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

YTHDF2 Gene

protein-coding   GIFtS: 52
GCID: GC01P029063

YTH Domain Family, Member 2

(Previous name: YTH domain family 2)
  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 Family, Member 21 2     YTH Domain Family 21
High-Glucose-Regulated Protein 82 3     9430020E02Rik2
Renal Carcinoma Antigen NY-REN-22 3     NY-REN-22
HGRG82 3     YTH Domain Family Protein 22
CLL-Associated Antigen KW-142 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 Gene:
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)

GeneCards Summary for YTHDF2 Gene: 
YTHDF2 (YTH domain family, member 2) is a protein-coding gene. Diseases associated with YTHDF2 include acute myeloid leukemia, and myeloid leukemia. An important paralog of this gene is YTHDF1.




(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_000001.10  NC_018912.2  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 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: 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

Explore proteomics data for YTHDF2 at MOPED 

Post-translational modifications:

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

  • YTHDF2 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    YTHDF2 Protein Expression
    REFSEQ proteins (3 alternative transcripts): 
    NP_001166299.1  NP_001166599.1  NP_057342.2  

    ENSEMBL proteins: 
     ENSP00000474446   ENSP00000362918   ENSP00000474784   ENSP00000444660   ENSP00000439394  

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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 Q9Y5A9

    ProtoNet protein and cluster: Q9Y5A9

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

    UniProtKB/Swiss-Prot: YTHD2_HUMAN, Q9Y5A9
    Similarity: Contains 1 YTH domain


    YTHDF2 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

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

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for YTHDF2 
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    SwitchGear 3'UTR luciferase reporter plasmidYTHDF2 3' UTR sequence
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    (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 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, 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 YTHDF2 (YTHD2)

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

    (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 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
    miRNA
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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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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat YTHDF2
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat YTHDF2

    Additional mRNA 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):

    CB305414 BQ642076 BX442178 AI650357 AI468335 AI500186 BU634093 AA278406 
    AI920785 CB147652 BX461087 AW292279 BX450710 AA128950 AA112736 CB306475 
    BQ182901 BM989398 BF792382 CA440052 AI355344 H84221 CR594279 BM978544 

    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 <intensity>2/3
    CGAP TAG: TGCAGGTGTG
    YTHDF2 Expression
    About this image


    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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    (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 7/16 species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ythdf21 , 5 YTH domain family 21, 5 95.68(n)1
    99.65(a)1
      4 (64.92 cM)5
    2135411  NM_145393.41  NP_663368.31 
     1321849125 
    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
    Uncharacterized protein
    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
    --
    25(a)
    1 → many
    3R(20859866-20864801)
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes YDR374C6
    Putative protein of unknown function
    29(a)
    1 → many
    IV(1223474-1224394)
    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  YTHDF32  
    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, 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

    10/731 SNPs in YTHDF2 are shown (see all 731)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1996553621,2
    --27324897(+) CCCCC-/GCCCCC 3 -- int10--------
    rs1465690761,2
    C--27331462(+) TGTTT-/TTGTTGTT 3 -- cds10--------
    rs112998641,2
    C--27336595(+) ACTTTC/-CAACT 3 -- int13Minor allele frequency- -:0.17NA CSA 6
    rs2004040631,2
    --27340286(+) TGTGT-/GTATTTTT 3 -- int10--------
    rs1460190111,2
    C--27343114(+) TATTT-/TTTTTT 3 -- int10--------
    rs106592131,2
    C--27344590(+) GTTTT-/TTGAGAG 3 -- int10--------
    rs114231181,2
    C--27346957(+) ACGCC-/CAGCTA 3 -- int10--------
    rs1137077781,2
    C--27347013(+) GGATGG/-TCTCA 3 -- int11Minor allele frequency- -:0.00CSA 2
    rs339140741,2
    C--29061384(+) CCGGC-/TTTTTT 2 -- us2k11Minor allele frequency- T:0.00NA 2
    rs350731931,2
    C--29072237(+) CCCGCC/-CCCCC 3 -- int11Minor allele frequency- -:0.00NA 2

    HapMap Linkage Disequilibrium report for YTHDF2 (29063133 - 29096287 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for YTHDF2:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2745830CNV Deletion23290073
    nsv509080CNV Insertion20534489
    nsv160265CNV Loss16902084


    Human Gene Mutation Database (HGMD): YTHDF2
    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
    OMIM gene information: 610640    OMIM disorders: --

    5 diseases for YTHDF2:    About MalaCards
    acute myeloid leukemia    myeloid leukemia    leukemia    renal cell carcinoma
    breast cancer


    YTHDF2 for disorders           About GeneDecksing

    Genetic Association Database (GAD): YTHDF2
    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)
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    PubMed articles for YTHDF2 gene, integrated from 9 sources (see all 35):
    (articles sorted by number of sources associating them with YTHDF2)
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    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. A polymorphism of the YTHDF2 gene (1p35) located in an Alu-rich genomic domain is associated with human longevity. (PubMed id 16799135)1, 4 Cardelli M....Franceschi C. (2006)
    3. Interlaboratory reproducibility of large-scale human p rotein-complex analysis by standardized AP-MS. (PubMed id 23455922)1 Varjosalo M....Superti-Furga G. (2013)
    4. Identification of the hypoxia-inducible factor 2a nucl ear interactome in melanoma cells reveals master proteins involved in melanoma d evelopment. (PubMed id 23275444)1 Steunou A.L....Nieto L. (2013)
    5. 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)
    6. A high-throughput approach for measuring temporal chan ges in the interactome. (PubMed id 22863883)1 Kristensen A.R....Foster L.J. (2012)
    7. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (2012)
    8. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    9. 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)
    10. 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)

    (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)
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    Entrez Gene: 51441 HGNC: 31675 AceView: YTHDF2 Ensembl:ENSG00000198492 euGenes: HUgn51441
    ECgene: YTHDF2 H-InvDB: YTHDF2

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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    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.)
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    Patent Information for YTHDF2 gene:
    Search GeneIP for patents involving YTHDF2

    GeneCards and IP:
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