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    Tyw1 tRNA-yW synthesizing protein 1 homolog (S. cerevisiae) [ Mus musculus (house mouse) ]

    Gene ID: 100929, updated on 30-Apr-2024

    Summary

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    Official Symbol
    Tyw1provided by MGI
    Official Full Name
    tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)provided by MGI
    Primary source
    MGI:MGI:2141161
    See related
    Ensembl:ENSMUSG00000056310 AllianceGenome:MGI:2141161
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Rsafd1
    Summary
    Predicted to enable several functions, including 4 iron, 4 sulfur cluster binding activity; FMN binding activity; and tRNA-4-demethylwyosine synthase activity. Predicted to be involved in wybutosine biosynthetic process. Predicted to act upstream of or within tRNA processing. Is expressed in several structures, including alimentary system; brain; cardiovascular system; genitourinary system; and respiratory system. Orthologous to several human genes including TYW1 (tRNA-yW synthesizing protein 1 homolog). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 3.3), placenta adult (RPKM 3.0) and 28 other tissues See more
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    Genomic context

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    Location:
    5 G1.3; 5 69.0 cM
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (130284460..130370408)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (130255572..130341568)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E11304 Neighboring gene STARR-positive B cell enhancer ABC_E11728 Neighboring gene STARR-positive B cell enhancer mm9_chr5:130730118-130730418 Neighboring gene STARR-positive B cell enhancer ABC_E234 Neighboring gene STARR-positive B cell enhancer ABC_E279 Neighboring gene transmembrane protein 248 Neighboring gene predicted gene 6598 Neighboring gene STARR-seq mESC enhancer starr_14473 Neighboring gene SBDS ribosome maturation factor Neighboring gene STARR-seq mESC enhancer starr_14474 Neighboring gene RIKEN cDNA A330070K13 gene Neighboring gene predicted gene, 40336 Neighboring gene calneuron 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Functional consequences of necdin nucleocytoplasmic localization. Lavi-Itzkovitz A, et al. PLoS One, 2012. PMID 22442722, Free PMC Article
    2. Construction of long-transcript enriched cDNA libraries from submicrogram amounts of total RNAs by a universal PCR amplification method. Piao Y, et al. Genome Res, 2001 Sep. PMID 11544199, Free PMC Article
    3. Fancd2 in vivo interaction network reveals a non-canonical role in mitochondrial function. Zhang T, et al. Sci Rep, 2017 Apr 5. PMID 28378742, Free PMC Article
    4. BioID screening of biotinylation sites using the avidin-like protein Tamavidin 2-REV identifies global interactors of stimulator of interferon genes (STING). Motani K, et al. J Biol Chem, 2020 Aug 7. PMID 32554809, Free PMC Article
    5. The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data. Koscielny G, et al. Nucleic Acids Res, 2014 Jan. PMID 24194600, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (2) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    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 catalytic activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables iron-sulfur cluster binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables lyase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleotide 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
    acts_upstream_of_or_within tRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in tRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    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
    NP_001015876.1
    NP_001411703.1
    NP_001411704.1
    NP_001411705.1
    NP_001411706.1
    NP_001411707.1
    NP_001411708.1
    NP_001411709.1
    NP_001411711.1
    NP_849228.1

    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_001015876.3 → NP_001015876.1  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 isoform 1

      See identical proteins and their annotated locations for NP_001015876.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC113029
      Consensus CDS
      CCDS19712.1
      UniProtKB/Swiss-Prot
      Q3TRC5, Q8BJM7, Q8BLG4, Q8R0C7
      Related
      ENSMUSP00000037173.7, ENSMUST00000040213.13
      Conserved Domains (2) summary
      PRK13762
      Location:340 → 652
      PRK13762; 4-demethylwyosine synthase TYW1
      pfam00258
      Location:73 → 224
      Flavodoxin_1

    2. NM_001424774.1 → NP_001411703.1  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC113029
      UniProtKB/Swiss-Prot
      Q3TRC5, Q8BJM7, Q8BLG4, Q8R0C7

    3. NM_001424775.1 → NP_001411704.1  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC113029

    4. NM_001424776.1 → NP_001411705.1  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC113029

    5. NM_001424777.1 → NP_001411706.1  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC113029

    6. NM_001424778.1 → NP_001411707.1  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC113029

    7. NM_001424779.1 → NP_001411708.1  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC113029

    8. NM_001424780.1 → NP_001411709.1  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC113029

    9. NM_001424782.1 → NP_001411711.1  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC113029

    10. NM_178897.4 → NP_849228.1  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 isoform 2

      See identical proteins and their annotated locations for NP_849228.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has multiple differences in its 3' end, compared to variant 1, which results in a protein (isoform 2) with a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC113029, AK045279
      Consensus CDS
      CCDS19711.1
      UniProtKB/TrEMBL
      A0A0R4J0L2
      Related
      ENSMUSP00000047318.6, ENSMUST00000044204.12
      Conserved Domains (2) summary
      PRK13762
      Location:340 → 374
      PRK13762; 4-demethylwyosine synthase TYW1
      pfam00258
      Location:73 → 224
      Flavodoxin_1

    RNA

    1. NR_153350.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice junction 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)
      AC113029

    2. NR_188930.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC113029

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000071.7 Reference GRCm39 C57BL/6J

      Range
      130284460..130370408
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_868551.4 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BJM7.1 GenPept UniProtKB/Swiss-Prot:Q8BJM7

    Gene LinkOut

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