SMG5 is involved in nonsense-mediated mRNA decay (Ohnishi et al., 2003 [PubMed 14636577]).[supplied by OMIM, Mar 2008] See more...

Aliases for SMG5 Gene

Aliases for SMG5 Gene

  • SMG5 Nonsense Mediated MRNA Decay Factor 2 3 5
  • EST1-Like Protein B 3 4
  • Protein SMG5 3 4
  • LPTS-RP1 3 4
  • EST1B 3 4
  • Smg-5 Homolog, Nonsense Mediated MRNA Decay Factor (C. Elegans) 2
  • EST1 Telomerase Component Homolog B (S. Cerevisiae) 2
  • Smg-5 Homolog, Nonsense Mediated MRNA Decay Factor 3
  • SMG5, Nonsense Mediated MRNA Decay Factor 2
  • EST1 Telomerase Component Homolog B 3
  • Ever Shorter Telomeres 1B 3
  • LPTS Interacting Protein 3
  • LPTS-Interacting Protein 4
  • Est1p-Like Protein B 3
  • SMG-5 Homolog 4
  • KIAA1089 4
  • LPTSRP1 3
  • HSMG-5 4
  • SMG-5 3

External Ids for SMG5 Gene

Previous GeneCards Identifiers for SMG5 Gene

  • GC01M154485
  • GC01M156219
  • GC01M127580
  • GC01M156253
  • GC01M156255

Summaries for SMG5 Gene

Entrez Gene Summary for SMG5 Gene

  • SMG5 is involved in nonsense-mediated mRNA decay (Ohnishi et al., 2003 [PubMed 14636577]).[supplied by OMIM, Mar 2008]

GeneCards Summary for SMG5 Gene

SMG5 (SMG5 Nonsense Mediated MRNA Decay Factor) is a Protein Coding gene. Diseases associated with SMG5 include Pancreatic Adenosquamous Carcinoma and Carnitine Palmitoyltransferase I Deficiency. Among its related pathways are Gene Expression and mRNA surveillance pathway. Gene Ontology (GO) annotations related to this gene include protein phosphatase 2A binding. An important paralog of this gene is SMG7.

UniProtKB/Swiss-Prot Summary for SMG5 Gene

  • Plays a role in nonsense-mediated mRNA decay. Does not have RNase activity by itself. Promotes dephosphorylation of UPF1. Together with SMG7 is thought to provide a link to the mRNA degradation machinery involving exonucleolytic pathways, and to serve as an adapter for UPF1 to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation. Necessary for TERT activity.

Gene Wiki entry for SMG5 Gene

Additional gene information for SMG5 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SMG5 Gene

Genomics for SMG5 Gene

GeneHancer (GH) Regulatory Elements for SMG5 Gene

Promoters and enhancers for SMG5 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J156281 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 523.4 -0.4 -373 4.4 RXRA ZBTB40 ZNF217 EP300 TCF12 SIN3A MYC USF1 POLR2G SP1 SMG5 TMEM79 KHDC4 GLMP CCT3 MSTO2P MSTO1 ENSG00000271267 GON4L RRNAD1
GH01J156290 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 500.4 -8.9 -8889 2.3 TCF12 NRF1 USF1 POLR2G NCOR1 KDM6A TCF7 ZBTB25 SKI TEAD1 SMG5 PAQR6 GLMP BGLAP TSACC CCT3 MIR9-1 C1orf61 LAMTOR2 UBQLN4
GH01J156245 Promoter/Enhancer 1.4 Ensembl ENCODE CraniofacialAtlas dbSUPER 71.5 +36.9 36884 1.2 POLR2G EZH2 POLR2A RBM14 SRSF1 TFDP1 GABPB1 ZFHX2 ELF1 ZGPAT SMG5 GLMP KHDC4 MSTO2P MSTO1 CLK2 ENSG00000271267 GON4L RRNAD1 ASH1L-AS1
GH01J156249 Promoter/Enhancer 0.5 EPDnew dbSUPER 71.4 +33.2 33226 0.1 PAQR6 piR-56522 SMG5
GH01J156262 Enhancer 0.8 Ensembl ENCODE dbSUPER 21.9 +19.8 19829 1.5 FOS FOSL1 JUND PBX3 BCL3 MYC GLMP SMG5 PAQR6 BGLAP PMF1 SEMA4A SLC25A44 ENSG00000252236 LMNA MEX3A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SMG5 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SMG5

Top Transcription factor binding sites by QIAGEN in the SMG5 gene promoter:
  • CUTL1
  • HOXA5
  • Lmo2
  • Max
  • Nkx2-5
  • PPAR-alpha
  • PPAR-gamma1
  • SRF
  • SRF (504 AA)
  • YY1

Genomic Locations for SMG5 Gene

Genomic Locations for SMG5 Gene
chr1:156,249,224-156,282,885
(GRCh38/hg38)
Size:
33,662 bases
Orientation:
Minus strand
chr1:156,219,015-156,252,620
(GRCh37/hg19)
Size:
33,606 bases
Orientation:
Minus strand

Genomic View for SMG5 Gene

Genes around SMG5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMG5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMG5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMG5 Gene

Proteins for SMG5 Gene

  • Protein details for SMG5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UPR3-SMG5_HUMAN
    Recommended name:
    Protein SMG5
    Protein Accession:
    Q9UPR3
    Secondary Accessions:
    • D3DVB7
    • Q5QJE7
    • Q659C7
    • Q8IXC0
    • Q8IY09
    • Q96IJ7

    Protein attributes for SMG5 Gene

    Size:
    1016 amino acids
    Molecular mass:
    113928 Da
    Quaternary structure:
    • Interacts with TERT, PPP2CA and SMG1. Part of a complex that contains SMG1, SMG5, SMG7, PPP2CA, a short isoform of UPF3A (isoform UPF3AS, but not isoform UPF3AL) and phosphorylated UPF1. Not detected in complexes that contain unphosphorylated UPF1.
    SequenceCaution:
    • Sequence=BAA83041.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SMG5 Gene

neXtProt entry for SMG5 Gene

Post-translational modifications for SMG5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SMG5 Gene

No data available for DME Specific Peptides for SMG5 Gene

Domains & Families for SMG5 Gene

Gene Families for SMG5 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for SMG5 Gene

Suggested Antigen Peptide Sequences for SMG5 Gene

GenScript: Design optimal peptide antigens:
  • Smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans) (Q5TCL0_HUMAN)
  • SMG-5 homolog (SMG5_HUMAN)
genes like me logo Genes that share domains with SMG5: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SMG5 Gene

Function for SMG5 Gene

Molecular function for SMG5 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in nonsense-mediated mRNA decay. Does not have RNase activity by itself. Promotes dephosphorylation of UPF1. Together with SMG7 is thought to provide a link to the mRNA degradation machinery involving exonucleolytic pathways, and to serve as an adapter for UPF1 to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation. Necessary for TERT activity.

Phenotypes From GWAS Catalog for SMG5 Gene

Gene Ontology (GO) - Molecular Function for SMG5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA,IPI 12699629
GO:0031625 ubiquitin protein ligase binding IPI 16809764
GO:0042162 telomeric DNA binding IDA 17916692
GO:0042826 histone deacetylase binding IPI 16809764
GO:0051721 protein phosphatase 2A binding IDA 14636577
genes like me logo Genes that share ontologies with SMG5: view
genes like me logo Genes that share phenotypes with SMG5: view

Animal Model Products

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SMG5 Gene

Localization for SMG5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMG5 Gene

Cytoplasm. Nucleus. Note=Predominantly cytoplasmic, and nuclear. Shuttles between nucleus and cytoplasm. Detected in cytoplasmic mRNA decay bodies.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SMG5 gene
Compartment Confidence
nucleus 4
cytosol 4
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytoplasmic bodies (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SMG5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 14636577
GO:0005697 telomerase holoenzyme complex IBA 21873635
GO:0005737 cytoplasm IDA 14636577
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with SMG5: view

Pathways & Interactions for SMG5 Gene

genes like me logo Genes that share pathways with SMG5: view

Pathways by source for SMG5 Gene

Gene Ontology (GO) - Biological Process for SMG5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS 16488880
GO:0006406 mRNA export from nucleus TAS 16488880
GO:0007004 telomere maintenance via telomerase IBA 21873635
GO:0032204 regulation of telomere maintenance IMP 16809764
GO:0032210 regulation of telomere maintenance via telomerase IBA,TAS 16507993
genes like me logo Genes that share ontologies with SMG5: view

No data available for SIGNOR curated interactions for SMG5 Gene

Drugs & Compounds for SMG5 Gene

No Compound Related Data Available

Transcripts for SMG5 Gene

mRNA/cDNA for SMG5 Gene

5 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SMG5 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19a · 19b · 19c ^ 20 ^
SP1: - - -
SP2: - - - - - -
SP3: -
SP4: - -
SP5:
SP6:
SP7:
SP8:
SP9:

ExUns: 21 ^ 22 ^ 23 ^ 24a · 24b ^ 25 ^ 26a · 26b · 26c
SP1: -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for SMG5 Gene

GeneLoc Exon Structure for
SMG5

Expression for SMG5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SMG5 Gene

Protein differential expression in normal tissues from HIPED for SMG5 Gene

This gene is overexpressed in Lung (44.0), Placenta (9.2), and Pancreas (6.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SMG5 Gene



Protein tissue co-expression partners for SMG5 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SMG5

SOURCE GeneReport for Unigene cluster for SMG5 Gene:

Hs.516837

mRNA Expression by UniProt/SwissProt for SMG5 Gene:

Q9UPR3-SMG5_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for SMG5 Gene

  • Nervous system(4.6)
  • Liver(4.3)
  • Muscle(4.3)
  • Lung(2.9)
genes like me logo Genes that share expression patterns with SMG5: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SMG5 Gene

Orthologs for SMG5 Gene

This gene was present in the common ancestor of animals.

Orthologs for SMG5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SMG5 31 30
  • 99.84 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SMG5 31 30
  • 93.01 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SMG5 31 30
  • 90.87 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SMG5 31
  • 89 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Smg5 17 31 30
  • 88.18 (n)
rat
(Rattus norvegicus)
Mammalia Smg5 30
  • 87.95 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SMG5 31
  • 60 (a)
OneToOne
chicken
(Gallus gallus)
Aves SMG5 31 30
  • 75.35 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SMG5 31
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia smg5 30
  • 71.21 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.16535 30
zebrafish
(Danio rerio)
Actinopterygii smg5 31
  • 63 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Smg5 31
  • 19 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 37 (a)
OneToMany
-- 31
  • 24 (a)
OneToMany
Species where no ortholog for SMG5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SMG5 Gene

ENSEMBL:
Gene Tree for SMG5 (if available)
TreeFam:
Gene Tree for SMG5 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SMG5: view image

Paralogs for SMG5 Gene

Paralogs for SMG5 Gene

Pseudogenes.org Pseudogenes for SMG5 Gene

genes like me logo Genes that share paralogs with SMG5: view

Variants for SMG5 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SMG5 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs17853821 - p.Asn1004Asp

Additional dbSNP identifiers (rs#s) for SMG5 Gene

Structural Variations from Database of Genomic Variants (DGV) for SMG5 Gene

Variant ID Type Subtype PubMed ID
nsv509524 CNV insertion 20534489
nsv547968 CNV loss 21841781

Variation tolerance for SMG5 Gene

Residual Variation Intolerance Score: 4.73% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.85; 48.10% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SMG5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMG5

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMG5 Gene

Disorders for SMG5 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SMG5 Gene - From: DISEASES

Disorder Aliases PubMed IDs
pancreatic adenosquamous carcinoma
  • adenosquamous carcinoma of pancreas
carnitine palmitoyltransferase i deficiency
  • carnitine palmitoyltransferase ia deficiency
ullrich congenital muscular dystrophy 1
  • ucmd1
- elite association - COSMIC cancer census association via MalaCards
Search SMG5 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SMG5

genes like me logo Genes that share disorders with SMG5: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SMG5 Gene

Publications for SMG5 Gene

  1. SMG7 acts as a molecular link between mRNA surveillance and mRNA decay. (PMID: 15546618) Unterholzner L … Izaurralde E (Molecular cell 2004) 3 4 23 54
  2. Functional conservation of the telomerase protein Est1p in humans. (PMID: 12699629) Snow BE … Harrington L (Current biology : CB 2003) 2 3 4 54
  3. Phosphorylation of hUPF1 induces formation of mRNA surveillance complexes containing hSMG-5 and hSMG-7. (PMID: 14636577) Ohnishi T … Ohno S (Molecular cell 2003) 3 4 23 54
  4. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 54
  5. Structures of the PIN domains of SMG6 and SMG5 reveal a nuclease within the mRNA surveillance complex. (PMID: 17053788) Glavan F … Conti E (The EMBO journal 2006) 3 4 54

Products for SMG5 Gene

Sources for SMG5 Gene