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

    Gene ID: 229512, updated on 28-Oct-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, Oct 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

    Gene LinkOut

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

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