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    SMG5 SMG5 nonsense mediated mRNA decay factor [ Homo sapiens (human) ]

    Gene ID: 23381, updated on 5-Mar-2024

    Summary

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    Official Symbol
    SMG5provided by HGNC
    Official Full Name
    SMG5 nonsense mediated mRNA decay factorprovided by HGNC
    Primary source
    HGNC:HGNC:24644
    See related
    Ensembl:ENSG00000198952 MIM:610962; AllianceGenome:HGNC:24644
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    EST1B; SMG-5; LPTSRP1; LPTS-RP1
    Summary
    SMG5 is involved in nonsense-mediated mRNA decay (Ohnishi et al., 2003 [PubMed 14636577]).[supplied by OMIM, Mar 2008]
    Expression
    Ubiquitous expression in heart (RPKM 16.7), testis (RPKM 16.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1q22
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (156249224..156291516, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (155387685..155429979, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (156219015..156261307, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene PMF1-BGLAP readthrough Neighboring gene BGLAP promoter region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1423 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1424 Neighboring gene Sharpr-MPRA regulatory region 3040 Neighboring gene bone gamma-carboxyglutamate protein Neighboring gene progestin and adipoQ receptor family member 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156250697-156251670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1425 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:156252643-156253614 Neighboring gene transmembrane protein 79 Neighboring gene Sharpr-MPRA regulatory regions 9834 and 13552 Neighboring gene glycosylated lysosomal membrane protein Neighboring gene VHL like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. SMG5-SMG7 authorize nonsense-mediated mRNA decay by enabling SMG6 endonucleolytic activity. Boehm V, et al. Nat Commun, 2021 Jun 25. PMID 34172724, Free PMC Article
    2. MicroRNA 433 regulates nonsense-mediated mRNA decay by targeting SMG5 mRNA. Jin Y, et al. BMC Mol Biol, 2016 Jul 29. PMID 27473591, Free PMC Article
    3. SMG7 acts as a molecular link between mRNA surveillance and mRNA decay. Unterholzner L, et al. Mol Cell, 2004 Nov 19. PMID 15546618
    4. Dissecting the functions of SMG5, SMG7, and PNRC2 in nonsense-mediated mRNA decay of human cells. Nicholson P, et al. RNA, 2018 Apr. PMID 29348139, Free PMC Article
    5. The host nonsense-mediated mRNA decay pathway restricts Mammalian RNA virus replication. Balistreri G, et al. Cell Host Microbe, 2014 Sep 10. PMID 25211080

    See all (51) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Pan-Cancer Analysis of the Prognostic and Immunological Role of SMG5: A Biomarker for Cancers.
      Title: Pan-Cancer Analysis of the Prognostic and Immunological Role of SMG5: A Biomarker for Cancers.
    2. Overexpression of TMEM79 combined with SMG5 is related to prognosis, tumor immune infiltration and drug sensitivity in hepatocellular carcinoma.
      Title: Overexpression of TMEM79 combined with SMG5 is related to prognosis, tumor immune infiltration and drug sensitivity in hepatocellular carcinoma.
    3. SMG5-SMG7 authorize nonsense-mediated mRNA decay by enabling SMG6 endonucleolytic activity.
      Title: SMG5-SMG7 authorize nonsense-mediated mRNA decay by enabling SMG6 endonucleolytic activity.
    4. The authors found no evidence for the existence of a physical or functional interaction between SMG5 and PNRC2.
      Title: Dissecting the functions of SMG5, SMG7, and PNRC2 in nonsense-mediated mRNA decay of human cells.
    5. This study highlights that miR-433 represses nonsense mediated mRNA decay. The miR-433 targets 3'-UTR of SMG5 and represses the expression of SMG5, whereas nonsense-mediated mRNA decay activity is decreased when SMG5 is decreased.
      Title: MicroRNA 433 regulates nonsense-mediated mRNA decay by targeting SMG5 mRNA.
    6. Depletion of nonsense-mediated mRNA decay pathway components Upf1, Smg5, and Smg7 led to increased levels of viral proteins and and virus release.
      Title: The host nonsense-mediated mRNA decay pathway restricts Mammalian RNA virus replication.
    7. The study demonstrates that SMG5-SMG7 and SMG6 exhibit different and non-overlapping modes of UPF1 recognition, thus pointing at distinguished roles in integrating the complex nonsense-mediated mRNA decay interaction network.
      Title: Phospho-dependent and phospho-independent interactions of the helicase UPF1 with the NMD factors SMG5-SMG7 and SMG6.
    8. Data show that phosphorylated hUPF1, the human ortholog of UPF1/SMG-2, forms a complex with human orthologs of the Caenorhabditis elegans proteins SMG-5 and SMG-7.
      Title: Phosphorylation of hUPF1 induces formation of mRNA surveillance complexes containing hSMG-5 and hSMG-7.
    9. HDAC8 regulation of hEST1B protein stability modulates total telomerase enzymatic activity
      Title: Histone deacetylase 8 safeguards the human ever-shorter telomeres 1B (hEST1B) protein from ubiquitin-mediated degradation.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study of hematological and biochemical traits in a Japanese population.
    EBI GWAS Catalog
    Multiple nonglycemic genomic loci are newly associated with blood level of glycated hemoglobin in East Asians.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    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

    • FLJ12287, FLJ34864, KIAA1089

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables histone deacetylase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein phosphatase 2A binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables telomerase RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables telomerase RNA binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables telomeric DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables telomeric DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ubiquitin protein ligase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mRNA export from nucleus TAS
    Traceable Author Statement
    more info
    		 PubMed 
    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 TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of dephosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of telomere maintenance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of telomere maintenance via telomerase TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 telomerase component homolog B
    EST1-like protein B
    Est1p-like protein B
    LPTS interacting protein
    ever shorter telomeres 1B
    protein SMG5
    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_001323614.2 → NP_001310543.1  nonsense-mediated mRNA decay factor SMG5 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL135927, AL589685
      Conserved Domains (4) summary
      cd09884
      Location:802 → 960
      PIN_Smg5; PIN domain of human telomerase-binding protein EST1, Smg5, and other similar eukaryotic homologs
      sd00006
      Location:172 → 206
      TPR; TPR repeat [structural motif]
      pfam10373
      Location:197 → 412
      EST1_DNA_bind; Est1 DNA/RNA binding domain
      pfam10374
      Location:77 → 187
      EST1; Telomerase activating protein Est1

    2. NM_001323615.2 → NP_001310544.1  nonsense-mediated mRNA decay factor SMG5 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL135927, AL589685
      Conserved Domains (4) summary
      cd09884
      Location:809 → 967
      PIN_Smg5; PIN domain of human telomerase-binding protein EST1, Smg5, and other similar eukaryotic homologs
      sd00006
      Location:172 → 206
      TPR; TPR repeat [structural motif]
      pfam10373
      Location:197 → 375
      EST1_DNA_bind; Est1 DNA/RNA binding domain
      pfam10374
      Location:77 → 187
      EST1; Telomerase activating protein Est1

    3. NM_001323616.2 → NP_001310545.1  nonsense-mediated mRNA decay factor SMG5 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL135927, AL589685
      Conserved Domains (4) summary
      cd09884
      Location:789 → 947
      PIN_Smg5; PIN domain of human telomerase-binding protein EST1, Smg5, and other similar eukaryotic homologs
      sd00006
      Location:106 → 140
      TPR; TPR repeat [structural motif]
      pfam10373
      Location:131 → 346
      EST1_DNA_bind; Est1 DNA/RNA binding domain
      pfam10374
      Location:11 → 121
      EST1; Telomerase activating protein Est1

    4. NM_001323617.2 → NP_001310546.1  nonsense-mediated mRNA decay factor SMG5 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL135927, AL589685
      Conserved Domains (4) summary
      cd09884
      Location:789 → 947
      PIN_Smg5; PIN domain of human telomerase-binding protein EST1, Smg5, and other similar eukaryotic homologs
      sd00006
      Location:106 → 140
      TPR; TPR repeat [structural motif]
      pfam10373
      Location:131 → 346
      EST1_DNA_bind; Est1 DNA/RNA binding domain
      pfam10374
      Location:11 → 121
      EST1; Telomerase activating protein Est1

    5. NM_015327.3 → NP_056142.2  nonsense-mediated mRNA decay factor SMG5 isoform 1

      See identical proteins and their annotated locations for NP_056142.2

      Status: VALIDATED

      Source sequence(s)
      AB029012, BC038296, CT000143
      Consensus CDS
      CCDS1137.1
      UniProtKB/Swiss-Prot
      D3DVB7, Q5QJE7, Q659C7, Q8IXC0, Q8IY09, Q96IJ7, Q9UPR3
      Related
      ENSP00000355261.5, ENST00000361813.5
      Conserved Domains (4) summary
      cd09884
      Location:855 → 1013
      PIN_Smg5; PIN domain of human telomerase-binding protein EST1, Smg5, and other similar eukaryotic homologs
      sd00006
      Location:172 → 206
      TPR; TPR repeat [structural motif]
      pfam10373
      Location:197 → 412
      EST1_DNA_bind; Est1 DNA/RNA binding domain
      pfam10374
      Location:77 → 187
      EST1; Telomerase activating protein Est1

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      156249224..156291516 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      155387685..155429979 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UPR3.3 GenPept UniProtKB/Swiss-Prot:Q9UPR3

    Gene LinkOut

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

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