Human Gene CTU2 (uc002flm.3) Description and Page Index
  Description: Homo sapiens cytosolic thiouridylase subunit 2 homolog (S. pombe) (CTU2), transcript variant 1, mRNA.
RefSeq Summary (NM_001012759): 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].
Transcript (Including UTRs)
   Position: hg19 chr16:88,772,891-88,781,786 Size: 8,896 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr16:88,772,939-88,781,659 Size: 8,721 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:88,772,891-88,781,786)mRNA (may differ from genome)Protein (515 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: CTU2_HUMAN
DESCRIPTION: RecName: Full=Cytoplasmic tRNA 2-thiolation protein 2;
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.
PATHWAY: tRNA modification; 5-methoxycarbonylmethyl-2-thiouridine- tRNA biosynthesis.
SUBUNIT: Component of a complex at least composed of URM1, CTU2/NCS2 and CTU1/ATPBD3.
SUBCELLULAR LOCATION: Cytoplasm.
SIMILARITY: Belongs to the CTU2/NCS2 family.

-  MalaCards Disease Associations
  MalaCards Gene Search: CTU2
Diseases sorted by gene-association score: phobia, specific (11), exotropia (5)

-  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: 8.03 RPKM in Testis
Total median expression: 258.59 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -15.5048-0.323 Picture PostScript Text
3' UTR -39.50127-0.311 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
IPR014729 - Rossmann-like_a/b/a_fold
IPR019407 - Thiouridylase_cyt_su2

Pfam Domains:
PF10288 - Cytoplasmic tRNA 2-thiolation protein 2

SCOP Domains:
52402 - Adenine nucleotide alpha hydrolases-like

ModBase Predicted Comparative 3D Structure on Q2VPK5
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000049 tRNA binding
GO:0005515 protein binding
GO:0016783 sulfurtransferase activity

Biological Process:
GO:0002098 tRNA wobble uridine modification
GO:0002143 tRNA wobble position uridine thiolation
GO:0008033 tRNA processing
GO:0034227 tRNA thio-modification

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0032991 macromolecular complex


-  Descriptions from all associated GenBank mRNAs
  BC121805 - Homo sapiens chromosome 16 open reading frame 84, mRNA (cDNA clone MGC:148063 IMAGE:40107956), complete cds.
BC125269 - Homo sapiens chromosome 16 open reading frame 84, mRNA (cDNA clone MGC:148064 IMAGE:40107964), complete cds.
LF384489 - JP 2014500723-A/191992: Polycomb-Associated Non-Coding RNAs.
BC157881 - Homo sapiens chromosome 16 open reading frame 84, mRNA (cDNA clone MGC:189706 IMAGE:8862703), complete cds.
AK299521 - Homo sapiens cDNA FLJ59594 complete cds.
BC108659 - Homo sapiens chromosome 16 open reading frame 84, mRNA (cDNA clone MGC:131681 IMAGE:6167465), complete cds.
BC021056 - Homo sapiens chromosome 16 open reading frame 84, mRNA (cDNA clone IMAGE:2989282).
BC063512 - Homo sapiens chromosome 16 open reading frame 84, mRNA (cDNA clone IMAGE:3877613), with apparent retained intron.
BC080540 - Homo sapiens chromosome 16 open reading frame 84, mRNA (cDNA clone IMAGE:5458809), partial cds.
BC021829 - Homo sapiens chromosome 16 open reading frame 84, mRNA (cDNA clone IMAGE:3452981), containing frame-shift errors.
BC044951 - Homo sapiens chromosome 16 open reading frame 84, mRNA (cDNA clone IMAGE:5225154), with apparent retained intron.
JD023425 - Sequence 4449 from Patent EP1572962.
JD031461 - Sequence 12485 from Patent EP1572962.
JD389519 - Sequence 370543 from Patent EP1572962.
JD051720 - Sequence 32744 from Patent EP1572962.
JD398516 - Sequence 379540 from Patent EP1572962.
JD173306 - Sequence 154330 from Patent EP1572962.
JD056670 - Sequence 37694 from Patent EP1572962.
JD497199 - Sequence 478223 from Patent EP1572962.
MA620066 - JP 2018138019-A/191992: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q2VPK5 (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: B2RXK0, C16orf84, CTU2_HUMAN, NCS2, NM_001012759, NP_001012777, Q0P511, Q2VPK5, Q66K78, Q6P4C8, Q86SV4
UCSC ID: uc002flm.3
RefSeq Accession: NM_001012759
Protein: Q2VPK5 (aka CTU2_HUMAN)
CCDS: CCDS45545.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001012759.1
exon count: 15CDS single in 3' UTR: no RNA size: 1740
ORF size: 1548CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3179.00frame shift in genome: no % Coverage: 99.02
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.