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YTHDC1 YTH N6-methyladenosine RNA binding protein C1 [ Homo sapiens (human) ]

Gene ID: 91746, updated on 3-Nov-2024

Summary

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Official Symbol
YTHDC1provided by HGNC
Official Full Name
YTH N6-methyladenosine RNA binding protein C1provided by HGNC
Primary source
HGNC:HGNC:30626
See related
Ensembl:ENSG00000083896 MIM:617283; AllianceGenome:HGNC:30626
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
YT521; YT521-B
Summary
Enables N6-methyladenosine-containing RNA reader activity and RNA binding activity. Involved in gene expression and regulation of gene expression. Located in nuclear speck and plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in bone marrow (RPKM 22.7), ovary (RPKM 15.2) and 25 other tissues See more
Orthologs
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Genomic context

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See YTHDC1 in Genome Data Viewer
Location:
4q13.2
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (68310387..68350090, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (71751442..71791158, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (69176105..69215808, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene UDP glucuronosyltransferase family 2 member B11 pseudogene Neighboring gene apolipoprotein O pseudogene 4 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:69215177-69215756 Neighboring gene uncharacterized LOC124900917 Neighboring gene metallothionein 2 pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. The Effect of N6-Methyladenosine Regulators and m6A Reader YTHDC1-Mediated N6-Methyladenosine Modification Is Involved in Oxidative Stress in Human Aortic Dissection. Yin F, et al. Oxid Med Cell Longev, 2023. PMID 36819785, Free PMC Article
  2. YTHDC1 gene polymorphisms and neuroblastoma susceptibility in Chinese children. Li Y, et al. Aging (Albany NY), 2021 Dec 12. PMID 34897032, Free PMC Article
  3. YTHDC1 gene polymorphisms and Wilms tumor susceptibility in Chinese children: A five-center case-control study. Lin A, et al. Gene, 2021 May 30. PMID 33737126
  4. Atomistic and Thermodynamic Analysis of N6-Methyladenosine (m(6)A) Recognition by the Reader Domain of YTHDC1. Li Y, et al. J Chem Theory Comput, 2021 Feb 9. PMID 33472367
  5. Downregulation of m(6) A reader YTHDC2 promotes tumor progression and predicts poor prognosis in non-small cell lung cancer. Sun S, et al. Thorac Cancer, 2020 Nov. PMID 32956555, Free PMC Article

See all (146) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. METTL3 mediates m6A modification of lncRNA CRNDE to promote ATG10 expression and improve brain ischemia/reperfusion injury through YTHDC1.
    Title: METTL3 mediates m6A modification of lncRNA CRNDE to promote ATG10 expression and improve brain ischemia/reperfusion injury through YTHDC1.
  2. YTHDC1 inhibits osteoclast differentiation to alleviate osteoporosis by enhancing PTPN6 messenger RNA stability in an m6A-hUR-dependent manner.
    Title: YTHDC1 inhibits osteoclast differentiation to alleviate osteoporosis by enhancing PTPN6 messenger RNA stability in an m6A-hUR-dependent manner.
  3. m[6]A Reader YTHDC1 Impairs Respiratory Syncytial Virus Infection by Downregulating Membrane CX3CR1 Expression.
    Title: m(6)A Reader YTHDC1 Impairs Respiratory Syncytial Virus Infection by Downregulating Membrane CX3CR1 Expression.
  4. KAP1 stabilizes MYCN mRNA and promotes neuroblastoma tumorigenicity by protecting the RNA m[6]A reader YTHDC1 protein degradation.
    Title: KAP1 stabilizes MYCN mRNA and promotes neuroblastoma tumorigenicity by protecting the RNA m(6)A reader YTHDC1 protein degradation.
  5. YTHDC1-dependent m6A modification modulated FOXM1 promotes glycolysis and tumor progression through CENPA in triple-negative breast cancer.
    Title: YTHDC1-dependent m6A modification modulated FOXM1 promotes glycolysis and tumor progression through CENPA in triple-negative breast cancer.
  6. Recruitment of PVT1 Enhances YTHDC1-Mediated m6A Modification of IL-33 in Hyperoxia-Induced Lung Injury During Bronchopulmonary Dysplasia.
    Title: Recruitment of PVT1 Enhances YTHDC1-Mediated m6A Modification of IL-33 in Hyperoxia-Induced Lung Injury During Bronchopulmonary Dysplasia.
  7. YTHDC1 promotes the malignant progression of gastric cancer by promoting ROD1 translocation to the nucleus.
    Title: YTHDC1 promotes the malignant progression of gastric cancer by promoting ROD1 translocation to the nucleus.
  8. KIAA1429 facilitates metastasis via m6A-YTHDC1-dependent RND3 down-regulation in hepatocellular carcinoma cells.
    Title: KIAA1429 facilitates metastasis via m6A-YTHDC1-dependent RND3 down-regulation in hepatocellular carcinoma cells.
  9. YTHDC1-Modified m6A Methylation of Hsa_circ_0102678 Promotes Keratinocyte Inflammation Induced by Cutibacterium acnes Biofilm through Regulating miR-146a/TRAF6 and IRAK1 Axis.
    Title: YTHDC1-Modified m6A Methylation of Hsa_circ_0102678 Promotes Keratinocyte Inflammation Induced by Cutibacterium acnes Biofilm through Regulating miR-146a/TRAF6 and IRAK1 Axis.
  10. YTHDC1 as a tumor progression suppressor through modulating FSP1-dependent ferroptosis suppression in lung cancer.
    Title: YTHDC1 as a tumor progression suppressor through modulating FSP1-dependent ferroptosis suppression in lung cancer.
Submit: New GeneRIF Correction See all GeneRIFs (48)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2019-04-24)

ClinGen Genome Curation Page
Haploinsufficency

Little evidence for dosage pathogenicity (Last evaluated 2019-04-24)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1966

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables N6-methyladenosine-containing RNA reader activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables N6-methyladenosine-containing RNA reader activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA binding HDA PubMed 
enables RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in dosage compensation by inactivation of X chromosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in in utero embryonic development IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA alternative polyadenylation IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA export from nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mRNA splice site recognition IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in post-transcriptional regulation of gene expression ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in primary follicle stage IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of alternative mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in spermatogenesis IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in nuclear speck IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
YTH domain-containing protein 1
Names
YTH domain containing 1
putative splicing factor YT521
splicing factor YT521
splicing factor YT521-B

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001031732.4 → NP_001026902.1  YTH domain-containing protein 1 isoform 1

    See identical proteins and their annotated locations for NP_001026902.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AC074378
    Consensus CDS
    CCDS33992.1
    UniProtKB/Swiss-Prot
    Q4W5Q3, Q7Z622, Q8TF35, Q96MU7
    Related
    ENSP00000339245.4, ENST00000344157.9
    Conserved Domains (1) summary
    pfam04146
    Location:355 → 493
    YTH; YT521-B-like domain

  2. NM_001330698.2 → NP_001317627.1  YTH domain-containing protein 1 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is longer compared to isoform 1.
    Source sequence(s)
    AC074378
    Consensus CDS
    CCDS82929.1
    UniProtKB/TrEMBL
    J3QR07
    Related
    ENSP00000463982.1, ENST00000579690.5
    Conserved Domains (1) summary
    pfam04146
    Location:355 → 492
    YTH; YT521-B-like domain

  3. NM_133370.4 → NP_588611.2  YTH domain-containing protein 1 isoform 2

    See identical proteins and their annotated locations for NP_588611.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC074378
    Consensus CDS
    CCDS3522.2
    UniProtKB/Swiss-Prot
    Q96MU7
    Related
    ENSP00000347888.3, ENST00000355665.7
    Conserved Domains (1) summary
    pfam04146
    Location:337 → 474
    YTH; YT521-B-like domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    68310387..68350090 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005265708.4 → XP_005265765.1  YTH domain-containing protein 1 isoform X1

    See identical proteins and their annotated locations for XP_005265765.1

    Conserved Domains (1) summary
    pfam04146
    Location:337 → 474
    YTH; YT521-B-like domain

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_167250.2 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    4029..43732 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054328548.1 → XP_054184523.1  YTH domain-containing protein 1 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    71751442..71791158 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054351241.1 → XP_054207216.1  YTH domain-containing protein 1 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96MU7.3 GenPept UniProtKB/Swiss-Prot:Q96MU7

Gene LinkOut

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