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

Gene ID: 240255, updated on 14-May-2024

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
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Genomic context

See Ythdc2 in Genome Data Viewer
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_000084.7Genomic Context describing neighboring genes Neighboring gene mutated in colorectal cancers Neighboring gene STARR-seq mESC enhancer starr_44470 Neighboring gene predicted gene, 52347 Neighboring gene STARR-seq mESC enhancer starr_44475 Neighboring gene STARR-seq mESC enhancer starr_44477 Neighboring gene RIKEN cDNA A930012L18 gene Neighboring gene STARR-seq mESC enhancer starr_44478 Neighboring gene STARR-seq mESC enhancer starr_44479 Neighboring gene STARR-seq mESC enhancer starr_44481 Neighboring gene STARR-seq mESC enhancer starr_44482 Neighboring gene STARR-seq mESC enhancer starr_44483 Neighboring gene STARR-seq mESC enhancer starr_44484 Neighboring gene STARR-seq mESC enhancer starr_44486 Neighboring gene predicted gene, 31706 Neighboring gene mortality factor 4 like 1 pseudogene Neighboring gene DnaJ (Hsp40) homolog, subfamily C, member 30 pseudogene

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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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

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

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
XP_006525978.1
XP_030106314.1

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)

  1. NM_001163013.2NP_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:61119
    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:831916
    HA2; Helicase associated domain (HA2) Add an annotation
    cd00046
    Location:225364
    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:502587
    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:625757
    Helicase_C; Helicase conserved C-terminal domain
    pfam04146
    Location:13041434
    YTH; YT521-B-like domain
    pfam07717
    Location:9541081
    OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold
    pfam13637
    Location:524574
    Ank_4; Ankyrin repeats (many copies)
    sd00045
    Location:520552
    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

  1. NC_000084.7 Reference GRCm39 C57BL/6J

    Range
    44961521..45022782
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Conserved Domains (7) summary
    PHA02653
    Location:6139
    PHA02653; RNA helicase NPH-II; Provisional
    COG0666
    Location:189294
    ANKYR; Ankyrin repeat [Signal transduction mechanisms]
    COG1643
    Location:318716
    HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]
    sd00045
    Location:205237
    ANK; ANK repeat [structural motif]
    pfam04146
    Location:9891119
    YTH; YT521-B-like domain
    pfam07717
    Location:671766
    OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold
    cl28899
    Location:168
    DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
  2. XM_006525915.4XP_006525978.1  3'-5' RNA helicase YTHDC2 isoform X2

    Conserved Domains (3) summary
    COG1643
    Location:77475
    HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]
    pfam04146
    Location:748878
    YTH; YT521-B-like domain
    pfam07717
    Location:430525
    OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold

RNA

  1. XR_385990.5 RNA Sequence