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

    Gene ID: 229512, updated on 23-Jun-2021

    Summary

    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
    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
    BC024683; mKIAA1089
    Expression
    Ubiquitous expression in testis adult (RPKM 31.0), thymus adult (RPKM 24.5) and 28 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Smg5 in Genome Data Viewer
    Location:
    3; 3 F1
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    109 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)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 3 NC_000069.5 (88140182..88166259)

    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

    Expression

    • 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

    Variation

    Alleles

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC30464, MGC56792, MGC118167

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables histone deacetylase binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein phosphatase 2A binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables telomerase RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables telomerase RNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables telomeric DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables telomeric DNA binding ISO
    Inferred from Sequence Orthology
    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
    PubMed 
    involved_in regulation of dephosphorylation 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 cytoplasm 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
    PubMed 

    General protein information

    Preferred Names
    protein SMG5
    Names
    EST1-like protein B
    Smg-5 homolog, nonsense mediated mRNA decay factor

    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_178246.3NP_839977.2  protein 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
      Q6ZPY2
      UniProtKB/TrEMBL
      Q3UZS1
      Related
      ENSMUSP00000001451.6, ENSMUST00000001451.11
      Conserved Domains (4) summary
      sd00006
      Location:172206
      TPR; TPR repeat [structural motif]
      pfam10373
      Location:197411
      EST1_DNA_bind; Est1 DNA/RNA binding domain
      pfam10374
      Location:77187
      EST1; Telomerase activating protein Est1
      cl14812
      Location:8561014
      PIN_SF; PIN (PilT N terminus) domain: Superfamily

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

    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_006501343.5XP_006501406.1  protein SMG5 isoform X1

      Conserved Domains (3) summary
      cd09884
      Location:8421000
      PIN_Smg5-like; VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar eukaryotic homologs
      pfam10373
      Location:183382
      EST1_DNA_bind; Est1 DNA/RNA binding domain
      pfam10374
      Location:77174
      EST1; Telomerase activating protein Est1
    2. XM_011240087.4XP_011238389.1  protein SMG5 isoform X2

      Conserved Domains (3) summary
      cd09884
      Location:790948
      PIN_Smg5-like; VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar eukaryotic homologs
      pfam10373
      Location:131330
      EST1_DNA_bind; Est1 DNA/RNA binding domain
      pfam10374
      Location:11122
      EST1; Telomerase activating protein Est1
    3. XM_036163050.1XP_036018943.1  protein SMG5 isoform X4

      Conserved Domains (3) summary
      cd09884
      Location:595753
      PIN_Smg5-like; VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar eukaryotic homologs
      pfam10373
      Location:2150
      EST1_DNA_bind; Est1 DNA/RNA binding domain
      NF033845
      Location:208311
      MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB
    4. XM_006501345.4XP_006501408.1  protein SMG5 isoform X4

      Conserved Domains (3) summary
      cd09884
      Location:595753
      PIN_Smg5-like; VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar eukaryotic homologs
      pfam10373
      Location:2150
      EST1_DNA_bind; Est1 DNA/RNA binding domain
      NF033845
      Location:208311
      MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB
    5. XM_036163049.1XP_036018942.1  protein SMG5 isoform X3

      Conserved Domains (4) summary
      cd09884
      Location:776934
      PIN_Smg5-like; VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar eukaryotic homologs
      pfam10373
      Location:117331
      EST1_DNA_bind; Est1 DNA/RNA binding domain
      pfam10374
      Location:11108
      EST1; Telomerase activating protein Est1
      NF033845
      Location:389492
      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.
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