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    Ythdf3 YTH N6-methyladenosine RNA binding protein 3 [ Mus musculus (house mouse) ]

    Gene ID: 229096, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Ythdf3provided by MGI
    Official Full Name
    YTH N6-methyladenosine RNA binding protein 3provided by MGI
    Primary source
    MGI:MGI:1918850
    See related
    Ensembl:ENSMUSG00000047213 AllianceGenome:MGI:1918850
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    9130022A11Rik
    Summary
    Predicted to enable N6-methyladenosine-containing RNA binding activity; mRNA binding activity; and ribosome binding activity. Involved in mRNA destabilization and negative regulation of type I interferon-mediated signaling pathway. Located in cytoplasm. Orthologous to human YTHDF3 (YTH N6-methyladenosine RNA binding protein 3). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 17.9), limb E14.5 (RPKM 16.0) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    3 A1; 3 4.04 cM
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (16237309..16271201)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (16183148..16217037)

    Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_07029 Neighboring gene STARR-seq mESC enhancer starr_07030 Neighboring gene phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoribosylaminoimidazole, succinocarboxamide synthetase pseudogene Neighboring gene predicted gene 5150 Neighboring gene STARR-seq mESC enhancer starr_07031 Neighboring gene STARR-seq mESC enhancer starr_07032 Neighboring gene STARR-seq mESC enhancer starr_07033 Neighboring gene STARR-seq mESC enhancer starr_07034 Neighboring gene STARR-seq mESC enhancer starr_07036 Neighboring gene STARR-seq mESC enhancer starr_07037 Neighboring gene STARR-positive B cell enhancer ABC_E2660 Neighboring gene STARR-seq mESC enhancer starr_07038 Neighboring gene STARR-seq mESC enhancer starr_07039 Neighboring gene STARR-seq mESC enhancer starr_07040 Neighboring gene STARR-seq mESC enhancer starr_07041 Neighboring gene STARR-seq mESC enhancer starr_07042 Neighboring gene STARR-seq mESC enhancer starr_07043 Neighboring gene STARR-seq mESC enhancer starr_07044 Neighboring gene STARR-seq mESC enhancer starr_07045 Neighboring gene STARR-seq mESC enhancer starr_07046 Neighboring gene STARR-seq mESC enhancer starr_07050 Neighboring gene STARR-seq mESC enhancer starr_07051 Neighboring gene STARR-seq mESC enhancer starr_07052 Neighboring gene STARR-seq mESC enhancer starr_07053 Neighboring gene STARR-seq mESC enhancer starr_07054 Neighboring gene STARR-seq mESC enhancer starr_07055 Neighboring gene predicted gene, 30223 Neighboring gene predicted gene, 26485 Neighboring gene predicted gene, 42184

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. The m6A reader YTHDF3-mediated PRDX3 translation alleviates liver fibrosis. Sun R, et al. Redox Biol, 2022 Aug. PMID 35779442, Free PMC Article
    2. YTHDF2 suppresses the plasmablast genetic program and promotes germinal center formation. Grenov A, et al. Cell Rep, 2022 May 3. PMID 35508130, Free PMC Article
    3. RNA-binding protein YTHDF3 suppresses interferon-dependent antiviral responses by promoting FOXO3 translation. Zhang Y, et al. Proc Natl Acad Sci U S A, 2019 Jan 15. PMID 30591559, Free PMC Article
    4. Context-dependent functional compensation between Ythdf m(6)A reader proteins. Lasman L, et al. Genes Dev, 2020 Oct 1. PMID 32943573, Free PMC Article
    5. m(6)A modification controls the innate immune response to infection by targeting type I interferons. Winkler R, et al. Nat Immunol, 2019 Feb. PMID 30559377

    See all (33) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. METTL3-mediated m[6]A modification of SOX4 regulates osteoblast proliferation and differentiation via YTHDF3 recognition.
      Title: METTL3-mediated m(6)A modification of SOX4 regulates osteoblast proliferation and differentiation via YTHDF3 recognition.
    2. The m6A reader YTHDF3-mediated PRDX3 translation alleviates liver fibrosis.
      Title: The m6A reader YTHDF3-mediated PRDX3 translation alleviates liver fibrosis.
    3. findings uncover the role of YTHDF3 as a negative regulator of antiviral immunity through the translational promotion of FOXO3 mRNA under homeostatic conditions, adding insight into the networks of RNA-binding protein-RNA interactions in homeostatically maintaining host antiviral immune function and preventing inflammatory response.
      Title: RNA-binding protein YTHDF3 suppresses interferon-dependent antiviral responses by promoting FOXO3 translation.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables N6-methyladenosine-containing RNA reader activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables N6-methyladenosine-containing RNA reader activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ribosome binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in mRNA destabilization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA destabilization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mRNA destabilization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of type I interferon-mediated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in organelle assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of translation ISO
    Inferred from Sequence Orthology
    more info
    		  
    NOT involved_in positive regulation of translational initiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of mRNA stability IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of mRNA stability ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of trophoblast cell migration ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in stress granule assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in P-body ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasmic stress granule ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    YTH domain-containing family protein 3
    Names
    YTH domain family 3

    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_001145919.2 → NP_001139391.1  YTH domain-containing family protein 3 isoform 2

      See identical proteins and their annotated locations for NP_001139391.1

      Status: VALIDATED

      Source sequence(s)
      BC067040, CJ066078
      Consensus CDS
      CCDS50869.1
      UniProtKB/Swiss-Prot
      Q3UVI5, Q6NXJ6, Q6NXJ8, Q8BKB6, Q8BYK6
      UniProtKB/TrEMBL
      Q7TN20
      Related
      ENSMUSP00000103982.3, ENSMUST00000108345.9
      Conserved Domains (1) summary
      pfam04146
      Location:417 → 550
      YTH; YT521-B-like domain

    2. NM_001358041.1 → NP_001344970.1  YTH domain-containing family protein 3 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AK053736, BC067040, CJ066078
      Consensus CDS
      CCDS89615.1
      UniProtKB/TrEMBL
      Q7TN20
      Related
      ENSMUSP00000141610.2, ENSMUST00000191774.6
      Conserved Domains (1) summary
      pfam04146
      Location:421 → 554
      YTH; YT521-B-like domain

    3. NM_001358042.1 → NP_001344971.1  YTH domain-containing family protein 3 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC122053, BC067040
      UniProtKB/TrEMBL
      Q7TN20
      Conserved Domains (1) summary
      pfam04146
      Location:366 → 499
      YTH; YT521-B-like domain

    4. NM_001358043.1 → NP_001344972.1  YTH domain-containing family protein 3 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC122053, BC067040
      UniProtKB/TrEMBL
      Q7TN20
      Conserved Domains (1) summary
      pfam04146
      Location:366 → 499
      YTH; YT521-B-like domain

    5. NM_172677.4 → NP_766265.3  YTH domain-containing family protein 3 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AK137245, BC067040, CJ066078
      Consensus CDS
      CCDS38396.1
      UniProtKB/Swiss-Prot
      Q8BYK6
      Related
      ENSMUSP00000103983.3, ENSMUST00000108346.5
      Conserved Domains (1) summary
      pfam04146
      Location:428 → 561
      YTH; YT521-B-like domain

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000069.7 Reference GRCm39 C57BL/6J

      Range
      16237309..16271201
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006535442.5 → XP_006535505.1  YTH domain-containing family protein 3 isoform X1

      Conserved Domains (1) summary
      pfam04146
      Location:432 → 565
      YTH; YT521-B-like domain

    2. XM_036163023.1 → XP_036018916.1  YTH domain-containing family protein 3 isoform X2

      UniProtKB/TrEMBL
      Q7TN20
      Conserved Domains (1) summary
      pfam04146
      Location:366 → 499
      YTH; YT521-B-like domain

    3. XM_036163024.1 → XP_036018917.1  YTH domain-containing family protein 3 isoform X2

      UniProtKB/TrEMBL
      Q7TN20
      Conserved Domains (1) summary
      pfam04146
      Location:366 → 499
      YTH; YT521-B-like domain

    4. XM_036163025.1 → XP_036018918.1  YTH domain-containing family protein 3 isoform X2

      UniProtKB/TrEMBL
      Q7TN20
      Conserved Domains (1) summary
      pfam04146
      Location:366 → 499
      YTH; YT521-B-like domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BYK6.2 GenPept UniProtKB/Swiss-Prot:Q8BYK6

    Gene LinkOut

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