Ythdc1 YTH domain containing 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Ythdc1provided by MGI
Official Full Name: YTH domain containing 1provided by MGI
Primary source: MGI:MGI:2443713
See related: Ensembl:ENSMUSG00000035851 AllianceGenome:MGI:2443713
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: mKIAA1966; A730098D12Rik
Summary: Predicted to enable N6-methyladenosine-containing RNA binding activity and mRNA binding activity. Involved in posttranscriptional regulation of gene expression. Acts upstream of or within gamete generation; in utero embryonic development; and regulation of mRNA processing. Located in nucleus. Orthologous to human YTHDC1 (YTH domain containing 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in CNS E11.5 (RPKM 13.3), CNS E14 (RPKM 10.4) and 26 other tissues See more
Orthologs: human all
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Genomic context

Location:: 5 E1; 5 43.56 cM

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	5	NC_000071.7 (86951349..86984518)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	5	NC_000071.6 (86803980..86836659)

Chromosome 5 - NC_000071.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

YTHDC1 delays cellular senescence and pulmonary fibrosis by activating ATR in an m6A-independent manner.
Title: YTHDC1 delays cellular senescence and pulmonary fibrosis by activating ATR in an m6A-independent manner.
The m6A reader YTHDC1 regulates muscle stem cell proliferation via PI4K-Akt-mTOR signalling.
Title: The m6A reader YTHDC1 regulates muscle stem cell proliferation via PI4K-Akt-mTOR signalling.
The nuclear m6A reader YTHDC1 is essential for embryo viability and germline development in mouse. YTHDC1 plays a critical role in processing of pre-mRNA transcripts in the oocyte nucleus.
Title: Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development.
SILENCING M 6 A READER YTHDC1 REDUCES INFLAMMATORY RESPONSE IN SEPSIS-INDUCED CARDIOMYOPATHY BY INHIBITING SERPINA3N EXPRESSION.
Title: SILENCING M 6 A READER YTHDC1 REDUCES INFLAMMATORY RESPONSE IN SEPSIS-INDUCED CARDIOMYOPATHY BY INHIBITING SERPINA3N EXPRESSION.
Nuclear m6A reader YTHDC1 promotes muscle stem cell activation/proliferation by regulating mRNA splicing and nuclear export.
Title: Nuclear m6A reader YTHDC1 promotes muscle stem cell activation/proliferation by regulating mRNA splicing and nuclear export.
Reduction of mRNA m[6]A associates with glucose metabolism via YTHDC1 in human and mice.
Title: Reduction of mRNA m(6)A associates with glucose metabolism via YTHDC1 in human and mice.
m(6)A reader YTHDC1 modulates autophagy by targeting SQSTM1 in diabetic skin.
Title: m(6)A reader YTHDC1 modulates autophagy by targeting SQSTM1 in diabetic skin.
The RNA m(6)A reader YTHDC1 silences retrotransposons and guards ES cell identity.
Title: The RNA m(6)A reader YTHDC1 silences retrotransposons and guards ES cell identity.

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Variation

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Alleles

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

Targeted (4) 1 citation
Endonuclease-mediated (4) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH126854 (e-PCR)
- UniSTS:208432

AU022537 (e-PCR)
- UniSTS:207816

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 protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within RNA splicing	IEA Inferred from Electronic Annotation more info
involved_in dosage compensation by inactivation of X chromosome	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within in utero embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mRNA alternative polyadenylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA export from nucleus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in mRNA splice site recognition	ISO Inferred from Sequence Orthology more info
involved_in mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
involved_in post-transcriptional regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within primary follicle stage	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of alternative mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of alternative mRNA splicing, via spliceosome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within spermatogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
is_active_in nucleoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: YTH domain-containing protein 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)

NM_001347375.1 → NP_001334304.1 YTH domain-containing protein 1 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 4. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 4.

Source sequence(s)

AC102016

Consensus CDS

CCDS84898.1

UniProtKB/Swiss-Prot

E9Q5K9

Related

ENSMUSP00000113951.2, ENSMUST00000120498.8
NM_001347376.1 → NP_001334305.1 YTH domain-containing protein 1 isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks two alternate in-frame exons compared to variant 4. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 4.

Source sequence(s)

AC102016

Consensus CDS

CCDS84899.1

UniProtKB/Swiss-Prot

E9Q5K9

Related

ENSMUSP00000113000.2, ENSMUST00000119339.8
NM_001359907.1 → NP_001346836.1 YTH domain-containing protein 1 isoform 4

Status: VALIDATED

Description

Transcript Variant: This variant (4) encodes the longest isoform (4).

Source sequence(s)

AC102016

Conserved Domains (1) summary

pfam04146
Location:368 → 506

YTH; YT521-B-like domain
NM_001359908.1 → NP_001346837.1 YTH domain-containing protein 1 isoform 5

Status: VALIDATED

Description

Transcript Variant: This variant (5) lacks an alternate in-frame exon compared to variant 4. The resulting isoform (5) has the same N- and C-termini but is shorter compared to isoform 4.

Source sequence(s)

AC102016

Conserved Domains (1) summary

pfam04146
Location:350 → 488

YTH; YT521-B-like domain
NM_177680.4 → NP_808348.2 YTH domain-containing protein 1 isoform 1

See identical proteins and their annotated locations for NP_808348.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) lacks an alternate in-frame exon and uses an alternate in-frame splice junction compared to variant 4. The resulting isoform (1) has the same N- and C-termini but is shorter compared to isoform 4.

Source sequence(s)

AC102016

Consensus CDS

CCDS39127.1

UniProtKB/Swiss-Prot

E9PW44, E9Q5K9, E9Q7Z8, Q69Z54, Q80V25, Q8R5E6

Related

ENSMUSP00000039133.8, ENSMUST00000038384.8

Conserved Domains (1) summary

pfam04146
Location:356 → 493

YTH; YT521-B-like domain

RNA

NR_153372.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (6) contains an alternate exon compared to variant 4. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC102016

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_000071.7 Reference GRCm39 C57BL/6J

Range

86951349..86984518

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006534867.5 → XP_006534930.1 YTH domain-containing protein 1 isoform X4

Conserved Domains (1) summary

pfam04146
Location:368 → 505

YTH; YT521-B-like domain
XM_006534863.3 → XP_006534926.1 YTH domain-containing protein 1 isoform X1

Conserved Domains (1) summary

pfam04146
Location:368 → 505

YTH; YT521-B-like domain
XM_030254395.2 → XP_030110255.1 YTH domain-containing protein 1 isoform X5

Conserved Domains (1) summary

pfam04146
Location:368 → 505

YTH; YT521-B-like domain
XM_006534865.3 → XP_006534928.1 YTH domain-containing protein 1 isoform X2

Conserved Domains (1) summary

pfam04146
Location:350 → 487

YTH; YT521-B-like domain
XM_017320843.2 → XP_017176332.1 YTH domain-containing protein 1 isoform X3

Conserved Domains (1) summary

pfam04146
Location:338 → 475

YTH; YT521-B-like domain