Human Gene YTHDF2 (uc021okf.1) Description and Page Index
  Description: Homo sapiens YTH domain family, member 2 (YTHDF2), transcript variant 2, mRNA.
RefSeq Summary (NM_001173128): 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].
Transcript (Including UTRs)
   Position: hg19 chr1:29,063,133-29,096,287 Size: 33,155 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr1:29,063,633-29,095,464 Size: 31,832 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:29,063,133-29,096,287)mRNA (may differ from genome)Protein (579 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: YTHD2_HUMAN
DESCRIPTION: RecName: Full=YTH domain family protein 2; AltName: Full=CLL-associated antigen KW-14; AltName: Full=High-glucose-regulated protein 8; AltName: Full=Renal carcinoma antigen NY-REN-2;
SIMILARITY: Contains 1 YTH domain.
SEQUENCE CAUTION: Sequence=AAD42861.1; Type=Frameshift; Positions=565; Sequence=AAF08813.1; Type=Frameshift; Positions=565;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): YTHDF2
CDC HuGE Published Literature: YTHDF2
Positive Disease Associations: longevity
Related Studies:
  1. longevity
    Cardelli, M. et al. 2006, A Polymorphism of the YTHDF2 Gene (1p35) Located in an Alu-Rich Genomic Domain Is Associated With Human Longevity, J Gerontol A Biol Sci Med Sci 2006 61(6) 547-56. [PubMed 16799135]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 26.84 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 778.48 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -136.60263-0.519 Picture PostScript Text
3' UTR -200.26823-0.243 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR007275 - YTH_domain

Pfam Domains:
PF04146 - YT521-B-like domain

ModBase Predicted Comparative 3D Structure on Q9Y5A9
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding
GO:1990247 N6-methyladenosine-containing RNA binding

Biological Process:
GO:0001556 oocyte maturation
GO:0006959 humoral immune response
GO:0030154 cell differentiation
GO:0043488 regulation of mRNA stability
GO:0045746 negative regulation of Notch signaling pathway
GO:0048477 oogenesis
GO:0048598 embryonic morphogenesis
GO:0061157 mRNA destabilization
GO:0098508 endothelial to hematopoietic transition
GO:1902036 regulation of hematopoietic stem cell differentiation
GO:1903538 regulation of meiotic cell cycle process involved in oocyte maturation
GO:1903679 positive regulation of cap-independent translational initiation

Cellular Component:
GO:0000932 P-body
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005815 microtubule organizing center
GO:0005829 cytosol
GO:0036464 cytoplasmic ribonucleoprotein granule


-  Descriptions from all associated GenBank mRNAs
  BC002559 - Homo sapiens YTH domain family, member 2, mRNA (cDNA clone MGC:739 IMAGE:3139250), complete cds.
AK292581 - Homo sapiens cDNA FLJ76954 complete cds, highly similar to Homo sapiens high-glucose-regulated protein 8, mRNA.
AK303833 - Homo sapiens cDNA FLJ53486 complete cds, highly similar to YTH domain protein 2.
AF432214 - Homo sapiens CLL-associated antigen KW-14 mRNA, complete cds.
AF155095 - Homo sapiens NY-REN-2 antigen mRNA, complete cds.
AF192968 - Homo sapiens high-glucose-regulated protein 8 (HGRG8) mRNA, complete cds.
JD148133 - Sequence 129157 from Patent EP1572962.
JD341220 - Sequence 322244 from Patent EP1572962.
DQ895352 - Synthetic construct Homo sapiens clone IMAGE:100009812; FLH183544.01L; RZPDo839D11141D YTH domain family, member 2 (YTHDF2) gene, encodes complete protein.
DQ892157 - Synthetic construct clone IMAGE:100004787; FLH183548.01X; RZPDo839D11142D YTH domain family, member 2 (YTHDF2) gene, encodes complete protein.
KJ893914 - Synthetic construct Homo sapiens clone ccsbBroadEn_03308 YTHDF2 gene, encodes complete protein.
CU678040 - Synthetic construct Homo sapiens gateway clone IMAGE:100017715 5' read YTHDF2 mRNA.
AB451484 - Homo sapiens YTHDF2 mRNA for high glucose-regulated protein 8, partial cds, clone: FLJ80394SAAF.
AB451335 - Homo sapiens YTHDF2 mRNA for high glucose-regulated protein 8, complete cds, clone: FLJ80394SAAN.
AK074276 - Homo sapiens cDNA FLJ23696 fis, clone HEP10522, highly similar to Homo sapiens NY-REN-2 antigen mRNA.
JD046726 - Sequence 27750 from Patent EP1572962.
JD333838 - Sequence 314862 from Patent EP1572962.
JD538685 - Sequence 519709 from Patent EP1572962.
JD208242 - Sequence 189266 from Patent EP1572962.
JD063691 - Sequence 44715 from Patent EP1572962.
JD120143 - Sequence 101167 from Patent EP1572962.
JD132190 - Sequence 113214 from Patent EP1572962.
JD435183 - Sequence 416207 from Patent EP1572962.
EU093085 - Homo sapiens RUNX1/YTHDF2 fusion mRNA, partial sequence.
JD330697 - Sequence 311721 from Patent EP1572962.
JD037919 - Sequence 18943 from Patent EP1572962.
JD299162 - Sequence 280186 from Patent EP1572962.
JD284068 - Sequence 265092 from Patent EP1572962.
JD235808 - Sequence 216832 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NKG4, A8K966, B4E1G7, D3DPM8, HGRG8, NM_001173128, NP_001166299, Q5VSZ9, Q8TDH0, Q9BUJ5, Q9Y5A9, YTHD2_HUMAN
UCSC ID: uc021okf.1
RefSeq Accession: NM_001173128
Protein: Q9Y5A9 (aka YTHD2_HUMAN or YTH2_HUMAN)
CCDS: CCDS41296.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001173128.1
exon count: 6CDS single in 3' UTR: no RNA size: 2830
ORF size: 1740CDS single in intron: no Alignment % ID: 99.96
txCdsPredict score: 3680.00frame shift in genome: no % Coverage: 99.86
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.