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

    Gene ID: 23381, updated on 9-Dec-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SMG5 in Genome Data Viewer
    Location:
    1q22
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (156249224..156291516, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (155387685..155429979, complement)
    RS_2024_09 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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 
    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

    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)

    NEW Try the new Transcript table

    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_001323614.2NP_001310543.1  nonsense-mediated mRNA decay factor SMG5 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL135927, AL589685
      Conserved Domains (4) summary
      cd09884
      Location:802960
      PIN_Smg5; PIN domain of human telomerase-binding protein EST1, Smg5, and other similar eukaryotic homologs
      sd00006
      Location:172206
      TPR; TPR repeat [structural motif]
      pfam10373
      Location:197412
      EST1_DNA_bind; Est1 DNA/RNA binding domain
      pfam10374
      Location:77187
      EST1; Telomerase activating protein Est1
    2. NM_001323615.2NP_001310544.1  nonsense-mediated mRNA decay factor SMG5 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL135927, AL589685
      Conserved Domains (4) summary
      cd09884
      Location:809967
      PIN_Smg5; PIN domain of human telomerase-binding protein EST1, Smg5, and other similar eukaryotic homologs
      sd00006
      Location:172206
      TPR; TPR repeat [structural motif]
      pfam10373
      Location:197375
      EST1_DNA_bind; Est1 DNA/RNA binding domain
      pfam10374
      Location:77187
      EST1; Telomerase activating protein Est1
    3. NM_001323616.2NP_001310545.1  nonsense-mediated mRNA decay factor SMG5 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL135927, AL589685
      Conserved Domains (4) summary
      cd09884
      Location:789947
      PIN_Smg5; PIN domain of human telomerase-binding protein EST1, Smg5, and other similar eukaryotic homologs
      sd00006
      Location:106140
      TPR; TPR repeat [structural motif]
      pfam10373
      Location:131346
      EST1_DNA_bind; Est1 DNA/RNA binding domain
      pfam10374
      Location:11121
      EST1; Telomerase activating protein Est1
    4. NM_001323617.2NP_001310546.1  nonsense-mediated mRNA decay factor SMG5 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL135927, AL589685
      Conserved Domains (4) summary
      cd09884
      Location:789947
      PIN_Smg5; PIN domain of human telomerase-binding protein EST1, Smg5, and other similar eukaryotic homologs
      sd00006
      Location:106140
      TPR; TPR repeat [structural motif]
      pfam10373
      Location:131346
      EST1_DNA_bind; Est1 DNA/RNA binding domain
      pfam10374
      Location:11121
      EST1; Telomerase activating protein Est1
    5. NM_015327.3NP_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:8551013
      PIN_Smg5; PIN domain of human telomerase-binding protein EST1, Smg5, and other similar eukaryotic homologs
      sd00006
      Location:172206
      TPR; TPR repeat [structural motif]
      pfam10373
      Location:197412
      EST1_DNA_bind; Est1 DNA/RNA binding domain
      pfam10374
      Location:77187
      EST1; Telomerase activating protein Est1

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    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)