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    TYW1B tRNA-yW synthesizing protein 1 homolog B [ Homo sapiens (human) ]

    Gene ID: 441250, updated on 3-Apr-2024

    Summary

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    Official Symbol
    TYW1Bprovided by HGNC
    Official Full Name
    tRNA-yW synthesizing protein 1 homolog Bprovided by HGNC
    Primary source
    HGNC:HGNC:33908
    See related
    Ensembl:ENSG00000277149 AllianceGenome:HGNC:33908
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RSAFD2; LINC00069; NCRNA00069
    Summary
    Wybutosine is a hypermodified guanosine found in phenylalanine tRNA. Wybutosine functions to stabilize codon-anticodon interactions during ribosome decoding and therefore supports the maintenance of the reading frame. In yeast, the homolog of this gene is essential for the synthesis of wybutosine. The human genome contains two closely related genes that putatively function in wybutosine synthesis. The open reading frame of this locus is disrupted in some individuals. Thus, this locus appears to be an evolving pseudogene, but may still be functional in some members of the population. [provided by RefSeq, Apr 2014]
    Expression
    Ubiquitous expression in ovary (RPKM 3.5), thyroid (RPKM 3.4) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    Location:
    7q11.22-q11.23
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (72574513..72828200, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (73793064..74052329, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (72039498..72298779, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene calneuron 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:71406788-71407288 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:71407289-71407789 Neighboring gene ribosomal protein S28 pseudogene 6 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_99965 Neighboring gene ATP binding cassette subfamily F member 2 pseudogene 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:71689607-71689762 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:71730468-71731047 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:71778325-71778516 Neighboring gene MPRA-validated peak6577 silencer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:71870231-71871430 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:71911988-71912488 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:71912489-71912989 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26117 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:72087779-72088278 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:72120413-72120929 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26118 Neighboring gene MPRA-validated peak6582 silencer Neighboring gene microRNA 4650-2 Neighboring gene transmembrane protein 68-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:72291163-72291664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:72291665-72292164 Neighboring gene Sharpr-MPRA regulatory region 3958 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26119 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:72308407-72308549 Neighboring gene RNA, 7SL, cytoplasmic 377, pseudogene Neighboring gene RNA, 7SL, cytoplasmic 625, pseudogene Neighboring gene SBDS pseudogene 1

    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. Discovery of a gene family critical to wyosine base formation in a subset of phenylalanine-specific transfer RNAs. Waas WF, et al. J Biol Chem, 2005 Nov 11. PMID 16162496
    2. Ribonucleome analysis identified enzyme genes responsible for wybutosine synthesis. Noma A, et al. Nucleic Acids Symp Ser (Oxf), 2006. PMID 17150819
    3. Biological, clinical and population relevance of 95 loci for blood lipids. Teslovich TM, et al. Nature, 2010 Aug 5. PMID 20686565, Free PMC Article
    4. Discovery and refinement of loci associated with lipid levels. Willer CJ, et al. Nat Genet, 2013 Nov. PMID 24097068, Free PMC Article
    5. C5orf51 is a component of the MON1-CCZ1 complex and controls RAB7A localization and stability during mitophagy. Yan BR, et al. Autophagy, 2022 Apr. PMID 34432599, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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
    Biological, clinical and population relevance of 95 loci for blood lipids.
    EBI GWAS Catalog
    Discovery and refinement of loci associated with lipid levels.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC87315

    Gene Ontology Provided by GOA

    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 metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables tRNA-4-demethylwyosine synthase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    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 TYW1B
    Names
    long intergenic non-protein coding RNA 69
    radical S-adenosyl methionine and flavodoxin domain-containing protein 2
    radical S-adenosyl methionine and flavodoxin domains 1
    tRNA wybutosine-synthesizing protein 1 homolog B
    tRNA-yW synthesizing protein 1 homolog B (non-protein coding)
    NP_001138912.2
    NP_001399108.1
    NP_001399109.1
    NP_001399110.1
    NP_001399111.1

    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_001145440.3 → NP_001138912.2  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1B isoform 1

      Status: REVIEWED

      Source sequence(s)
      AI984113, BC068520, BC106019, DA769764
      Consensus CDS
      CCDS69309.1
      UniProtKB/Swiss-Prot
      A0A087WZB2, A6NG09, B4DFY2, Q3KQX2, Q6NUM6
      Related
      ENSP00000482502.1, ENST00000620995.5
      Conserved Domains (2) summary
      PRK13762
      Location:339 → 592
      PRK13762; 4-demethylwyosine synthase TYW1
      pfam00258
      Location:44 → 186
      Flavodoxin_1

    2. NM_001412179.1 → NP_001399108.1  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1B isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC091738, AC092536, AC211469

    3. NM_001412180.1 → NP_001399109.1  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1B isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC091738, AC092536, AC211469

    4. NM_001412181.1 → NP_001399110.1  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1B isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC211469

    5. NM_001412182.1 → NP_001399111.1  S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1B isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC091738, AC092536, AC211469

    RNA

    1. NR_178064.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1, non-coding) uses the same exon combination as variant 1 but represents the allele encoded by the T2T-CHM13v2.0 genome assembly. This variant is represented as non-coding because a frameshift results in a premature stop codon.
      Source sequence(s)
      CP068271

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      72574513..72828200 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      73793064..74052329 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001145441.1: Suppressed sequence

      Description
      NM_001145441.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

    2. NR_027031.1: Suppressed sequence

      Description
      NR_027031.1: This RefSeq was permanently suppressed because the transcript represents an alternate, non-coding haplotype and is out-of-scope.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6NUM6.4 GenPept UniProtKB/Swiss-Prot:Q6NUM6

    Gene LinkOut

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

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