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    TYW3 tRNA-yW synthesizing protein 3 homolog [ Homo sapiens (human) ]

    Gene ID: 127253, updated on 5-Mar-2024

    Summary

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    Official Symbol
    TYW3provided by HGNC
    Official Full Name
    tRNA-yW synthesizing protein 3 homologprovided by HGNC
    Primary source
    HGNC:HGNC:24757
    See related
    Ensembl:ENSG00000162623 MIM:611245; AllianceGenome:HGNC:24757
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    C1orf171
    Summary
    Wybutosine (yW) is a hypermodified guanosine at the 3-prime position adjacent to the anticodon of phenylalanine tRNA that stabilizes codon-anticodon interactions during decoding on the ribosome. TYW3 is the human homolog of a yeast gene essential for yW synthesis (Noma and Suzuki, 2006).[supplied by OMIM, Mar 2008]
    Expression
    Ubiquitous expression in thyroid (RPKM 10.1), ovary (RPKM 8.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1p31.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (74733152..74766677)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (74574793..74608590)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (75198836..75232361)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ERICH3 antisense RNA 1 Neighboring gene glutamate rich 3 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:75187729-75188286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1199 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:75198416-75199126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1201 Neighboring gene crystallin zeta Neighboring gene NANOG hESC enhancer GRCh37_chr1:75311356-75311857 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:75342688-75343188 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:75343189-75343689 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:75417464-75418002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:75452641-75453140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:75548004-75548706 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:75548707-75549409 Neighboring gene Sharpr-MPRA regulatory region 8849 Neighboring gene MPRA-validated peak288 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:75597021-75598220 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:75600378-75600890 Neighboring gene LHX8 antisense RNA 1 Neighboring gene LIM homeobox 8 Neighboring gene RNA, U6 small nuclear 622, pseudogene

    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. Genome-wide association analysis identifies TYW3/CRYZ and NDST4 loci associated with circulating resistin levels. Qi Q, et al. Hum Mol Genet, 2012 Nov 1. PMID 22843503, Free PMC Article
    2. Ribonucleome analysis identified enzyme genes responsible for wybutosine synthesis. Noma A, et al. Nucleic Acids Symp Ser (Oxf), 2006. PMID 17150819
    3. Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. Perry JR, et al. Nature, 2014 Oct 2. PMID 25231870, Free PMC Article
    4. Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. Fox CS, et al. PLoS Genet, 2012. PMID 22589738, Free PMC Article
    5. Mapping the mammalian ribosome quality control complex interactome using proximity labeling approaches. Zuzow N, et al. Mol Biol Cell, 2018 May 15. PMID 29540532, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    EBI GWAS Catalog

    Description
    Genome-wide association analysis identifies TYW3/CRYZ and NDST4 loci associated with circulating resistin levels.
    EBI GWAS Catalog
    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    EBI GWAS Catalog
    Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
    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

    • FLJ40918

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables tRNA methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in tRNA methylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in wybutosine biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    tRNA wybutosine-synthesizing protein 3 homolog
    Names
    tRNA(Phe) 7-((3-amino-3-carboxypropyl)-4-demethylwyosine(37)-N(4))-methyltransferase
    tRNA-yW-synthesizing protein 3
    NP_001156388.1
    NP_612476.1
    XP_006710410.1

    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_001162916.2 → NP_001156388.1  tRNA wybutosine-synthesizing protein 3 homolog isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the CDS, as compared to variant 1. The resulting isoform (2) lacks an internal segment, as compared to isoform 1.
      Source sequence(s)
      AC091611, AK299849, BC009514, BM680331, DA033034
      Consensus CDS
      CCDS53334.1
      UniProtKB/Swiss-Prot
      Q6IPR3
      UniProtKB/TrEMBL
      Q96GE7
      Related
      ENSP00000407025.2, ENST00000457880.6
      Conserved Domains (1) summary
      pfam02676
      Location:10 → 160
      TYW3; Methyltransferase TYW3

    2. NM_138467.3 → NP_612476.1  tRNA wybutosine-synthesizing protein 3 homolog isoform 1

      See identical proteins and their annotated locations for NP_612476.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC091611, AK098237, BC071765, BM680331
      Consensus CDS
      CCDS666.1
      UniProtKB/Swiss-Prot
      B4DSP9, E9PGR7, Q5HYJ0, Q6IPR3, Q8N7L1
      Related
      ENSP00000359904.3, ENST00000370867.8
      Conserved Domains (1) summary
      pfam02676
      Location:10 → 193
      TYW3; Methyltransferase TYW3

    RNA

    1. NR_027962.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) has an alternate 5' exon, as compared to variant 1. The resulting transcript is a nonsense-mediated mRNA decay candidate, and is unlikely to make a functional protein.
      Source sequence(s)
      AC091611, AK311272, BC009514, BM680331

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      74733152..74766677
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006710347.3 → XP_006710410.1  tRNA wybutosine-synthesizing protein 3 homolog isoform X1

      See identical proteins and their annotated locations for XP_006710410.1

      UniProtKB/Swiss-Prot
      B4DSP9, E9PGR7, Q5HYJ0, Q6IPR3, Q8N7L1
      Conserved Domains (1) summary
      pfam02676
      Location:10 → 193
      TYW3; Methyltransferase TYW3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      74574793..74608590
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6IPR3.2 GenPept UniProtKB/Swiss-Prot:Q6IPR3

    Gene LinkOut

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