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

    Gene ID: 129450, updated on 28-Oct-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 tRNA(Phe) (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, Oct 2024]
    Expression
    Ubiquitous expression in bone marrow (RPKM 2.6), thyroid (RPKM 2.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TYW5 in Genome Data Viewer
    Location:
    2q33.1
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (199928913..199955491, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (200412544..200439116, complement)
    RS_2024_09 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 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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    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 iron ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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