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

Gene ID: 441250, updated on 2-Nov-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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See TYW1B in Genome Data Viewer
Location:
7q11.22-q11.23
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (72574513..72828200, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (73793064..74052329, complement)
RS_2024_09 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 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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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)

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_2024_08

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

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