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Aliases for YTHDC1 Gene

Aliases for YTHDC1 Gene

  • YTH Domain Containing 1 2 3 5
  • Splicing Factor YT521 3 4
  • YT521-B 3 4
  • YT521 3 4
  • YTH Domain-Containing Protein 1 3
  • Putative Splicing Factor YT521 3
  • Splicing Factor YT521-B 3
  • KIAA1966 4

External Ids for YTHDC1 Gene

Previous GeneCards Identifiers for YTHDC1 Gene

  • GC04M069008
  • GC04M068858
  • GC04M069176
  • GC04M065089

Summaries for YTHDC1 Gene

GeneCards Summary for YTHDC1 Gene

YTHDC1 (YTH Domain Containing 1) is a Protein Coding gene. GO annotations related to this gene include poly(A) RNA binding and N6-methyladenosine-containing RNA binding.

UniProtKB/Swiss-Prot for YTHDC1 Gene

  • Regulator of alternative splicing that specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs (PubMed:26318451, PubMed:26876937, PubMed:25242552). 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, PubMed:25242552). Acts as a key regulator of exon-inclusion or exon-skipping during alternative splicing via interaction with mRNA splicing factors SRSF3 and SRSF10 (PubMed:26876937). Specifically binds m6A-containing mRNAs and promotes recruitment of SRSF3 to its mRNA-binding elements adjacent to m6A sites, leading to exon-inclusion during alternative splicing (PubMed:26876937). In contrast, interaction with SRSF3 prevents interaction with SRSF10, a splicing factor that promotes exon skipping: this prevents SRSF10 from binding to its mRNA-binding sites close to m6A-containing regions, leading to inhibit exon skipping during alternative splicing (PubMed:26876937). May also regulate alternative splice site selection (PubMed:20167602).

Gene Wiki entry for YTHDC1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for YTHDC1 Gene

Genomics for YTHDC1 Gene

Regulatory Elements for YTHDC1 Gene

Enhancers for YTHDC1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH04G068372 1.4 Ensembl ENCODE dbSUPER 12.8 -23.2 -23241 2.0 ELF3 FOXA2 CHAMP1 YY1 RARA ETS1 TCF12 ZNF143 HCFC1 CEBPB YTHDC1 MT2P1
GH04G068376 1 ENCODE dbSUPER 12.7 -26.1 -26072 0.2 CTCF SIN3A RAD21 SMC3 ZNF143 MIXL1 ZNF654 TRIM22 REST MNT YTHDC1 MT2P1
GH04G068266 1 Ensembl ENCODE 11 +82.3 82349 1.6 ETV1 JUN BACH1 ZNF175 ZNF644 FOSL1 ZNF316 GATA2 NFE2 SMARCE1 TMPRSS11B YTHDC1 GCOM2 ENSG00000250642
GH04G068271 0.9 Ensembl ENCODE 11 +76.9 76926 2.8 CTCF ZNF654 PKNOX1 TRIM22 REST CHD7 RAD21 HDAC2 SMC3 POU5F1 TMPRSS11B YTHDC1 GCOM2 ENSG00000250642
GH04G068267 0.6 ENCODE 11 +83.6 83558 0.4 MEF2D ZNF639 PKNOX1 GATA2 PBX2 FOXJ2 IRF1 TMPRSS11B YTHDC1 GCOM2 ENSG00000250642
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around YTHDC1 on UCSC Golden Path with GeneCards custom track

Promoters for YTHDC1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000168927 906 2801 HDGF PKNOX1 FOXA2 CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1

Genomic Location for YTHDC1 Gene

Chromosome:
4
Start:
68,310,387 bp from pter
End:
68,350,106 bp from pter
Size:
39,720 bases
Orientation:
Minus strand

Genomic View for YTHDC1 Gene

Genes around YTHDC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
YTHDC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for YTHDC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for YTHDC1 Gene

Proteins for YTHDC1 Gene

  • Protein details for YTHDC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96MU7-YTDC1_HUMAN
    Recommended name:
    YTH domain-containing protein 1
    Protein Accession:
    Q96MU7
    Secondary Accessions:
    • Q4W5Q3
    • Q7Z622
    • Q8TF35

    Protein attributes for YTHDC1 Gene

    Size:
    727 amino acids
    Molecular mass:
    84700 Da
    Quaternary structure:
    • Interacts with KHDRBS1/SAM68 (By similarity). Interacts with SRSF1 (By similarity). Interacts with SRSF2 (By similarity). Interacts with TRA2B (By similarity). Interacts with SRSF3 (PubMed:26876937). Interacts with SRSF10 (PubMed:26876937). Interacts with KHDRBS3 (By similarity). Interacts with EMD (PubMed:12755701). Interacts with RBMX (PubMed:19282290).
    SequenceCaution:
    • Sequence=AAY41024.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=BAB71181.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for YTHDC1 Gene

    Alternative splice isoforms for YTHDC1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for YTHDC1 Gene

Post-translational modifications for YTHDC1 Gene

No data available for DME Specific Peptides for YTHDC1 Gene

Domains & Families for YTHDC1 Gene

Protein Domains for YTHDC1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for YTHDC1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96MU7

UniProtKB/Swiss-Prot:

YTDC1_HUMAN :
  • The YTH domain mediates RNA-binding.
Domain:
  • The YTH domain mediates RNA-binding.
genes like me logo Genes that share domains with YTHDC1: view

No data available for Gene Families for YTHDC1 Gene

Function for YTHDC1 Gene

Molecular function for YTHDC1 Gene

UniProtKB/Swiss-Prot Function:
Regulator of alternative splicing that specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs (PubMed:26318451, PubMed:26876937, PubMed:25242552). 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, PubMed:25242552). Acts as a key regulator of exon-inclusion or exon-skipping during alternative splicing via interaction with mRNA splicing factors SRSF3 and SRSF10 (PubMed:26876937). Specifically binds m6A-containing mRNAs and promotes recruitment of SRSF3 to its mRNA-binding elements adjacent to m6A sites, leading to exon-inclusion during alternative splicing (PubMed:26876937). In contrast, interaction with SRSF3 prevents interaction with SRSF10, a splicing factor that promotes exon skipping: this prevents SRSF10 from binding to its mRNA-binding sites close to m6A-containing regions, leading to inhibit exon skipping during alternative splicing (PubMed:26876937). May also regulate alternative splice site selection (PubMed:20167602).

Gene Ontology (GO) - Molecular Function for YTHDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA,IEA 20167602
GO:0005515 protein binding IPI 19282290
GO:1990247 N6-methyladenosine-containing RNA binding IEA,IDA 25242552
genes like me logo Genes that share ontologies with YTHDC1: view
genes like me logo Genes that share phenotypes with YTHDC1: view

Animal Model Products

miRNA for YTHDC1 Gene

miRTarBase miRNAs that target YTHDC1

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for YTHDC1 Gene

Localization for YTHDC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for YTHDC1 Gene

Nucleus. Nucleus speckle. Note=Localizes to a novel subnuclear structure, the YT bodies. {ECO:0000250 UniProtKB:Q9QY02}.

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 YTHDC1 gene
Compartment Confidence
plasma membrane 5
nucleus 5

Gene Ontology (GO) - Cellular Components for YTHDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 20167602
GO:0005654 nucleoplasm IDA --
GO:0005886 plasma membrane IDA --
GO:0016604 nuclear body IEA --
GO:0016607 nuclear speck IDA,IEA 26876937
genes like me logo Genes that share ontologies with YTHDC1: view

Pathways & Interactions for YTHDC1 Gene

SuperPathways for YTHDC1 Gene

No Data Available

SIGNOR curated interactions for YTHDC1 Gene

Is inactivated by:

Gene Ontology (GO) - Biological Process for YTHDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006376 mRNA splice site selection IDA 20167602
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
GO:0048024 regulation of mRNA splicing, via spliceosome IDA 26876937
genes like me logo Genes that share ontologies with YTHDC1: view

No data available for Pathways by source for YTHDC1 Gene

Drugs & Compounds for YTHDC1 Gene

No Compound Related Data Available

Transcripts for YTHDC1 Gene

mRNA/cDNA for YTHDC1 Gene

Unigene Clusters for YTHDC1 Gene

YTH domain containing 1:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for YTHDC1 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b · 13c ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20a ·
SP1: - - -
SP2: - - -
SP3: - - -
SP4: -
SP5: -
SP6: -
SP7: - -
SP8: - -
SP9:
SP10: -
SP11: -
SP12:
SP13:

ExUns: 20b · 20c ^ 21 ^ 22a · 22b · 22c ^ 23a · 23b
SP1: - -
SP2:
SP3: -
SP4:
SP5:
SP6: - -
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:

Relevant External Links for YTHDC1 Gene

GeneLoc Exon Structure for
YTHDC1
ECgene alternative splicing isoforms for
YTHDC1

Expression for YTHDC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for YTHDC1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for YTHDC1 Gene

This gene is overexpressed in Testis (16.6), CD8 Tcells (7.9), Fetal testis (7.1), Fetal ovary (6.6), and Peripheral blood mononuclear cells (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for YTHDC1 Gene



Protein tissue co-expression partners for YTHDC1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of YTHDC1 Gene:

YTHDC1

SOURCE GeneReport for Unigene cluster for YTHDC1 Gene:

Hs.175955

Evidence on tissue expression from TISSUES for YTHDC1 Gene

  • Nervous system(4.7)
  • Liver(4.3)
  • Skin(4.3)
genes like me logo Genes that share expression patterns with YTHDC1: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for YTHDC1 Gene

Orthologs for YTHDC1 Gene

This gene was present in the common ancestor of animals.

Orthologs for YTHDC1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia YTHDC1 34 35
  • 99.68 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 94 (a)
OneToMany
-- 35
  • 69 (a)
OneToMany
-- 35
  • 62 (a)
OneToMany
-- 35
  • 59 (a)
OneToMany
-- 35
  • 51 (a)
OneToMany
dog
(Canis familiaris)
Mammalia YTHDC1 34 35
  • 92.97 (n)
cow
(Bos Taurus)
Mammalia YTHDC1 34 35
  • 92.92 (n)
rat
(Rattus norvegicus)
Mammalia Ythdc1 34
  • 92.61 (n)
mouse
(Mus musculus)
Mammalia Ythdc1 34 16 35
  • 92.06 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia YTHDC1 35
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves YTHDC1 35
  • 81 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia YTHDC1 35
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ythdc1 34
  • 76.96 (n)
Str.6830 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.7841 34
zebrafish
(Danio rerio)
Actinopterygii ythdc1 34 35
  • 75.81 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.776 34
fruit fly
(Drosophila melanogaster)
Insecta YT521-B 35
  • 28 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.1604 34
Species where no ortholog for YTHDC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • rice (Oryza sativa)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for YTHDC1 Gene

ENSEMBL:
Gene Tree for YTHDC1 (if available)
TreeFam:
Gene Tree for YTHDC1 (if available)

Paralogs for YTHDC1 Gene

No data available for Paralogs for YTHDC1 Gene

Variants for YTHDC1 Gene

Sequence variations from dbSNP and Humsavar for YTHDC1 Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type
rs1000006100 -- 68,320,322(+) CTTAA(C/T)TTTTT intron-variant
rs1000119963 -- 68,319,757(+) ATGTA(C/T)ATGTA intron-variant
rs1000245662 -- 68,313,438(+) ATTTG(A/G)AGGGG nc-transcript-variant, utr-variant-3-prime
rs1000309499 -- 68,349,511(+) CCCTA(A/C)TGAGA intron-variant
rs1000336601 -- 68,327,001(+) GGAGG(C/T)TGAGG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for YTHDC1 Gene

Variant ID Type Subtype PubMed ID
dgv88n17 CNV loss 16327808
esv2759258 CNV gain+loss 17122850
nsv1073769 CNV deletion 25765185
nsv1119002 CNV deletion 24896259
nsv1122086 CNV deletion 24896259
nsv594506 CNV loss 21841781

Variation tolerance for YTHDC1 Gene

Residual Variation Intolerance Score: 18.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.39; 63.59% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for YTHDC1 Gene

Human Gene Mutation Database (HGMD)
YTHDC1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
YTHDC1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for YTHDC1 Gene

Disorders for YTHDC1 Gene

Relevant External Links for YTHDC1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
YTHDC1

No disorders were found for YTHDC1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for YTHDC1 Gene

Publications for YTHDC1 Gene

  1. Emerin interacts in vitro with the splicing-associated factor, YT521- B. (PMID: 12755701) Wilkinson F.L. … Morris G.E. (Eur. J. Biochem. 2003) 3 4 22 64
  2. YTH: a new domain in nuclear proteins. (PMID: 12368078) Stoilov P. … Stamm S. (Trends Biochem. Sci. 2002) 2 3 22 64
  3. Nuclear m(6)A Reader YTHDC1 Regulates mRNA Splicing. (PMID: 26876937) Xiao W. … Yang Y.G. (Mol. Cell 2016) 3 4 64
  4. 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. (J. Biol. Chem. 2015) 3 4 64
  5. Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain. (PMID: 25242552) Xu C. … Min J. (Nat. Chem. Biol. 2014) 3 4 64

Products for YTHDC1 Gene

Sources for YTHDC1 Gene

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