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Aliases for YTHDC2 Gene

Aliases for YTHDC2 Gene

  • YTH Domain Containing 2 2 3 5
  • Probable ATP-Dependent RNA Helicase YTHDC2 3
  • CsA-Associated Helicase-Like Protein 3
  • YTH Domain-Containing Protein 2 4
  • EC 3.6.4.13 4
  • EC 3.6.1 56
  • CAHL 3

External Ids for YTHDC2 Gene

Previous GeneCards Identifiers for YTHDC2 Gene

  • GC05P112926
  • GC05P112877
  • GC05P108032

Summaries for YTHDC2 Gene

Entrez Gene Summary for YTHDC2 Gene

  • This gene encodes a member of the DEAH (Asp-Glu-Ala-His) subfamily of proteins, part of the DEAD (Asp-Glu-Ala-Asp) box family of RNA helicases. The encoded protein binds to N6-methyladenosine, a common modified RNA nucleotide that is enriched in the stop codons and 3' UTRs of eukaryotic messenger RNAs. Binding of proteins to this modified nucleotide may regulate mRNA translation and stability. This gene may be associated with susceptibility to pancreatic cancer in human patients, and knockdown of this gene resulted in reduced proliferation in a human liver cancer cell line. [provided by RefSeq, Sep 2016]

GeneCards Summary for YTHDC2 Gene

YTHDC2 (YTH Domain Containing 2) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and helicase activity. An important paralog of this gene is DHX57.

UniProtKB/Swiss-Prot for YTHDC2 Gene

  • Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs affecting the translation efficiency and mRNA abundance of its targets (PubMed:26318451). Is required for proper spermatocyte development (By similarity). M6A is a modification present at internal sites of mRNAs and some non-coding RNAs and plays a role in the efficiency of mRNA splicing, processing and stability (PubMed:26318451). When associated with MEIOC, binds transcripts that regulate the mitotic cell cycle inhibiting progression into metaphase, thereby allowing meiotic prophase to proceed normally (By similarity).

Additional gene information for YTHDC2 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for YTHDC2 Gene

Genomics for YTHDC2 Gene

GeneHancer (GH) Regulatory Elements for YTHDC2 Gene

Promoters and enhancers for YTHDC2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05I113513 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 561.7 +0.3 287 1.9 PKNOX1 FOXA2 ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 POLR2B ZNF766 YTHDC2 GC05M113600
GH05I113515 Enhancer 0.4 Ensembl 562.2 +1.8 1818 0.2 ZNF362 PRDM10 YTHDC2 GC05M113600
GH05I112973 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 42.2 -536.8 -536757 7.4 FEZF1 DMAP1 YY1 SLC30A9 E2F8 ZNF143 ZNF548 SP3 NFYC ZNF610 DCP2 LOC105379126 YTHDC2 MCC PIR41975
GH05I113487 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 42.4 -24.9 -24915 3.1 ZNF493 SIN3A DMAP1 GLI4 ZNF2 GLIS2 FOS RUNX3 YY2 ZHX2 MCC YTHDC2 ENSG00000272389 TSSK1B
GH05I113202 Enhancer 1.4 Ensembl ENCODE dbSUPER 39.4 -309.3 -309283 3.5 PKNOX1 FOXA2 ARID4B FEZF1 ZNF2 YY1 ZNF213 FOS SP3 REST YTHDC2 GC05M113150 PIR40347 MCC
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around YTHDC2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the YTHDC2 gene promoter:

Genomic Locations for YTHDC2 Gene

Genomic Locations for YTHDC2 Gene
chr5:113,513,683-113,595,287
(GRCh38/hg38)
Size:
81,605 bases
Orientation:
Plus strand
chr5:112,849,380-112,930,984
(GRCh37/hg19)

Genomic View for YTHDC2 Gene

Genes around YTHDC2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
YTHDC2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for YTHDC2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for YTHDC2 Gene

Proteins for YTHDC2 Gene

  • Protein details for YTHDC2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H6S0-YTDC2_HUMAN
    Recommended name:
    Probable ATP-dependent RNA helicase YTHDC2
    Protein Accession:
    Q9H6S0
    Secondary Accessions:
    • B2RP66

    Protein attributes for YTHDC2 Gene

    Size:
    1430 amino acids
    Molecular mass:
    160248 Da
    Quaternary structure:
    • Interacts with MEIOC; binds transcripts that regulate the mitotic cell cycle inhibiting progression into metaphase, thereby allowing meiotic prophase to proceed normally.
    SequenceCaution:
    • Sequence=BAB15183.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for YTHDC2 Gene

neXtProt entry for YTHDC2 Gene

Selected DME Specific Peptides for YTHDC2 Gene

Q9H6S0:
  • GAVLIFLPG
  • VDEVHER
  • ILSTNIAE
  • TNIAETS
  • GKTTQIPQ
  • TGSGKTTQ

Post-translational modifications for YTHDC2 Gene

  • Ubiquitination at posLast=13071307

Domains & Families for YTHDC2 Gene

Gene Families for YTHDC2 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for YTHDC2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9H6S0

UniProtKB/Swiss-Prot:

YTDC2_HUMAN :
  • The YTH domain mediates RNA-binding.
  • Belongs to the DEAD box helicase family. DEAH subfamily.
Domain:
  • The YTH domain mediates RNA-binding.
Family:
  • Belongs to the DEAD box helicase family. DEAH subfamily.
genes like me logo Genes that share domains with YTHDC2: view

Function for YTHDC2 Gene

Molecular function for YTHDC2 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate.
UniProtKB/Swiss-Prot Function:
Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs affecting the translation efficiency and mRNA abundance of its targets (PubMed:26318451). Is required for proper spermatocyte development (By similarity). M6A is a modification present at internal sites of mRNAs and some non-coding RNAs and plays a role in the efficiency of mRNA splicing, processing and stability (PubMed:26318451). When associated with MEIOC, binds transcripts that regulate the mitotic cell cycle inhibiting progression into metaphase, thereby allowing meiotic prophase to proceed normally (By similarity).

Enzyme Numbers (IUBMB) for YTHDC2 Gene

Phenotypes From GWAS Catalog for YTHDC2 Gene

Gene Ontology (GO) - Molecular Function for YTHDC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding HDA,IDA 22658674
GO:0004004 ATP-dependent RNA helicase activity IBA --
GO:0004386 helicase activity IEA --
GO:0005515 protein binding IPI 21903422
genes like me logo Genes that share ontologies with YTHDC2: view
genes like me logo Genes that share phenotypes with YTHDC2: view

Animal Model Products

miRNA for YTHDC2 Gene

miRTarBase miRNAs that target YTHDC2

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for YTHDC2 Gene

Localization for YTHDC2 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for YTHDC2 gene
Compartment Confidence
endoplasmic reticulum 4
nucleus 3
cytosol 3
plasma membrane 1
cytoskeleton 1
mitochondrion 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytoplasmic bodies (2)
  • Nuclear bodies (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for YTHDC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005783 colocalizes_with endoplasmic reticulum IDA 21559518
genes like me logo Genes that share ontologies with YTHDC2: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for YTHDC2 Gene

Pathways & Interactions for YTHDC2 Gene

SuperPathways for YTHDC2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for YTHDC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006396 RNA processing IBA --
GO:0034612 response to tumor necrosis factor IDA 21559518
GO:0044829 positive regulation by host of viral genome replication IMP 21559518
GO:0070555 response to interleukin-1 IDA 21559518
genes like me logo Genes that share ontologies with YTHDC2: view

No data available for Pathways by source and SIGNOR curated interactions for YTHDC2 Gene

Drugs & Compounds for YTHDC2 Gene

(3) Drugs for YTHDC2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
ATP Investigational Nutra Agonist 0

(1) Additional Compounds for YTHDC2 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 58-64-0
genes like me logo Genes that share compounds with YTHDC2: view

Transcripts for YTHDC2 Gene

Unigene Clusters for YTHDC2 Gene

YTH domain containing 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for YTHDC2 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b · 13c ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18a · 18b ^ 19 ^
SP1:
SP2: -
SP3:
SP4: - -
SP5:
SP6:
SP7: - - - -
SP8:

ExUns: 20a · 20b ^ 21a · 21b · 21c ^ 22a · 22b ^ 23
SP1: - -
SP2:
SP3: - -
SP4:
SP5:
SP6:
SP7:
SP8:

Relevant External Links for YTHDC2 Gene

GeneLoc Exon Structure for
YTHDC2
ECgene alternative splicing isoforms for
YTHDC2

Expression for YTHDC2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for YTHDC2 Gene

Protein differential expression in normal tissues from HIPED for YTHDC2 Gene

This gene is overexpressed in Pancreatic juice (25.6), Ovary (8.7), and Cerebrospinal fluid (7.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for YTHDC2 Gene



NURSA nuclear receptor signaling pathways regulating expression of YTHDC2 Gene:

YTHDC2

SOURCE GeneReport for Unigene cluster for YTHDC2 Gene:

Hs.231942

Evidence on tissue expression from TISSUES for YTHDC2 Gene

  • Nervous system(4.3)
  • Adrenal gland(2.2)
genes like me logo Genes that share expression patterns with YTHDC2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for YTHDC2 Gene

Orthologs for YTHDC2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for YTHDC2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia YTHDC2 33 34
  • 99.6 (n)
dog
(Canis familiaris)
Mammalia YTHDC2 34
  • 95 (a)
OneToOne
LOC474641 33
  • 93.78 (n)
oppossum
(Monodelphis domestica)
Mammalia YTHDC2 34
  • 95 (a)
OneToOne
cow
(Bos Taurus)
Mammalia YTHDC2 33 34
  • 93.4 (n)
mouse
(Mus musculus)
Mammalia Ythdc2 33 16 34
  • 91.33 (n)
rat
(Rattus norvegicus)
Mammalia Ythdc2 33
  • 89.91 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia YTHDC2 34
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves YTHDC2 33 34
  • 77.93 (n)
lizard
(Anolis carolinensis)
Reptilia YTHDC2 34
  • 90 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ythdc2 33
  • 73.84 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC567114 33
  • 62.4 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007953 33
  • 49.92 (n)
fruit fly
(Drosophila melanogaster)
Insecta bgcn 34
  • 23 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea F52B5.3 34
  • 23 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons HVT1 33
  • 48.66 (n)
rice
(Oryza sativa)
Liliopsida Os01g0767700 33
  • 49.24 (n)
Os.45507 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 38 (a)
OneToOne
Species where no ortholog for YTHDC2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for YTHDC2 Gene

ENSEMBL:
Gene Tree for YTHDC2 (if available)
TreeFam:
Gene Tree for YTHDC2 (if available)

Paralogs for YTHDC2 Gene

Paralogs for YTHDC2 Gene

(2) SIMAP similar genes for YTHDC2 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with YTHDC2: view

Variants for YTHDC2 Gene

Sequence variations from dbSNP and Humsavar for YTHDC2 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs193921121 uncertain-significance, Malignant tumor of prostate 113,564,033(+) C/A coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs1000009974 -- 113,591,728(+) A/G genic_downstream_transcript_variant, intron_variant
rs1000058056 -- 113,583,673(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000068100 -- 113,514,241(+) G/C intron_variant
rs1000100343 -- 113,514,516(+) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for YTHDC2 Gene

Variant ID Type Subtype PubMed ID
nsv956498 CNV deletion 24416366
nsv599396 CNV loss 21841781
nsv520674 CNV gain 19592680
nsv1161279 CNV duplication 26073780
nsv1120512 CNV tandem duplication 24896259
nsv1033202 CNV gain 25217958
esv3890710 CNV gain 25118596
esv3566475 CNV deletion 23714750
esv2763910 CNV gain+loss 21179565
esv2752057 CNV gain 17911159
esv2730608 CNV deletion 23290073
esv2730606 CNV deletion 23290073
esv2730605 CNV deletion 23290073
esv2730604 CNV deletion 23290073
esv2540445 CNV deletion 19546169
esv2162364 CNV deletion 18987734
esv1743798 CNV deletion 17803354
dgv953e201 CNV deletion 23290073
dgv5783n100 CNV gain 25217958
dgv3149n106 CNV deletion 24896259
dgv208n6 CNV deletion 16902084

Variation tolerance for YTHDC2 Gene

Residual Variation Intolerance Score: 11.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.52; 91.12% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for YTHDC2 Gene

Human Gene Mutation Database (HGMD)
YTHDC2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
YTHDC2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for YTHDC2 Gene

Disorders for YTHDC2 Gene

Additional Disease Information for YTHDC2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for YTHDC2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for YTHDC2 Gene

Publications for YTHDC2 Gene

  1. Structural Basis for the Discriminative Recognition of N6-Methyladenosine RNA by the Human YT521-B Homology Domain Family of Proteins. (PMID: 26318451) Xu C … Min J (The Journal of biological chemistry 2015) 3 4 58
  2. Genome-wide association study identifies genetic variants influencing F-cell levels in sickle-cell patients. (PMID: 21326311) Bhatnagar P … Keefer JR (Journal of human genetics 2011) 3 44 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for YTHDC2 Gene

Sources for YTHDC2 Gene

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