U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Smg5 SMG5 nonsense mediated mRNA decay factor [ Rattus norvegicus (Norway rat) ]

Gene ID: 681012, updated on 4-Jan-2025

Summary

Go to the top of the page Help
Official Symbol
Smg5provided by RGD
Official Full Name
SMG5 nonsense mediated mRNA decay factorprovided by RGD
Primary source
RGD:1584731
See related
EnsemblRapid:ENSRNOG00000019590 AllianceGenome:RGD:1584731
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
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, Jan 2025]
Expression
Biased expression in Thymus (RPKM 138.5), Spleen (RPKM 134.2) and 9 other tissues See more
Orthologs
human mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See Smg5 in Genome Data Viewer
Location:
2q34
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (176102812..176129925)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (173804987..173832102)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (187708247..187735355)

Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene glycosylated lysosomal membrane protein Neighboring gene transmembrane protein 79 Neighboring gene progestin and adipoQ receptor family member 6 Neighboring gene bone gamma-carboxyglutamate protein

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. An anchor site-type defect in human telomerase that disrupts telomere length maintenance and cellular immortalization. Moriarty TJ, et al. Mol Biol Cell, 2005 Jul. PMID 15857955, Free PMC Article
  2. Phosphorylation of hUPF1 induces formation of mRNA surveillance complexes containing hSMG-5 and hSMG-7. Ohnishi T, et al. Mol Cell, 2003 Nov. PMID 14636577
  3. Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends. Azzalin CM, et al. Science, 2007 Nov 2. PMID 17916692
  4. Histone deacetylase 8 safeguards the human ever-shorter telomeres 1B (hEST1B) protein from ubiquitin-mediated degradation. Lee H, et al. Mol Cell Biol, 2006 Jul. PMID 16809764, Free PMC Article
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

See all (6) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

Go to the top of the page Help

Markers

Homology

Gene Ontology Provided by RGD

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
  
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 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
  
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
  

General protein information

Go to the top of the page Help
Preferred Names
nonsense-mediated mRNA decay factor SMG5
Names
Smg-5 homolog, nonsense mediated mRNA decay factor
protein SMG5

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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_001427645.1 → NP_001414574.1  nonsense-mediated mRNA decay factor SMG5

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000002
    UniProtKB/TrEMBL
    A6J668, E9PU03
    Related
    ENSRNOP00000026514.7, ENSRNOT00000026514.10

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086020.1 Reference GRCr8

    Range
    176102812..176129925
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039103754.2 → XP_038959682.1  nonsense-mediated mRNA decay factor SMG5 isoform X2

    Conserved Domains (3) summary
    pfam10373
    Location:198 → 412
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:78 → 189
    EST1; Telomerase activating protein Est1
    NF033845
    Location:470 → 573
    MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

  2. XM_039103751.2 → XP_038959679.1  nonsense-mediated mRNA decay factor SMG5 isoform X1

    UniProtKB/TrEMBL
    A6J668
    Conserved Domains (4) summary
    cd09884
    Location:857 → 1015
    PIN_Smg5-like; VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar eukaryotic homologs
    pfam10373
    Location:198 → 412
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:78 → 189
    EST1; Telomerase activating protein Est1
    NF033845
    Location:470 → 573
    MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB
Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

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

Chemical Information
Molecular Biology Databases
Research Materials
Tools