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

Gene ID: 287522, updated on 27-Nov-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, Nov 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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