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

Gene ID: 100929, updated on 8-Feb-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

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