Free for academic non-profit institutions. Other users need a Commercial license

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. Among its related pathways are Chromatin Regulation / Acetylation. Gene Ontology (GO) annotations related to this gene include 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). Involved in S-adenosyl-L-methionine homeostasis by regulating expression of MAT2A transcripts, probably by binding m6A-containing MAT2A mRNAs (By similarity).

Gene Wiki entry for YTHDC1 Gene

Additional gene information 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

GeneHancer (GH) Regulatory Elements for YTHDC1 Gene

Promoters and enhancers for YTHDC1 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
GH04J068346 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 664.8 +1.3 1318 5.2 HDGF PKNOX1 CLOCK FOXA2 SMAD1 ARID4B SIN3A DMAP1 ZNF2 IRF4 YTHDC1 CENPC UBA6 ENSG00000270257 UGT2B29P TMPRSS11BNL APOOP4
GH04J068377 Promoter/Enhancer 1 EPDnew dbSUPER 662.7 -26.3 -26339 0.1 ZNF217 CTCF ZGPAT SIN3A MNT YTHDC1 MT2P1 TMPRSS11E
GH04J067697 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 13.2 +649.9 649917 4.8 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 YBX1 YY1 POLR2B UBA6 UBA6-AS1 CENPC YTHDC1 ENSG00000270257 STAP1 TMPRSS11D GC04P067653
GH04J067720 Enhancer 1.4 Ensembl ENCODE dbSUPER 22.8 +628.5 628472 2.4 PKNOX1 ATF1 ARNT YY1 TCF12 ZNF766 FOS ATF7 KDM4B CAVIN1 PIR61967 PIR51733 UBA6 CENPC YTHDC1 UBA6-AS1 ENSG00000270257 GNRHR LOC100419862 GC04P067653
GH04J067543 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 13.5 +805.0 804973 2.8 HDGF PKNOX1 SMAD1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 CENPC UBA6 YTHDC1 LOC101927237 ENSG00000270257 STAP1 GCOM2 GC04M067379
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around YTHDC1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the YTHDC1 gene promoter:
  • YY1
  • MEF-2A
  • aMEF-2
  • RSRFC4
  • AP-2gamma
  • AP-2beta
  • AP-2alphaA

Genomic Locations for YTHDC1 Gene

Genomic Locations for YTHDC1 Gene
chr4:68,310,387-68,350,106
(GRCh38/hg38)
Size:
39,720 bases
Orientation:
Minus strand
chr4:69,176,105-69,215,824
(GRCh37/hg19)
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

Antibody Products

  • Boster Bio Antibodies for YTHDC1
  • Santa Cruz Biotechnology (SCBT) Antibodies for YTHDC1

No data available for DME Specific Peptides for YTHDC1 Gene

Domains & Families for YTHDC1 Gene

Gene Families for YTHDC1 Gene

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

Protein Domains for YTHDC1 Gene

Blocks:
InterPro:
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

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). Involved in S-adenosyl-L-methionine homeostasis by regulating expression of MAT2A transcripts, probably by binding m6A-containing MAT2A mRNAs (By similarity).

Phenotypes From GWAS Catalog for YTHDC1 Gene

Gene Ontology (GO) - Molecular Function for YTHDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA,IDA 20167602
GO:0005515 protein binding IPI 19282290
GO:1990247 N6-methyladenosine-containing RNA binding IDA,IEA 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

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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Plasma membrane (2)
See all subcellular structures

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,IEA --
GO:0005886 plasma membrane IDA --
GO:0016604 nuclear body IEA --
GO:0016607 nuclear speck IEA,IDA 26876937
genes like me logo Genes that share ontologies with YTHDC1: view

Pathways & Interactions for YTHDC1 Gene

genes like me logo Genes that share pathways with YTHDC1: view

Pathways by source for YTHDC1 Gene

1 Cell Signaling Technology pathway for YTHDC1 Gene

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:0010608 posttranscriptional regulation of gene expression ISS,IEA --
GO:0048024 regulation of mRNA splicing, via spliceosome IDA 26876937
genes like me logo Genes that share ontologies with YTHDC1: view

Drugs & Compounds for YTHDC1 Gene

No Compound Related Data Available

Transcripts for YTHDC1 Gene

mRNA/cDNA for YTHDC1 Gene

(7) REFSEQ mRNAs :
(9) Additional mRNA sequences :
(11) Selected AceView cDNA sequences:
(7) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for YTHDC1 Gene

YTH domain containing 1:
Representative Sequences:

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, 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

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 33
  • 99.68 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 94 (a)
OneToMany
-- 34
  • 69 (a)
OneToMany
-- 34
  • 62 (a)
OneToMany
-- 34
  • 59 (a)
OneToMany
-- 34
  • 51 (a)
OneToMany
dog
(Canis familiaris)
Mammalia YTHDC1 34 33
  • 92.97 (n)
OneToOne
cow
(Bos Taurus)
Mammalia YTHDC1 34 33
  • 92.92 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ythdc1 33
  • 92.61 (n)
mouse
(Mus musculus)
Mammalia Ythdc1 16 34 33
  • 92.06 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia YTHDC1 34
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves YTHDC1 34
  • 81 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia YTHDC1 34
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ythdc1 33
  • 76.96 (n)
Str.6830 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.7841 33
zebrafish
(Danio rerio)
Actinopterygii ythdc1 34 33
  • 75.81 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.776 33
fruit fly
(Drosophila melanogaster)
Insecta YT521-B 34
  • 28 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea Cin.1604 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.1604 33
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)
Aminode:
Evolutionary constrained regions (ECRs) for YTHDC1: view image

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 Variation AA Info Type
rs1000006100 -- 68,320,322(-) T/C intron_variant
rs1000119963 -- 68,319,757(-) T/C intron_variant
rs1000245662 -- 68,313,438(-) G/A 3_prime_UTR_variant, non_coding_transcript_variant
rs1000309499 -- 68,349,511(-) C/A intron_variant
rs1000336601 -- 68,327,001(-) C/T 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)

Additional Variant Information 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

Additional Disease Information for 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 FL … Morris GE (European journal of biochemistry 2003) 3 4 22 58
  2. YTH: a new domain in nuclear proteins. (PMID: 12368078) Stoilov P … Stamm S (Trends in biochemical sciences 2002) 2 3 22 58
  3. Nuclear m(6)A Reader YTHDC1 Regulates mRNA Splicing. (PMID: 26876937) Xiao W … Yang YG (Molecular cell 2016) 3 4 58
  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 (The Journal of biological chemistry 2015) 3 4 58
  5. Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain. (PMID: 25242552) Xu C … Min J (Nature chemical biology 2014) 3 4 58

Products for YTHDC1 Gene

Sources for YTHDC1 Gene

Content
Loading form....