Tbio YTHDC1 YTH domain-containing protein 1

Protein Summary

Description

Regulator of alternative splicing that specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs (PubMed:26318451, PubMed:26876937, PubMed:25242552, PubMed:28984244). M6A is a modification present at internal sites of mRNAs and some non-coding RNAs and plays a role in the efficiency of mRNA splicing, processing and stability (PubMed:26318451, PubMed:25242552). Acts as a key regulator of exon-inclusion or exon-skipping during alternative splicing via interaction with mRNA splicing factors SRSF3 and SRSF10 (PubMed:26876937). Specifically binds m6A-containing mRNAs and promotes recruitment of SRSF3 to its mRNA-binding elements adjacent to m6A sites, leading to exon-inclusion during alternative splicing (PubMed:26876937). In contrast, interaction with SRSF3 prevents interaction with SRSF10, a splicing factor that promotes exon skipping: this prevents SRSF10 from binding to its mRNA-binding sites close to m6A-containing regions, leading to inhibit exon skipping during alternative splicing (PubMed:26876937). May also regulate alternative splice site selection (PubMed:20167602). Also involved in nuclear export of m6A-containing mRNAs via interaction with SRSF3: interaction with SRSF3 facilitates m6A-containing mRNA-binding to both SRSF3 and NXF1, promoting mRNA nuclear export (PubMed:28984244). Also recognizes and binds m6A on other RNA molecules (PubMed:27602518). Involved in random X inactivation mediated by Xist RNA: recognizes and binds m6A-containing Xist and promotes transcription repression activity of Xist (PubMed:27602518). Involved in S-adenosyl-L-methionine homeostasis by regulating expression of MAT2A transcripts, probably by binding m6A-containing MAT2A mRNAs (By similarity).

Uniprot Accession IDs

• Q96MU7
• Q4W5Q3
• Q7Z622
• Q8TF35

Gene Name

• YTHDC1

Ensembl ID

• ENST00000344157
• ENSP00000339245
• ENSG00000083896
• ENST00000355665
• ENSP00000347888
• ENST00000613637
• ENSP00000484604
• ENSG00000275272
• ENST00000615500
• ENSP00000479213

Symbol

• KIAA1966
• YT521
• YT521
• YT521-B

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
transcription factor perturbation	0.96
kinase	0.9
virus perturbation	0.88
ligand (protein) perturbation	0.83
microRNA	0.8

Protein Classes

No PANTHER Classes or DTO Classes found

IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 76.99   (req: < 5)

Gene RIFs: 10   (req: <= 3)

Antibodies: 79   (req: <= 50)

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 76.99   (req: >= 5)

Gene RIFs: 10   (req: > 3)

Antibodies: 79   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 7

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 0

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

Expression Data (0 Tissues)

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No expression data found

Protein Sequence and Structure

Residue Counts

Protein Sequence

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Related Tools (4)

Target Illumination GWAS Analytics (TIGA)

TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.

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GENEVA

GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.

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GlyGen

GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.

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ARCHS4

ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.

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Approved Drugs (0)

No approved drugs found

Active Ligands (0)

No active ligands found

Protein-Protein Interactions (88)

Explore Interacting Targets

1 – 10 of 88

• See Interactions on String-DB

ZC3H18

Tdark

Novelty:  0.3515546

p_int:  0.999978451

p_ni:  0.000021549

p_wrong:  1e-9

Score:  0.288

Data Source:  BioPlex,STRINGDB

LARP4B

Tbio

Novelty:  0.11363794

p_int:  0.999771855

p_ni:  0.000228136

p_wrong:  9e-9

Score:  0.224

Data Source:  BioPlex,STRINGDB

APOBEC3D

Tbio

Novelty:  0.01102619

p_int:  0.999455736

p_ni:  0.000544214

p_wrong:  4.9e-8

Score:  0.192

Data Source:  BioPlex,STRINGDB

ELAVL2

Tbio

Novelty:  0.00370708

p_int:  0.999181411

p_ni:  0.000818586

p_wrong:  3e-9

Score:  0.415

Data Source:  BioPlex,STRINGDB

CLK2

Tchem

Family:  Kinase

Novelty:  0.13068449

p_int:  0.998972753

p_ni:  0.001027247

Score:  0.757

Data Source:  BioPlex,STRINGDB

SNIP1

Tbio

Novelty:  0.01865867

p_int:  0.995713167

p_ni:  0.004286833

Score:  0.277

Data Source:  BioPlex,STRINGDB

SAP18

Tbio

Family:  Enzyme

Novelty:  0.03918373

p_int:  0.991854346

p_ni:  0.008145415

p_wrong:  2.39e-7

Score:  0.155

Data Source:  BioPlex,STRINGDB

CLK3

Tchem

Family:  Kinase

Novelty:  0.03466191

p_int:  0.987439268

p_ni:  0.012560614

p_wrong:  1.18e-7

Score:  0.798

Data Source:  BioPlex,STRINGDB

RBM47

Tbio

Novelty:  0.04787234

p_int:  0.981208727

p_ni:  0.018791248

p_wrong:  2.6e-8

Data Source:  BioPlex

FBXW11

Tbio

Novelty:  0.0715377

p_int:  0.976488693

p_ni:  0.023499323

p_wrong:  0.000011985

Score:  0.358

Data Source:  BioPlex,STRINGDB

Nearest Tclin Targets

Nearest Tclin calculations are only available for targets with KEGG Pathway annotations.

Pathways (0)

No pathways found

Viral Interactions (0)

No viral interactions found

Gene Ontology Terms (11)

Functions (2)

Components (4)

Processes (5)

Find Similar Targets

Items per page:

10

1 – 2 of 2

GO Term	Evidence	Assigned by
N6-methyladenosine-containing RNA binding	Inferred from Direct Assay (IDA)	UniProtKB
RNA binding	Inferred from Direct Assay (IDA)	UniProtKB

Disease Associations (null)

No disease associations found

GWAS Traits (10)

Items per page:

5

1 – 5 of 10

GWAS Trait	EFO ID	ENSG ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
IGF-1 measurement	EFO_0004627	ENSG00000083896	1	1	1		32.7
IGF-1 measurement	EFO_0004627	ENSG00000275272	1	1	1		32.7
total cholesterol measurement	EFO_0004574	ENSG00000083896	1	1	1		31.1
total cholesterol measurement	EFO_0004574	ENSG00000275272	1	1	1		31.1
low density lipoprotein cholesterol measurement	EFO_0004611	ENSG00000275272	1	1	1		17.6

Items per page:

5

1 – 5 of 10

GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
IGF-1 measurement	EFO_0004627	1		32.7
IGF-1 measurement	EFO_0004627	1		32.7
total cholesterol measurement	EFO_0004574	1		31.1
total cholesterol measurement	EFO_0004574	1		31.1
low density lipoprotein cholesterol measurement	EFO_0004611	1		17.6

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UniProt Keyword Find Similar Targets

No Header	No Header
3D-structure
Alternative splicing
Complete proteome
Isopeptide bond
mRNA processing
mRNA splicing
Nucleus
Phosphoprotein
Polymorphism
Reference proteome

GWAS Trait Find Similar Targets

No Header	No Header
apolipoprotein A 1 measurement
apolipoprotein B measurement
IGF-1 measurement
low density lipoprotein cholesterol measurement
total cholesterol measurement

MGI Phenotype Find Similar Targets

No Header	No Header
cellular phenotype
endocrine/exocrine gland phenotype
mortality/aging
reproductive system phenotype

IDG Resources

No IDG generated resources found

Orthologs (11)

1 – 5 of 11

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	YTH domain containing 1	VGNC:12940	461291
Macaque	YTH domain containing 1		709717
Mouse	YTH domain containing 1	MGI:2443713	231386
Rat	YTH domain containing 1	RGD:621706	170956
Dog	YTH domain containing 1	VGNC:48503	475161

Species	Name	OMA	EggNOG	Inparanoid
Chimp	YTH domain containing 1
Macaque	YTH domain containing 1
Mouse	YTH domain containing 1
Rat	YTH domain containing 1
Dog	YTH domain containing 1

Publication Statistics

PubMed Score 76.99

PubMed score by year

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PubTator Score 16.23

PubTator score by year

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Related Publications

Text Mined References (33)

GeneRif Annotations (10)

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10

0 of 0

PMID	Year	Title