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

YTHDF2 Gene

protein-coding   GIFtS: 51
GCID: GC01P029063

YTH domain family, member 2

(Previous name: YTH domain family 2 )
 Explore 6 diseases affiliated with
YTHDF2 via our new
 Human Malady Compendium 
Biological research products
for YTHDF2
    

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

Aliases
YTH Domain Family, Member 21 2     CLL-Associated Antigen KW-142 3
HGRG81 2 3     YTH Domain Family 21
NY-REN-21 2     9430020E02Rik2
High-Glucose-Regulated Protein 82 3     YTH Domain Family Protein 22
Renal Carcinoma Antigen NY-REN-22 3     

External Ids:    HGNC: 316751   Entrez Gene: 514412   Ensembl: ENSG000001984927   OMIM: 6106405   UniProtKB: Q9Y5A93   

Export aliases for YTHDF2 gene to outside databases

Previous GC identifers: GC01P028751 GC01P028884 GC01P028935 GC01P027315


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

Entrez Gene summary for YTHDF2:
This gene encodes a member of the YTH (YT521-B homology) superfamily containing YTH domain. The YTH domain is typical
for the eukaryotes and is particularly abundant in plants. The YTH domain is usually located in the middle of the
protein sequence and may function in binding to RNA. In addition to a YTH domain, this protein has a proline rich
region which may be involved in signal transduction. An Alu-rich domain has been identified in one of the introns of
this gene, which is thought to be associated with human longevity. In addition, reciprocal translocations between this
gene and the Runx1 (AML1) gene on chromosome 21 has been observed in patients with acute myeloid leukemia. This gene
was initially mapped to chromosome 14, which was later turned out to be a pseudogene. Alternatively spliced transcript
variants encoding different isoforms have been identified in this gene. (provided by RefSeq, Oct 2012)




(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_000001.10  NC_018912.1  NT_004610.19  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the YTHDF2 gene promoter:
         HFH-3   AML1a   AP-2alpha isoform 2   E4BP4   C/EBPalpha   PPAR-alpha   FOXI1   S8   AP-2alpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidYTHDF2 promoter sequence
   Search SABiosciences Chromatin IP Primers for YTHDF2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat YTHDF2


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

Entrez Gene cytogenetic band: 1p35   Ensembl cytogenetic band:  1p35.3   HGNC cytogenetic band: 1p35

YTHDF2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
YTHDF2 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P029063:  view genomic region     (about GC identifiers)

Start:
29,063,133 bp from pter      End:
29,096,287 bp from pter
Size:
33,155 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: YTHD2_HUMAN, Q9Y5A9 (See protein sequence)
Recommended Name: YTH domain family protein 2  
Size: 579 amino acids; 62334 Da
Sequence caution: Sequence=AAD42861.1; Type=Frameshift; Positions=565; Sequence=AAF08813.1; Type=Frameshift;
Positions=565;
Secondary accessions: A6NKG4 A8K966 B4E1G7 D3DPM8 Q5VSZ9 Q8TDH0 Q9BUJ5
Alternative splicing: 2 isoforms:  Q9Y5A9-1   Q9Y5A9-2   (May be due to intron retention. No experimental confirmation available)

Explore the universe of human proteins at neXtProt for YTHDF2: NX_Q9Y5A9

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9Y5A9

  • YTHDF2 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (3 alternative transcripts): 
    NP_001166299.1  NP_001166599.1  NP_057342.2  

    ENSEMBL proteins: 
     ENSP00000362918   ENSP00000444660   ENSP00000439394  

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

    YTHDF2 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR007275 YTH_domain

    Graphical View of Domain Structure for InterPro Entry Q9Y5A9

    ProtoNet protein and cluster: Q9Y5A9

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

    UniProtKB/Swiss-Prot: YTHD2_HUMAN, Q9Y5A9
    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,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    miRNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for YTHDF2

    2 GenomeRNAi human phenotypes for YTHDF2:
     Decreased viability with pacli  Increased gamma-H2AX phosphory 


    (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 YTHDF2

    STRING Interaction Network Preview (showing 5 interactants - click image to see 8)

    5/22 Interacting proteins for YTHDF2 (Q9Y5A93 ENSP000003629184) via UniProtKB, MINT, STRING, and/or I2D (see all 22)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HNRNPH1P319433, ENSP000003491684I2D: score=1 STRING: ENSP00000349168
    MEPCEQ7L2J03, ENSP000003085464I2D: score=1 STRING: ENSP00000308546
    SMAD3P840223, ENSP000003329734I2D: score=1 STRING: ENSP00000332973
    HNRNPA1P096513, ENSP000003418264I2D: score=1 STRING: ENSP00000341826
    POT1Q9NUX53, ENSP000003502494I2D: score=1 STRING: ENSP00000350249
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006959humoral immune response TAS10508479


    YTHDF2 for ontologies           About GeneDecksing



    (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 YTHDF2
    Search CenterWatch for drugs/clinical trials and news about YTHDF2 / YTHD2 

    (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, 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 YTHDF2 gene (3 alternative transcripts): 
    NM_001172828.1  NM_001173128.1  NM_016258.2  

    Unigene Cluster for YTHDF2:

    YTH domain family, member 2
    Hs.532286  [show with all ESTs]
    Unigene Representative Sequence: NM_016258
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000474884 ENST00000373812(uc001brc.3 uc010ofx.2 uc001bre.3)
    ENST00000478283 ENST00000496288 ENST00000475796 ENST00000476976 ENST00000468863
    ENST00000542507(uc021okf.1) ENST00000541996

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    8/33 QIAGEN miScript miRNA Assays for microRNAs that regulate YTHDF2 (see all 33):
    hsa-miR-3607-3p hsa-miR-200a hsa-miR-301a hsa-miR-519a hsa-miR-141 hsa-miR-130b hsa-miR-181b hsa-miR-301b
    SwitchGear 3'UTR luciferase reporter plasmidYTHDF2 3' UTR sequence
    Inhib. RNA
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    Additional cDNA sequence: 

    AB451335.1 AB451484.1 AF155095.1 AF192968.1 AK074276.1 AK292581.1 AK303833.1 BC002559.2 

    23 DOTS entries:

    DT.448634  DT.202769  DT.95166815  DT.100884786  DT.100884782  DT.120759786  DT.100884776  DT.100884781 
    DT.120759785  DT.121431552  DT.97847970  DT.121431566  DT.99971591  DT.100721532  DT.100884785  DT.101964561 
    DT.121431538  DT.121431544  DT.121431549  DT.95166788  DT.95166857  DT.97777074  DT.91812378 

    24/448 AceView cDNA sequences (see all 448):

    BX461087 BE748735 BU680187 BU623451 CB147652 BQ182901 BQ575200 AI968258 
    BM824921 BX346894 AA825580 AW473215 CD364914 BX461086 CA438638 CB160717 
    AW192011 AA100514 BF792382 AI468335 AI027080 BQ020122 AI282952 BQ946104 

    GeneLoc Exon Structure

    5/7 Alternative Splicing Database (ASD) splice patterns (SP) for YTHDF2 (see all 7)    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c · 6d · 6e ^ 7 ^ 8
    SP1:        -           -     -                                   -         
    SP2:                    -     -                                             
    SP3:                                                                        
    SP4:                                                                        
    SP5:                    -     -                                             


    ECgene alternative splicing isoforms for YTHDF2

    (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

    YTHDF2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TGCAGGTGTG

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    YTHDF2 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    Head MesenchymeBranchial Arch 1Cranial Neural Crest CellsNeural Crest
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See YTHDF2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for YTHDF2

    SOURCE GeneReport for Unigene cluster: Hs.532286
        SABiosciences Custom PCR Arrays for YTHDF2
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    In Situ
    Assay Products:
     

     
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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)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for YTHDF2 gene from 6/23 species (see all 23)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves YTHDF21 YTH domain family, member 2 82.94(n)
    93.87(a)
      419583  XM_003642575.1  XP_003642623.1 
    lizard
    (Anolis carolinensis)
    Reptilia YTHDF26
    --
    92(a)
    1 ↔ 1
    GL344007.1(85722-96786)
    zebrafish
    (Danio rerio)
    Actinopterygii zgc562242 hypothetical protein MGC56224 80.26(n)   393220  BC047846.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG64226
    --
    26(a)
    1 → many
    3R(20859866-20864801)
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons ECT16
    ECT36
    (see all 11)
    uncharacterized protein
    evolutionarily conserved C-terminal region 3 prote...
    (see all 11)
    25(a)
    23(a)
    (see all 11)
    many ↔ many
    many ↔ many
    (see all 11)
    3(1021260-1024009)
    5(24557201-24559879)
    rice
    (Oryza sativa)
    Liliopsida Os.87832 Oryza sativa (japonica cultivar-group) cDNA cloneJ more 77.31(n)    AK072392.1 


    ENSEMBL Gene Tree for YTHDF2 (if available)
    TreeFam Gene Tree for YTHDF2 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for YTHDF2 gene
    YTHDF12  
    4 SIMAP similar genes for YTHDF2 using alignment to 2 protein entries:     YTHD2_HUMAN (see all proteins):
    DKFZp451A052    YTHDF3    DKFZp451J085    YTHDF1

    YTHDF2 for paralogs           About GeneDecksing


    2 Pseudogenes.org Pseudogenes for YTHDF2
    PGOHUM00000248146 PGOHUM00000257209


    (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

    10/585 NCBI SNPs in YTHDF2 are shown (see all 585    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs749336121,2
    F,--27314733(+) GTCTCC/AATTAA 3 -- us2k11Minor allele frequency- A:0.03WA 118
    rs172622931,2
    C,F,H,--27315091(+) ACAGAG/ATCTCG 3 -- us2k113Minor allele frequency- A:0.04NA NS EA 1506
    rs120680751,2
    C,F,H,--27315384(+) TGCATG/AAGGTG 3 -- us2k119Minor allele frequency- A:0.14NS EA NA WA 2034
    rs13180001,2
    C,H,--27315841(+) CTGGTC/AGTCCC 3 -- ut51 us2k19Minor allele frequency- A:0.01MN NS EA NA 902
    rs617875671,2
    C,F,--27316691(+) TCTTCC/TTCACT 3 -- int13Minor allele frequency- T:0.25NA 124
    rs726638601,2
    C,--27317596(+) GATTCA/TTTTTT 3 -- int10--------
    rs754647711,2
    F,--27318506(+) ACGTAG/ATGTCA 3 -- int11Minor allele frequency- A:0.02NA 120
    rs109151911,2
    C,F,--27318761(+) CCATGC/GCCGGC 3 -- int15Minor allele frequency- G:0.31NA WA CSA 126
    rs789122821,2
    --27320917(+) GGAACG/AGCTGT 3 -- int11Minor allele frequency- A:0.01WA 118
    rs783621821,2
    C,F,--27321331(+) ATTCTC/TCTGCC 3 -- int12Minor allele frequency- T:0.50WA 4

    HapMap Linkage Disequilibrium report for YTHDF2 (29063133 - 29096287 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for YTHDF2
         1 CNV: 5481
    Human Gene Mutation Database (HGMD): YTHDF2

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing YTHDF2
    DNA2.0 Custom Variant and Variant Library Synthesis for YTHDF2

    (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

    YTHDF2 for disorders           About GeneDecksing

    OMIM gene information: 610640    OMIM disorders: --

    6 diseases for YTHDF2:    About MalaCards
    acute myeloid leukemia    myeloid leukemia    renal carcinoma    leukemia
    carcinoma    renal cell carcinoma

    Human Genome Epidemiology (HuGE) Navigator: YTHDF2 (1 document)

    Export disorders for YTHDF2 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 YTHDF2 gene, integrated from 9 sources (see all 29):
    (articles sorted by number of sources associating them with YTHDF2)
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    world of online information

    1. Antigens recognized by autologous antibody in patients with renal- cell carcinoma. (PubMed id 10508479)1, 2, 3 Scanlan M.J....Old L.J. (1999)
    2. Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (2012)
    3. A high-throughput approach for measuring temporal chan ges in the interactome. (PubMed id 22863883)1 Kristensen A.R....Foster L.J. (2012)
    4. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    5. 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)
    6. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
    7. Identification of proteins associated with ligand-acti vated estrogen receptor a in human breast cancer cell nuclei by tandem affinity purification and nano LC-MS/MS. (PubMed id 21182205)1 Tarallo R....Weisz A. (2011)
    8. 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)
    9. Interactions of pathological hallmark proteins: tubul in polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (2011)
    10. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (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: 51441 HGNC: 31675 AceView: YTHDF2 Ensembl:ENSG00000198492 euGenes: HUgn51441
    ECgene: YTHDF2 H-InvDB: YTHDF2

    (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 YTHDF2 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for YTHDF2 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for YTHDF2 gene:
    Search GeneIP for patents involving YTHDF2

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



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