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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

YTHDC1 Gene

protein-coding   GIFtS: 44
GCID: GC04M069176

YTH Domain Containing 1

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

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     

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, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for YTHDC1 Gene: 
YTHDC1 (YTH domain containing 1) is a protein-coding gene. Diseases associated with YTHDC1 include emery-dreifuss muscular dystrophy, and muscular dystrophy. GO annotations related to this gene include protein binding.

UniProtKB/Swiss-Prot: YTDC1_HUMAN, Q96MU7
Function: May be part of a signal transduction pathway that influences splice site selection (By similarity)

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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000004.11  NT_022778.16  NT_167250.1  NC_018915.2  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for YTHDC1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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_1   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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

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
Subcellular location: Nucleus (By similarity). Note=Localizes to a novel subnuclear structure, the YT bodies (By
similarity)
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:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q96MU7

  • YTHDC1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    YTHDC1 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_001026902.1  NP_588611.2  

    ENSEMBL proteins: 
     ENSP00000448618   ENSP00000447653  

    Human Recombinant Protein Products for YTHDC1: 
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    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for YTHDC1 

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

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

    YTHDC1 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    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
    Similarity: Contains 1 YTH domain


    YTHDC1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: YTDC1_HUMAN, Q96MU7
    Function: May be part of a signal transduction pathway that influences splice site selection (By similarity)

         Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI19282290
         
    YTHDC1 for ontologies           About GeneDecksing


    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:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for YTHDC1 
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    SwitchGear 3'UTR luciferase reporter plasmidYTHDC1 3' UTR sequence
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for YTHDC1


    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for YTHDC1

    5/18 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): 2 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006397mRNA processing IEA--
    GO:0008380RNA splicing IEA--

    YTHDC1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for YTHDC1 (YTDC1)

    Search CenterWatch for drugs/clinical trials and news about 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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    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
    Products:
         
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    8/89 QIAGEN miScript miRNA 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
    Inhib. RNA
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    DNA2.0 Custom Codon Optimized Gene Synthesis Service for YTHDC1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat YTHDC1
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    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat YTHDC1
      QIAGEN 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 

    24/271 AceView cDNA sequences (see all 271):

    AB075846 AA247204 AW590232 BU616437 BU508352 BQ717244 CA448429 CA436862 
    CA422945 BQ029994 BQ231724 BM697583 AA983531 CA441501 AL598932 BU622854 
    AK098515 CA441489 BM990404 AI867928 AI681009 AI824570 AV705969 T30693 

    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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    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


    See YTHDC1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for YTHDC1

    SOURCE GeneReport for Unigene cluster: Hs.175955
        SABiosciences Custom PCR Arrays for YTHDC1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for YTHDC1

    (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)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for YTHDC1 gene from 3/10 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 93.11(n)1
    97.25(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 69.28(n)
    73.49(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)
    About This Section
      --

    (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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/931 SNPs in YTHDC1 are shown (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

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    3 diseases for YTHDC1:    About MalaCards
    emery-dreifuss muscular dystrophy    muscular dystrophy    hypoxia


    YTHDC1 for disorders           About GeneDecksing


    Export disorders for YTHDC1 gene to outside databases

    (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)
    About This Section

    PubMed articles for YTHDC1 gene, integrated from 9 sources (see all 33):
    (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. (2003)
    2. YTH: a new domain in nuclear proteins. (PubMed id 12368078)1, 3, 9 Stoilov P....Stamm S. (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. (2009)
    4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (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. (2005)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (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. (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. (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. (1999)
    10. The evaluation of the FOXO1, KLF9 and YT521 genes expr ession in human endometrial cancer. (PubMed id 23865345)1 Korani M....Maleki J. (2013)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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
    Entrez Gene: 91746 HGNC: 30626 AceView: YT521 Ensembl:ENSG00000257413 euGenes: HUgn91746
    ECgene: YTHDC1 H-InvDB: YTHDC1

    (According to HUGE)
    About This Section
    HUGE: KIAA1966

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    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
    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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