Aliases for YTHDC1 Gene

Aliases for YTHDC1 Gene

  • YTH Domain Containing 1 2 3 5
  • YTH Domain-Containing Protein 1 3 4
  • Splicing Factor YT521 3 4
  • YT521-B 3 4
  • YT521 3 4
  • 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. An important paralog of this gene is YTHDF1.

UniProtKB/Swiss-Prot Summary for YTHDC1 Gene

  • Regulator of alternative splicing that specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs (PubMed:26318451, PubMed:26876937, PubMed:25242552, PubMed:28984244). 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). Also involved in nuclear export of m6A-containing mRNAs via interaction with SRSF3: interaction with SRSF3 facilitates m6A-containing mRNA-binding to both SRSF3 and NXF1, promoting mRNA nuclear export (PubMed:28984244). Also recognizes and binds m6A on other RNA molecules (PubMed:27602518). Involved in random X inactivation mediated by Xist RNA: recognizes and binds m6A-containing Xist and promotes transcription repression activity of Xist (PubMed:27602518). 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 , Rfam classification 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 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 533.5 +1.4 1419 5.4 EP300 FOXK2 HNRNPK ZBTB40 ZNF217 SIN3A NRF1 TCF12 POLR2G SP1 YTHDC1 HSALNG0034917 lnc-TMPRSS11E-5 CENPC UBA6 ENSG00000270257 UGT2B29P TMPRSS11BNL RF00017-4323
GH04J068376 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE dbSUPER 512.8 -26.3 -26295 0.8 ZNF217 CTCF REST RAD21 TRIM22 SMC3 SIN3A KLF9 EBF1 RB1 YTHDC1 MT2P1 RF00004-087
GH04J069025 Enhancer 0.8 ENCODE 22.7 -675.5 -675539 0.7 CTCF POLR2G RAD21 SKI KMT2B FOXA2 SMC3 ZNF205 DRAP1 SMAD4 YTHDC1 UGT2B7 LOC100422020 UGT2B26P lnc-UGT2A3-9
GH04J068372 Promoter/Enhancer 1.2 ENCODE CraniofacialAtlas dbSUPER 12.8 -23.2 -23240 2 NFYB POLR2A HCFC1 CEBPG FOS YY1 SPI1 NR2C1 ETS1 FOSL1 YTHDC1 MT2P1 lnc-TMPRSS11E-5
GH04J068815 Promoter/Enhancer 1.2 EPDnew Ensembl 11.7 -466.4 -466367 1.1 TCF12 POLR2G KDM6A TCF7 ZBTB25 SKI TEAD1 ZKSCAN8 FOXA2 ZSCAN9 UGT2B10 YTHDC1 ENSG00000272626 ENSG00000251424
- 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

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for YTHDC1

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

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, PubMed:28984244). Interacts with SRSF10 (PubMed:26876937). Interacts with KHDRBS3 (By similarity). Interacts with EMD (PubMed:12755701). Interacts with RBMX (PubMed:19282290). Interacts with ZCCHC8 (PubMed:28984244).
    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

Gene Families for YTHDC1 Gene

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

Protein Domains for YTHDC1 Gene

Blocks:
  • YT521-B-like protein
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for YTHDC1 Gene

GenScript: Design optimal peptide antigens:
  • Putative splicing factor YT521 (YTDC1_HUMAN)

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, PubMed:28984244). 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). Also involved in nuclear export of m6A-containing mRNAs via interaction with SRSF3: interaction with SRSF3 facilitates m6A-containing mRNA-binding to both SRSF3 and NXF1, promoting mRNA nuclear export (PubMed:28984244). Also recognizes and binds m6A on other RNA molecules (PubMed:27602518). Involved in random X inactivation mediated by Xist RNA: recognizes and binds m6A-containing Xist and promotes transcription repression activity of Xist (PubMed:27602518). 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 IDA,IEA 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 Models for YTHDC1 Gene

MGI Knock Outs for YTHDC1:

Animal Model Products

CRISPR Products

miRNA for YTHDC1 Gene

miRTarBase miRNAs that target YTHDC1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , 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
nucleus 5
plasma membrane 4
extracellular 1
cytoskeleton 1
mitochondrion 1
cytosol 1
golgi apparatus 1

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:0001673 male germ cell nucleus IEA --
GO:0005634 nucleus IEA,IDA 20167602
GO:0005654 nucleoplasm IDA,IEA --
GO:0005886 plasma membrane IDA --
GO:0016604 nuclear body IEA --
genes like me logo Genes that share ontologies with YTHDC1: view

Pathways & Interactions for YTHDC1 Gene

PathCards logo

SuperPathways 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:0000398 mRNA splicing, via spliceosome IEA --
GO:0006376 mRNA splice site selection IDA 20167602
GO:0006397 mRNA processing IEA --
GO:0006406 mRNA export from nucleus IDA 28984244
GO:0007283 spermatogenesis IEA --
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

3 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR 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

Expression for YTHDC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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 31 30
  • 99.68 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 94 (a)
OneToMany
-- 31
  • 69 (a)
OneToMany
-- 31
  • 62 (a)
OneToMany
-- 31
  • 59 (a)
OneToMany
-- 31
  • 51 (a)
OneToMany
dog
(Canis familiaris)
Mammalia YTHDC1 31 30
  • 92.97 (n)
OneToOne
cow
(Bos Taurus)
Mammalia YTHDC1 31 30
  • 92.92 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ythdc1 30
  • 92.61 (n)
mouse
(Mus musculus)
Mammalia Ythdc1 17 31 30
  • 92.06 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia YTHDC1 31
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves YTHDC1 31
  • 81 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia YTHDC1 31
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ythdc1 30
  • 76.96 (n)
Str.6830 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.7841 30
zebrafish
(Danio rerio)
Actinopterygii ythdc1 31 30
  • 75.81 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.776 30
fruit fly
(Drosophila melanogaster)
Insecta YT521-B 31
  • 28 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea Cin.1604 30
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.1604 30
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

Paralogs for YTHDC1 Gene

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

Variants for YTHDC1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for YTHDC1 Gene

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
rs3813832 - p.His183Arg

Additional dbSNP identifiers (rs#s) for YTHDC1 Gene

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

No publications were found for YTHDC1 Gene.

Products for YTHDC1 Gene

Sources for YTHDC1 Gene