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CTU2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CTU2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for CTU2 Gene

Proteins for CTU2 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for CTU2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q2VPK5-CTU2_HUMAN
    Recommended name:
    Cytoplasmic tRNA 2-thiolation protein 2
    Protein Accession:
    Q2VPK5
    Secondary Accessions:
    • B2RXK0
    • Q0P511
    • Q66K78
    • Q6P4C8
    • Q86SV4

    Protein attributes for CTU2 Gene

    Size:
    515 amino acids
    Molecular mass:
    56107 Da
    Quaternary structure:
    • Component of a complex at least composed of URM1, CTU2/NCS2 and CTU1/ATPBD3.
    Miscellaneous:
    • [Isoform 3]: Incomplete sequence.

    Alternative splice isoforms for CTU2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CTU2 Gene

Protein Expression for CTU2 Gene

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

Post-translational modifications for CTU2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CTU2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CTU2 Gene

Domains & Families for CTU2 Gene

Gene Families for CTU2 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for CTU2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CTU2 Gene

GenScript: Design optimal peptide antigens:
  • Cytoplasmic tRNA 2-thiolation protein 2 (CTU2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q2VPK5

UniProtKB/Swiss-Prot:

CTU2_HUMAN :
  • Belongs to the CTU2/NCS2 family.
Family:
  • Belongs to the CTU2/NCS2 family.
genes like me logo Genes that share domains with CTU2: view

Function for CTU2 Gene

Products:

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

Molecular function for CTU2 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). May act by forming a heterodimer with CTU1/ATPBD3 that ligates sulfur from thiocarboxylated URM1 onto the uridine of tRNAs at wobble position.

Phenotypes From GWAS Catalog for CTU2 Gene

Gene Ontology (GO) - Molecular Function for CTU2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000049 tRNA binding IEA --
GO:0005515 protein binding IPI 19017811
GO:0016779 nucleotidyltransferase activity IEA --
GO:0016783 sulfurtransferase activity IBA 21873635
genes like me logo Genes that share ontologies with CTU2: view
genes like me logo Genes that share phenotypes with CTU2: view

Human Phenotype Ontology for CTU2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CTU2 Gene

MGI Knock Outs for CTU2:
  • Ctu2 Ctu2<tm1(KOMP)Wtsi>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CTU2

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for CTU2 Gene

Localization for CTU2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CTU2 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 CTU2 gene
Compartment Confidence
cytosol 4
mitochondrion 3
nucleus 3
plasma membrane 1
extracellular 1
cytoskeleton 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CTU2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0032991 protein-containing complex IDA 19017811
genes like me logo Genes that share ontologies with CTU2: view

Pathways & Interactions for CTU2 Gene

genes like me logo Genes that share pathways with CTU2: view

Pathways by source for CTU2 Gene

1 KEGG pathway for CTU2 Gene

UniProtKB/Swiss-Prot Q2VPK5-CTU2_HUMAN

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

Gene Ontology (GO) - Biological Process for CTU2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002098 tRNA wobble uridine modification IEA,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 CTU2: view

No data available for SIGNOR curated interactions for CTU2 Gene

Drugs & Compounds for CTU2 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for CTU2 Gene

Products:

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

mRNA/cDNA for CTU2 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CTU2

Alternative Splicing Database (ASD) splice patterns (SP) for CTU2 Gene

No ASD Table

Relevant External Links for CTU2 Gene

GeneLoc Exon Structure for
CTU2

Expression for CTU2 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CTU2 Gene

mRNA expression in normal human tissues for CTU2 Gene
mRNA expression by GTEx for CTU2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CTU2 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (18.9) and Blymphocyte (15.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CTU2 Gene



Protein tissue co-expression partners for CTU2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CTU2

SOURCE GeneReport for Unigene cluster for CTU2 Gene:

Hs.592074

Evidence on tissue expression from TISSUES for CTU2 Gene

  • Nervous system(4.4)
  • Skin(4.4)
genes like me logo Genes that share expression patterns with CTU2: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CTU2 Gene

Orthologs for CTU2 Gene

This gene was present in the common ancestor of animals.

Orthologs for CTU2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia CTU2 30 31
  • 99.03 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia CTU2 30 31
  • 81.47 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia CTU2 30 31
  • 80.48 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Ctu2 30 17 31
  • 79.07 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Ctu2 30
  • 78.44 (n)
Oppossum
(Monodelphis domestica)
 Mammalia CTU2 31
  • 65 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia CTU2 31
  • 59 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves CTU2 30 31
  • 63.85 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia CTU2 31
  • 53 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia ctu2 30
  • 56.53 (n)
Zebrafish
(Danio rerio)
 Actinopterygii ctu2 30 31
  • 58.18 (n)
 OneToOne
wufe06e11 30
Fruit Fly
(Drosophila melanogaster)
 Insecta CG10189 30 31
  • 46.23 (n)
 OneToOne
African malaria mosquito
(Anopheles gambiae)
 Insecta CTU2_ANOGA 30
  • 46.11 (n)
Sea Squirt
(Ciona savignyi)
 Ascidiacea CSA.3713 31
  • 38 (a)
 OneToMany
-- 31
  • 27 (a)
 OneToMany
Species where no ortholog for CTU2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • 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 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)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for CTU2 Gene

ENSEMBL:
Gene Tree for CTU2 (if available)
TreeFam:
Gene Tree for CTU2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CTU2: view image

Paralogs for CTU2 Gene

No data available for Paralogs for CTU2 Gene

Variants for CTU2 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CTU2 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
635409 Pathogenic: MICROCEPHALY, FACIAL DYSMORPHISM, RENAL AGENESIS, AND AMBIGUOUS GENITALIA SYNDROME 88,714,590(+) G/GT FRAMESHIFT_VARIANT
635410 Pathogenic: MICROCEPHALY, FACIAL DYSMORPHISM, RENAL AGENESIS, AND AMBIGUOUS GENITALIA SYNDROME 88,709,982(+) T/C MISSENSE_VARIANT,INTRON_VARIANT
635411 Pathogenic: MICROCEPHALY, FACIAL DYSMORPHISM, RENAL AGENESIS, AND AMBIGUOUS GENITALIA SYNDROME 88,715,213(+) CTGAT/C FRAMESHIFT_VARIANT
637954 Pathogenic: MICROCEPHALY, FACIAL DYSMORPHISM, RENAL AGENESIS, AND AMBIGUOUS GENITALIA SYNDROME 88,710,287(+) G/A INTRON_VARIANT
713607 Benign: not provided 88,714,864(+) G/A MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for CTU2 Gene

Structural Variations from Database of Genomic Variants (DGV) for CTU2 Gene

Variant ID Type Subtype PubMed ID
dgv3064n100 CNV gain 25217958
dgv3065n100 CNV gain 25217958
esv1056304 CNV insertion 17803354
esv2715025 CNV deletion 23290073
esv2715026 CNV deletion 23290073
esv3553875 CNV deletion 23714750
nsv1061256 CNV gain 25217958
nsv1063024 CNV gain 25217958
nsv1065973 CNV loss 25217958
nsv1119453 CNV insertion 24896259
nsv1160442 CNV deletion 26073780
nsv1927 CNV insertion 18451855
nsv471113 CNV loss 18288195
nsv471114 CNV gain 18288195
nsv482951 CNV loss 15286789
nsv499595 CNV gain 21111241
nsv517643 CNV loss 19592680
nsv833327 CNV loss 17160897
nsv952070 CNV deletion 24416366

Variation tolerance for CTU2 Gene

Residual Variation Intolerance Score: 97% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 17.35; 98.16% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CTU2 Gene

Human Gene Mutation Database (HGMD)
CTU2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CTU2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CTU2 Gene

Disorders for CTU2 Gene

MalaCards: The human disease database

(14) MalaCards diseases for CTU2 Gene - From: OMIM, ClinVar, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search CTU2 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CTU2_HUMAN
  • Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome (MFRG) [MIM:618142]: An autosomal dominant syndrome characterized by primary microcephaly, ambiguous male genitalia, dysmorphic facies, polydactyly, and unilateral renal agenesis. Variable brain, cardiac, and skeletal anomalies are present, including corpus callosum agenesis or dysgenesis, lissencephaly, atrial and ventricular septal defects, patent ductus arteriosus, hypoplastic right ventricle, and joint contractures. {ECO:0000269 PubMed:26633546}. Note=The disease may be caused by mutations affecting the gene represented in this entry. A homozygous synonymous variant at codon 247 has been identified in 3 consanguineous families. This variant impairs normal splicing, causing a frameshift resulting in a premature termination codon. {ECO:0000269 PubMed:26633546}.

Additional Disease Information for CTU2

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with CTU2: view

No data available for Genatlas for CTU2 Gene

Publications for CTU2 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. PLEKHA4/kramer Attenuates Dishevelled Ubiquitination to Modulate Wnt and Planar Cell Polarity Signaling. (PMID: 31091453) Shami Shah A … Baskin JM (Cell reports 2019) 3
  3. Biallelic variants in CTU2 cause DREAM-PL syndrome and impair thiolation of tRNA wobble U34. (PMID: 31301155) Shaheen R … Alkuraya FS (Human mutation 2019) 3
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3
  5. Accelerating matchmaking of novel dysmorphology syndromes through clinical and genomic characterization of a large cohort. (PMID: 26633546) Shaheen R … Alkuraya FS (Genetics in medicine : official journal of the American College of Medical Genetics 2016) 4

ExternalLinks

View latest publications for CTU2 gene in Mastermind

Products for CTU2 Gene

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