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

Gene ID: 103677, updated on 8-Mar-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; endoribonuclease 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. Orthologous to human SMG6 (SMG6 nonsense mediated mRNA decay factor). [provided by Alliance of Genome Resources, Apr 2022]
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. 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
  3. 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
  4. Cell Type-Specific Role of RNA Nuclease SMG6 in Neurogenesis. Guerra GM, et al. Cells, 2021 Nov 30. PMID 34943873, Free PMC Article
  5. The TRIM9/TRIM67 neuronal interactome reveals novel activators of morphogenesis. Menon S, et al. Mol Biol Cell, 2021 Feb 15. PMID 33378226, Free PMC Article

See all (28) 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)
  • Transgenic (1) 
  • Gene trapped (1) 
  • Targeted (3)  1 citation
  • Endonuclease-mediated (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 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 endonuclease activity IEA
Inferred from Electronic Annotation
more info
  
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables nuclease activity 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 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
  
Process Evidence Code Pubs
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 regulation of telomere maintenance ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in chromosome IEA
Inferred from Electronic Annotation
more info
  
located_in chromosome, telomeric region IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in cytosol ISO
Inferred from Sequence Orthology
more info
  
part_of exon-exon junction complex ISO
Inferred from Sequence Orthology
more info
  
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
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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