Aliases for SHISA9 Gene

Aliases for SHISA9 Gene

  • Shisa Family Member 9 2 3 5
  • Protein Shisa-9 3 4
  • Cystine-Knot AMPAR Modulating Protein 3
  • Shisa Homolog 9 (Xenopus Laevis) 2
  • Shisa Homolog 9 3
  • CKAMP44 3
  • SHISA9 5

External Ids for SHISA9 Gene

Previous GeneCards Identifiers for SHISA9 Gene

  • GC16P012995
  • GC16P012912

Summaries for SHISA9 Gene

GeneCards Summary for SHISA9 Gene

SHISA9 (Shisa Family Member 9) is a Protein Coding gene. Diseases associated with SHISA9 include Tarp Syndrome and Kagami-Ogata Syndrome. An important paralog of this gene is SHISA6.

UniProtKB/Swiss-Prot Summary for SHISA9 Gene

  • 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).

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SHISA9 Gene

Genomics for SHISA9 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SHISA9 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J012900 Promoter/Enhancer 1.2 EPDnew Ensembl ENCODE 259.3 +1.0 1002 4.8 SIN3A CTBP1 BHLHE40 CTCF TAF1 ZNF398 EZH2 ZBTB33 POLR2A ELF1 SHISA9 HSALNG0109666 HSALNG0109667
GH16J012916 Enhancer 0.7 Ensembl ENCODE 41.1 +16.0 16027 2.1 MAFF NFE2 NFE2L2 MAFG MAFK HMBOX1 EMSY SHISA9 lnc-SNX29-3 HSALNG0109668
GH16J012898 Enhancer 0.7 ENCODE 8.4 -2.2 -2227 1.6 ZNF217 SIX4 CTCF CUX1 CTBP1 SIN3A RAD21 SMARCE1 MAZ PKNOX1 HSALNG0109663 HSALNG0109666 SHISA9 CPPED1
GH16J012998 Enhancer 0.6 ENCODE 7.3 +98.3 98335 3.5 JUND LCORL ATF2 NFIB JUN NFIA CREB1 ATF7 ATF3 USF2 SHISA9 KR153242 piR-39858-230 ERCC4
GH16J012994 Enhancer 0.4 Ensembl ENCODE 6.8 +93.8 93779 2.7 HLF SHISA9 KR153242 piR-39858-230 ERCC4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SHISA9 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SHISA9

Genomic Locations for SHISA9 Gene

Latest Assembly
661,830 bases
Plus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
338,819 bases
Plus strand

(GRCh37/hg19 by Ensembl)
338,796 bases
Plus strand

Genomic View for SHISA9 Gene

Genes around SHISA9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SHISA9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SHISA9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SHISA9 Gene

Proteins for SHISA9 Gene

  • Protein details for SHISA9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein shisa-9
    Protein Accession:
    Secondary Accessions:
    • C9J314
    • C9JCE9

    Protein attributes for SHISA9 Gene

    424 amino acids
    Molecular mass:
    46925 Da
    Quaternary structure:
    • 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.

    Alternative splice isoforms for SHISA9 Gene


neXtProt entry for SHISA9 Gene

Post-translational modifications for SHISA9 Gene

  • Glycosylation at Asn89, Asn116, and Asn45
  • Modification sites at PhosphoSitePlus

Other Protein References for SHISA9 Gene

No data available for DME Specific Peptides for SHISA9 Gene

Domains & Families for SHISA9 Gene

Gene Families for SHISA9 Gene

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

Protein Domains for SHISA9 Gene


Suggested Antigen Peptide Sequences for SHISA9 Gene

GenScript: Design optimal peptide antigens:
  • Protein shisa-9 (SHSA9_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the shisa family. SHISA9 subfamily.
  • Belongs to the shisa family. SHISA9 subfamily.
genes like me logo Genes that share domains with SHISA9: view

Function for SHISA9 Gene

Molecular function for SHISA9 Gene

UniProtKB/Swiss-Prot 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).

Phenotypes From GWAS Catalog for SHISA9 Gene

Gene Ontology (GO) - Molecular Function for SHISA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030165 PDZ domain binding IEA --
genes like me logo Genes that share ontologies with SHISA9: view

Phenotypes for SHISA9 Gene

genes like me logo Genes that share phenotypes with SHISA9: view

Animal Models for SHISA9 Gene

MGI Knock Outs for SHISA9:

Animal Models for research

  • Taconic Biosciences Mouse Models for SHISA9

miRNA for SHISA9 Gene

miRTarBase miRNAs that target SHISA9

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SHISA9

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SHISA9 Gene

Localization for SHISA9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SHISA9 Gene

Cell projection, dendritic spine membrane. Single-pass type I membrane protein. Cell junction, synapse.

Subcellular locations from

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 SHISA9 gene
Compartment Confidence
plasma membrane 4
extracellular 1
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
endosome 1
cytosol 1
golgi apparatus 1
lysosome 0

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for SHISA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0008328 ionotropic glutamate receptor complex ISS --
GO:0014069 postsynaptic density IBA 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SHISA9: view

Pathways & Interactions for SHISA9 Gene

PathCards logo

SuperPathways for SHISA9 Gene

No Data Available

Interacting Proteins for SHISA9 Gene

Gene Ontology (GO) - Biological Process for SHISA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0048172 regulation of short-term neuronal synaptic plasticity ISS --
GO:0098962 regulation of postsynaptic neurotransmitter receptor activity IEA --
GO:2000311 regulation of AMPA receptor activity IBA 21873635
genes like me logo Genes that share ontologies with SHISA9: view

No data available for Pathways by source and SIGNOR curated interactions for SHISA9 Gene

Drugs & Compounds for SHISA9 Gene

No Compound Related Data Available

Transcripts for SHISA9 Gene

mRNA/cDNA for SHISA9 Gene

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

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SHISA9

Alternative Splicing Database (ASD) splice patterns (SP) for SHISA9 Gene

No ASD Table

Relevant External Links for SHISA9 Gene

GeneLoc Exon Structure for

Expression for SHISA9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SHISA9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SHISA9 Gene

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x6.2), Brain - Anterior cingulate cortex (BA24) (x5.7), Brain - Frontal Cortex (BA9) (x5.4), Brain - Caudate (basal ganglia) (x4.7), Brain - Hypothalamus (x4.6), and Brain - Putamen (basal ganglia) (x4.4).

Protein differential expression in normal tissues from HIPED for SHISA9 Gene

This gene is overexpressed in Frontal cortex (68.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SHISA9 Gene

Protein tissue co-expression partners for SHISA9 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SHISA9

SOURCE GeneReport for Unigene cluster for SHISA9 Gene:


Evidence on tissue expression from TISSUES for SHISA9 Gene

  • Nervous system(4.7)
genes like me logo Genes that share expression patterns with SHISA9: view

Primer products for research

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SHISA9 Gene

Orthologs for SHISA9 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SHISA9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SHISA9 30 31
  • 99.44 (n)
(Bos Taurus)
Mammalia SHISA9 31
  • 97 (a)
(Canis familiaris)
Mammalia SHISA9 30 31
  • 93.63 (n)
(Mus musculus)
Mammalia Shisa9 30 17 31
  • 90.88 (n)
(Rattus norvegicus)
Mammalia Shisa9 30
  • 89.47 (n)
(Monodelphis domestica)
Mammalia SHISA9 31
  • 65 (a)
(Gallus gallus)
Aves SHISA9 30
  • 71.25 (n)
(Anolis carolinensis)
Reptilia -- 31
  • 23 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia shisa9 30
  • 68 (n)
(Danio rerio)
Actinopterygii shisa9a 30 31
  • 63.43 (n)
shisa9b 31
  • 42 (a)
Species where no ortholog for SHISA9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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)
  • Fruit Fly (Drosophila melanogaster)
  • 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)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (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)
  • Worm (Caenorhabditis elegans)

Evolution for SHISA9 Gene

Gene Tree for SHISA9 (if available)
Gene Tree for SHISA9 (if available)
Evolutionary constrained regions (ECRs) for SHISA9: view image

Paralogs for SHISA9 Gene

Paralogs for SHISA9 Gene

(2) SIMAP similar genes for SHISA9 Gene using alignment to 3 proteins:

  • H0YM01_HUMAN
genes like me logo Genes that share paralogs with SHISA9: view

Variants for SHISA9 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SHISA9 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SHISA9 Gene

Variant ID Type Subtype PubMed ID
dgv1300n106 CNV deletion 24896259
dgv461n67 CNV gain 20364138
dgv4912n54 CNV loss 21841781
dgv4913n54 CNV loss 21841781
dgv4914n54 CNV loss 21841781
dgv4915n54 CNV loss 21841781
esv1005806 CNV deletion 20482838
esv1009468 CNV deletion 20482838
esv1257667 CNV deletion 17803354
esv22866 CNV gain+loss 19812545
esv2365778 CNV deletion 18987734
esv2453404 CNV deletion 19546169
esv2665133 CNV deletion 23128226
esv2713990 CNV deletion 23290073
esv2713991 CNV deletion 23290073
esv2713992 CNV deletion 23290073
esv2713993 CNV deletion 23290073
esv2713994 CNV deletion 23290073
esv2713995 CNV deletion 23290073
esv275394 CNV loss 21479260
esv3203790 CNV deletion 24192839
esv3553136 CNV deletion 23714750
esv3553142 CNV deletion 23714750
esv3582012 CNV loss 25503493
esv3637976 CNV loss 21293372
esv9240 CNV loss 19470904
nsv1038320 CNV gain 25217958
nsv1044706 CNV loss 25217958
nsv1070329 CNV deletion 25765185
nsv1108989 CNV deletion 24896259
nsv1118567 CNV duplication 24896259
nsv1121516 CNV deletion 24896259
nsv1737 CNV deletion 18451855
nsv1738 CNV insertion 18451855
nsv474463 CNV novel sequence insertion 20440878
nsv478920 CNV novel sequence insertion 20440878
nsv511565 CNV loss 21212237
nsv512425 CNV loss 21212237
nsv571482 CNV loss 21841781
nsv819710 CNV gain 19587683
nsv820320 CNV deletion 20802225
nsv827557 CNV gain 20364138
nsv827558 CNV loss 20364138
nsv833142 CNV loss 17160897
nsv952925 CNV deletion 24416366

Variation tolerance for SHISA9 Gene

Gene Damage Index Score: 1.74; 33.02% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SHISA9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SHISA9 Gene

Disorders for SHISA9 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SHISA9 Gene - From: COP

Disorder Aliases PubMed IDs
tarp syndrome
  • tarps
kagami-ogata syndrome
  • uniparental disomy, paternal, chromosome 14
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SHISA9

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with SHISA9: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SHISA9 Gene

Publications for SHISA9 Gene

  1. Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs. (PMID: 20195266) Adkins DE … van den Oord EJ (Molecular psychiatry 2011) 3 41
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  3. Identification of loci associated with schizophrenia by genome-wide association and follow-up. (PMID: 18677311) O'Donovan MC … Molecular Genetics of Schizophrenia Collaboration (Nature genetics 2008) 3 41
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. (PMID: 30021884) Fasci D … Heck AJR (Molecular & cellular proteomics : MCP 2018) 3

Products for SHISA9 Gene

Sources for SHISA9 Gene