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YTHDC1 Gene

protein-coding   GIFtS: 46
GCID: GC04M069176

YTH Domain Containing 1

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
YTH Domain Containing 11 2     Splicing Factor YT521-B2
Putative Splicing Factor YT5212 3     YTH Domain-Containing Protein 12
YT5212 3     KIAA19663
YT521-B2 3     

External Ids:    HGNC: 306261   Entrez Gene: 917462   Ensembl: ENSG000002574137   UniProtKB: Q96MU73   

Export aliases for YTHDC1 gene to outside databases

Previous GC identifers: GC04M069008 GC04M068858 GC04M065089


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for YTHDC1 Gene:
YTHDC1 (YTH domain containing 1) is a protein-coding gene.

UniProtKB/Swiss-Prot: YTDC1_HUMAN, Q96MU7
Function: RNA-binding protein that regulates alternative splice site selection

Gene Wiki entry for YTHDC1 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000004.11  NT_016354.20  NT_167250.2  NC_018915.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the YTHDC1 gene promoter:
         MEF-2A   AP-2beta   aMEF-2   AP-2gamma   AP-2alphaA   RSRFC4   YY1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidYTHDC1 promoter sequence
   Search Chromatin IP Primers for YTHDC1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat YTHDC1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 4q13.2   Ensembl cytogenetic band:  HSCHR4_1q13.2   HGNC cytogenetic band: 4q13.3

YTHDC1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
YTHDC1 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04M069176:  view genomic region     (about GC identifiers)

Start:
69,176,103 bp from pter      End:
69,215,824 bp from pter
Size:
39,722 bases      Orientation:
minus strand

1 alternative location:
Chr4-,NT_167250 6,027-45,746     

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: YTDC1_HUMAN, Q96MU7 (See protein sequence)
Recommended Name: YTH domain-containing protein 1  
Size: 727 amino acids; 84700 Da
Subunit: Interacts with EMD, KHDRBS1/SAM68, KHDRBS3, TRA2B/SFRS10, SC35 and SF2 (By similarity). Interacts with
RBMX
Sequence caution: Sequence=AAY41024.1; Type=Erroneous gene model prediction; Sequence=BAB71181.1; Type=Erroneous
initiation;
1 PDB 3D structure from and Proteopedia for YTHDC1:
2YUD (3D)    
Secondary accessions: Q4W5Q3 Q7Z622 Q8TF35
Alternative splicing: 2 isoforms:  Q96MU7-1   Q96MU7-2   

Explore the universe of human proteins at neXtProt for YTHDC1: NX_Q96MU7

Explore proteomics data for YTHDC1 at MOPED

Post-translational modifications: 

  • Tyrosine phosphorylated (By similarity)1
  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See YTHDC1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001026902.1  NP_588611.2  

    ENSEMBL proteins: 
     ENSP00000448618   ENSP00000447653  

    YTHDC1 Human Recombinant Protein Products:

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    antibodies-online peptides for YTHDC1

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    antibodies-online antibodies for YTHDC1 (2 products) 

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR007275 YTH_domain

    Graphical View of Domain Structure for InterPro Entry Q96MU7

    ProtoNet protein and cluster: Q96MU7

    1 Blocks protein domain: IPB007275 YT521-B-like protein

    UniProtKB/Swiss-Prot: YTDC1_HUMAN, Q96MU7
    Domain: The YTH domain mediates RNA-binding (PubMed:20167602)
    Similarity: Contains 1 YTH domain


    Find genes that share domains with YTHDC1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: YTDC1_HUMAN, Q96MU7
    Function: RNA-binding protein that regulates alternative splice site selection

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003723RNA binding IDA--
    GO:0005515protein binding IPI19282290
    GO:0044822poly(A) RNA binding IDA--
         
    Find genes that share ontologies with YTHDC1           About GenesLikeMe


    Phenotypes:
         6 GenomeRNAi human phenotypes for YTHDC1:
     Decreased cell number  Decreased influenza A virus in  Decreased viability of wild-ty  G0/1 arrest 
     Increased circadian period len  Increased gamma-H2AX phosphory 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for YTHDC1

    miRNA
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    miRTarBase miRNAs that target YTHDC1:
    hsa-mir-20a-3p (MIRT038967), hsa-mir-103a-3p (MIRT027037), hsa-mir-1 (MIRT023492), hsa-mir-19b-3p (MIRT031105), hsa-mir-100-5p (MIRT048400), hsa-mir-93-5p (MIRT027989), hsa-mir-16-5p (MIRT031379), hsa-let-7b-5p (MIRT052150)

    Block miRNA regulation of human, mouse, rat YTHDC1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate YTHDC1 (see all 89):
    hsa-miR-520f hsa-miR-300 hsa-miR-15a hsa-miR-200a hsa-miR-605 hsa-miR-30d hsa-miR-30a hsa-miR-3613-3p
    SwitchGear 3'UTR luciferase reporter plasmidYTHDC1 3' UTR sequence
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    YTDC1_HUMAN, Q96MU7: Nucleus. Note=Localizes to a novel subnuclear structure, the YT bodies
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    plasma membrane1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--

    Find genes that share ontologies with YTHDC1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for YTHDC1
    Interactions:

        Search GeneGlobe Interaction Network for YTHDC1

    Selected Interacting proteins for YTHDC1 (Q96MU71, 3) via UniProtKB, MINT, STRING, and/or I2D (see all 18)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ABL1P005193I2D: score=3 
    EMDP504023I2D: score=3 
    FYNP062413I2D: score=3 
    KHDRBS1Q076663I2D: score=2 
    KHDRBS3O755253I2D: score=2 
    About this table

    Gene Ontology (GO): 3 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006376mRNA splice site selection IDA--
    GO:0006397mRNA processing ----
    GO:0008380RNA splicing ----

    Find genes that share ontologies with YTHDC1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for YTHDC1 (YTDC1)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for YTHDC1 gene (2 alternative transcripts): 
    NM_001031732.2  NM_133370.2  

    Unigene Cluster for YTHDC1:

    YTH domain containing 1
    Hs.175955  [show with all ESTs]
    Unigene Representative Sequence: NM_001031732
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000552105 ENST00000550485
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate YTHDC1 (see all 89):
    hsa-miR-520f hsa-miR-300 hsa-miR-15a hsa-miR-200a hsa-miR-605 hsa-miR-30d hsa-miR-30a hsa-miR-3613-3p
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      QuantiTect SYBR Green Assays in human, mouse, rat YTHDC1
      QuantiFast Probe-based Assays in human, mouse, rat YTHDC1

    Additional mRNA sequence: 

    AB075846.1 AK056430.1 AK090836.1 AK098515.1 AL049340.1 AL157447.1 AL832559.1 BC041119.1 
    BC053863.1 

    20 DOTS entries:

    DT.319276  DT.95226740  DT.208534  DT.100030794  DT.319271  DT.92410275  DT.40206935  DT.95095287 
    DT.121236845  DT.100680976  DT.92434776  DT.97826357  DT.92419278  DT.92434777  DT.310195  DT.95226769 
    DT.99939310  DT.121236835  DT.310194  DT.91754711 

    Selected AceView cDNA sequences (see all 271):

    CB152758 AV650131 AK098515 BM677688 AV705969 AI989475 CA436862 BM800137 
    AA294839 CD365942 AI681009 BC041119 AW590232 BQ720809 CA448429 AL598932 
    CA441489 BQ029994 AA381681 F12326 BQ020998 CA393259 CB216292 AI383836 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    YTHDC1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TAGTTGCACA
    YTHDC1 Expression
    About this image


    YTHDC1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 5) fully expand
     
     Bone (Muscoskeletal System)
             Bone Marrow
     
     Ovary (Reproductive System)
     
     Pancreas (Endocrine System)
     
     Uterus (Reproductive System)
     
     Spleen (Hematopoietic System)
    YTHDC1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    YTHDC1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.175955
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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for YTHDC1 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ythdc11 , 5 YTH domain containing 11, 5 92.06(n)1
    94.2(a)1
      5 (43.56 cM)5
    2313861  NM_177680.31  NP_808348.21 
     868042215 
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.78412 Xenopus laevis transcribed sequence with weak similarity more 80.5(n)    BX852085.1 
    zebrafish
    (Danio rerio)
    Actinopterygii ythdc11 YTH domain containing 1 75.81(n)
    86.68(a)
      492769  NM_001007410.1  NP_001007411.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for YTHDC1 (see all 931)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 4 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs68318891,2
    C,F,H--69072268(+) tcataT/Cagaat 2 -- ds500111Minor allele frequency- C:0.05NS EA NA WA 1208
    rs1124052351,2
    C--69072299(+) TTCCCC/AACAAT 2 -- ds50011Minor allele frequency- A:0.50CSA 2
    rs1461429101,2
    C--69072301(+) CCCAAA/CAATTT 2 -- ds50010--------
    rs1931665171,2
    --69072324(+) CCATAA/GCTTAC 2 -- ds50010--------
    rs1172974921,2
    C,F--69072369(+) TGTCGC/TCCAGG 2 -- ds50011Minor allele frequency- T:0.14EA 120
    rs1853443231,2
    --69072373(+) GCCCAG/TGCTGG 2 -- ds50010--------
    rs1889562101,2
    --69072422(+) CTCCCA/GGGTTC 2 -- ds50010--------
    rs1437835501,2
    --69072440(+) TCTCCC/TGCCTC 2 -- ds50010--------
    rs1926177181,2
    --69072463(+) ACCTGG/TGATTA 2 -- ds50010--------
    rs1836559721,2
    --69072473(+) ACAGGC/TATGCG 2 -- ds50010--------

    HapMap Linkage Disequilibrium report for YTHDC1 (69176103 - 69215824 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for YTHDC1:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv88n17CNV Loss16327808
    dgv1626e1CNV Complex17122850
    dgv1628e1CNV Complex17122850

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing YTHDC1
    DNA2.0 Custom Variant and Variant Library Synthesis for YTHDC1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for YTHDC1 gene, integrated from 10 sources (see all 36):
    (articles sorted by number of sources associating them with YTHDC1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Emerin interacts in vitro with the splicing-associated factor, YT521- B. (PubMed id 12755701)1, 2, 9 Wilkinson F.L.... Morris G.E. (Eur. J. Biochem. 2003)
    2. YTH: a new domain in nuclear proteins. (PubMed id 12368078)1, 3, 9 Stoilov P....Stamm S. (Trends Biochem. Sci. 2002)
    3. Heterogeneous nuclear ribonucleoprotein G regulates splice site selection by binding to CC(A/C)-rich regions in pre-mRNA. (PubMed id 19282290)1, 2 Heinrich B.... Stamm S. (J. Biol. Chem. 2009)
    4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (Cell 2006)
    5. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)1, 2 Hillier L.W.... Wilson R.K. (Nature 2005)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    7. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    8. Prediction of the coding sequences of unidentified human genes. XXII. The complete sequences of 50 new cDNA clones which code for large proteins. (PubMed id 11853319)1, 2 Nagase T.... Ohara O. (DNA Res. 2001)
    9. The interaction and colocalization of Sam68 with the splicing-associated factor YT521-B in nuclear dots is regulated by the Src family kinase p59(fyn). (PubMed id 10564280)1, 3 Hartmann A.M....Stamm S. (Mol. Biol. Cell 1999)
    10. The protein interaction landscape of the human CMGC kinase group. (PubMed id 23602568)1 Varjosalo M....Gstaiger M. (Cell Rep 2013)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section

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    Entrez Gene: 91746 HGNC: 30626 AceView: YT521 Ensembl:ENSG00000257413 euGenes: HUgn91746
    ECgene: YTHDC1 H-InvDB: YTHDC1

    (According to HUGE)
    About This Section

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    HUGE: KIAA1966

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for YTHDC1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

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    Patent Information for YTHDC1 gene:
    Search GeneIP for patents involving YTHDC1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from genOway)
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