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

Gene ID: 23381, updated on 7-Dec-2018

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
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

Genomic context

See SMG5 in Genome Data Viewer
Location:
1q22
Exon count:
25
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (156249224..156291498, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (156219015..156252676, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene PMF1-BGLAP readthrough Neighboring gene BGLAP promoter region Neighboring gene bone gamma-carboxyglutamate protein Neighboring gene progestin and adipoQ receptor family member 6 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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ12287, FLJ34864, KIAA1089

Gene Ontology Provided by GOA

Function Evidence Code Pubs
histone deacetylase binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein phosphatase 2A binding IDA
Inferred from Direct Assay
more info
PubMed 
telomerase RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
telomerase RNA binding IPI
Inferred from Physical Interaction
more info
PubMed 
telomeric DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
telomeric DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
RNA phosphodiester bond hydrolysis IEA
Inferred from Electronic Annotation
more info
 
mRNA export from nucleus TAS
Traceable Author Statement
more info
PubMed 
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS
Traceable Author Statement
more info
PubMed 
regulation of dephosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of telomere maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of telomere maintenance via telomerase IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of telomere maintenance via telomerase TAS
Traceable Author Statement
more info
PubMed 
telomere maintenance via telomerase IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
telomerase holoenzyme complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
protein SMG5
Names
EST1 telomerase component homolog B
EST1-like protein B
Est1p-like protein B
LPTS interacting protein
ever shorter telomeres 1B
smg-5 homolog, nonsense mediated mRNA decay factor

NCBI Reference Sequences (RefSeq)

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_001323614.1NP_001310543.1  protein 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_001323615.1NP_001310544.1  protein 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_001323616.1NP_001310545.1  protein 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_001323617.1NP_001310546.1  protein 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  protein 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
    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: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    156249224..156291498 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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