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    Ythdc1 YTH N6-methyladenosine RNA binding protein C1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 170956, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Ythdc1provided by RGD
    Official Full Name
    YTH N6-methyladenosine RNA binding protein C1provided by RGD
    Primary source
    RGD:621706
    See related
    Ensembl:ENSRNOG00000001996 AllianceGenome:RGD:621706
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Yt521
    Summary
    Enables N6-methyladenosine-containing RNA binding activity. Involved in mRNA splicing, via spliceosome. Located in nuclear body. Orthologous to human YTHDC1 (YTH domain containing 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 184.9), Lung (RPKM 128.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    14p21
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 14 NC_086032.1 (21540276..21570724, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 14 NC_051349.1 (21185438..21215934, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 14 NC_005113.4 (22971834..23002326, complement)

    Chromosome 14 - NC_086032.1Genomic Context describing neighboring genes Neighboring gene UDP glucuronosyltransferase 2 family, polypeptide B10 Neighboring gene heat shock protein 90 alpha family class A member 1, pseudogene 3 Neighboring gene UDP glucuronosyltransferase 2 family, polypeptide B34 like 1 Neighboring gene transmembrane serine protease 11E Neighboring gene uncharacterized LOC134481834 Neighboring gene ribosomal protein L23a, pseudogene 20

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Solution structure of the YTH domain in complex with N6-methyladenosine RNA: a reader of methylated RNA. Theler D, et al. Nucleic Acids Res, 2014 Dec 16. PMID 25389274, Free PMC Article
    2. Methyltransferase-like 3 modulates visceral hypersensitivity through regulating the nuclear export of circKcnk9 in YTHDC1-dependent manner. Lin W, et al. Mol Pain, 2022 Apr. PMID 36443649, Free PMC Article
    3. YTHDC1 mitigates ischemic stroke by promoting Akt phosphorylation through destabilizing PTEN mRNA. Zhang Z, et al. Cell Death Dis, 2020 Nov 13. PMID 33188203, Free PMC Article
    4. Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain. Xu C, et al. Nat Chem Biol, 2014 Nov. PMID 25242552
    5. The YTH domain is a novel RNA binding domain. Zhang Z, et al. J Biol Chem, 2010 May 7. PMID 20167602, Free PMC Article

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Methyltransferase-like 3 modulates visceral hypersensitivity through regulating the nuclear export of circKcnk9 in YTHDC1-dependent manner.
      Title: Methyltransferase-like 3 modulates visceral hypersensitivity through regulating the nuclear export of circKcnk9 in YTHDC1-dependent manner.
    2. YTHDC1 mitigates ischemic stroke by promoting Akt phosphorylation through destabilizing PTEN mRNA.
      Title: YTHDC1 mitigates ischemic stroke by promoting Akt phosphorylation through destabilizing PTEN mRNA.
    3. The YTH domain of YT521-B binds sequence-specifically a GA-containing sequence with a 50-fold affinity increase when the adenine is N6 methylated.
      Title: Solution structure of the YTH domain in complex with N6-methyladenosine RNA: a reader of methylated RNA.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

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

    General protein information

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    Preferred Names
    YTH domain-containing protein 1
    Names
    RA301-binding protein
    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_133423.1 → NP_596914.1  YTH domain-containing protein 1

      See identical proteins and their annotated locations for NP_596914.1

      Status: PROVISIONAL

      Source sequence(s)
      AF144731
      UniProtKB/Swiss-Prot
      G3V690, O54729, Q9QY02
      Related
      ENSRNOP00000095873.1, ENSRNOT00000119155.1
      Conserved Domains (1) summary
      pfam04146
      Location:358 → 495
      YTH; YT521-B-like domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086032.1 Reference GRCr8

      Range
      21540276..21570724 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006250808.4 → XP_006250870.1  YTH domain-containing protein 1 isoform X7

      See identical proteins and their annotated locations for XP_006250870.1

      UniProtKB/Swiss-Prot
      G3V690, O54729, Q9QY02
      UniProtKB/TrEMBL
      A6JCQ7
      Related
      ENSRNOP00000080807.1
      Conserved Domains (2) summary
      pfam04146
      Location:340 → 477
      YTH; YT521-B-like domain
      cl11266
      Location:2 → 98
      EssA; WXG100 protein secretion system (Wss), protein EssA

    2. XM_063272837.1 → XP_063128907.1  YTH domain-containing protein 1 isoform X6

    3. XM_006250806.4 → XP_006250868.1  YTH domain-containing protein 1 isoform X4

      UniProtKB/Swiss-Prot
      G3V690, O54729, Q9QY02
      Conserved Domains (2) summary
      pfam04146
      Location:358 → 495
      YTH; YT521-B-like domain
      cl11266
      Location:2 → 98
      EssA; WXG100 protein secretion system (Wss), protein EssA

    4. XM_039091592.2 → XP_038947520.1  YTH domain-containing protein 1 isoform X5

      UniProtKB/Swiss-Prot
      G3V690, O54729, Q9QY02
      Conserved Domains (1) summary
      cd21134
      Location:353 → 489
      YTH; YTH (YT521-B homology) domains are RNA-binding domains that belong to the PUA superfamily

    5. XM_039091591.2 → XP_038947519.1  YTH domain-containing protein 1 isoform X3

      UniProtKB/Swiss-Prot
      G3V690, O54729, Q9QY02
      Conserved Domains (1) summary
      cd21134
      Location:353 → 489
      YTH; YTH (YT521-B homology) domains are RNA-binding domains that belong to the PUA superfamily

    6. XM_039091590.2 → XP_038947518.1  YTH domain-containing protein 1 isoform X2

      UniProtKB/Swiss-Prot
      G3V690, O54729, Q9QY02
      Conserved Domains (1) summary
      cd21134
      Location:371 → 507
      YTH; YTH (YT521-B homology) domains are RNA-binding domains that belong to the PUA superfamily

    7. XM_063272838.1 → XP_063128908.1  YTH domain-containing protein 1 isoform X9

    8. XM_006250805.5 → XP_006250867.1  YTH domain-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      G3V690, O54729, Q9QY02
      UniProtKB/TrEMBL
      A0A8I6GG56
      Related
      ENSRNOP00000087598.1
      Conserved Domains (1) summary
      pfam04146
      Location:370 → 507
      YTH; YT521-B-like domain

    9. XM_008769990.4 → XP_008768212.2  YTH domain-containing protein 1 isoform X8

      UniProtKB/Swiss-Prot
      G3V690, O54729, Q9QY02
      Conserved Domains (1) summary
      cd21134
      Location:371 → 507
      YTH; YTH (YT521-B homology) domains are RNA-binding domains that belong to the PUA superfamily

    10. XM_039091594.2 → XP_038947522.1  YTH domain-containing protein 1 isoform X10

      Conserved Domains (1) summary
      cd21134
      Location:371 → 507
      YTH; YTH (YT521-B homology) domains are RNA-binding domains that belong to the PUA superfamily
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9QY02.2 GenPept UniProtKB/Swiss-Prot:Q9QY02

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