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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
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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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