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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

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