Human Gene SMG9 (ENST00000270066.11) from GENCODE V44
  Description: Homo sapiens SMG9 nonsense mediated mRNA decay factor (SMG9), mRNA. (from RefSeq NM_019108)
RefSeq Summary (NM_019108): 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]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments.
Gencode Transcript: ENST00000270066.11
Gencode Gene: ENSG00000105771.14
Transcript (Including UTRs)
   Position: hg38 chr19:43,727,983-43,754,962 Size: 26,980 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg38 chr19:43,731,596-43,750,741 Size: 19,146 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr19:43,727,983-43,754,962)mRNA (may differ from genome)Protein (520 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Protein SMG9; AltName: Full=Protein smg-9 homolog;
FUNCTION: Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. 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.
SUBUNIT: 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.
INTERACTION: Self; NbExp=3; IntAct=EBI-2872322, EBI-2872322; Q8ND04:SMG8; NbExp=4; IntAct=EBI-2872322, EBI-3903643;
PTM: Phosphorylated by SMG1.
SIMILARITY: Belongs to the SMG9 family.
SEQUENCE CAUTION: Sequence=AAC17932.1; Type=Erroneous gene model prediction;

-  Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

-  MalaCards Disease Associations
  MalaCards Gene Search: SMG9
Diseases sorted by gene-association score: heart and brain malformation syndrome* (519)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 31.87 RPKM in Testis
Total median expression: 455.45 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -114.60315-0.364 Picture PostScript Text
3' UTR -1309.503613-0.362 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR019354 - Smg8/Smg9

Pfam Domains:
PF10220 - Smg8_Smg9

ModBase Predicted Comparative 3D Structure on Q9H0W8
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0042802 identical protein binding

Biological Process:
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
GO:0001654 eye development
GO:0007420 brain development
GO:0007507 heart development

Cellular Component:
GO:0005622 intracellular
GO:0005829 cytosol

-  Descriptions from all associated GenBank mRNAs
  JD497756 - Sequence 478780 from Patent EP1572962.
JD196127 - Sequence 177151 from Patent EP1572962.
JD222901 - Sequence 203925 from Patent EP1572962.
BC008869 - Homo sapiens chromosome 19 open reading frame 61, mRNA (cDNA clone MGC:15017 IMAGE:4131601), complete cds.
AL136606 - Homo sapiens mRNA; cDNA DKFZp564H1322 (from clone DKFZp564H1322).
AK022948 - Homo sapiens cDNA FLJ12886 fis, clone NT2RP2004041, weakly similar to SYNAPSINS IA AND IB.
AK309830 - Homo sapiens cDNA, FLJ99871.
DQ587315 - Homo sapiens piRNA piR-54427, complete sequence.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9H0W8 (Reactome details) participates in the following event(s):

R-HSA-927832 UPF1 binds an mRNP with a termination codon preceding an Exon Junction Complex
R-HSA-927889 SMG1 phosphorylates UPF1 (enhanced by Exon Junction Complex)
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
R-HSA-927802 Nonsense-Mediated Decay (NMD)
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: C19orf61, ENST00000270066.1, ENST00000270066.10, ENST00000270066.2, ENST00000270066.3, ENST00000270066.4, ENST00000270066.5, ENST00000270066.6, ENST00000270066.7, ENST00000270066.8, ENST00000270066.9, NM_019108, O60429, Q9H0W8, Q9H9A9, SMG9_HUMAN, uc002oxj.1, uc002oxj.2, uc002oxj.3, uc002oxj.4
UCSC ID: ENST00000270066.11
RefSeq Accession: NM_019108
Protein: Q9H0W8 (aka SMG9_HUMAN)
CCDS: CCDS33043.2

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.