Human Gene SHISA9 (ENST00000558583.3_5) from GENCODE V47lift37
  Description: shisa family member 9, transcript variant 1 (from RefSeq NM_001145204.3)
Gencode Transcript: ENST00000558583.3_5
Gencode Gene: ENSG00000237515.10_11
Transcript (Including UTRs)
   Position: hg19 chr16:12,995,455-13,334,273 Size: 338,819 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr16:12,995,922-13,329,266 Size: 333,345 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:12,995,455-13,334,273)mRNA (may differ from genome)Protein (424 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SHSA9_HUMAN
DESCRIPTION: RecName: Full=Protein shisa-9; Flags: Precursor;
FUNCTION: Regulator of short-term neuronal synaptic plasticity in the dentate gyrus. Associates with AMPA receptors (ionotropic glutamate receptors) in synaptic spines and promotes AMPA receptor desensitization at excitatory synapses (By similarity).
SUBUNIT: Component of some AMPA receptors (ionotropic glutamate receptors) complex, at least composed of some AMPA receptor (GRIA1, GRIA2 and/or GRIA3), CACNG2 and SHISA9, as well as low level of DLG4 (By similarity).
SUBCELLULAR LOCATION: Cell projection, dendritic spine membrane; Single-pass type I membrane protein (By similarity). Cell junction, synapse (By similarity).
SIMILARITY: Belongs to the shisa family. SHISA9 subfamily.

-  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


+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 3.12 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 26.00 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -243.20467-0.521 Picture PostScript Text
3' UTR -1316.325007-0.263 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
IPR026910 - Shisa

Pfam Domains:
PF13908 - Wnt and FGF inhibitory regulator

ModBase Predicted Comparative 3D Structure on B4DS77
FrontTopSide
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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0030165 PDZ domain binding

Biological Process:
GO:0048172 regulation of short-term neuronal synaptic plasticity
GO:2000311 regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity

Cellular Component:
GO:0005886 plasma membrane
GO:0008328 ionotropic glutamate receptor complex
GO:0014069 postsynaptic density
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0032281 AMPA glutamate receptor complex
GO:0032591 dendritic spine membrane
GO:0042995 cell projection
GO:0045202 synapse
GO:0045211 postsynaptic membrane


-  Descriptions from all associated GenBank mRNAs
  AK299610 - Homo sapiens cDNA FLJ58277 complete cds.
AK309038 - Homo sapiens cDNA, FLJ99079.
CR627300 - Homo sapiens mRNA; cDNA DKFZp686E24206 (from clone DKFZp686E24206).
CR749545 - Homo sapiens mRNA; cDNA DKFZp686D24206 (from clone DKFZp686D24206).
AK026131 - Homo sapiens cDNA: FLJ22478 fis, clone HRC10816.
JD335429 - Sequence 316453 from Patent EP1572962.
JD106065 - Sequence 87089 from Patent EP1572962.
JD069147 - Sequence 50171 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B4DS77, C9J314, C9JCE9, ENST00000558583.1, ENST00000558583.2, NM_001145204, SHSA9_HUMAN, uc325lpy.1, uc325lpy.2
UCSC ID: ENST00000558583.3_5
RefSeq Accession: NM_001145204.3
Protein: B4DS77 (aka SHSA9_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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