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    Smg6 SMG6 nonsense mediated mRNA decay factor [ Mus musculus (house mouse) ]

    Gene ID: 103677, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Smg6provided by MGI
    Official Full Name
    SMG6 nonsense mediated mRNA decay factorprovided by MGI
    Primary source
    MGI:MGI:2144117
    See related
    Ensembl:ENSMUSG00000038290 AllianceGenome:MGI:2144117
    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
    Summary
    Predicted to enable several functions, including DNA polymerase binding activity; RNA endonuclease activity; and nucleic acid binding activity. Predicted to be involved in negative regulation of telomere capping and nuclear-transcribed mRNA catabolic process, nonsense-mediated decay. Predicted to be located in cytosol and nucleolus. Predicted to be part of exon-exon junction complex and telomerase holoenzyme complex. Is expressed in 1-cell stage embryo; 4-cell stage embryo; compacted morula; and cortical plate. Orthologous to human SMG6 (SMG6 nonsense mediated mRNA decay factor). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in testis adult (RPKM 16.7), thymus adult (RPKM 12.4) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Smg6 in Genome Data Viewer
    Location:
    11 B5; 11 45.76 cM
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (74816665..75055274)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (74925854..75164448)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene small G protein signaling modulator 2 Neighboring gene microRNA 6926 Neighboring gene small nucleolar RNA, C/D box 91A Neighboring gene TSR1 20S rRNA accumulation Neighboring gene serine racemase Neighboring gene STARR-seq mESC enhancer starr_29979 Neighboring gene predicted gene, 22733 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:74826503-74826738 Neighboring gene ribosomal protein S12, pseudogene 19 Neighboring gene SMT3 suppressor of mif two 3 homolog 2 pseudogene Neighboring gene predicted gene, 51907 Neighboring gene RIKEN cDNA 1700016P03 gene Neighboring gene STARR-positive B cell enhancer ABC_E10686 Neighboring gene microRNA 212 Neighboring gene microRNA 132 Neighboring gene hypermethylated in cancer 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. SMG6 localizes to the chromatoid body and shapes the male germ cell transcriptome to drive spermatogenesis. Lehtiniemi T, et al. Nucleic Acids Res, 2022 Nov 11. PMID 36259644, Free PMC Article
    2. A conditional Smg6 mutant mouse model reveals circadian clock regulation through the nonsense-mediated mRNA decay pathway. Katsioudi G, et al. Sci Adv, 2023 Jan 13. PMID 36638184, Free PMC Article
    3. Smg6/Est1 licenses embryonic stem cell differentiation via nonsense-mediated mRNA decay. Li T, et al. EMBO J, 2015 Jun 12. PMID 25770585, Free PMC Article
    4. CFIm-mediated alternative polyadenylation safeguards the development of mammalian pre-implantation embryos. Li N, et al. Stem Cell Reports, 2023 Jan 10. PMID 36563685, Free PMC Article
    5. Cell Type-Specific Role of RNA Nuclease SMG6 in Neurogenesis. Guerra GM, et al. Cells, 2021 Nov 30. PMID 34943873, Free PMC Article

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SMG6 localizes to the chromatoid body and shapes the male germ cell transcriptome to drive spermatogenesis.
      Title: SMG6 localizes to the chromatoid body and shapes the male germ cell transcriptome to drive spermatogenesis.
    2. Cell Type-Specific Role of RNA Nuclease SMG6 in Neurogenesis.
      Title: Cell Type-Specific Role of RNA Nuclease SMG6 in Neurogenesis.
    3. Smg6/Est1 licenses embryonic stem cell differentiation via nonsense-mediated mRNA decay.
      Title: Smg6/Est1 licenses embryonic stem cell differentiation via nonsense-mediated mRNA decay.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Gene trapped (1) 
    • Targeted (3)  1 citation
    • Transgenic (1) 

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC7717

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA polymerase binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA polymerase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA endonuclease activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA endonuclease activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ribonucleoprotein complex binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ribonucleoprotein complex binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables telomerase RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables telomerase RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables telomerase RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables telomeric DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables telomeric DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables telomeric DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of telomere capping IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of telomere capping ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of telomere maintenance ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of telomere maintenance ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in chromosome, telomeric region IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of exon-exon junction complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of exon-exon junction complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleolus 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
    		  
    part_of telomerase holoenzyme complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    telomerase-binding protein EST1A
    Names
    EST1-like protein A
    Smg-6 homolog, nonsense mediated mRNA decay factor
    ever shorter telomeres 1A
    nonsense mediated mRNA decay factor SMG6
    telomerase subunit EST1A
    NP_001002764.1
    XP_011246962.1
    XP_036012083.1

    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_001002764.2 → NP_001002764.1  telomerase-binding protein EST1A

      See identical proteins and their annotated locations for NP_001002764.1

      Status: VALIDATED

      Source sequence(s)
      BC066040, BY109058
      Consensus CDS
      CCDS25039.1
      UniProtKB/Swiss-Prot
      P61406, Q5NC64
      Related
      ENSMUSP00000043555.7, ENSMUST00000045281.13
      Conserved Domains (4) summary
      cd09885
      Location:1240 → 1415
      PIN_Smg6; PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs
      pfam10373
      Location:750 → 1102
      EST1_DNA_bind; Est1 DNA/RNA binding domain
      pfam10374
      Location:637 → 740
      EST1; Telomerase activating protein Est1
      pfam12868
      Location:479 → 552
      DUF3824; Domain of unknwon function (DUF3824)

    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_000077.7 Reference GRCm39 C57BL/6J

      Range
      74816665..75055274
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011248660.3 → XP_011246962.1  telomerase-binding protein EST1A isoform X2

      Conserved Domains (2) summary
      cd09885
      Location:333 → 508
      PIN_Smg6-like; VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs
      pfam10373
      Location:1 → 195
      EST1_DNA_bind; Est1 DNA/RNA binding domain

    2. XM_036156190.1 → XP_036012083.1  telomerase-binding protein EST1A isoform X1

      Conserved Domains (3) summary
      cd09885
      Location:1227 → 1402
      PIN_Smg6-like; VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs
      pfam10373
      Location:737 → 1089
      EST1_DNA_bind; Est1 DNA/RNA binding domain
      pfam10374
      Location:624 → 729
      EST1; Telomerase activating protein Est1
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P61406.1 GenPept UniProtKB/Swiss-Prot:P61406

    Gene LinkOut

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

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