Ythdc2 YTH domain containing 2 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Ythdc2provided by MGI
Official Full Name: YTH domain containing 2provided by MGI
Primary source: MGI:MGI:2448561
See related: Ensembl:ENSMUSG00000034653 AllianceGenome:MGI:2448561
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: mYTHDC2; 3010002F02Rik
Summary: Enables 3'-5' RNA helicase activity and N6-methyladenosine-containing RNA binding activity. Involved in germline cell cycle switching, mitotic to meiotic cell cycle; oocyte development; and spermatid development. Located in cytoplasm and ribonucleoprotein granule. Is expressed in germ cell of ovary; ovary; seminiferous tubule; spermatocyte; and testis. Orthologous to human YTHDC2 (YTH domain containing 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in CNS E18 (RPKM 1.7), CNS E14 (RPKM 1.6) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 18 B3; 18 23.81 cM

Exon count:: 30

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	18	NC_000084.7 (44961521..45022782)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	18	NC_000084.6 (44827730..44889720)

Chromosome 18 - NC_000084.7 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?

The m[6]A reader YTHDC2 maintains visual function and retinal photoreceptor survival through modulating translation of PPEF2 and PDE6B.
Title: The m(6)A reader YTHDC2 maintains visual function and retinal photoreceptor survival through modulating translation of PPEF2 and PDE6B.
The m[6]A reader YTHDC2 promotes SIRT3 expression by reducing the stabilization of KDM5B to improve mitochondrial metabolic reprogramming in diabetic peripheral neuropathy.
Title: The m(6)A reader YTHDC2 promotes SIRT3 expression by reducing the stabilization of KDM5B to improve mitochondrial metabolic reprogramming in diabetic peripheral neuropathy.
Mettl3-mediated m(6) A modification of Lrp2 facilitates neurogenesis through Ythdc2 and elicits antidepressant-like effects.
Title: Mettl3-mediated m(6) A modification of Lrp2 facilitates neurogenesis through Ythdc2 and elicits antidepressant-like effects.
YTHDC2 is required for meiotic progression through the pachytene stage. Inducible inactivation of YTHDC2 causes a massively dysregulated transcriptome in pachytene cells and altered transcripts in YTHDC2-deficient cells encode microtubule network proteins. Depletion of YTHDC2 leads to telomere clustering in pachytene cells.
Title: YTHDC2 is essential for pachytene progression and prevents aberrant microtubule-driven telomere clustering in male meiosis.
N(6) -Methyladenosine Reader Protein YT521-B Homology Domain-Containing 2 Suppresses Liver Steatosis by Regulation of mRNA Stability of Lipogenic Genes.
Title: N(6) -Methyladenosine Reader Protein YT521-B Homology Domain-Containing 2 Suppresses Liver Steatosis by Regulation of mRNA Stability of Lipogenic Genes.
Results suggest that mRNA m(6)A modification and YTHDC2 expression are essential for meiotic initiation and progression in female germ cells.
Title: Critical roles of mRNA m(6)A modification and YTHDC2 expression for meiotic initiation and progression in female germ cells.
The authors propose that regulation of gene expression by YTHDC2-MEIOC is an evolutionarily ancient strategy for controlling the germline transition into meiosis.
Title: ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2.
The authors show that the mammalian YTHDC2 facilitates a clean switch from mitosis to meiosis in mouse germ cells, revealing a conserved role for YTHDC2 in this critical cell fate transition.
Title: The conserved RNA helicase YTHDC2 regulates the transition from proliferation to differentiation in the germline.
YTHDC2 is an N(6)-methyladenosine-binding protein that plays critical roles during spermatogenesis.
Title: Ythdc2 is an N(6)-methyladenosine binding protein that regulates mammalian spermatogenesis.
studies reveal a role for YTHDC2 in modulating the levels of m(6)A-modified germline transcripts to maintain a gene expression program that is conducive for progression through meiosis.
Title: Regulation of m(6)A Transcripts by the 3'→5' RNA Helicase YTHDC2 Is Essential for a Successful Meiotic Program in the Mammalian Germline.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Variation

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Alleles

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

Targeted (4) 1 citation
Chemically induced (ENU) (1) 1 citation
Endonuclease-mediated (12) 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 3'-5' RNA helicase activity	IDA Inferred from Direct Assay more info	PubMed
enables 3'-5' RNA helicase activity	ISO Inferred from Sequence Orthology more info
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP-dependent activity, acting on RNA	ISO Inferred from Sequence Orthology more info
enables N6-methyladenosine-containing RNA reader activity	IDA Inferred from Direct Assay more info	PubMed
enables N6-methyladenosine-containing RNA reader activity	ISO Inferred from Sequence Orthology more info
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA helicase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase binding	ISO Inferred from Sequence Orthology more info
enables helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in germline cell cycle switching, mitotic to meiotic cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within meiotic cell cycle	IEA Inferred from Electronic Annotation more info
involved_in oocyte development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within oogenesis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation by host of viral genome replication	ISO Inferred from Sequence Orthology more info
involved_in response to interleukin-1	ISO Inferred from Sequence Orthology more info
involved_in response to tumor necrosis factor	ISO Inferred from Sequence Orthology more info
involved_in spermatid development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within spermatogenesis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
is_active_in intracellular anatomical structure	IBA Inferred from Biological aspect of Ancestor more info
located_in ribonucleoprotein granule	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: 3'-5' RNA helicase YTHDC2

Names: YTH domain-containing protein C2; keen to exit meiosis leaving testes under-populated protein; ketu; probable ATP-dependent RNA helicase YTHDC2

NP_001156485.1

EC 3.6.4.13

XP_006525978.1

EC 3.6.4.13

XP_030106314.1

EC 3.6.4.13

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_001163013.2 → NP_001156485.1 3'-5' RNA helicase YTHDC2

See identical proteins and their annotated locations for NP_001156485.1

Status: VALIDATED

Source sequence(s)

AC134472, AC137150

Consensus CDS

CCDS50278.1

UniProtKB/Swiss-Prot

B2RR83

Related

ENSMUSP00000048340.8, ENSMUST00000037763.11

Conserved Domains (9) summary

cd06007
Location:61 → 119

R3H_DEXH_helicase; R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may function as ATP-dependent DNA or RNA helicases. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine ...

smart00847
Location:831 → 916

HA2; Helicase associated domain (HA2) Add an annotation

cd00046
Location:225 → 364

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00204
Location:502 → 587

ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...

pfam00271
Location:625 → 757

Helicase_C; Helicase conserved C-terminal domain

pfam04146
Location:1304 → 1434

YTH; YT521-B-like domain

pfam07717
Location:954 → 1081

OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold

pfam13637
Location:524 → 574

Ank_4; Ankyrin repeats (many copies)

sd00045
Location:520 → 552

ANK; ANK repeat [structural motif]

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_000084.7 Reference GRCm39 C57BL/6J

Range

44961521..45022782

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030250454.1 → XP_030106314.1 3'-5' RNA helicase YTHDC2 isoform X1

Conserved Domains (7) summary

PHA02653
Location:6 → 139

PHA02653; RNA helicase NPH-II; Provisional

COG0666
Location:189 → 294

ANKYR; Ankyrin repeat [Signal transduction mechanisms]

COG1643
Location:318 → 716

HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]

sd00045
Location:205 → 237

ANK; ANK repeat [structural motif]

pfam04146
Location:989 → 1119

YTH; YT521-B-like domain

pfam07717
Location:671 → 766

OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold

cl28899
Location:1 → 68

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
XM_006525915.4 → XP_006525978.1 3'-5' RNA helicase YTHDC2 isoform X2

Conserved Domains (3) summary

COG1643
Location:77 → 475

HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]

pfam04146
Location:748 → 878

YTH; YT521-B-like domain

pfam07717
Location:430 → 525

OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold