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

YTHDC2 Gene

protein-coding   GIFtS: 48
GCID: GC05P112877

YTH domain containing 2

 Explore 2 diseases affiliated with
YTHDC2 via our new
 Human Malady Compendium 
Biological research products
for YTHDC2
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
YTH Domain Containing 21 2     CsA-Associated Helicase-Like Protein2
DKFZp564A1861     Probable ATP-Dependent RNA Helicase YTHDC22
FLJ100531     EC 3.6.4.133
FLJ21941     EC 3.6.18
CAHL2     

External Ids:    HGNC: 247211   Entrez Gene: 648482   Ensembl: ENSG000000471887   UniProtKB: Q9H6S03   

Export aliases for YTHDC2 gene to outside databases

Previous GC identifers: GC05P112926 GC05P108032


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

  --

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000005.9  NC_018916.1  NT_034772.6  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the YTHDC2 gene promoter:
         ISGF-3   POU3F1   NCX/Ncx   C/EBPalpha   GATA-1   CREB   PPAR-gamma1   deltaCREB   PPAR-gamma2   ATF   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidYTHDC2 promoter sequence
   Search SABiosciences Chromatin IP Primers for YTHDC2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat YTHDC2


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

Entrez Gene cytogenetic band: 5q22.2   Ensembl cytogenetic band:  5q22.2   HGNC cytogenetic band: 5q22.3

YTHDC2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
YTHDC2 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P112877:  view genomic region     (about GC identifiers)

Start:
112,849,380 bp from pter      End:
112,930,984 bp from pter
Size:
81,605 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: YTDC2_HUMAN, Q9H6S0 (See protein sequence)
Recommended Name: Probable ATP-dependent RNA helicase YTHDC2  
Size: 1430 amino acids; 160248 Da
Sequence caution: Sequence=BAB15183.1; Type=Erroneous initiation;
1 PDB 3D structure from and Proteopedia for YTHDC2:
2YU6 (3D)    
Secondary accessions: B2RP66

Explore the universe of human proteins at neXtProt for YTHDC2: NX_Q9H6S0

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9H6S0

  • 4/6 DME Specific Peptides for YTHDC2 (Q9H6S0) (see all 6)
     TNIAETS  VDEVHER  GKTTQIPQ  ILSTNIAE 

    YTHDC2 Protein expression data from MOPED and PaxDb:    About this image 
    YTHDC2 Protein Expression
    REFSEQ proteins: NP_073739.3  
    ENSEMBL proteins: 
     ENSP00000161863   ENSP00000426644   ENSP00000423101   ENSP00000422916  

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    Uscn Proteins for YTHDC2


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

    YTHDC2 for domains           About GeneDecksing

    5/9 InterPro domains/families (see all 9):
     IPR007502 Helicase-assoc_dom
     IPR011545 DNA/RNA_helicase_DEAD/DEAH_N
     IPR011709 DUF1605
     IPR001374 R3H_ss-bd
     IPR020683 Ankyrin_rpt-contain_dom

    Graphical View of Domain Structure for InterPro Entry Q9H6S0

    ProtoNet protein and cluster: Q9H6S0

    UniProtKB/Swiss-Prot: YTDC2_HUMAN, Q9H6S0
    Similarity: Belongs to the DEAD box helicase family. DEAH subfamily
    Similarity: Contains 2 ANK repeats
    Similarity: Contains 1 helicase ATP-binding domain
    Similarity: Contains 1 helicase C-terminal domain
    Similarity: Contains 1 R3H domain
    Similarity: Contains 1 YTH domain


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

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: YTDC2_HUMAN, Q9H6S0
    Catalytic activity: ATP + H(2)O = ADP + phosphate

         Enzyme Numbers (IUBMB): EC 3.6.12 EC 3.6.4.131

         Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding IEA--
    GO:0005515protein binding IPI--
    GO:0005524ATP binding IEA--
    GO:0008026ATP-dependent helicase activity IEA--
         
    YTHDC2 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for YTHDC2:
     Decreased p24 protein expressi 

    Animal Models:
       inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for YTHDC2 

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    hsa-miR-495 hsa-miR-607 hsa-miR-181c hsa-miR-520d-5p hsa-miR-4328 hsa-miR-148b hsa-miR-513c hsa-miR-129-3p
    SwitchGear 3'UTR luciferase reporter plasmidYTHDC2 3' UTR sequence
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for YTHDC2


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for YTHDC2

    STRING Interaction Network Preview (showing 5 interactants - click image to see 9)

    5/593 Interacting proteins for YTHDC2 (Q9H6S01, 2, 3 ENSP000001618634) via UniProtKB, MINT, STRING, and/or I2D (see all 593)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SQSTM1Q135012, 3MINT-7945693 I2D: score=1 
    IRF4Q153061, 3, ENSP000003703434EBI-1057466,EBI-751345 I2D: score=1 STRING: ENSP00000370343
    USP42Q9H9J43, ENSP000003019624I2D: score=2 STRING: ENSP00000301962
    IRAK1P516173, ENSP000003589974I2D: score=1 STRING: ENSP00000358997
    LYARQ9NX583, ENSP000003459174I2D: score=1 STRING: ENSP00000345917
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 YTHDC2
    Search CenterWatch for drugs/clinical trials and news about YTHDC2 / YTDC2 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, Sirion Biotech, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for YTHDC2 gene: 
    NM_022828.3  

    Unigene Cluster for YTHDC2:

    YTH domain containing 2
    Hs.231942  [show with all ESTs]
    Unigene Representative Sequence: NM_022828
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000161863(uc003kqn.3) ENST00000503857(uc010jcf.2) ENST00000515883(uc010jce.2)
    ENST00000514720 ENST00000506333 ENST00000512600 ENST00000507567

    miRNA
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    8/20 QIAGEN miScript miRNA Assays for microRNAs that regulate YTHDC2 (see all 20):
    hsa-miR-495 hsa-miR-607 hsa-miR-181c hsa-miR-520d-5p hsa-miR-4328 hsa-miR-148b hsa-miR-513c hsa-miR-129-3p
    SwitchGear 3'UTR luciferase reporter plasmidYTHDC2 3' UTR sequence
    Inhib. RNA
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    Additional cDNA sequence: 

    AK025593.1 AK096486.1 AK131450.1 AK225316.1 AK310855.1 AL049305.1 BC019100.2 BC137285.1 

    11 DOTS entries:

    DT.91754242  DT.40131006  DT.113188  DT.100022403  DT.91754228  DT.95272922  DT.100012653  DT.120812363 
    DT.97793725  DT.91660640  DT.95272923 

    24/168 AceView cDNA sequences (see all 168):

    AA922641 AI207209 BU183816 BG203583 AI992372 AA282082 BC019100 BF056966 
    CR614354 AA976570 AK095368 AI887563 AI332392 AW514633 AA309730 BX437705 
    AA283156 AI434990 AA976993 BX095474 CB268902 AI219789 AI367658 NM_022828 

    GeneLoc Exon Structure

    5/8 Alternative Splicing Database (ASD) splice patterns (SP) for YTHDC2 (see all 8)    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b · 13c ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18a · 18b ^ 19 ^
    SP1:                                                                                                                                                            
    SP2:              -                                                                                                                                             
    SP3:                                                                                                                                                            
    SP4:                                                                                                                          -     -                           
    SP5:                                                                                                                                                            

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


    ECgene alternative splicing isoforms for YTHDC2

    (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

    YTHDC2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TACTTAATAG
    YTHDC2 Expression
    About this image
    See YTHDC2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for YTHDC2

    SOURCE GeneReport for Unigene cluster: Hs.231942
        SABiosciences Custom PCR Arrays for YTHDC2

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for YTHDC2

    (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 eukaryotes.

    Orthologs for YTHDC2 gene from 8/22 species (see all 22)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ythdc21 , 5 YTH domain containing 21, 5 91.59(n)1
    97.06(a)1
      18 (23.81 cM)5
    2402551  NM_001163013.11  NP_001156485.11 
     448286655 
    chicken
    (Gallus gallus)
    Aves YTHDC21 YTH domain containing 2 78.67(n)
    81.4(a)
      415602  XM_413970.3  XP_413970.2 
    lizard
    (Anolis carolinensis)
    Reptilia YTHDC26
    --
    90(a)
    1 ↔ 1
    GL343193.1(7347220-7380577)
    zebrafish
    (Danio rerio)
    Actinopterygii LOC5671141 probable ATP-dependent RNA helicase YTHDC2-like 63.15(n)
    70.15(a)
      567114  XM_690404.5  XP_695496.5 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG89156
    bgcn6
    benign gonial cell neoplasm
    23(a)
    14(a)
    1 ↔ 1
    possible ortholog
    X(17135300-17139045)
    2R(19740801-19746314)
    worm
    (Caenorhabditis elegans)
    Secernentea F52B5.36
    Protein F52B5.3
    20(a)
    1 ↔ 1
    I(8318339-8323976)
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons HVT11 protein helicase in vascular tissue and tapetum 48.62(n)
    37.61(a)
      817631  NM_179823.3  NP_850154.2 
    rice
    (Oryza sativa)
    Liliopsida Os.455072 Oryza sativa (japonica cultivar-group) putative ATP-dependent more 74(n)    NM_184116.1 


    ENSEMBL Gene Tree for YTHDC2 (if available)
    TreeFam Gene Tree for YTHDC2 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for YTHDC2 gene
    DHX402  DHX572  DHX352  DHX92  DHX292  DHX362  DHX302  TDRD92  
    DHX332  DHX162  DHX382  DHX82  
    2 SIMAP similar genes for YTHDC2 using alignment to 4 protein entries:     YTDC2_HUMAN (see all proteins):
    PPP1R12A    DHX36

    YTHDC2 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/1701 NCBI SNPs in YTHDC2 are shown (see all 1701    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1424750901,2
    C,Fother112868683(+) GTTGCC/TGCAGA 2 A syn12Minor allele frequency- T:0.00NA EU 5871
    rs785184161,2
    C--112847398(+) GTTCCA/GGAGAA 1 -- us2k10--------
    rs1381880261,2
    C--112847519(+) GGGTG-/GGAGGAGG 1 -- us2k10--------
    rs1908920091,2
    --112847595(+) GTCAAC/TTTTAT 1 -- us2k10--------
    rs757975321,2
    F--112847647(+) TGCTCG/ATATGC 1 -- us2k11Minor allele frequency- A:0.03WA 118
    rs785982281,2
    --112847650(+) TCGTAC/TGCCAC 1 -- us2k10--------
    rs1471091391,2
    --112847653(+) TATGCC/TACAAG 1 -- us2k10--------
    rs18200581,2
    C,F--112847671(-) TGATAT/AGCCTG 1 -- us2k11Minor allele frequency- A:0.03NA 120
    rs1379449671,2
    --112847694(+) CCCCAG/TTTCTT 1 -- us2k10--------
    rs68715671,2
    C--112847801(+) CAGAAC/TAAGCT 1 -- us2k1 tfbs30--------

    HapMap Linkage Disequilibrium report for YTHDC2 (112849380 - 112930984 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 7 variations for YTHDC2
         3 CNVs: 99258 51530 8495
         4 Indels: 12737 46749 27770 12738

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    (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.)
    About This Section

    YTHDC2 for disorders           About GeneDecksing

    2 diseases for YTHDC2:    About MalaCards
    hepatitis c    hepatitis

    Human Genome Epidemiology (HuGE) Navigator: YTHDC2 (2 documents)

    Export disorders for YTHDC2 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 YTHDC2 gene, integrated from 9 sources (see all 22):
    (articles sorted by number of sources associating them with YTHDC2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (2002)
    3. Functional proteomics establishes the interaction of S IRT7 with chromatin remodeling complexes and expands its role in regulation of R NA polymerase I transcription. (PubMed id 22586326)1 Tsai Y.C....Cristea I.M. (2012)
    4. Mapping a dynamic innate immunity protein interaction network regulating type I interferon production. (PubMed id 21903422)1 Li S....Dorf M.E. (2011)
    5. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    6. Cyclosporin A associated helicase-like protein facili tates the association of hepatitis C virus RNA polymerase with its cellular cyc lophilin B. (PubMed id 21559518)1 Morohashi K....Sugawara F. (2011)
    7. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    8. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
    9. Genome-wide association study identifies genetic vari ants influencing F-cell levels in sickle-cell patients. (PubMed id 21326311)1 Bhatnagar P....Keefer J.R. (2011)
    10. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. (PubMed id 21406692)2 Rigbolt K.T....Blagoev B. (2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 64848 HGNC: 24721 AceView: YTHDC2 Ensembl:ENSG00000047188 euGenes: HUgn64848
    ECgene: YTHDC2 H-InvDB: YTHDC2

    (According to HUGE)
    About This Section
      --

    (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 YTHDC2 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 YTHDC2 gene:
    Search GeneIP for patents involving YTHDC2

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



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