Human Gene YTHDC1 (ENST00000344157.9_7) from GENCODE V47lift37
  Description: YTH domain containing 1, transcript variant 1 (from RefSeq NM_001031732.4)
Gencode Transcript: ENST00000344157.9_7
Gencode Gene: ENSG00000083896.13_13
Transcript (Including UTRs)
   Position: hg19 chr4:69,176,105-69,215,808 Size: 39,704 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg19 chr4:69,179,817-69,215,471 Size: 35,655 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:69,176,105-69,215,808)mRNA (may differ from genome)Protein (727 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: YTDC1_HUMAN
DESCRIPTION: RecName: Full=YTH domain-containing protein 1; AltName: Full=Putative splicing factor YT521;
FUNCTION: May be part of a signal transduction pathway that influences splice site selection (By similarity).
SUBUNIT: Interacts with EMD, KHDRBS1/SAM68, KHDRBS3, TRA2B/SFRS10, SC35 and SF2 (By similarity). Interacts with RBMX.
SUBCELLULAR LOCATION: Nucleus (By similarity). Note=Localizes to a novel subnuclear structure, the YT bodies (By similarity).
SIMILARITY: Contains 1 YTH domain.
SEQUENCE CAUTION: Sequence=AAY41024.1; Type=Erroneous gene model prediction; Sequence=BAB71181.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • C517041 (4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)
  • C049325 1,2-dithiol-3-thione
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • C016403 2,4-dinitrotoluene
  • C049584 2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine
  • C030370 2-methoxy-5-(2',3',4'-trimethoxyphenyl)tropone
  • D000082 Acetaminophen
  • D016604 Aflatoxin B1
  • D000643 Ammonium Chloride
  • D017638 Asbestos, Crocidolite
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 24.93 RPKM in Ovary
Total median expression: 720.07 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -149.70337-0.444 Picture PostScript Text
3' UTR -924.503712-0.249 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

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2YUD - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q96MU7
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 DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  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:0006376 mRNA splice site selection
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0010608 posttranscriptional regulation of gene expression
GO:0048024 regulation of mRNA splicing, via spliceosome

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005886 plasma membrane
GO:0016607 nuclear speck


-  Descriptions from all associated GenBank mRNAs
  AK056430 - Homo sapiens cDNA FLJ31868 fis, clone NT2RP7001962, highly similar to Rattus norvegicus YT521 mRNA for RNA splicing-related protein.
BC053863 - Homo sapiens YTH domain containing 1, mRNA (cDNA clone MGC:61557 IMAGE:4933750), complete cds.
BC041119 - Homo sapiens YTH domain containing 1, mRNA (cDNA clone MGC:47781 IMAGE:5541053), complete cds.
KJ895165 - Synthetic construct Homo sapiens clone ccsbBroadEn_04559 YTHDC1 gene, encodes complete protein.
AB384654 - Synthetic construct DNA, clone: pF1KA1966, Homo sapiens YTHDC1 gene for YTH domain-containing protein 1, complete cds, without stop codon, in Flexi system.
CU691958 - Synthetic construct Homo sapiens gateway clone IMAGE:100022718 5' read YTHDC1 mRNA.
AL157447 - Homo sapiens mRNA; cDNA DKFZp761C1811 (from clone DKFZp761C1811).
AK090836 - Homo sapiens cDNA FLJ33517 fis, clone BRAMY2005708.
AB075846 - Homo sapiens mRNA for KIAA1966 protein.
JD416212 - Sequence 397236 from Patent EP1572962.
JD397726 - Sequence 378750 from Patent EP1572962.
AL832559 - Homo sapiens mRNA; cDNA DKFZp547E1518 (from clone DKFZp547E1518).
AK098515 - Homo sapiens cDNA FLJ25649 fis, clone SYN01041, highly similar to Rattus norvegicus YT521 mRNA for RNA splicing-related protein.
JD562685 - Sequence 543709 from Patent EP1572962.
JD377617 - Sequence 358641 from Patent EP1572962.
JD314201 - Sequence 295225 from Patent EP1572962.
JD023889 - Sequence 4913 from Patent EP1572962.
JD288780 - Sequence 269804 from Patent EP1572962.
JD506952 - Sequence 487976 from Patent EP1572962.
JD348828 - Sequence 329852 from Patent EP1572962.
JD273560 - Sequence 254584 from Patent EP1572962.
JD073916 - Sequence 54940 from Patent EP1572962.
JD215507 - Sequence 196531 from Patent EP1572962.
JD541195 - Sequence 522219 from Patent EP1572962.
JD449543 - Sequence 430567 from Patent EP1572962.
JD075887 - Sequence 56911 from Patent EP1572962.
JD396575 - Sequence 377599 from Patent EP1572962.
JD129200 - Sequence 110224 from Patent EP1572962.
JD251810 - Sequence 232834 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000344157.1, ENST00000344157.2, ENST00000344157.3, ENST00000344157.4, ENST00000344157.5, ENST00000344157.6, ENST00000344157.7, ENST00000344157.8, KIAA1966 , NM_001031732, Q4W5Q3, Q7Z622, Q8TF35, Q96MU7, uc317wwa.1, uc317wwa.2, YT521 , YTDC1_HUMAN, YTHDC1
UCSC ID: ENST00000344157.9_7
RefSeq Accession: NM_001031732.4
Protein: Q96MU7 (aka YTDC1_HUMAN)

-  Gene Model Information
  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.