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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
    mouse all
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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)

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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