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] See more...

Aliases for TYW1 Gene

Aliases for TYW1 Gene

  • TRNA-YW Synthesizing Protein 1 Homolog 2 3 5
  • Radical S-Adenosyl Methionine And Flavodoxin Domain-Containing Protein 1 3 4
  • S-Adenosyl-L-Methionine-Dependent TRNA 4-Demethylwyosine Synthase TYW1 3 4
  • Radical S-Adenosyl Methionine And Flavodoxin Domains 1 2 3
  • TRNA Wybutosine-Synthesizing Protein 1 Homolog 3 4
  • RSAFD1 3 4
  • S-Adenosyl-L-Methionine-Dependent TRNA 4-Demethylwyosine Synthase 3
  • TRNA-YW Synthesizing Protein 1 Homolog A (S. Cerevisiae) 2
  • TRNA-YW Synthesizing Protein 1 Homolog (S. Cerevisiae) 2
  • TRNA-YW Synthesizing Protein 1 Homolog A 3
  • TRNA-YW-Synthesizing Protein 4
  • EC 4.1.3.44 4
  • YPL207W 3
  • TYW1A 3

External Ids for TYW1 Gene

Previous HGNC Symbols for TYW1 Gene

  • RSAFD1

Previous GeneCards Identifiers for TYW1 Gene

  • GC07P066099
  • GC07P066460
  • GC07P062645

Summaries for TYW1 Gene

Entrez Gene Summary for TYW1 Gene

  • 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]

GeneCards Summary for TYW1 Gene

TYW1 (TRNA-YW Synthesizing Protein 1 Homolog) is a Protein Coding gene. Among its related pathways are tRNA processing and Gene Expression. Gene Ontology (GO) annotations related to this gene include oxidoreductase activity and 4 iron, 4 sulfur cluster binding. An important paralog of this gene is TYW1B.

UniProtKB/Swiss-Prot Summary for TYW1 Gene

  • Probable component of the wybutosine biosynthesis pathway. Wybutosine is a hyper modified guanosine with a tricyclic base found at the 3'-position adjacent to the anticodon of eukaryotic phenylalanine tRNA. Catalyzes the condensation of N-methylguanine with 2 carbon atoms from pyruvate to form the tricyclic 4-demethylwyosine, an intermediate in wybutosine biosynthesis (By similarity).

Additional gene information for TYW1 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TYW1 Gene

Genomics for TYW1 Gene

GeneHancer (GH) Regulatory Elements for TYW1 Gene

Promoters and enhancers for TYW1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TYW1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TYW1 gene promoter:
  • Elk-1
  • FOXO3
  • FOXO3a
  • FOXO3b
  • GATA-1
  • RORalpha1
  • RREB-1
  • SRF
  • SRF (504 AA)
  • STAT3

Genomic Locations for TYW1 Gene

Genomic Locations for TYW1 Gene
chr7:66,995,173-67,239,520
(GRCh38/hg38)
Size:
244,348 bases
Orientation:
Plus strand
chr7:66,460,160-66,704,501
(GRCh37/hg19)
Size:
244,342 bases
Orientation:
Plus strand

Genomic View for TYW1 Gene

Genes around TYW1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TYW1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TYW1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TYW1 Gene

Proteins for TYW1 Gene

  • Protein details for TYW1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NV66-TYW1_HUMAN
    Recommended name:
    S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1
    Protein Accession:
    Q9NV66
    Secondary Accessions:
    • Q6PJG8
    • Q75MG8
    • Q75MN3
    • Q86V12
    • Q8IVS7
    • Q9H9C4

    Protein attributes for TYW1 Gene

    Size:
    732 amino acids
    Molecular mass:
    83702 Da
    Cofactor:
    Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH15591.1; Type=Frameshift; Positions=663; Evidence={ECO:0000305}; Sequence=BAB14307.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for TYW1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TYW1 Gene

Post-translational modifications for TYW1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for TYW1 Gene

No data available for DME Specific Peptides for TYW1 Gene

Domains & Families for TYW1 Gene

Gene Families for TYW1 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for TYW1 Gene

GenScript: Design optimal peptide antigens:
  • tRNA-yW-synthesizing protein (TYW1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NV66

UniProtKB/Swiss-Prot:

TYW1_HUMAN :
  • Belongs to the TYW1 family.
Family:
  • Belongs to the TYW1 family.
genes like me logo Genes that share domains with TYW1: view

Function for TYW1 Gene

Molecular function for TYW1 Gene

UniProtKB/Swiss-Prot Function:
Probable component of the wybutosine biosynthesis pathway. Wybutosine is a hyper modified guanosine with a tricyclic base found at the 3'-position adjacent to the anticodon of eukaryotic phenylalanine tRNA. Catalyzes the condensation of N-methylguanine with 2 carbon atoms from pyruvate to form the tricyclic 4-demethylwyosine, an intermediate in wybutosine biosynthesis (By similarity).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=N(1)-methylguanosine(37) in tRNA(Phe) + pyruvate + S-adenosyl-L-methionine = 4-demethylwyosine(37) in tRNA(Phe) + 5'-deoxyadenosine + CO2 + H2O + L-methionine; Xref=Rhea:RHEA:36347, Rhea:RHEA-COMP:10164, Rhea:RHEA-COMP:10165, ChEBI:CHEBI:15361, ChEBI:CHEBI:15377, ChEBI:CHEBI:16526, ChEBI:CHEBI:17319, ChEBI:CHEBI:57844, ChEBI:CHEBI:59789, ChEBI:CHEBI:64315, ChEBI:CHEBI:73542; EC=4.1.3.44;.

Enzyme Numbers (IUBMB) for TYW1 Gene

Phenotypes From GWAS Catalog for TYW1 Gene

Gene Ontology (GO) - Molecular Function for TYW1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IEA --
GO:0010181 FMN binding IEA --
GO:0016829 lyase activity IEA --
GO:0046872 metal ion binding IEA --
GO:0051536 iron-sulfur cluster binding IEA --
genes like me logo Genes that share ontologies with TYW1: view
genes like me logo Genes that share phenotypes with TYW1: view

Animal Models for TYW1 Gene

MGI Knock Outs for TYW1:
  • Tyw1 Tyw1<tm1b(KOMP)Wtsi>

Animal Model Products

  • Taconic Biosciences Mouse Models for TYW1

CRISPR Products

miRNA for TYW1 Gene

miRTarBase miRNAs that target TYW1

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for TYW1 Gene

Localization for TYW1 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TYW1 gene
Compartment Confidence
cytosol 3
nucleus 2
peroxisome 1
endoplasmic reticulum 1
plasma membrane 0
extracellular 0
golgi apparatus 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TYW1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with TYW1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for TYW1 Gene

Pathways & Interactions for TYW1 Gene

genes like me logo Genes that share pathways with TYW1: view

UniProtKB/Swiss-Prot Q9NV66-TYW1_HUMAN

  • Pathway: tRNA modification; wybutosine-tRNA(Phe) biosynthesis.

Gene Ontology (GO) - Biological Process for TYW1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008033 tRNA processing IEA --
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with TYW1: view

No data available for SIGNOR curated interactions for TYW1 Gene

Drugs & Compounds for TYW1 Gene

(1) Drugs for TYW1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Flavin Mononucleotide Approved, Investigational Pharma 10

(1) Additional Compounds for TYW1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
s-adenosylmethionine
  • (3S)-5'-[(3-amino-3-Carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt
  • [1-(Adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium
  • Acylcarnitine
  • AdoMet
  • S-(5'-Deoxyadenosin-5'-yl)-L-methionine
485-80-3
genes like me logo Genes that share compounds with TYW1: view

Transcripts for TYW1 Gene

mRNA/cDNA for TYW1 Gene

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TYW1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13a · 13b
SP1:
SP2:
SP3:
SP4: -

Relevant External Links for TYW1 Gene

GeneLoc Exon Structure for
TYW1
ECgene alternative splicing isoforms for
TYW1

Expression for TYW1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TYW1 Gene

Protein differential expression in normal tissues from HIPED for TYW1 Gene

This gene is overexpressed in Spleen (65.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TYW1 Gene



Protein tissue co-expression partners for TYW1 Gene

NURSA nuclear receptor signaling pathways regulating expression of TYW1 Gene:

TYW1

SOURCE GeneReport for Unigene cluster for TYW1 Gene:

Hs.520917

Evidence on tissue expression from TISSUES for TYW1 Gene

  • Intestine(4.2)
  • Nervous system(2.4)
genes like me logo Genes that share expression patterns with TYW1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TYW1 Gene

Orthologs for TYW1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TYW1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TYW1 32
  • 98.94 (n)
-- 33
  • 96 (a)
OneToMany
dog
(Canis familiaris)
Mammalia -- 33
  • 88 (a)
OneToMany
TYW1 32
  • 87.02 (n)
cow
(Bos Taurus)
Mammalia TYW1 33 32
  • 86.59 (n)
OneToMany
mouse
(Mus musculus)
Mammalia Tyw1 17 33 32
  • 80.75 (n)
rat
(Rattus norvegicus)
Mammalia Tyw1 32
  • 80.39 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 33
  • 74 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 33
  • 68 (a)
OneToMany
chicken
(Gallus gallus)
Aves TYW1 32
  • 76.65 (n)
-- 33
  • 70 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia tyw1 32
  • 69.43 (n)
Str.7207 32
zebrafish
(Danio rerio)
Actinopterygii tyw1 33 32
  • 68.26 (n)
OneToMany
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFL099W 32
  • 52.57 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TYW1 35 33 32
  • 50.53 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G75200 32
  • 56.09 (n)
soybean
(Glycine max)
eudicotyledons Gma.17994 32
rice
(Oryza sativa)
Liliopsida Os03g0775300 32
  • 56.72 (n)
Os.33461 32
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8783 33
  • 57 (a)
OneToMany
Cin.5664 32
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPCC1020.08 32
  • 55.49 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU06633 32
  • 50.48 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5664 32
Species where no ortholog for TYW1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for TYW1 Gene

ENSEMBL:
Gene Tree for TYW1 (if available)
TreeFam:
Gene Tree for TYW1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TYW1: view image

Paralogs for TYW1 Gene

Paralogs for TYW1 Gene

(1) SIMAP similar genes for TYW1 Gene using alignment to 2 proteins:

  • TYW1_HUMAN
  • C9J9Q4_HUMAN

Pseudogenes.org Pseudogenes for TYW1 Gene

genes like me logo Genes that share paralogs with TYW1: view

Variants for TYW1 Gene

Sequence variations from dbSNP and Humsavar for TYW1 Gene

SNP ID Clin Chr 07 pos Variation AA Info Type
rs113993990 pathogenic, Shwachman syndrome, not provided 66,995,298(+) CC/C upstream_transcript_variant
rs28942099 uncertain-significance, Shwachman syndrome 66,995,394(+) G/T upstream_transcript_variant
rs373730800 pathogenic, Shwachman syndrome 66,995,320(+) T/C/G upstream_transcript_variant
rs772797192 pathogenic, not provided 66,995,405(+) T/ upstream_transcript_variant
rs1131691842 likely-pathogenic, not provided 66,995,323(+) T/C upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for TYW1 Gene

Variant ID Type Subtype PubMed ID
dgv11434n54 CNV loss 21841781
dgv11435n54 CNV loss 21841781
dgv1299e214 CNV gain 21293372
dgv1300e214 CNV gain 21293372
dgv3579n106 CNV deletion 24896259
esv2253832 CNV deletion 18987734
esv23402 CNV loss 19812545
esv2422035 CNV deletion 20811451
esv2467105 CNV deletion 19546169
esv26455 CNV loss 19812545
esv2660507 CNV deletion 23128226
esv2666250 CNV deletion 23128226
esv2759535 CNV gain 17122850
esv33653 CNV loss 17666407
esv3541815 CNV deletion 23714750
esv3571892 CNV loss 25503493
esv3571893 CNV loss 25503493
esv3571894 CNV loss 25503493
esv3571895 CNV loss 25503493
esv3571896 CNV loss 25503493
esv3613538 CNV loss 21293372
esv3613541 CNV loss 21293372
esv3613543 CNV loss 21293372
esv3891136 CNV gain 25118596
esv3891138 CNV gain 25118596
nsv1032237 CNV loss 25217958
nsv1032575 CNV gain 25217958
nsv1109885 CNV deletion 24896259
nsv1109886 CNV deletion 24896259
nsv1119126 CNV deletion 24896259
nsv1140797 CNV deletion 24896259
nsv1142671 CNV deletion 24896259
nsv1146102 OTHER inversion 26484159
nsv1161553 OTHER complex 26073780
nsv441983 CNV loss 18776908
nsv509205 CNV insertion 20534489
nsv5774 CNV insertion 18451855
nsv607415 CNV loss 21841781
nsv607418 CNV loss 21841781
nsv607423 CNV loss 21841781
nsv824151 CNV loss 20364138
nsv831019 CNV loss 17160897
nsv966838 CNV duplication 23825009
nsv970518 CNV duplication 23825009
nsv981515 CNV duplication 23825009
nsv981516 CNV duplication 23825009

Variation tolerance for TYW1 Gene

Residual Variation Intolerance Score: 76.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.17; 90.39% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TYW1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TYW1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TYW1 Gene

Disorders for TYW1 Gene

Additional Disease Information for TYW1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for TYW1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for TYW1 Gene

Publications for TYW1 Gene

  1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 43 56
  2. Ribonucleome analysis identified enzyme genes responsible for wybutosine synthesis. (PMID: 17150819) Noma A … Suzuki T (Nucleic acids symposium series (2004) 2006) 2 3 56
  3. Discovery of a gene family critical to wyosine base formation in a subset of phenylalanine-specific transfer RNAs. (PMID: 16162496) Waas WF … Schimmel P (The Journal of biological chemistry 2005) 2 3 56
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 56
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 56

Products for TYW1 Gene

Sources for TYW1 Gene