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Ythdc1 YTH domain containing 1 [ Mus musculus (house mouse) ]

Gene ID: 231386, updated on 5-Mar-2024

Summary

Official Symbol
Ythdc1provided by MGI
Official Full Name
YTH domain containing 1provided by MGI
Primary source
MGI:MGI:2443713
See related
Ensembl:ENSMUSG00000035851 AllianceGenome:MGI:2443713
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
mKIAA1966; A730098D12Rik
Summary
Predicted to enable N6-methyladenosine-containing RNA binding activity and mRNA binding activity. Involved in posttranscriptional regulation of gene expression. Acts upstream of or within gamete generation; in utero embryonic development; and regulation of mRNA processing. Located in nucleus. Orthologous to human YTHDC1 (YTH domain containing 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 13.3), CNS E14 (RPKM 10.4) and 26 other tissues See more
Orthologs
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Genomic context

See Ythdc1 in Genome Data Viewer
Location:
5 E1; 5 43.56 cM
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (86951349..86984518)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (86803980..86836659)

Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene transmembrane protease, serine 11B Neighboring gene transmembrane protease, serine 11e Neighboring gene STARR-seq mESC enhancer starr_13551 Neighboring gene STARR-seq mESC enhancer starr_13552 Neighboring gene STARR-seq mESC enhancer starr_13553 Neighboring gene STARR-seq mESC enhancer starr_13554 Neighboring gene predicted gene, 21461 Neighboring gene UDP glucuronosyltransferase 2 family, polypeptide B34

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

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

General protein information

Preferred Names
YTH domain-containing protein 1

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_001347375.1NP_001334304.1  YTH domain-containing protein 1 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 4. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 4.
    Source sequence(s)
    AC102016
    Consensus CDS
    CCDS84898.1
    UniProtKB/Swiss-Prot
    E9Q5K9
    Related
    ENSMUSP00000113951.2, ENSMUST00000120498.8
  2. NM_001347376.1NP_001334305.1  YTH domain-containing protein 1 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks two alternate in-frame exons compared to variant 4. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 4.
    Source sequence(s)
    AC102016
    Consensus CDS
    CCDS84899.1
    UniProtKB/Swiss-Prot
    E9Q5K9
    Related
    ENSMUSP00000113000.2, ENSMUST00000119339.8
  3. NM_001359907.1NP_001346836.1  YTH domain-containing protein 1 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) encodes the longest isoform (4).
    Source sequence(s)
    AC102016
    Conserved Domains (1) summary
    pfam04146
    Location:368506
    YTH; YT521-B-like domain
  4. NM_001359908.1NP_001346837.1  YTH domain-containing protein 1 isoform 5

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks an alternate in-frame exon compared to variant 4. The resulting isoform (5) has the same N- and C-termini but is shorter compared to isoform 4.
    Source sequence(s)
    AC102016
    Conserved Domains (1) summary
    pfam04146
    Location:350488
    YTH; YT521-B-like domain
  5. NM_177680.4NP_808348.2  YTH domain-containing protein 1 isoform 1

    See identical proteins and their annotated locations for NP_808348.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) lacks an alternate in-frame exon and uses an alternate in-frame splice junction compared to variant 4. The resulting isoform (1) has the same N- and C-termini but is shorter compared to isoform 4.
    Source sequence(s)
    AC102016
    Consensus CDS
    CCDS39127.1
    UniProtKB/Swiss-Prot
    E9PW44, E9Q5K9, E9Q7Z8, Q69Z54, Q80V25, Q8R5E6
    Related
    ENSMUSP00000039133.8, ENSMUST00000038384.8
    Conserved Domains (1) summary
    pfam04146
    Location:356493
    YTH; YT521-B-like domain

RNA

  1. NR_153372.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) contains an alternate exon compared to variant 4. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC102016

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000071.7 Reference GRCm39 C57BL/6J

    Range
    86951349..86984518
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006534867.5XP_006534930.1  YTH domain-containing protein 1 isoform X4

    Conserved Domains (1) summary
    pfam04146
    Location:368505
    YTH; YT521-B-like domain
  2. XM_006534863.3XP_006534926.1  YTH domain-containing protein 1 isoform X1

    Conserved Domains (1) summary
    pfam04146
    Location:368505
    YTH; YT521-B-like domain
  3. XM_030254395.2XP_030110255.1  YTH domain-containing protein 1 isoform X5

    Conserved Domains (1) summary
    pfam04146
    Location:368505
    YTH; YT521-B-like domain
  4. XM_006534865.3XP_006534928.1  YTH domain-containing protein 1 isoform X2

    Conserved Domains (1) summary
    pfam04146
    Location:350487
    YTH; YT521-B-like domain
  5. XM_017320843.2XP_017176332.1  YTH domain-containing protein 1 isoform X3

    Conserved Domains (1) summary
    pfam04146
    Location:338475
    YTH; YT521-B-like domain

RNA

  1. XR_004942503.1 RNA Sequence

  2. XR_389269.4 RNA Sequence

    Related
    ENSMUST00000156363.8
  3. XR_003955632.2 RNA Sequence