Human Gene CTU1 (ENST00000421832.3_7) from GENCODE V47lift37
  Description: cytosolic thiouridylase subunit 1 (from RefSeq NM_145232.4)
Gencode Transcript: ENST00000421832.3_7
Gencode Gene: ENSG00000142544.7_9
Transcript (Including UTRs)
   Position: hg19 chr19:51,600,863-51,611,666 Size: 10,804 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr19:51,601,858-51,607,826 Size: 5,969 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:51,600,863-51,611,666)mRNA (may differ from genome)Protein (348 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CTU1_HUMAN
DESCRIPTION: RecName: Full=Cytoplasmic tRNA 2-thiolation protein 1; EC=2.7.7.-; AltName: Full=ATP-binding domain-containing protein 3; AltName: Full=Cancer-associated gene protein; AltName: Full=Cytoplasmic tRNA adenylyltransferase 1;
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.
PATHWAY: tRNA modification; 5-methoxycarbonylmethyl-2-thiouridine- tRNA biosynthesis.
SUBUNIT: Component of a complex at least composed of URM1, CTU2/NCS2 and CTU1/ATPBD3. May form a heterodimer with CTU2/NCS2.
SUBCELLULAR LOCATION: Cytoplasm.
SIMILARITY: Belongs to the TtcA family. CTU1/NCS6/ATPBD3 subfamily.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 4.83 RPKM in Ovary
Total median expression: 114.22 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -38.3084-0.456 Picture PostScript Text
3' UTR -420.00995-0.422 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR012089 - 2-thiocytidine_tRNA_synth_TtcA
IPR014729 - Rossmann-like_a/b/a_fold
IPR011063 - tRNA-lysidine/thiocyt_synth

Pfam Domains:
PF01171 - PP-loop family
PF16503 - Zinc-ribbon

SCOP Domains:
52402 - Adenine nucleotide alpha hydrolases-like

ModBase Predicted Comparative 3D Structure on Q7Z7A3
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologGenome Browser
Gene DetailsGene Details Gene Details Gene Details
Gene SorterGene Sorter Gene Sorter Gene Sorter
 RGDEnsembl  SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000049 tRNA binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0016740 transferase activity

Biological Process:
GO:0002098 tRNA wobble uridine modification
GO:0008033 tRNA processing
GO:0034227 tRNA thio-modification

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AK291173 - Homo sapiens cDNA FLJ75680 complete cds.
BC009037 - Homo sapiens ATP binding domain 3, mRNA (cDNA clone MGC:17332 IMAGE:4182164), complete cds.
JD078818 - Sequence 59842 from Patent EP1572962.
JD485115 - Sequence 466139 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
PWY-7888 - tRNA-uridine 2-thiolation (cytoplasmic)

Reactome (by CSHL, EBI, and GO)

Protein Q7Z7A3 (Reactome details) participates in the following event(s):

R-HSA-6782264 CTU1:CTU2:URM1 thiolates uridine-34 in tRNAs
R-HSA-6782315 tRNA modification in the nucleus and cytosol
R-HSA-72306 tRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: A8K558, ATPBD3 , CTU1 , CTU1_HUMAN, ENST00000421832.1, ENST00000421832.2, NCS6 , NM_145232, Q7Z7A3, Q96GZ7, uc319rfy.1, uc319rfy.2
UCSC ID: ENST00000421832.3_7
RefSeq Accession: NM_145232.4
Protein: Q7Z7A3 (aka CTU1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.