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

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, Nov 2024]
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

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_000069.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Deletion of YTHDF1 (not YTHDF3) reduced brain and gut damage after traumatic brain injury.
Title: Deletion of YTHDF1 (not YTHDF3) reduced brain and gut damage after traumatic brain injury.
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.
The m6A reader YTHDF3-mediated PRDX3 translation alleviates liver fibrosis.
Title: The m6A reader YTHDF3-mediated PRDX3 translation alleviates liver fibrosis.
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)

Endonuclease-mediated (6) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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

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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)

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
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
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
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
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

NC_000069.7 Reference GRCm39 C57BL/6J

Range

16237309..16271201

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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