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YTHDC1 Gene

protein-coding   GIFtS: 51

GC04M068858
YTH domain containing 1
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
KIAA1966 1, 2, 3
YT521 1, 2, 3
YT521-B 1, 2
Descriptions
Putative splicing factor YT521 3
YTH domain containing 1 2
splicing factor YT521-B 2
External Ids
HGNC: 306261
Entrez Gene: 917462
UniProtKB: Q96MU73
Ensembl: ENSG000000838967
Search outside databases for aliases for YTHDC1 gene

Previous GC identifer: GC04M069008

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the YTHDC1 gene  

Entrez Gene cytogenetic band: 4q13.2   Ensembl cytogenetic band:  4q13.2   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)

GeneLoc gene densities for chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04M068858:     (about GC identifiers)

Start:
68,858,700 bp from pter
End:
68,898,419 bp from pter
Size:
39,720 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000004.10  NT_022778.15  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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)
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;
PDB structures from and Proteopedia :
2YUD (3D)    
Secondary accessions: Q4W5Q3 Q7Z622 Q8TF35
Alternative splicing: 2 isoforms:  Q96MU7-1   Q96MU7-2   

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


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


    ENSEMBL proteins: 
    ENSP00000347888 ENSP00000339245 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
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    Browse recombinant and purified proteins available from Enzo Life Sciences
    Browse Abcam for Recombinant Proteins
    Human Recombinant Proteins from Abnova (YTHDC1)
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

    1 Gene Ontology (GO) cellular component term (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634 nucleus IEA--
    About this table

    Antibodies for YTHDC1: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Browse Antibodies at Sigma-Aldrich
    Browse R&D Systems for Antibodies
    Search for antibodies at Abcam and the World's Antibody Gateway (free search engine of over 150 antibody companies)
    Browse Abnova for Monoclonal and Polyclonal Antibodies
    Search Novus for antibodies for YTHDC1

    Assays for YTHDC1: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    Browse R&D Systems for biochemical assays
    Browse biochemical assays available from Enzo Life Sciences

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    1 InterPro domain/family:
     IPR007275 YTH


       GeneDecks  YTHDC1 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q96MU7

    ProtoNet protein and cluster: Q96MU7

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

    UniProtKB/Swiss-Prot: YTDC1_HUMAN, Q96MU7
    Similarity: Contains 1 YTH domain

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (YTHDC1)
    Browse for Gene Knock-down Tools from Millipore
    Browse Abnova for Chimera RNAi Products
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_001031732

                  Applied Biosystems Silencer® siRNAs for YTHDC1

                  Sigma-Aldrich siRNA for YTHDC1  
                         Browse shRNA at Sigma-Aldrich  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Invitrogen Clones for YTHDC1
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                   OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_001031732
                                     Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_001031732
                                     untagged cDNA clones in CMV expression vector (see all 3): NM_001031732 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_001031732

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

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section



    5/9 Interacting proteins for YTHDC1 (ENSP000003392453) via UniProtKB, MINT, and/or STRING (see all 9 )
    InteractantInteraction Details
    GeneCardExternal ID(s)
    KHDRBS2ENSP000002811563STRING (score=.859)
    KHDRBS3ENSP000003481083STRING (score=.842)
    ABL1ENSP000003614233STRING (score=.772)
    SRCENSP000003626593STRING (score=.766)
    EMDENSP000003588573STRING (score=.754)
    About this table

    2 Gene Ontology (GO) biological process terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006397 mRNA processing IEA--
    GO:0008380 RNA splicing IEA--
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for YTHDC1

    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (YTHDC1)
    Browse for Gene Knock-down Tools from Millipore
    Browse Abnova for Chimera RNAi Products
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_001031732

                  Sigma-Aldrich siRNA for YTHDC1  
                         Browse shRNA at Sigma-Aldrich  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_001031732  NM_133370  

    REFSEQ mRNAs for YTHDC1 gene (2 alternative transcripts): 

    NM_001031732.2   NM_133370.2   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_001031732  NM_133370  

                   OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_001031732
                                     Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_001031732
                                     untagged cDNA clones in CMV expression vector (see all 3): NM_001031732 

    Additional cDNA sequence: 

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

    19 DOTS entries:

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

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

    AI521494 BU508352 CB152758 BQ020998 T30693 AA426223 AV654958 CA422945 
    AA247204 BM677688 AV650131 BU622854 CB216292 BM800137 CA436862 BQ231724 
    BC041119 CB151726 AI989475 BQ720809 F12326 BQ029994 CA448429 AI383836 

    highest scoring ESTs for YTHDC1:

    AI990739 AI082831 AI350438 AI380475 AI478440 AI798629 AI989475 AI990284 AK056430 AL120288 

    Unigene Cluster for YTHDC1:

    YTH domain containing 1
    Hs.175955  [show with all ESTs]
    Unigene Representative Sequence: NM_001031732


    GeneLoc Exon Structure

    5/13 Alternative Splicing Database (ASD) splice patterns (SP) for YTHDC1 (see all 13 )

    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:                                                                    -                                                                                       

    ExUns: 20b · 20c ^ 21 ^ 22a · 22b · 22c ^ 23a · 23b
    SP1:  -                 -                           
    SP2:                                                
    SP3:                    -                           
    SP4:                                                
    SP5:                                                

    About this scheme

    ECgene alternative splicing isoforms for YTHDC1

    2 Ensembl transcripts including schematic representations:
    ENST00000355665  ENST00000344157  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    YTHDC1 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for YTHDC1

    1 / 2 / 3

    13 probe-sets matching YTHDC1 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

    75055_i_at2, 3 U95-E 1 1.00 1.00 0.26 0.11 AI990284 0.80 1.00 0.91 1

    83578_at2, 3 U95-D 1 1.00 1.00 0.34 1.01 AI400684 0.60 1.00 0.82 1
    91604_at2, 3 U95-D 1 1.00 1.00 0.49 1.28 AI521494 0.60 1.00 0.82 1

    46050_r_at2, 3 U95-B 1 1.00 1.00 0.50 0.49 AL120288 0.80 1.00 0.91 1

    87919_at2, 3 U95-E 1 1.00 1.00 0.23 0.46 AI990739 1.00 1.00 1.00 1

    75057_r_at2, 3 U95-E 1 1.00 1.00 0.25 0.57 AI990284 0.80 1.00 0.91 1

    39897_at2, 3 U95-A 1 1.00 1.00 0.71 1.74 N36997 0.80 1.00 0.91 1

    212455_at2, 3 U133-A 1 1.00 1.00 -- -- N36997 0.80 1.00 0.91 1

    228556_at2, 3 U133-B 1 1.00 1.00 -- -- AI990739 1.00 1.00 1.00 1

    240459_at2, 3 U133-B 1 1.00 1.00 -- -- AW467048 0.40 1.00 0.76 1

    212455_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    228556_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    240459_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    GeneDecks  YTHDC1 for binary patterns associated with the probe-sets selected above  
    About GeneDecksing
    About this table    
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: TAGTTGCACA

    SOURCE GeneReport for Unigene cluster: Hs.175955
    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for YTHDC1 gene from 5/12 species (see all 12 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    YTHDC11   -- YTH domain containing 1 94.21(n)
    98.02(a)
    475161  XM_532391.2  XP_532391.2 
    chimpanzee
    (Pan troglodytes)
    YTHDC11   -- YTH domain containing 1 99.68(n)
    99.72(a)
    461291  XM_517262.2  XP_517262.2 
    cow
    (Bos taurus)
    YTHDC11   -- YTH domain containing 1 94.64(n)
    97.62(a)
    613858  NM_001046520.1  NP_001039985.1 
    rat
    (Rattus norvegicus)
    Yt5211   -- splicing factor YT521-B 92.7(n)
    96.69(a)
    170956  NM_133423.1  NP_596914.1 
    mouse
    (Mus musculus)
    Ythdc11, 5 55
    YTH domain containing 11, 5 93.11(n)1
    97.25(a)1
    2313861  NM_177680.31  NP_808348.21 
     AB2216195  AI1219745  (see all 20)
    About this table        Species with no ortholog for YTHDC1

    ENSEMBL Gene Tree for YTHDC1
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for YTHDC1 gene
    NSBP12  

    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/150 NCBI SNPs in YTHDC1 are shown (see all 150 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 60)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 4 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs17150811,2
    A,C,F,H,O68859393(+) ACATGT/CGCCTC 2 -- ut318Minor allele frequency- C:0.48MN NA EU EA WA 718
    rs22935951,2
    A,C,F,H68861515(-) GGCACA/GCTTTA 2 -- ut3110Minor allele frequency- G:0.42EU EA WA NA 1020
    rs100330581,2
    A,C,F,H68860003(+) GCCAAC/GAGAAT 2 -- ut3116Minor allele frequency- G:0.40EU EA WA NA 1474
    rs17150801,2
    A,C,F,H68858745(+) GACAAT/CAGTCA 2 -- ut314Minor allele frequency- C:0.42EU EA WA 410
    rs175922881,2
    C,F,H68859733(+) TCTAAA/CCTCGG 2 -- ut3115Minor allele frequency- C:0.11NA EU EA WA 1394
    rs38138321,2
    C,F,H68885675(+) TCTCAT/CGGTCA 2 R/H mis1 ese38Minor allele frequency- C:0.11NA EU EA WA 626
    rs68318891,2
    F,H68858211(+) tcataT/Cagaat 2 -- ng514Minor allele frequency- C:0.03EU EA WA 414
    --
    rs170892521,2
    F,H68859557(+) CTACAT/CGGACA 2 -- ut317Minor allele frequency- C:0.36NA EU EA WA 558
    --
    rs362158971,2
    F68898146(-) CGTGCT/ATCTGC 2 -- ut511Minor allele frequency- A:0.02EU 566
    --
    rs170892531,2
    F68860712(+) GTAGCT/CATCAT 2 -- ut313Minor allele frequency- C:0.03NA 130
    About this table

    HapMap Linkage Disequilibrium images for YTHDC1 (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

      --

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    10/22 PubMed articles for YTHDC1 gene (see all 22 ):
    (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, and/or H-InvDB)
    About This Section

    Entrez Gene: 91746 HGNC: 30626 AceView: YT521 Ensembl:ENSG00000083896 euGenes: HUgn91746
    ECgene: YTHDC1 H-InvDB: YTHDC1
    (According to HUGE)
    About This Section

    HUGE: KIAA1966
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

      --
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for YTHDC1:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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     Predesigned and custom siRNAs for YTHDC1 Browse antibodies at Sigma-Aldrich
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