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    Smg6 SMG6 nonsense mediated mRNA decay factor [ Rattus norvegicus (Norway rat) ]

    Gene ID: 287522, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Smg6provided by RGD
    Official Full Name
    SMG6 nonsense mediated mRNA decay factorprovided by RGD
    Primary source
    RGD:1595918
    See related
    EnsemblRapid:ENSRNOG00000003041 AllianceGenome:RGD:1595918
    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
    LRRGT00040; RGD1309609
    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. Orthologous to human SMG6 (SMG6 nonsense mediated mRNA decay factor). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 140.1), Lung (RPKM 95.3) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Smg6 in Genome Data Viewer
    Location:
    10q24
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (60284628..60512738)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (59786258..60014395)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (61526024..61542583) , (61771912..62007030)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORD91 family Neighboring gene small nucleolar RNA SNORD91 family Neighboring gene TSR1, ribosome maturation factor Neighboring gene U6 spliceosomal RNA Neighboring gene serine racemase Neighboring gene microRNA 212 Neighboring gene HIC ZBTB transcriptional repressor 1

    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. SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells. Eberle AB, et al. Nat Struct Mol Biol, 2009 Jan. PMID 19060897
    2. Mechanism of circRNA_SMG6 mediating lung macrophage ECM degradation via miR-570-3p in microplastics-induced emphysema. Sun X, et al. Environ Int, 2024 May. PMID 38685156
    3. SMG6 is the catalytic endonuclease that cleaves mRNAs containing nonsense codons in metazoan. Huntzinger E, et al. RNA, 2008 Dec. PMID 18974281, Free PMC Article
    4. Protein RNA and protein protein interactions mediate association of human EST1A/SMG6 with telomerase. Redon S, et al. Nucleic Acids Res, 2007. PMID 17940095, Free PMC Article
    5. A human homolog of yeast Est1 associates with telomerase and uncaps chromosome ends when overexpressed. Reichenbach P, et al. Curr Biol, 2003 Apr 1. PMID 12676087

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Mechanism of circRNA_SMG6 mediating lung macrophage ECM degradation via miR-570-3p in microplastics-induced emphysema.
      Title: Mechanism of circRNA_SMG6 mediating lung macrophage ECM degradation via miR-570-3p in microplastics-induced emphysema.
    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 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 manganese ion 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 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, 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
    Smg-6 homolog, nonsense mediated mRNA decay factor
    NP_001099278.1
    XP_038941437.1
    XP_038941439.1
    XP_063124744.1

    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_001105808.1 → NP_001099278.1  telomerase-binding protein EST1A

      See identical proteins and their annotated locations for NP_001099278.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473948
      UniProtKB/TrEMBL
      A6HGP2, D4A589
      Related
      ENSRNOP00000004058.9, ENSRNOT00000004058.10
      Conserved Domains (4) summary
      cd09885
      Location:1294 → 1469
      PIN_Smg6; PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs
      sd00006
      Location:818 → 848
      TPR; TPR repeat [structural motif]
      pfam10373
      Location:804 → 1156
      EST1_DNA_bind; Est1 DNA/RNA binding domain
      pfam10374
      Location:691 → 794
      EST1; Telomerase activating protein Est1

    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_086028.1 Reference GRCr8

      Range
      60284628..60512738
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039085511.2 → XP_038941439.1  telomerase-binding protein EST1A isoform X2

      Conserved Domains (2) summary
      cd09885
      Location:1232 → 1407
      PIN_Smg6-like; VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs
      pfam10373
      Location:770 → 1094
      EST1_DNA_bind; Est1 DNA/RNA binding domain

    2. XM_063268674.1 → XP_063124744.1  telomerase-binding protein EST1A isoform X3

    3. XM_039085509.2 → XP_038941437.1  telomerase-binding protein EST1A isoform X1

      Related
      ENSRNOP00000110705.1, ENSRNOT00000153551.1
      Conserved Domains (3) summary
      cd09885
      Location:1241 → 1416
      PIN_Smg6-like; VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs
      pfam10373
      Location:751 → 1103
      EST1_DNA_bind; Est1 DNA/RNA binding domain
      pfam10374
      Location:638 → 743
      EST1; Telomerase activating protein Est1

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001047876.1: Suppressed sequence

      Description
      NM_001047876.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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