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

Gene ID: 170956, updated on 2-May-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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See Ythdc1 in Genome Data Viewer
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 IEA
Inferred from Electronic Annotation
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 IEA
Inferred from Electronic Annotation
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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