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    TYW1 tRNA-yW synthesizing protein 1 homolog [ Homo sapiens (human) ]

    Gene ID: 55253, updated on 5-Mar-2024

    Summary

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    Official Symbol
    TYW1provided by HGNC
    Official Full Name
    tRNA-yW synthesizing protein 1 homologprovided by HGNC
    Primary source
    HGNC:HGNC:25598
    See related
    Ensembl:ENSG00000198874 MIM:611243; AllianceGenome:HGNC:25598
    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
    TYW1A; RSAFD1; YPL207W
    Summary
    Wybutosine (yW) is a hypermodified guanosine found in phenylalanine tRNA adjacent to the anticodon that stabilizes codon-anticodon interactions in the ribosome. In yeast, the homolog of this gene is essential for the synthesis of wybutosine. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
    Expression
    Ubiquitous expression in thyroid (RPKM 5.7), ovary (RPKM 5.0) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    Location:
    7q11.21
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (66996833..67239514)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (68216506..68459212)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (66461820..66704501)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26091 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18219 Neighboring gene RNA, 7SL, cytoplasmic 43, pseudogene Neighboring gene SBDS ribosome maturation factor Neighboring gene ReSE screen-validated silencer GRCh37_chr7:66522608-66522788 Neighboring gene uncharacterized LOC124901664 Neighboring gene microRNA 4650-1 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:66599529-66599706 Neighboring gene uncharacterized LOC124901666 Neighboring gene Sharpr-MPRA regulatory region 9636 Neighboring gene MPRA-validated peak6550 silencer Neighboring gene uncharacterized LOC124901665 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:66705704-66706246 Neighboring gene speedy/RINGO cell cycle regulator family member E21 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26092 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18220 Neighboring gene PMS1 homolog 2, mismatch repair system component pseudogene 4 Neighboring gene STAG3 cohesin complex component like 4 (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. Discovery of a gene family critical to wyosine base formation in a subset of phenylalanine-specific transfer RNAs. Waas WF, et al. J Biol Chem, 2005 Nov 11. PMID 16162496
    2. Ribonucleome analysis identified enzyme genes responsible for wybutosine synthesis. Noma A, et al. Nucleic Acids Symp Ser (Oxf), 2006. PMID 17150819
    3. MMS19 links cytoplasmic iron-sulfur cluster assembly to DNA metabolism. Gari K, et al. Science, 2012 Jul 13. PMID 22678361
    4. Protein interaction discovery using parallel analysis of translated ORFs (PLATO). Zhu J, et al. Nat Biotechnol, 2013 Apr. PMID 23503679, 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 (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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

    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

    • FLJ10900, MGC23001, MGC60291

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 4 iron, 4 sulfur cluster binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables FMN binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables tRNA-4-demethylwyosine synthase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in wybutosine biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1
    Names
    radical S-adenosyl methionine and flavodoxin domain-containing protein 1
    radical S-adenosyl methionine and flavodoxin domains 1
    tRNA wybutosine-synthesizing protein 1 homolog
    tRNA-yW synthesizing protein 1 homolog A
    NP_060734.2
    XP_011514674.1
    XP_016867881.1
    XP_047276524.1
    XP_047276525.1
    XP_054214549.1
    XP_054214550.1
    XP_054214551.1
    XP_054214552.1

    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.

    Genomic

    1. NG_033069.1 RefSeqGene

      Range
      5029..247710
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_018264.4 → NP_060734.2  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1

      See identical proteins and their annotated locations for NP_060734.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the functional protein.
      Source sequence(s)
      AC006480, AC073089, AC079920
      Consensus CDS
      CCDS5538.1
      UniProtKB/Swiss-Prot
      Q6PJG8, Q75MG8, Q75MN3, Q86V12, Q8IVS7, Q9H9C4, Q9NV66
      Related
      ENSP00000352645.5, ENST00000359626.10
      Conserved Domains (2) summary
      PRK13762
      Location:351 → 656
      PRK13762; 4-demethylwyosine synthase TYW1
      pfam00258
      Location:81 → 232
      Flavodoxin_1

    RNA

    1. NR_134540.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC015591, BC051888, BM678114, HY014014
      Related
      ENST00000361660.8

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      66996833..67239514
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017012392.3 → XP_016867881.1  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 isoform X3

      Conserved Domains (2) summary
      PRK13762
      Location:368 → 562
      PRK13762; 4-demethylwyosine synthase TYW1
      pfam00258
      Location:81 → 232
      Flavodoxin_1

    2. XM_011516372.4 → XP_011514674.1  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 isoform X1

      Conserved Domains (2) summary
      PRK13762
      Location:351 → 664
      PRK13762; 4-demethylwyosine synthase TYW1
      pfam00258
      Location:81 → 232
      Flavodoxin_1

    3. XM_047420568.1 → XP_047276524.1  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 isoform X2

    4. XM_047420569.1 → XP_047276525.1  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      68216506..68459212
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054358576.1 → XP_054214551.1  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 isoform X3

    2. XM_054358574.1 → XP_054214549.1  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 isoform X1

    3. XM_054358575.1 → XP_054214550.1  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 isoform X2

    4. XM_054358577.1 → XP_054214552.1  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NV66.2 GenPept UniProtKB/Swiss-Prot:Q9NV66

    Gene LinkOut

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

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