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Aliases for SMG9 Gene

Aliases for SMG9 Gene

  • SMG9, Nonsense Mediated MRNA Decay Factor 2 3 5
  • C19orf61 3 4
  • Smg-9 Homolog, Nonsense Mediated MRNA Decay Factor (C. Elegans) 2
  • Chromosome 19 Open Reading Frame 61 2
  • Protein Smg-9 Homolog 3
  • Protein SMG-9 4
  • Protein SMG9 3
  • F17127_1 3
  • HBMS 3

External Ids for SMG9 Gene

Previous HGNC Symbols for SMG9 Gene

  • C19orf61

Previous GeneCards Identifiers for SMG9 Gene

  • GC19M044236

Summaries for SMG9 Gene

Entrez Gene Summary for SMG9 Gene

  • This gene encodes a regulatory subunit of the SMG1 complex, which plays a critical role in nonsense-mediated mRNA decay (NMD). Binding of the encoded protein to the SMG1 complex kinase scaffold protein results in the inhibition of its kinase activity. Mutations in this gene cause a multiple congenital anomaly syndrome in human patients, characterized by brain malformation, congenital heart disease and other features. [provided by RefSeq, Jul 2016]

GeneCards Summary for SMG9 Gene

SMG9 (SMG9, Nonsense Mediated MRNA Decay Factor) is a Protein Coding gene. Diseases associated with SMG9 include Heart And Brain Malformation Syndrome. Among its related pathways are Gene Expression and Viral mRNA Translation. GO annotations related to this gene include identical protein binding.

UniProtKB/Swiss-Prot for SMG9 Gene

  • Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons (PubMed:19417104). Is recruited by release factors to stalled ribosomes together with SMG1 and SMG8 (forming the SMG1C protein kinase complex) and, in the SMG1C complex, is required for the efficient association between SMG1 and SMG8 (PubMed:19417104). Plays a role in brain, heart, and eye development (By similarity).

Additional gene information for SMG9 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMG9 Gene

Genomics for SMG9 Gene

Regulatory Elements for SMG9 Gene

Enhancers for SMG9 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH19H043762 2 FANTOM5 Ensembl ENCODE dbSUPER 31.3 -11.0 -10988 6 HDGF PKNOX1 SIN3A ZNF2 ZNF121 ZNF766 GLIS2 ELK1 ZNF143 ZNF207 ZNF180 ZNF45 PLAUR XRCC1 ZNF155 ZNF234 ZNF225 SMG9 ZNF224 ZNF230
GH19H043773 2 FANTOM5 Ensembl ENCODE dbSUPER 30.5 -24.9 -24912 12 YBX1 ZNF416 ZNF143 SP3 ZC3H11A ZFP41 MEF2D ZNF610 ZNF585B GLIS1 ZNF180 ZNF45 ZNF225 ZNF227 ZNF284 ZNF223 ZNF224 ZNF283 ZNF235 ZNF576
GH19H043744 1.6 FANTOM5 Ensembl ENCODE dbSUPER 36.9 +9.9 9876 1 HDGF CTCF ZNF792 RAD21 CC2D1A ZNF791 ZNF547 EED SCRT2 SMC3 SMG9 PLAUR ZNF180 ZNF45 ZNF224 ZNF155 ZNF234 KCNN4 ZNF284 IRGC
GH19H043751 1.7 FANTOM5 ENCODE dbSUPER 25.9 -0.9 -887 8 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF143 ZNF207 ZNF180 ZNF45 ZNF155 ZNF225 ZNF234 ZNF224 LOC100505715 ZNF284 SMG9 ZNF112
GH19H043901 1.1 ENCODE 20.2 -146.9 -146863 1 SIN3A ARID4B ZNF2 YY1 ZNF766 ZNF302 ZNF416 ZNF143 ZNF548 SP3 ZNF45 ZNF180 ZNF225 ZNF224 ZNF234 ZNF284 ZNF227 ZNF235 ZNF226 XRCC1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SMG9 on UCSC Golden Path with GeneCards custom track

Promoters for SMG9 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000110003 -10 2001 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF143 ZNF207

Genomic Location for SMG9 Gene

Chromosome:
19
Start:
43,727,992 bp from pter
End:
43,754,990 bp from pter
Size:
26,999 bases
Orientation:
Minus strand

Genomic View for SMG9 Gene

Genes around SMG9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMG9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMG9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMG9 Gene

Proteins for SMG9 Gene

  • Protein details for SMG9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H0W8-SMG9_HUMAN
    Recommended name:
    Protein SMG9
    Protein Accession:
    Q9H0W8
    Secondary Accessions:
    • O60429
    • Q9H9A9

    Protein attributes for SMG9 Gene

    Size:
    520 amino acids
    Molecular mass:
    57651 Da
    Quaternary structure:
    • Component of the SMG1C complex composed of SMG1, SMG8 and SMG9. Self-associates to form homodimers and forms heterodimers with SMG8; these assembly forms may represent SMG1C intermediate forms.
    SequenceCaution:
    • Sequence=AAC17932.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for SMG9 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SMG9 Gene

Post-translational modifications for SMG9 Gene

No data available for DME Specific Peptides for SMG9 Gene

Domains & Families for SMG9 Gene

Gene Families for SMG9 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for SMG9 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SMG9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9H0W8

UniProtKB/Swiss-Prot:

SMG9_HUMAN :
  • Belongs to the SMG9 family.
Family:
  • Belongs to the SMG9 family.
genes like me logo Genes that share domains with SMG9: view

Function for SMG9 Gene

Molecular function for SMG9 Gene

UniProtKB/Swiss-Prot Function:
Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons (PubMed:19417104). Is recruited by release factors to stalled ribosomes together with SMG1 and SMG8 (forming the SMG1C protein kinase complex) and, in the SMG1C complex, is required for the efficient association between SMG1 and SMG8 (PubMed:19417104). Plays a role in brain, heart, and eye development (By similarity).

Phenotypes From GWAS Catalog for SMG9 Gene

Gene Ontology (GO) - Molecular Function for SMG9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 19417104
GO:0042802 identical protein binding IPI 20817927
genes like me logo Genes that share ontologies with SMG9: view
genes like me logo Genes that share phenotypes with SMG9: view

Human Phenotype Ontology for SMG9 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SMG9 Gene

MGI Knock Outs for SMG9:
  • Smg9 tm1b(EUCOMM)Wtsi

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SMG9
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for SMG9 Gene

Localization for SMG9 Gene

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 SMG9 gene
Compartment Confidence
cytosol 5
plasma membrane 3
mitochondrion 3
nucleus 3
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Mitochondria (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SMG9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IDA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with SMG9: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for SMG9 Gene

Pathways & Interactions for SMG9 Gene

genes like me logo Genes that share pathways with SMG9: view

Gene Ontology (GO) - Biological Process for SMG9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS --
GO:0001654 eye development ISS --
GO:0007420 brain development ISS --
GO:0007507 heart development ISS --
genes like me logo Genes that share ontologies with SMG9: view

No data available for SIGNOR curated interactions for SMG9 Gene

Drugs & Compounds for SMG9 Gene

No Compound Related Data Available

Transcripts for SMG9 Gene

Unigene Clusters for SMG9 Gene

Smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SMG9
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for SMG9 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c · 2d · 2e ^ 3 ^ 4 ^ 5a · 5b · 5c · 5d ^ 6a · 6b · 6c · 6d ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13a ·
SP1: - - - - - - -
SP2: - - - - - - -
SP3:
SP4:
SP5: - - - - - -
SP6: - - - - -
SP7: - -
SP8: -
SP9:
SP10:
SP11:

ExUns: 13b ^ 14a · 14b ^ 15a · 15b ^ 16a · 16b ^ 17
SP1: - -
SP2: -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for SMG9 Gene

GeneLoc Exon Structure for
SMG9
ECgene alternative splicing isoforms for
SMG9

Expression for SMG9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SMG9 Gene

Protein differential expression in normal tissues from HIPED for SMG9 Gene

This gene is overexpressed in CD8 Tcells (10.8), Pancreas (8.4), Fetal Brain (7.9), and Lymph node (7.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SMG9 Gene



Protein tissue co-expression partners for SMG9 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SMG9 Gene:

SMG9

SOURCE GeneReport for Unigene cluster for SMG9 Gene:

Hs.466875

Evidence on tissue expression from TISSUES for SMG9 Gene

  • Nervous system(4.7)
  • Liver(4.2)
  • Muscle(4.2)
  • Heart(2.8)
genes like me logo Genes that share expression patterns with SMG9: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SMG9 Gene

Orthologs for SMG9 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SMG9 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SMG9 33 34
  • 99.49 (n)
dog
(Canis familiaris)
Mammalia SMG9 33 34
  • 92.69 (n)
cow
(Bos Taurus)
Mammalia SMG9 33 34
  • 91.15 (n)
oppossum
(Monodelphis domestica)
Mammalia SMG9 34
  • 89 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Smg9 33 16 34
  • 88.14 (n)
rat
(Rattus norvegicus)
Mammalia Smg9 33
  • 87.31 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SMG9 34
  • 51 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SMG9 34
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia smg9 33
  • 70.58 (n)
Str.16189 33
zebrafish
(Danio rerio)
Actinopterygii SMG9 34
  • 74 (a)
OneToOne
si:dkey-79d12.3 33
  • 69.77 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG3857 34
  • 23 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea smg-9 34
  • 22 (a)
OneToOne
rice
(Oryza sativa)
Liliopsida Os06g0114600 33
  • 47.68 (n)
Species where no ortholog for SMG9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • chicken (Gallus gallus)
  • 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 blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)

Evolution for SMG9 Gene

ENSEMBL:
Gene Tree for SMG9 (if available)
TreeFam:
Gene Tree for SMG9 (if available)

Paralogs for SMG9 Gene

No data available for Paralogs for SMG9 Gene

Variants for SMG9 Gene

Sequence variations from dbSNP and Humsavar for SMG9 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs869312741 Pathogenic 43,747,509(-) TGCCC(-/CC)AGAGC reference, frameshift-variant, utr-variant-5-prime
rs869312742 Pathogenic 43,744,768(-) AGGTG(A/G)GGGGC intron-variant
rs1000059131 -- 43,738,642(+) GTGAG(C/G)TCACC intron-variant
rs1000069713 -- 43,754,659(+) CTAAC(A/G)CGGCT upstream-variant-2KB, utr-variant-5-prime
rs1000102087 -- 43,754,500(+) ACCCA(A/C/G)TATCG intron-variant, utr-variant-5-prime

Structural Variations from Database of Genomic Variants (DGV) for SMG9 Gene

Variant ID Type Subtype PubMed ID
nsv509745 CNV insertion 20534489
nsv833839 CNV loss 17160897

Variation tolerance for SMG9 Gene

Residual Variation Intolerance Score: 24.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.76; 33.25% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SMG9 Gene

Human Gene Mutation Database (HGMD)
SMG9
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMG9

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMG9 Gene

Disorders for SMG9 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SMG9 Gene - From: HGMD, OMIM, and GeneCards

Disorder Aliases PubMed IDs
heart and brain malformation syndrome
  • hbms
- elite association - COSMIC cancer census association via MalaCards
Search SMG9 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SMG9_HUMAN
  • Heart and brain malformation syndrome (HBMS) [MIM:616920]: An autosomal recessive syndrome characterized by multiple congenital anomalies such as cardiac defects, brain malformations, including cerebellar vermis hypoplasia, hypoplastic corpus callosum and Dandy-Walker malformation, profoundly delayed psychomotor development, microphthalmia, and facial dysmorphism. {ECO:0000269 PubMed:27018474}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SMG9

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SMG9
genes like me logo Genes that share disorders with SMG9: view

No data available for Genatlas for SMG9 Gene

Publications for SMG9 Gene

  1. SMG-8 and SMG-9, two novel subunits of the SMG-1 complex, regulate remodeling of the mRNA surveillance complex during nonsense-mediated mRNA decay. (PMID: 19417104) Yamashita A … Ohno S (Genes & development 2009) 2 3 4 60
  2. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S … Poustka A (Genome research 2001) 2 3 4 60
  3. Mutations in SMG9, Encoding an Essential Component of Nonsense-Mediated Decay Machinery, Cause a Multiple Congenital Anomaly Syndrome in Humans and Mice. (PMID: 27018474) Shaheen R … Alkuraya FS (American journal of human genetics 2016) 3 4 60
  4. Characterization of SMG-9, an essential component of the nonsense-mediated mRNA decay SMG1C complex. (PMID: 20817927) Fernández IS … Llorca O (Nucleic acids research 2011) 3 4 60
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60

Products for SMG9 Gene

Sources for SMG9 Gene

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