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    CTU2 cytosolic thiouridylase subunit 2 [ Homo sapiens (human) ]

    Gene ID: 348180, updated on 6-May-2024

    Summary

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    Official Symbol
    CTU2provided by HGNC
    Official Full Name
    cytosolic thiouridylase subunit 2provided by HGNC
    Primary source
    HGNC:HGNC:28005
    See related
    Ensembl:ENSG00000174177 MIM:617057; AllianceGenome:HGNC:28005
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    MFRG; NCS2; UPF0432; C16orf84
    Summary
    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]
    Expression
    Ubiquitous expression in testis (RPKM 3.9), brain (RPKM 2.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    16q24.3
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (88706503..88715396)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (94775662..94785864)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (88772911..88781804)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene SNAI3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88743941-88744698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88744699-88745454 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88747432-88748253 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7867 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7868 Neighboring gene snail family transcriptional repressor 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:88756108-88756282 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7869 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11366 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11367 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11368 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:88772291-88772928 Neighboring gene ring finger protein 166 Neighboring gene microRNA 4722 Neighboring gene piezo type mechanosensitive ion channel component 1 (Er blood group) Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7872 Neighboring gene HSP90AB1 associated lncRNA 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Biallelic variants in CTU2 cause DREAM-PL syndrome and impair thiolation of tRNA wobble U34. Shaheen R, et al. Hum Mutat, 2019 Nov. PMID 31301155
    2. A genome-wide association study of autism using the Simons Simplex Collection: Does reducing phenotypic heterogeneity in autism increase genetic homogeneity? Chaste P, et al. Biol Psychiatry, 2015 May 1. PMID 25534755, Free PMC Article
    3. A functional proteomics approach links the ubiquitin-related modifier Urm1 to a tRNA modification pathway. Schlieker CD, et al. Proc Natl Acad Sci U S A, 2008 Nov 25. PMID 19017811, Free PMC Article
    4. HectD1 controls hematopoietic stem cell regeneration by coordinating ribosome assembly and protein synthesis. Lv K, et al. Cell Stem Cell, 2021 Jul 1. PMID 33711283, Free PMC Article
    5. Human CIA2A-FAM96A and CIA2B-FAM96B integrate iron homeostasis and maturation of different subsets of cytosolic-nuclear iron-sulfur proteins. Stehling O, et al. Cell Metab, 2013 Aug 6. PMID 23891004, Free PMC Article

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Activation of CTU2 expression by LXR promotes the development of hepatocellular carcinoma.
      Title: Activation of CTU2 expression by LXR promotes the development of hepatocellular carcinoma.
    2. Our data establish a recognizable CTU2-linked autosomal recessive syndrome in humans characterized by defective thiolation of the wobble uridine. The potential deleterious consequences for the translational efficiency and fidelity during development as a mechanism for pathogenicity represent an attractive target of future investigations.
      Title: Biallelic variants in CTU2 cause DREAM-PL syndrome and impair thiolation of tRNA wobble U34.
    3. Identifies the product of this gene as being involved in tRNA modification.
      Title: A functional proteomics approach links the ubiquitin-related modifier Urm1 to a tRNA modification pathway.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome
    MedGen: C4748348 OMIM: 618142 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    A Genome-wide Association Study of Autism Using the Simons Simplex Collection: Does Reducing Phenotypic Heterogeneity in Autism Increase Genetic Homogeneity?
    EBI GWAS Catalog
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC131681, MGC148063, MGC148064

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables nucleotidyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sulfurtransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables tRNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in protein urmylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in tRNA thio-modification NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in tRNA wobble position uridine thiolation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in tRNA wobble uridine modification NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    cytoplasmic tRNA 2-thiolation protein 2
    Names
    cytosolic thiouridylase subunit 2 homolog

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001012759.3 → NP_001012777.1  cytoplasmic tRNA 2-thiolation protein 2 isoform 1

      See identical proteins and their annotated locations for NP_001012777.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) uses an alternate in-frame splice site in the 5' coding region, compared to variant 3. It encodes isoform 1, which lacks an internal in-frame segment and is shorter, compared to isoform 3.
      Source sequence(s)
      AA448486, AC138028, BC080540, BC125269
      Consensus CDS
      CCDS45545.1
      UniProtKB/Swiss-Prot
      B2RXK0, Q0P511, Q2VPK5, Q66K78, Q6P4C8, Q86SV4
      Related
      ENSP00000388320.2, ENST00000453996.7
      Conserved Domains (1) summary
      pfam10288
      Location:341 → 468
      CTU2; Cytoplasmic tRNA 2-thiolation protein 2

    2. NM_001012762.3 → NP_001012780.1  cytoplasmic tRNA 2-thiolation protein 2 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region and lacks an alternate exon in the 3' coding region, resulting in a frameshift and an early stop codon, compared to variant 3. The encoded isoform 2 is shorter and has a distinct C-terminus, compared to isoform 3.
      Source sequence(s)
      AA448486, AC138028, BC021829, BC080540, BC121805
      Consensus CDS
      CCDS32506.1
      UniProtKB/Swiss-Prot
      Q2VPK5
      Related
      ENSP00000308617.5, ENST00000312060.9
      Conserved Domains (1) summary
      pfam10288
      Location:341 → 468
      CTU2; Cytoplasmic tRNA 2-thiolation protein 2

    3. NM_001318507.2 → NP_001305436.1  cytoplasmic tRNA 2-thiolation protein 2 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (3).
      Source sequence(s)
      AA448486, AC138028, BC063512, BC080540, BI520274
      Consensus CDS
      CCDS82026.1
      UniProtKB/TrEMBL
      H3BSW6
      Related
      ENSP00000456908.1, ENST00000567949.5
      Conserved Domains (1) summary
      pfam10288
      Location:412 → 539
      CTU2; Cytoplasmic tRNA 2-thiolation protein 2

    4. NM_001318513.2 → NP_001305442.1  cytoplasmic tRNA 2-thiolation protein 2 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, uses a downstream start codon and uses an alternate in-frame splice site in the 5' coding region, compared to variant 3. It encodes isoform 4, which is shorter than isoform 3.
      Source sequence(s)
      AA448486, AC138028, BC080540, BC121805, BC125269
      UniProtKB/Swiss-Prot
      Q2VPK5
      Conserved Domains (1) summary
      pfam10288
      Location:254 → 381
      CTU2; Cytoplasmic tRNA 2-thiolation protein 2

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      88706503..88715396
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      94775662..94785864
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q2VPK5.1 GenPept UniProtKB/Swiss-Prot:Q2VPK5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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