Human Gene YTHDF3 (ENST00000539294.6_10) from GENCODE V47lift37

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Description: YTH N6-methyladenosine RNA binding protein 3, transcript variant 1 (from RefSeq NM_152758.6)
Gencode Transcript: ENST00000539294.6_10
Gencode Gene: ENSG00000185728.17_20
Transcript (Including UTRs)
Position: hg19 chr8:64,081,180-64,125,344 Size: 44,165 Total Exon Count: 6 Strand: +
Coding Region
Position: hg19 chr8:64,081,437-64,122,264 Size: 40,828 Coding Exon Count: 6

Page Index	Sequence and Links	UniProtKB Comments	Primers	CTD	Gene Alleles
RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species	GO Annotations
mRNA Descriptions	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr8:64,081,180-64,125,344)			mRNA (may differ from genome)		Protein (584 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	MGI	OMIM	PubMed	UniProtKB	Wikipedia
BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: YTHD3_HUMAN DESCRIPTION: RecName: Full=YTH domain family protein 3; INTERACTION: P04591:gag (xeno); NbExp=2; IntAct=EBI-2849837, EBI-6179727; SIMILARITY: Contains 1 YTH domain.

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 C016403 2,4-dinitrotoluene D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide D001564 Benzo(a)pyrene D019327 Copper Sulfate D005839 Gentamicins D007213 Indomethacin D013749 Tetrachlorodibenzodioxin D014501 Uranium C053541 bicalutamide C006780 bisphenol A C006253 pirinixic acid C005460 uranyl acetate C088658 zoledronic acid

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 18.39 RPKM in Cells - Cultured fibroblasts Total median expression: 520.98 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

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-112.60	257	-0.438	Picture	PostScript	Text
3' UTR	-725.00	3080	-0.235	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

ModBase Predicted Comparative 3D Structure on Q7Z739


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0003723 RNA binding GO:0005515 protein binding GO:0043022 ribosome binding GO:1990247 N6-methyladenosine-containing RNA binding Biological Process: GO:0045727 positive regulation of translation GO:0045948 positive regulation of translational initiation GO:0061157 mRNA destabilization Cellular Component: GO:0005737 cytoplasm GO:0005829 cytosol

Descriptions from all associated GenBank mRNAs


	BC052970 - Homo sapiens YTH domain family, member 3, mRNA (cDNA clone MGC:54324 IMAGE:6044054), complete cds. AK127574 - Homo sapiens cDNA FLJ45669 fis, clone CTONG3003669, highly similar to YTH domain protein 3. AL832005 - Homo sapiens mRNA; cDNA DKFZp451O193 (from clone DKFZp451O193). BX537996 - Homo sapiens mRNA; cDNA DKFZp451M1911 (from clone DKFZp451M1911). AL831816 - Homo sapiens mRNA; cDNA DKFZp451A052 (from clone DKFZp451A052). AK056219 - Homo sapiens cDNA FLJ31657 fis, clone NT2RI2004304, moderately similar to Homo sapiens NY-REN-2 antigen mRNA. BC037492 - Homo sapiens cDNA clone IMAGE:5260578, containing frame-shift errors. AL832335 - Homo sapiens mRNA; cDNA DKFZp451J085 (from clone DKFZp451J085). CU690942 - Synthetic construct Homo sapiens gateway clone IMAGE:100021491 5' read YTHDF3 mRNA. AB463357 - Synthetic construct DNA, clone: pF1KB8698, Homo sapiens YTHDF3 gene for YTH domain family, member 3, without stop codon, in Flexi system. AM393482 - Synthetic construct Homo sapiens clone IMAGE:100002145 for hypothetical protein (YTHDF3 gene). AM393861 - Synthetic construct Homo sapiens clone IMAGE:100002144 for hypothetical protein (YTHDF3 gene). KJ895899 - Synthetic construct Homo sapiens clone ccsbBroadEn_05293 YTHDF3 gene, encodes complete protein. AK093081 - Homo sapiens cDNA FLJ35762 fis, clone TESTI2004793, moderately similar to Homo sapiens NY-REN-2 antigen mRNA. AX747908 - Sequence 1433 from Patent EP1308459. AK298544 - Homo sapiens cDNA FLJ56221 complete cds, highly similar to YTH domain protein 3. AL832369 - Homo sapiens mRNA; cDNA DKFZp451B107 (from clone DKFZp451B107). JD093132 - Sequence 74156 from Patent EP1572962. JD282567 - Sequence 263591 from Patent EP1572962. JD470562 - Sequence 451586 from Patent EP1572962. JD391617 - Sequence 372641 from Patent EP1572962. JD440484 - Sequence 421508 from Patent EP1572962. JD460707 - Sequence 441731 from Patent EP1572962. JD075638 - Sequence 56662 from Patent EP1572962. JD503944 - Sequence 484968 from Patent EP1572962. JD552420 - Sequence 533444 from Patent EP1572962. JD514584 - Sequence 495608 from Patent EP1572962. JD290005 - Sequence 271029 from Patent EP1572962. AK002173 - Homo sapiens cDNA FLJ11311 fis, clone PLACE1010102. AL050081 - Homo sapiens mRNA; cDNA DKFZp566J2146 (from clone DKFZp566J2146).

Other Names for This Gene


	Alternate Gene Symbols: B3KXL4, ENST00000539294.1, ENST00000539294.2, ENST00000539294.3, ENST00000539294.4, ENST00000539294.5, NM_152758, Q63Z37, Q659A3, Q7Z739, uc324rfk.1, uc324rfk.2, YTHD3_HUMAN, YTHDF3 UCSC ID: ENST00000539294.6_10 RefSeq Accession: NM_152758.6 Protein: Q7Z739 (aka YTHD3_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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