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YTHDF2 YTH N6-methyladenosine RNA binding protein F2 [ Homo sapiens (human) ]

Gene ID: 51441, updated on 16-Apr-2024

Summary

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Official Symbol
YTHDF2provided by HGNC
Official Full Name
YTH N6-methyladenosine RNA binding protein F2provided by HGNC
Primary source
HGNC:HGNC:31675
See related
Ensembl:ENSG00000198492 MIM:610640; AllianceGenome:HGNC:31675
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DF2; CAHL; HGRG8; NY-REN-2
Summary
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]
Expression
Ubiquitous expression in bone marrow (RPKM 23.8), testis (RPKM 20.2) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
1p35.3
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (28736624..28769775)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (28578615..28611771)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (29063136..29096287)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 545 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 546 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 547 Neighboring gene TAF12 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 603 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:28998036-28998554 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:29007753-29008252 Neighboring gene small Cajal body-specific RNA 24 Neighboring gene RNA, U11 small nuclear Neighboring gene glucocorticoid modulatory element binding protein 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:29061369-29062268 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 604 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:29063168-29064066 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:29069801-29070309 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:29074507-29074730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:29075305-29075826 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:29075827-29076347 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:29081023-29081522 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:29089259-29089760 Neighboring gene Sharpr-MPRA regulatory region 15715 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 606 Neighboring gene NANOG hESC enhancer GRCh37_chr1:29133560-29134067 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:29141619-29142120 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:29161670-29162170 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:29162171-29162671 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:29181461-29181962 Neighboring gene opioid receptor delta 1 Neighboring gene GATA motif-containing MPRA enhancer 282 Neighboring gene CRISPRi-validated cis-regulatory element chr1.4082 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 548 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 549 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 550 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 551 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 608 Neighboring gene uncharacterized LOC124903886 Neighboring gene erythrocyte membrane protein band 4.1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. The m6A Reader YTHDF2 Promotes Bladder Cancer Progression by Suppressing RIG-I-Mediated Immune Response. Zhang L, et al. Cancer Res, 2023 Jun 2. PMID 36939388, Free PMC Article
  2. YTHDF2 Is Downregulated in Response to Host Shutoff Induced by DNA Virus Infection and Regulates Interferon-Stimulated Gene Expression. Hesser CR, et al. J Virol, 2023 Mar 30. PMID 36916936, Free PMC Article
  3. O-GlcNAcylation of YTHDF2 promotes HBV-related hepatocellular carcinoma progression in an N(6)-methyladenosine-dependent manner. Yang Y, et al. Signal Transduct Target Ther, 2023 Feb 10. PMID 36765030, Free PMC Article
  4. N6-Methyladenosine Reader YTHDF2 Enhances Non-Small-Cell Lung Cancer Cell Proliferation and Metastasis through Mediating circ_SFMBT2 Degradation. Xu J, et al. Contrast Media Mol Imaging, 2022. PMID 35924072, Free PMC Article
  5. Expression and clinical significance of the m6A reader YTHDF2 in peripheral blood mononuclear cells from rheumatoid arthritis patients. Yao F, et al. J Immunotoxicol, 2022 Dec. PMID 35776431

See all (204) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. YTHDF2 Is a Therapeutic Target for HCC by Suppressing Immune Evasion and Angiogenesis Through ETV5/PD-L1/VEGFA Axis.
    Title: YTHDF2 Is a Therapeutic Target for HCC by Suppressing Immune Evasion and Angiogenesis Through ETV5/PD-L1/VEGFA Axis.
  2. METTL3/YTHDF2 m6A axis mediates the progression of diabetic nephropathy through epigenetically suppressing PINK1 and mitophagy.
    Title: METTL3/YTHDF2 m6A axis mediates the progression of diabetic nephropathy through epigenetically suppressing PINK1 and mitophagy.
  3. FOXM1 Participates in Scleral Remodeling in Myopia by Upregulating APOA1 Expression Through METTL3/YTHDF2.
    Title: FOXM1 Participates in Scleral Remodeling in Myopia by Upregulating APOA1 Expression Through METTL3/YTHDF2.
  4. Epitranscriptional regulation of TGF-beta pseudoreceptor BAMBI by m6A/YTHDF2 drives extrinsic radioresistance.
    Title: Epitranscriptional regulation of TGF-β pseudoreceptor BAMBI by m6A/YTHDF2 drives extrinsic radioresistance.
  5. YTHDF2 promotes gallbladder cancer progression and gemcitabine resistance via m6A-dependent DAPK3 degradation.
    Title: YTHDF2 promotes gallbladder cancer progression and gemcitabine resistance via m6A-dependent DAPK3 degradation.
  6. METTL3-regulated m6A modification impairs the decidualization of endometrial stromal cells by regulating YTHDF2-mediated degradation of FOXO1 mRNA in endometriosis-related infertility.
    Title: METTL3-regulated m6A modification impairs the decidualization of endometrial stromal cells by regulating YTHDF2-mediated degradation of FOXO1 mRNA in endometriosis-related infertility.
  7. YTHDF2 facilitates aggresome formation via UPF1 in an m[6]A-independent manner.
    Title: YTHDF2 facilitates aggresome formation via UPF1 in an m(6)A-independent manner.
  8. HSP90beta Impedes STUB1-Induced Ubiquitination of YTHDF2 to Drive Sorafenib Resistance in Hepatocellular Carcinoma.
    Title: HSP90β Impedes STUB1-Induced Ubiquitination of YTHDF2 to Drive Sorafenib Resistance in Hepatocellular Carcinoma.
  9. YTHDF2 negatively correlates with tumor immune infiltration in small cell lung cancer.
    Title: YTHDF2 negatively correlates with tumor immune infiltration in small cell lung cancer.
  10. Diagnostic value and immune infiltration characterization of YTHDF2 as a critical m6A regulator in osteoarthritic synovitis.
    Title: Diagnostic value and immune infiltration characterization of YTHDF2 as a critical m6A regulator in osteoarthritic synovitis.
Submit: New GeneRIF Correction See all GeneRIFs (86)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables C5-methylcytidine-containing RNA reader activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables N6-methyladenosine-containing RNA reader activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables N6-methyladenosine-containing RNA reader activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA binding HDA PubMed 
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell cycle IEA
Inferred from Electronic Annotation
more info
  
involved_in embryonic morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in endothelial to hematopoietic transition ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in gamete generation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in hematopoietic stem cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in humoral immune response TAS
Traceable Author Statement
more info
 PubMed 
involved_in innate immune response IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mRNA destabilization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mRNA destabilization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mRNA destabilization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of Notch signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of stem cell differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of type I interferon-mediated signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in oocyte maturation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in organelle assembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of cap-independent translational initiation IDA
Inferred from Direct Assay
more info
 PubMed 
NOT involved_in positive regulation of translational initiation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of cell adhesion ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of hematopoietic stem cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of mRNA stability IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of mRNA stability IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of meiotic cell cycle process involved in oocyte maturation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of neurogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of neurogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of rRNA processing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in spermatogonial cell division ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in stress granule assembly IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in P-body IDA
Inferred from Direct Assay
more info
 PubMed 
located_in centriolar satellite IDA
Inferred from Direct Assay
more info
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasmic ribonucleoprotein granule IDA
Inferred from Direct Assay
more info
  
located_in cytoplasmic stress granule IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
YTH domain-containing family protein 2
Names
9430020E02Rik
CLL-associated antigen KW-14
YTH N(6)-methyladenosine RNA binding protein 2
YTH N6-methyladenosine RNA binding protein 2
YTH domain family, member 2
high-glucose-regulated protein 8
renal carcinoma antigen NY-REN-2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_016746.2 RefSeqGene

    Range
    5318..38153
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001172828.2 → NP_001166299.1  YTH domain-containing family protein 2 isoform 2

    See identical proteins and their annotated locations for NP_001166299.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an exon in the 5' region, which results in a downstream AUG start codon, as compared to variant 1. The resulting isoform (2) is shorter at the N-terminus, as compared to isoform 1.
    Source sequence(s)
    AL356786, AL645729
    Consensus CDS
    CCDS53287.1
    UniProtKB/TrEMBL
    B5BU99
    Related
    ENSP00000439394.1, ENST00000541996.5
    Conserved Domains (1) summary
    pfam04146
    Location:361 → 494
    YTH; YT521-B-like domain

  2. NM_001173128.2 → NP_001166599.1  YTH domain-containing family protein 2 isoform 1

    See identical proteins and their annotated locations for NP_001166599.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has a split 5' UTR exon, as compared to variant 1. Both variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AL356786, AL645729
    Consensus CDS
    CCDS41296.1
    UniProtKB/Swiss-Prot
    A6NKG4, A8K966, B4E1G7, D3DPM8, Q5VSZ9, Q8TDH0, Q9BUJ5, Q9Y5A9
    UniProtKB/TrEMBL
    B5BU99
    Related
    ENSP00000444660.1, ENST00000542507.5
    Conserved Domains (1) summary
    pfam04146
    Location:411 → 544
    YTH; YT521-B-like domain

  3. NM_016258.3 → NP_057342.2  YTH domain-containing family protein 2 isoform 1

    See identical proteins and their annotated locations for NP_057342.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AL356786, AL645729
    Consensus CDS
    CCDS41296.1
    UniProtKB/Swiss-Prot
    A6NKG4, A8K966, B4E1G7, D3DPM8, Q5VSZ9, Q8TDH0, Q9BUJ5, Q9Y5A9
    UniProtKB/TrEMBL
    B5BU99
    Related
    ENSP00000362918.3, ENST00000373812.8
    Conserved Domains (1) summary
    pfam04146
    Location:411 → 544
    YTH; YT521-B-like domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    28736624..28769775
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    28578615..28611771
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y5A9.2 GenPept UniProtKB/Swiss-Prot:Q9Y5A9

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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