Human Gene YTHDC2 (ENST00000161863.9_4) from GENCODE V47lift37

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Description: YTH domain containing 2, transcript variant 1 (from RefSeq NM_022828.5)
Gencode Transcript: ENST00000161863.9_4
Gencode Gene: ENSG00000047188.16_7
Transcript (Including UTRs)
Position: hg19 chr5:112,849,391-112,930,981 Size: 81,591 Total Exon Count: 30 Strand: +
Coding Region
Position: hg19 chr5:112,849,593-112,929,080 Size: 79,488 Coding Exon Count: 29

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 (chr5:112,849,391-112,930,981)			mRNA (may differ from genome)		Protein (1430 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: YTDC2_HUMAN DESCRIPTION: RecName: Full=Probable ATP-dependent RNA helicase YTHDC2; EC=3.6.4.13; CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate. INTERACTION: Q99J34:Irak1 (xeno); NbExp=2; IntAct=EBI-1057466, EBI-6117042; Q15306:IRF4; NbExp=2; IntAct=EBI-1057466, EBI-751345; SIMILARITY: Belongs to the DEAD box helicase family. DEAH subfamily. SIMILARITY: Contains 2 ANK repeats. SIMILARITY: Contains 1 helicase ATP-binding domain. SIMILARITY: Contains 1 helicase C-terminal domain. SIMILARITY: Contains 1 R3H domain. SIMILARITY: Contains 1 YTH domain. SEQUENCE CAUTION: Sequence=BAB15183.1; 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 D000082 Acetaminophen D016604 Aflatoxin B1 D019327 Copper Sulfate D010936 Plant Extracts D011374 Progesterone D013749 Tetrachlorodibenzodioxin C045651 epigallocatechin gallate C027373 potassium chromate(VI)

Common Gene Haplotype Alleles


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


	Highest median expression: 13.69 RPKM in Brain - Cerebellar Hemisphere Total median expression: 384.40 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	-85.00	202	-0.421	Picture	PostScript	Text
3' UTR	-353.10	1810	-0.195	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
IPR002110 - Ankyrin_rpt
IPR020683 - Ankyrin_rpt-contain_dom
IPR011545 - DNA/RNA_helicase_DEAD/DEAH_N
IPR011709 - DUF1605
IPR007502 - Helicase-assoc_dom
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
IPR001374 - R3H_ss-bd
IPR007275 - YTH_domain

Pfam Domains:
PF00270 - DEAD/DEAH box helicase
PF00271 - Helicase conserved C-terminal domain
PF01424 - R3H domain
PF04146 - YT521-B-like domain
PF04408 - Helicase associated domain (HA2)
PF07717 - Oligonucleotide/oligosaccharide-binding (OB)-fold

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases
53795 - PEP carboxykinase-like
48403 - Ankyrin repeat
82708 - R3H domain

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

2YU6 - NMR MuPIT

ModBase Predicted Comparative 3D Structure on Q9H6S0


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	Genome Browser	No ortholog
Gene Details	Gene Details			Gene Details
Gene Sorter	Gene Sorter			Gene Sorter
	RGD	Ensembl		WormBase
				Protein Sequence
				Alignment

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0000166 nucleotide binding GO:0003676 nucleic acid binding GO:0003723 RNA binding GO:0004004 ATP-dependent RNA helicase activity GO:0004386 helicase activity GO:0005515 protein binding GO:0005524 ATP binding GO:0008186 RNA-dependent ATPase activity GO:0016787 hydrolase activity GO:0070063 RNA polymerase binding GO:1990247 N6-methyladenosine-containing RNA binding Biological Process: GO:0006396 RNA processing GO:0034612 response to tumor necrosis factor GO:0044829 positive regulation by host of viral genome replication GO:0070555 response to interleukin-1 Cellular Component: GO:0005737 cytoplasm GO:0005783 endoplasmic reticulum

Descriptions from all associated GenBank mRNAs


	AK096486 - Homo sapiens cDNA FLJ39167 fis, clone OCBBF2002865, weakly similar to DOSAGE COMPENSATION REGULATOR. AK310855 - Homo sapiens cDNA, FLJ17897. BC019100 - Homo sapiens YTH domain containing 2, mRNA (cDNA clone IMAGE:4909312), partial cds. BC137285 - Homo sapiens YTH domain containing 2, mRNA (cDNA clone MGC:168905 IMAGE:9021282), complete cds. AK131450 - Homo sapiens cDNA FLJ16598 fis, clone TESTI4006473, weakly similar to ATP-dependent RNA helicase A. AK225316 - Homo sapiens mRNA for YTH domain containing 2 variant, clone: HEP04512. AK025593 - Homo sapiens cDNA: FLJ21940 fis, clone HEP04512. JD081270 - Sequence 62294 from Patent EP1572962. JD475178 - Sequence 456202 from Patent EP1572962. JD280548 - Sequence 261572 from Patent EP1572962. JD501418 - Sequence 482442 from Patent EP1572962. CR627037 - Homo sapiens mRNA; cDNA DKFZp686K16112 (from clone DKFZp686K16112). AK095368 - Homo sapiens cDNA FLJ38049 fis, clone CTONG2014280. AK000915 - Homo sapiens cDNA FLJ10053 fis, clone HEMBA1001303. JD048853 - Sequence 29877 from Patent EP1572962. JD245557 - Sequence 226581 from Patent EP1572962. JD559750 - Sequence 540774 from Patent EP1572962. AL049305 - Homo sapiens mRNA; cDNA DKFZp564A186 (from clone DKFZp564A186). JD172162 - Sequence 153186 from Patent EP1572962. JD083876 - Sequence 64900 from Patent EP1572962. JD321406 - Sequence 302430 from Patent EP1572962. JD036426 - Sequence 17450 from Patent EP1572962. JD410557 - Sequence 391581 from Patent EP1572962. JD553514 - Sequence 534538 from Patent EP1572962. JD416670 - Sequence 397694 from Patent EP1572962. JD386619 - Sequence 367643 from Patent EP1572962. JD555763 - Sequence 536787 from Patent EP1572962. JD524325 - Sequence 505349 from Patent EP1572962. JD244314 - Sequence 225338 from Patent EP1572962.

Other Names for This Gene


	Alternate Gene Symbols: B2RP66, ENST00000161863.1, ENST00000161863.2, ENST00000161863.3, ENST00000161863.4, ENST00000161863.5, ENST00000161863.6, ENST00000161863.7, ENST00000161863.8, NM_022828, Q9H6S0, uc317ccp.1, uc317ccp.2, YTDC2_HUMAN, YTHDC2 UCSC ID: ENST00000161863.9_4 RefSeq Accession: NM_022828.5 Protein: Q9H6S0 (aka YTDC2_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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