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

    Gene ID: 229096, updated on 9-Dec-2024

    Summary

    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 reader 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. Is expressed in brain; cerebral cortex ventricular layer; cortical plate; intestine; and liver. Orthologous to human YTHDF3 (YTH N6-methyladenosine RNA binding protein F3). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 17.9), limb E14.5 (RPKM 16.0) and 28 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Ythdf3 in Genome Data Viewer
    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

    Expression

    • 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

    Variation

    Alleles

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 N6-methyladenosine-containing RNA reader activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables RNA binding IEA
    Inferred from Electronic Annotation
    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
     
    enables ribosome binding ISS
    Inferred from Sequence or Structural Similarity
    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 mRNA destabilization ISS
    Inferred from Sequence or Structural Similarity
    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 organelle assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of translation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of translation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    NOT involved_in positive regulation of translational initiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of translational initiation ISO
    Inferred from Sequence Orthology
    more info
     
    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 regulation of trophoblast cell migration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in stress granule assembly ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in stress granule assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in P-body ISO
    Inferred from Sequence Orthology
    more info
     
    located_in P-body ISS
    Inferred from Sequence or Structural Similarity
    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
     
    located_in cytoplasmic stress granule ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001145919.2NP_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:417550
      YTH; YT521-B-like domain
    2. NM_001358041.1NP_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:421554
      YTH; YT521-B-like domain
    3. NM_001358042.1NP_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:366499
      YTH; YT521-B-like domain
    4. NM_001358043.1NP_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:366499
      YTH; YT521-B-like domain
    5. NM_172677.4NP_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:428561
      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_006535442.5XP_006535505.1  YTH domain-containing family protein 3 isoform X1

      Conserved Domains (1) summary
      pfam04146
      Location:432565
      YTH; YT521-B-like domain
    2. XM_036163023.1XP_036018916.1  YTH domain-containing family protein 3 isoform X2

      UniProtKB/TrEMBL
      Q7TN20
      Conserved Domains (1) summary
      pfam04146
      Location:366499
      YTH; YT521-B-like domain
    3. XM_036163024.1XP_036018917.1  YTH domain-containing family protein 3 isoform X2

      UniProtKB/TrEMBL
      Q7TN20
      Conserved Domains (1) summary
      pfam04146
      Location:366499
      YTH; YT521-B-like domain
    4. XM_036163025.1XP_036018918.1  YTH domain-containing family protein 3 isoform X2

      UniProtKB/TrEMBL
      Q7TN20
      Conserved Domains (1) summary
      pfam04146
      Location:366499
      YTH; YT521-B-like domain