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Smg5 SMG5 nonsense mediated mRNA decay factor [ Mus musculus (house mouse) ]

Gene ID: 229512, updated on 2-Nov-2024

Summary

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Official Symbol
Smg5provided by MGI
Official Full Name
SMG5 nonsense mediated mRNA decay factorprovided by MGI
Primary source
MGI:MGI:2447364
See related
Ensembl:ENSMUSG00000001415 AllianceGenome:MGI:2447364
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
LPTS-RP1; mKIAA1089
Summary
Predicted to enable enzyme binding activity and nucleic acid binding activity. Predicted to be involved in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; regulation of dephosphorylation; and regulation of telomere maintenance. Predicted to be located in cytoplasm and nucleus. Predicted to be part of telomerase holoenzyme complex. Orthologous to human SMG5 (SMG5 nonsense mediated mRNA decay factor). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in testis adult (RPKM 31.0), thymus adult (RPKM 24.5) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Smg5 in Genome Data Viewer
Location:
3 F1; 3 38.8 cM
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (88242050..88269645)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (88336259..88362338)

Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene glycosylated lysosomal membrane protein Neighboring gene transmembrane protein 79 Neighboring gene progestin and adipoQ receptor family member VI Neighboring gene bone gamma-carboxyglutamate protein 3

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 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. RNA Surveillance Factor SMG5 Is Essential for Mouse Embryonic Stem Cell Differentiation. Chen C, et al. Biomolecules, 2024 Aug 17. PMID 39199410, 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. Tagging genes with cassette-exchange sites. Cobellis G, et al. Nucleic Acids Res, 2005 Mar 1. PMID 15741177, Free PMC Article
  4. New roles for the de-ubiquitylating enzyme OTUD4 in an RNA-protein network and RNA granules. Das R, et al. J Cell Sci, 2019 Jun 17. PMID 31138677, Free PMC Article
  5. Hdac4 Interactions in Huntington's Disease Viewed Through the Prism of Multiomics. Federspiel JD, et al. Mol Cell Proteomics, 2019 Aug 9. PMID 31040226, Free PMC Article

See all (26) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RNA Surveillance Factor SMG5 Is Essential for Mouse Embryonic Stem Cell Differentiation.
    Title: RNA Surveillance Factor SMG5 Is Essential for Mouse Embryonic Stem Cell Differentiation.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1) 
  • Targeted (2)  1 citation

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

  • MGC30464, MGC56792, MGC118167

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables histone deacetylase binding IEA
Inferred from Electronic Annotation
more info
  
enables histone deacetylase binding ISO
Inferred from Sequence Orthology
more info
  
enables protein phosphatase 2A binding ISO
Inferred from Sequence Orthology
more info
  
enables protein phosphatase 2A binding ISS
Inferred from Sequence or Structural Similarity
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 IEA
Inferred from Electronic Annotation
more info
  
enables telomeric DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables ubiquitin protein ligase binding IEA
Inferred from Electronic Annotation
more info
  
enables ubiquitin protein ligase binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
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 IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of dephosphorylation ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of dephosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of telomere maintenance IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of telomere maintenance ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
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
nonsense-mediated mRNA decay factor SMG5
Names
EST1-like protein B
LPTS-interacting protein
Smg-5 homolog, nonsense mediated mRNA decay factor
protein SMG5

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_178246.3 → NP_839977.2  nonsense-mediated mRNA decay factor SMG5

    See identical proteins and their annotated locations for NP_839977.2

    Status: VALIDATED

    Source sequence(s)
    AK133688, AK143911, AV146226, BB869373, BC066787
    Consensus CDS
    CCDS38480.1
    UniProtKB/Swiss-Prot
    Q497S2, Q6ZPY2, Q8R3S4
    Related
    ENSMUSP00000001451.6, ENSMUST00000001451.11
    Conserved Domains (4) summary
    sd00006
    Location:172 → 206
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:197 → 411
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:77 → 187
    EST1; Telomerase activating protein Est1
    cl14812
    Location:856 → 1014
    PIN_SF; PIN (PilT N terminus) domain: Superfamily

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_000069.7 Reference GRCm39 C57BL/6J

    Range
    88242050..88269645
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006501343.5 → XP_006501406.1  nonsense-mediated mRNA decay factor SMG5 isoform X1

    Conserved Domains (3) summary
    cd09884
    Location:842 → 1000
    PIN_Smg5-like; VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar eukaryotic homologs
    pfam10373
    Location:183 → 382
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:77 → 174
    EST1; Telomerase activating protein Est1

  2. XM_011240087.4 → XP_011238389.1  nonsense-mediated mRNA decay factor SMG5 isoform X2

    Conserved Domains (3) summary
    cd09884
    Location:790 → 948
    PIN_Smg5-like; VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar eukaryotic homologs
    pfam10373
    Location:131 → 330
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:11 → 122
    EST1; Telomerase activating protein Est1

  3. XM_036163050.1 → XP_036018943.1  nonsense-mediated mRNA decay factor SMG5 isoform X4

    UniProtKB/TrEMBL
    Q3UZS1
    Conserved Domains (3) summary
    cd09884
    Location:595 → 753
    PIN_Smg5-like; VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar eukaryotic homologs
    pfam10373
    Location:2 → 150
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    NF033845
    Location:208 → 311
    MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

  4. XM_006501345.4 → XP_006501408.1  nonsense-mediated mRNA decay factor SMG5 isoform X4

    UniProtKB/TrEMBL
    Q3UZS1
    Conserved Domains (3) summary
    cd09884
    Location:595 → 753
    PIN_Smg5-like; VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar eukaryotic homologs
    pfam10373
    Location:2 → 150
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    NF033845
    Location:208 → 311
    MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

  5. XM_036163049.1 → XP_036018942.1  nonsense-mediated mRNA decay factor SMG5 isoform X3

    Conserved Domains (4) summary
    cd09884
    Location:776 → 934
    PIN_Smg5-like; VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar eukaryotic homologs
    pfam10373
    Location:117 → 331
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:11 → 108
    EST1; Telomerase activating protein Est1
    NF033845
    Location:389 → 492
    MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

RNA

  1. XR_004941306.1 RNA Sequence

  2. XR_004941307.1 RNA Sequence

    Related
    ENSMUST00000192057.6

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_173188.1: Suppressed sequence

    Description
    NM_173188.1: This RefSeq was temporarily suppressed because the CDS was partial when compared to proteins in other species such as human.
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6ZPY2.2 GenPept UniProtKB/Swiss-Prot:Q6ZPY2

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