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TYW5 tRNA-yW synthesizing protein 5 [ Homo sapiens (human) ]

Gene ID: 129450, updated on 5-Mar-2024

Summary

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Official Symbol
TYW5provided by HGNC
Official Full Name
tRNA-yW synthesizing protein 5provided by HGNC
Primary source
HGNC:HGNC:26754
See related
Ensembl:ENSG00000162971 MIM:619882; AllianceGenome:HGNC:26754
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
hTYW5; C2orf60
Summary
Enables several functions, including iron ion binding activity; protein homodimerization activity; and tRNAPhe (7-(3-amino-3-carboxypropyl)wyosine37-C2)-hydroxylase activity. Involved in wybutosine biosynthetic process. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in bone marrow (RPKM 2.6), thyroid (RPKM 2.0) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
2q33.1
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (199928913..199955491, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (200412544..200439116, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (200793636..200820214, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927687 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16950 Neighboring gene RNA, 7SL, cytoplasmic 717, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:200786527-200787028 Neighboring gene chromosome 2 open reading frame 69 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:200819858-200821057 Neighboring gene uncharacterized LOC124906112 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:200844585-200845115 Neighboring gene matrix AAA peptidase interacting protein 1 Neighboring gene uncharacterized LOC124907962 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:200874708-200874865 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:200919369-200920289 Neighboring gene uncharacterized LOC105373833

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. Comprehensive and integrative analyses identify TYW5 as a schizophrenia risk gene. Zhang C, et al. BMC Med, 2022 May 9. PMID 35527273, Free PMC Article
  2. Regulatory variants at 2q33.1 confer schizophrenia risk by modulating distal gene TYW5 expression. Li S, et al. Brain, 2022 Apr 18. PMID 34581804, Free PMC Article
  3. Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification. Kato M, et al. Nucleic Acids Res, 2011 Mar. PMID 20972222, Free PMC Article
  4. Expanding role of the jumonji C domain as an RNA hydroxylase. Noma A, et al. J Biol Chem, 2010 Nov 5. PMID 20739293, Free PMC Article
  5. Genome-wide association analysis identifies 13 new risk loci for schizophrenia. Ripke S, et al. Nat Genet, 2013 Oct. PMID 23974872, Free PMC Article

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Comprehensive and integrative analyses identify TYW5 as a schizophrenia risk gene.
    Title: Comprehensive and integrative analyses identify TYW5 as a schizophrenia risk gene.
  2. Regulatory variants at 2q33.1 confer schizophrenia risk by modulating distal gene TYW5 expression.
    Title: Regulatory variants at 2q33.1 confer schizophrenia risk by modulating distal gene TYW5 expression.
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

EBI GWAS Catalog

Description
Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
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

  • FLJ37953, MGC70509

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 2-oxoglutarate-dependent dioxygenase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables iron ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein homodimerization activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables tRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables tRNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables tRNA(Phe) (7-(3-amino-3-carboxypropyl)wyosine37-C2)-hydroxylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in wybutosine biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in wybutosine biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
tRNA wybutosine-synthesizing protein 5
Names
jmjC domain-containing protein C2orf60
tRNA yW-synthesizing enzyme 5
tRNA(Phe) (7-(3-amino-3-carboxypropyl)wyosine(37)-C(2))-hydroxylase
NP_001034782.1
XP_047299227.1
XP_047299228.1
XP_047299229.1
XP_054196449.1
XP_054196450.1
XP_054196451.1

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_001039693.3 → NP_001034782.1  tRNA wybutosine-synthesizing protein 5

    See identical proteins and their annotated locations for NP_001034782.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and is the protein-coding transcript.
    Source sequence(s)
    AC097717, BC132835, BM673915
    Consensus CDS
    CCDS42795.1
    UniProtKB/Swiss-Prot
    A2RUC4, B2RNE3, Q8N1R2
    Related
    ENSP00000346627.4, ENST00000354611.9
    Conserved Domains (1) summary
    pfam13621
    Location:17 → 255
    Cupin_8; Cupin-like domain

RNA

  1. NR_004862.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice junction at the 3' end of the second exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC097717, BC025758, BM673915, BX647677

  2. NR_109905.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks three alternate internal exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC097717, AK095272, BM673915, HY182974

  3. NR_109906.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate splice junction at the 3' end of the second exon and lacks an alternate internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC097717, AK293064, BM673915

  4. NR_109907.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC097717, AK095272, BM673915

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    199928913..199955491 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047443271.1 → XP_047299227.1  tRNA wybutosine-synthesizing protein 5 isoform X1

  2. XM_047443272.1 → XP_047299228.1  tRNA wybutosine-synthesizing protein 5 isoform X2

  3. XM_047443273.1 → XP_047299229.1  tRNA wybutosine-synthesizing protein 5 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    200412544..200439116 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054340474.1 → XP_054196449.1  tRNA wybutosine-synthesizing protein 5 isoform X1

  2. XM_054340475.1 → XP_054196450.1  tRNA wybutosine-synthesizing protein 5 isoform X2

  3. XM_054340476.1 → XP_054196451.1  tRNA wybutosine-synthesizing protein 5 isoform X3

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_152382.1: Suppressed sequence

    Description
    NM_152382.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
A2RUC4.1 GenPept UniProtKB/Swiss-Prot:A2RUC4

Gene LinkOut

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