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

YTHDF3 Gene

protein-coding   GIFtS: 45
GCID: GC08P064081

YTH Domain Family, Member 3

(Previous name: YTH domain family 3)
  Search for YTHDF3
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 31 2
YTH Domain Family 31
YTH Domain Family Protein 32

External Ids:    HGNC: 264651   Entrez Gene: 2539432   Ensembl: ENSG000001857287   UniProtKB: Q7Z7393   

Export aliases for YTHDF3 gene to outside databases

Previous GC identifers: GC08P064132 GC08P064243 GC08P059569


(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 YTHDF3 Gene:
This gene encodes a member of the YTH (YT521-B homology) domain protein family. The YTH domain is common in
eukaryotes, is often found in the middle of the protein sequence, and may function in binding to RNA. Alternative
splicing results in multiple transcript variants. (provided by RefSeq, Apr 2013)

GeneCards Summary for YTHDF3 Gene: 
YTHDF3 (YTH domain family, member 3) is a protein-coding gene. GO annotations related to this gene include protein binding. An important paralog of this gene is YTHDF2.

Gene Wiki entry for YTHDF3 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_000008.10  NC_018919.2  NT_008183.19  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the YTHDF3 gene promoter:
         AhR   Egr-1   FOXD3   LCR-F1   Gfi-1   Arnt   AREB6   S8   Chx10   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidYTHDF3 promoter sequence
   Search SABiosciences Chromatin IP Primers for YTHDF3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat YTHDF3


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

Entrez Gene cytogenetic band: 8q12.3   Ensembl cytogenetic band:  8q12.3   HGNC cytogenetic band: 8q12.3

YTHDF3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
YTHDF3 gene location

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08P064081:  view genomic region     (about GC identifiers)

Start:
64,081,112 bp from pter      End:
64,125,346 bp from pter
Size:
44,235 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: YTHD3_HUMAN, Q7Z739 (See protein sequence)
Recommended Name: YTH domain family protein 3  
Size: 585 amino acids; 63861 Da
Secondary accessions: B3KXL4 Q63Z37 Q659A3

Explore the universe of human proteins at neXtProt for YTHDF3: NX_Q7Z739

Explore proteomics data for YTHDF3 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q7Z739

  • YTHDF3 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    YTHDF3 Protein Expression
    REFSEQ proteins (7 alternative transcripts): 
    NP_001264742.1  NP_001264743.1  NP_001264744.1  NP_001264745.1  NP_001264746.1  NP_001264747.1  NP_689971.4  

    ENSEMBL proteins: 
     ENSP00000473986   ENSP00000473317   ENSP00000474547   ENSP00000473496   ENSP00000473387  

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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 Q7Z739

    ProtoNet protein and cluster: Q7Z739

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

    UniProtKB/Swiss-Prot: YTHD3_HUMAN, Q7Z739
    Similarity: Contains 1 YTH domain


    YTHDF3 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

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI--
         
    YTHDF3 for ontologies           About GeneDecksing


    Animal Models:
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    SwitchGear 3'UTR luciferase reporter plasmidYTHDF3 3' UTR sequence
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for YTHDF3


    (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 YTHDF3

    2 Interacting proteins for YTHDF3 (Q7Z7391, 3) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    POT1Q9NUX53I2D: score=1 
    gagP045911EBI-2849837,EBI-6179727
    About this table

    (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 YTHDF3 (YTHD3)

    Search CenterWatch for drugs/clinical trials and news about YTHDF3 / YTHD3

    (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 YTHDF3 gene (7 alternative transcripts): 
    NM_001277813.1  NM_001277814.1  NM_001277815.1  NM_001277816.1  NM_001277817.1  NM_001277818.1  NM_152758.5  

    Unigene Cluster for YTHDF3:

    YTH domain family, member 3
    Hs.491861  [show with all ESTs]
    Unigene Representative Sequence: NM_152758
    16 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000521674(uc003xuy.3 uc010lys.3 uc003xuz.3) ENST00000522282
    ENST00000519428 ENST00000523455 ENST00000517371 ENST00000524135(uc003xva.3 uc011len.2)
    ENST00000518763 ENST00000518438 ENST00000517375 ENST00000521547 ENST00000520640
    ENST00000523056 ENST00000517303 ENST00000518373 ENST00000539294 ENST00000542911

    miRNA
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    8/115 QIAGEN miScript miRNA Assays for microRNAs that regulate YTHDF3 (see all 115):
    hsa-miR-582-3p hsa-miR-579 hsa-miR-520e hsa-miR-520f hsa-miR-3152-3p hsa-miR-106a hsa-miR-30d hsa-miR-30a
    SwitchGear 3'UTR luciferase reporter plasmidYTHDF3 3' UTR sequence
    Inhib. RNA
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    GenScript: all cDNA clones in your preferred vector: YTHDF3 (NM_152758)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for YTHDF3
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat YTHDF3
    Sirion Biotech Customized lentivirus for stable overexpression of YTHDF3 
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    Primer
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat YTHDF3

    Additional mRNA sequence: 

    AK002173.1 AK056219.1 AK093081.1 AK127574.1 AK298544.1 AL050081.1 AL831816.1 AL832005.1 
    AL832335.1 AL832369.1 BC037492.1 BC052970.1 BX537996.2 

    11 DOTS entries:

    DT.102825847  DT.91749167  DT.100652083  DT.95268981  DT.100652089  DT.100666742  DT.102825850  DT.95260348 
    DT.95268980  DT.95355192  DT.91808969 

    24/285 AceView cDNA sequences (see all 285):

    Z43691 AA128191 AI363820 AI373633 CB105178 CK904692 BU195196 CB046550 
    AI967934 AI659673 BM069441 AA287239 AA826923 AW196318 AI985539 AA908355 
    AA418619 BQ026584 AW169433 AK127574 CK904693 AW119122 BM697489 BQ637880 

    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

    YTHDF3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGAATTTGAA
    YTHDF3 Expression
    About this image


    See YTHDF3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for YTHDF3

    SOURCE GeneReport for Unigene cluster: Hs.491861
        SABiosciences Custom PCR Arrays for YTHDF3
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for YTHDF3

    (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 YTHDF3 gene from 8/15 species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ythdf31 , 5 YTH domain family 31, 5 96.41(n)1
    98.8(a)1
      3 (4.04 cM)5
    2290961  NM_172677.31  NP_766265.31 
     161831835 
    chicken
    (Gallus gallus)
    Aves YTHDF31 YTH domain family, member 3 90.39(n)
    96.4(a)
      421145  NM_001006391.1  NP_001006391.1 
    lizard
    (Anolis carolinensis)
    Reptilia YTHDF36
    YTH domain family, member 3
    94(a)
    1 ↔ 1
    4(29473027-29506059)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.89342 Transcribed sequence with weak similarity to protein more 82.49(n)    CF239562.1 
    zebrafish
    (Danio rerio)
    Actinopterygii BC045342.12   -- 78.42(n)   334191  BC045342.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG64226
    --
    27(a)
    1 → many
    3R(20859866-20864801)
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes YDR374C6
    Putative protein of unknown function
    28(a)
    1 → many
    IV(1223474-1224394)
    barley
    (Hordeum vulgare)
    Liliopsida Hv.55682 Transcribed sequence with weak similarity to protein more 73.48(n)    AV914848.1 


    ENSEMBL Gene Tree for YTHDF3 (if available)
    TreeFam Gene Tree for YTHDF3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for YTHDF3 gene
    YTHDF22  YTHDF12  
    4 SIMAP similar genes for YTHDF3 using alignment to 5 protein entries:     YTHD3_HUMAN (see all proteins):
    DKFZp451A052    DKFZp451J085    YTHDF2    YTHDF1

    YTHDF3 for paralogs           About GeneDecksing



    (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

    10/848 SNPs in YTHDF3 are shown (see all 848)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 8 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs339945941,2
    C--59587270(+) GTCAA-/GTCCAT 15 D ES fra1 int10--------
    rs78291861,2
    C--59589799(+) tatatT/Attttt 8 -- int11Minor allele frequency- A:0.50NA 2
    rs1999925731,2
    --59589799(+) TATAT-/ATTTTT 8 -- int10--------
    rs106995511,2
    C--59600118(+) CATTG-/AGTG  
            
    GTATT
    8 -- int10--------
    rs107106721,2
    C--64089234(+) CTCAGT/-TTTTT 8 -- int1 trp32Minor allele frequency- -:0.25NA CSA 4
    rs625101271,2
    --64092436(+) TGGGGC/TGGCCG 8 -- int10--------
    rs113813851,2
    C--64095514(+) TTTTT-/TCTTTT 8 -- int1 trp30--------
    rs606823711,2
    C--64096948(+) AACCT-/CTGTTAC 8 -- int10--------
    rs584198561,2
    C--64098729(+) TGTCAG/-ATCCA 15 /D /GS fra1 int12Minor allele frequency- -:0.00NA CSA 4
    rs725389821,2
    C--64098729(+) TGTCA-/GAATCC 15 D GS fra1 int10--------

    HapMap Linkage Disequilibrium report for YTHDF3 (64081112 - 64125346 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for YTHDF3:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2677763CNV Deletion23128226
    nsv890966CNV Loss21882294
    nsv831342CNV Gain17160897
    nsv890967CNV Gain21882294
    nsv890965CNV Gain+Loss21882294

    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

    YTHDF3 for disorders           About MalaCards

    YTHDF3 for disorders           About GeneDecksing

    Genetic Association Database (GAD): YTHDF3

    Export disorders for YTHDF3 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 YTHDF3 gene, integrated from 9 sources (see all 23):
    (articles sorted by number of sources associating them with YTHDF3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Initial characterization of the human central proteome. (PubMed id 21269460)1, 2 Burkard T.R.... Colinge J. (2011)
    2. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)1, 2 Olsen J.V....Mann M. (2010)
    3. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)1, 2 Dephoure N.... Gygi S.P. (2008)
    4. 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)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    6. 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)
    7. Replication study of 10 genes showing evidence for ass ociation with multiple sclerosis: validation of TMEM39A, IL12B and CBLB [correct ion of CLBL] genes. (PubMed id 22194214)1 Varade J....Urcelay E. (2012)
    8. Global landscape of HIV-human protein complexes. (PubMed id 22190034)1 Jager S....Krogan N.J. (2012)
    9. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    10. Concomitant duplications of opioid peptide and recepto r genes before the origin of jawed vertebrates. (PubMed id 20463905)1 Sundstrom G....Larhammar D. (2010)

    (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: 253943 HGNC: 26465 AceView: YTHDF3 Ensembl:ENSG00000185728 euGenes: HUgn253943
    ECgene: YTHDF3 H-InvDB: YTHDF3

    (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 YTHDF3 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 YTHDF3 gene:
    Search GeneIP for patents involving YTHDF3

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



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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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