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Aliases for YTHDF2 Gene

Aliases for YTHDF2 Gene

  • YTH N6-Methyladenosine RNA Binding Protein 2 2 3 5
  • YTH N(6)-Methyladenosine RNA Binding Protein 2 2 3
  • High-Glucose-Regulated Protein 8 3 4
  • Renal Carcinoma Antigen NY-REN-2 3 4
  • CLL-Associated Antigen KW-14 3 4
  • YTH Domain Family, Member 2 2 3
  • HGRG8 3 4
  • YTH Domain-Containing Family Protein 2 3
  • YTH Domain Family 2 2
  • 9430020E02Rik 3
  • NY-REN-2 3
  • CAHL 3

External Ids for YTHDF2 Gene

Previous GeneCards Identifiers for YTHDF2 Gene

  • GC01P028884
  • GC01P028935
  • GC01P029063
  • GC01P027315

Summaries for YTHDF2 Gene

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 N6-Methyladenosine RNA Binding Protein 2) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include N6-methyladenosine-containing RNA binding. An important paralog of this gene is YTHDF3.

UniProtKB/Swiss-Prot for YTHDF2 Gene

  • Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs, and regulates mRNA stability (PubMed:24284625, PubMed:26046440, PubMed:26318451). M6A is a modification present at internal sites of mRNAs and some non-coding RNAs and plays a role in mRNA stability and processing (PubMed:22575960, PubMed:24284625, PubMed:25412658, PubMed:25412661). Acts as a regulator of mRNA stability: binding to m6A-containing mRNAs results in the localization to mRNA decay sites, such as processing bodies (P-bodies), leading to mRNA degradation (PubMed:24284625, PubMed:26046440). Required maternally to regulate oocyte maturation: probably acts by binding to m6A-containing mRNAs, thereby regulating maternal transcript dosage during oocyte maturation, which is essential for the competence of oocytes to sustain early zygotic development (By similarity). Also involved in haematopoietic stem cells specification: acts by binding to m6A-containing mRNAs, leading to decrease Notch dignaling and promote endothelial to haematopoietic transition (By similarity). Also acts as a promoter of cap-independent mRNA translation following heat shock stress: upon stress, relocalizes to the nucleus and specifically binds mRNAs with some m6A methylation mark at their 5-UTR, protecting demethylation of mRNAs by FTO, thereby promoting cap-independent mRNA translation (PubMed:26458103).

Additional gene information for YTHDF2 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for YTHDF2 Gene

Genomics for YTHDF2 Gene

GeneHancer (GH) Regulatory Elements for YTHDF2 Gene

Promoters and enhancers for YTHDF2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I028735 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 575.7 +0.7 679 3.8 MLX FEZF1 DMAP1 YBX1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 YTHDF2 GC01P028737 GC01M028743 SRSF4 GMEB1 PHACTR4 SNHG12 TRNAU1AP ENSG00000231344 RCC1
GH01I028881 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 80.2 +148.6 148621 6.8 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 EPB41 LOC105376898 SRSF4 TRNAU1AP GMEB1 SNHG12 YTHDF2 PHACTR4 EYA3 TMEM200B
GH01I028647 Promoter/Enhancer 1.7 Ensembl ENCODE 96.9 -88.2 -88176 2.7 CLOCK ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ENSG00000270103 GC01P028651 GC01P028669 GC01P028670 GC01P028671 GC01P028672 RNU11 SRSF4 GMEB1 TRNAU1AP
GH01I029236 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 63.3 +502.1 502093 5.1 HDGF FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 ZNF207 ZNF143 DEK PTPRU SRSF4 GMEB1 TRNAU1AP YTHDF2 SNHG12 PHACTR4 TMEM200B RCC1 ENSG00000237934
GH01I028578 Promoter/Enhancer 1.6 Ensembl ENCODE 78.4 -155.4 -155421 4.5 ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC SNHG12 GC01M028584 GC01M028612 GC01M028618 GC01M028623 GC01M028624 GC01M028625 GC01M028628 PIR59489 SNORA16A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around YTHDF2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the YTHDF2 gene promoter:

Genomic Locations for YTHDF2 Gene

Genomic Locations for YTHDF2 Gene
chr1:28,736,621-28,769,775
(GRCh38/hg38)
Size:
33,155 bases
Orientation:
Plus strand
chr1:29,063,133-29,096,287
(GRCh37/hg19)

Genomic View for YTHDF2 Gene

Genes around YTHDF2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
YTHDF2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for YTHDF2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for YTHDF2 Gene

Proteins for YTHDF2 Gene

  • Protein details for YTHDF2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5A9-YTHD2_HUMAN
    Recommended name:
    YTH domain-containing family protein 2
    Protein Accession:
    Q9Y5A9
    Secondary Accessions:
    • A6NKG4
    • A8K966
    • B4E1G7
    • D3DPM8
    • Q5VSZ9
    • Q8TDH0
    • Q9BUJ5

    Protein attributes for YTHDF2 Gene

    Size:
    579 amino acids
    Molecular mass:
    62334 Da
    Quaternary structure:
    • Interacts with YTHDF3 (PubMed:28106072).
    SequenceCaution:
    • Sequence=AAD42861.1; Type=Frameshift; Positions=565; Evidence={ECO:0000305}; Sequence=AAF08813.1; Type=Frameshift; Positions=565; Evidence={ECO:0000305}; Sequence=AAL99921.1; Type=Miscellaneous discrepancy; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for YTHDF2 Gene

    Alternative splice isoforms for YTHDF2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for YTHDF2 Gene

Post-translational modifications for YTHDF2 Gene

  • Ubiquitination at posLast=401401 and posLast=408408

Other Protein References for YTHDF2 Gene

No data available for DME Specific Peptides for YTHDF2 Gene

Domains & Families for YTHDF2 Gene

Gene Families for YTHDF2 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for YTHDF2 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for YTHDF2 Gene

Graphical View of Domain Structure for InterPro Entry

Q9Y5A9

UniProtKB/Swiss-Prot:

YTHD2_HUMAN :
  • Belongs to the YTHDF2 family.
Family:
  • Belongs to the YTHDF2 family.
genes like me logo Genes that share domains with YTHDF2: view

Function for YTHDF2 Gene

Molecular function for YTHDF2 Gene

UniProtKB/Swiss-Prot Function:
Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs, and regulates mRNA stability (PubMed:24284625, PubMed:26046440, PubMed:26318451). M6A is a modification present at internal sites of mRNAs and some non-coding RNAs and plays a role in mRNA stability and processing (PubMed:22575960, PubMed:24284625, PubMed:25412658, PubMed:25412661). Acts as a regulator of mRNA stability: binding to m6A-containing mRNAs results in the localization to mRNA decay sites, such as processing bodies (P-bodies), leading to mRNA degradation (PubMed:24284625, PubMed:26046440). Required maternally to regulate oocyte maturation: probably acts by binding to m6A-containing mRNAs, thereby regulating maternal transcript dosage during oocyte maturation, which is essential for the competence of oocytes to sustain early zygotic development (By similarity). Also involved in haematopoietic stem cells specification: acts by binding to m6A-containing mRNAs, leading to decrease Notch dignaling and promote endothelial to haematopoietic transition (By similarity). Also acts as a promoter of cap-independent mRNA translation following heat shock stress: upon stress, relocalizes to the nucleus and specifically binds mRNAs with some m6A methylation mark at their 5-UTR, protecting demethylation of mRNAs by FTO, thereby promoting cap-independent mRNA translation (PubMed:26458103).
UniProtKB/Swiss-Prot Induction:
Following heat shock stress.

Phenotypes From GWAS Catalog for YTHDF2 Gene

Gene Ontology (GO) - Molecular Function for YTHDF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA,IDA 22658674
GO:0005515 protein binding IPI 24965446
GO:1990247 N6-methyladenosine-containing RNA binding IDA 22575960
genes like me logo Genes that share ontologies with YTHDF2: view
genes like me logo Genes that share phenotypes with YTHDF2: view

Animal Models for YTHDF2 Gene

MGI Knock Outs for YTHDF2:

Animal Model Products

miRNA for YTHDF2 Gene

miRTarBase miRNAs that target YTHDF2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for YTHDF2 Gene

Localization for YTHDF2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for YTHDF2 Gene

Cytoplasm, cytosol. Nucleus. Cytoplasm, P-body. Note=Localizes to the cytosol and relocates to the nucleus following heat shock stress (PubMed:26458103). {ECO:0000269 PubMed:26458103}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for YTHDF2 gene
Compartment Confidence
nucleus 5
cytosol 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (4)
  • Cytoplasmic bodies (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for YTHDF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000932 P-body IDA 24284625
GO:0005634 nucleus IDA,IEA 26458103
GO:0005737 cytoplasm IEA --
GO:0005815 microtubule organizing center IDA --
GO:0005829 cytosol IEA,IDA 26458103
genes like me logo Genes that share ontologies with YTHDF2: view

Pathways & Interactions for YTHDF2 Gene

SuperPathways for YTHDF2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for YTHDF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001556 oocyte maturation ISS --
GO:0006959 humoral immune response TAS 10508479
GO:0030154 cell differentiation IEA --
GO:0043488 regulation of mRNA stability IMP 24284625
GO:0045746 negative regulation of Notch signaling pathway ISS --
genes like me logo Genes that share ontologies with YTHDF2: view

No data available for Pathways by source and SIGNOR curated interactions for YTHDF2 Gene

Drugs & Compounds for YTHDF2 Gene

No Compound Related Data Available

Transcripts for YTHDF2 Gene

Unigene Clusters for YTHDF2 Gene

YTH domain family, member 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for YTHDF2 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c · 6d · 6e ^ 7 ^ 8
SP1: - - - -
SP2: - -
SP3:
SP4:
SP5: - -
SP6: - -
SP7: - - - - - - - -

Relevant External Links for YTHDF2 Gene

GeneLoc Exon Structure for
YTHDF2
ECgene alternative splicing isoforms for
YTHDF2

Expression for YTHDF2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for YTHDF2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for YTHDF2 Gene

This gene is overexpressed in Bone (16.7) and Breast (8.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for YTHDF2 Gene



Protein tissue co-expression partners for YTHDF2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of YTHDF2 Gene:

YTHDF2

SOURCE GeneReport for Unigene cluster for YTHDF2 Gene:

Hs.532286

Evidence on tissue expression from TISSUES for YTHDF2 Gene

  • Nervous system(4.7)
  • Skin(2.5)
  • Eye(2.3)
  • Kidney(2.2)
  • Liver(2.2)
  • Lung(2.2)
genes like me logo Genes that share expression patterns with YTHDF2: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for YTHDF2 Gene

Orthologs for YTHDF2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for YTHDF2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia YTHDF2 33 34
  • 99.94 (n)
cow
(Bos Taurus)
Mammalia YTHDF2 33 34
  • 97.24 (n)
dog
(Canis familiaris)
Mammalia YTHDF2 33 34
  • 96.74 (n)
oppossum
(Monodelphis domestica)
Mammalia YTHDF2 34
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ythdf2 33 16 34
  • 95.68 (n)
rat
(Rattus norvegicus)
Mammalia Ythdf2 33
  • 94.52 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia YTHDF2 34
  • 87 (a)
OneToOne
chicken
(Gallus gallus)
Aves YTHDF2 33 34
  • 82.86 (n)
lizard
(Anolis carolinensis)
Reptilia YTHDF2 34
  • 92 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ythdf2 33
  • 70.08 (n)
zebrafish
(Danio rerio)
Actinopterygii yth2 33 34
  • 72.81 (n)
zgc56224 33
fruit fly
(Drosophila melanogaster)
Insecta CG6422 34
  • 28 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes -- 34
  • 30 (a)
OneToMany
rice
(Oryza sativa)
Liliopsida Os.8783 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6332 34
  • 45 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4206 33
Species where no ortholog for YTHDF2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for YTHDF2 Gene

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

Paralogs for YTHDF2 Gene

Paralogs for YTHDF2 Gene

(4) SIMAP similar genes for YTHDF2 Gene using alignment to 4 proteins:

Pseudogenes.org Pseudogenes for YTHDF2 Gene

genes like me logo Genes that share paralogs with YTHDF2: view

Variants for YTHDF2 Gene

Sequence variations from dbSNP and Humsavar for YTHDF2 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000027443 -- 28,749,587(+) A/T intron_variant
rs1000028606 -- 28,755,085(+) T/G intron_variant
rs1000165075 -- 28,760,443(+) C/A/G/T intron_variant
rs1000284827 -- 28,739,264(+) C/G intron_variant
rs1000325863 -- 28,766,184(+) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for YTHDF2 Gene

Variant ID Type Subtype PubMed ID
esv2745830 CNV deletion 23290073
esv3585591 CNV loss 21293372
nsv160265 CNV deletion 16902084
nsv473498 CNV novel sequence insertion 20440878
nsv509080 CNV insertion 20534489
nsv945857 CNV duplication 23825009

Variation tolerance for YTHDF2 Gene

Residual Variation Intolerance Score: 12.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.35; 26.67% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for YTHDF2 Gene

Human Gene Mutation Database (HGMD)
YTHDF2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
YTHDF2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for YTHDF2 Gene

Disorders for YTHDF2 Gene

Additional Disease Information for YTHDF2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for YTHDF2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for YTHDF2 Gene

Publications for YTHDF2 Gene

  1. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. (PMID: 22575960) Dominissini D … Rechavi G (Nature 2012) 2 3 4 58
  2. Antigens recognized by autologous antibody in patients with renal-cell carcinoma. (PMID: 10508479) Scanlan MJ … Old LJ (International journal of cancer 1999) 2 3 4 58
  3. YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA. (PMID: 28106072) Shi H … He C (Cell research 2017) 3 4 58
  4. N(6)-methyladenosine Modulates Messenger RNA Translation Efficiency. (PMID: 26046440) Wang X … He C (Cell 2015) 3 4 58
  5. Structural Basis for the Discriminative Recognition of N6-Methyladenosine RNA by the Human YT521-B Homology Domain Family of Proteins. (PMID: 26318451) Xu C … Min J (The Journal of biological chemistry 2015) 3 4 58

Products for YTHDF2 Gene

Sources for YTHDF2 Gene

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