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Aliases for SHISA9 Gene

Aliases for SHISA9 Gene

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

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. An important paralog of this gene is SHISA6.

UniProtKB/Swiss-Prot 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 , fRNAdb sequence ontologies and piRNA Summary for SHISA9 Gene

Genomics for SHISA9 Gene

Regulatory Elements for SHISA9 Gene

Enhancers for SHISA9 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
GH16G012916 0.6 ENCODE 41.1 +16.0 16006 2.1 MAFG HMBOX1 NFE2 EMSY MAFK NFE2L2 SHISA9 GC16P012908 LOC105371092
GH16G012900 0.7 ENCODE 9.4 +0.7 667 3.4 CTCF MXI1 HDAC6 SUZ12 BHLHE40 HLF CHD1 SIN3A RBBP5 ZNF398 SHISA9 GC16P012908
GH16G012898 0.7 ENCODE 8.4 -2.2 -2249 1.6 SIX4 CTCF PKNOX1 NFIB RAD21 CTBP1 GATA3 FOS RCOR1 ZNF687 SHISA9 GC16P012881
GH16G012998 0.7 ENCODE 7.3 +98.3 98313 3.5 NFIA NFIB BACH1 MAFG NFXL1 ATF2 SREBF1 NFIC JUND ZNF316 SHISA9 LOC105371092 GC16P013153
GH16G012987 0.5 ENCODE 5.5 +86.7 86741 1.1 MTA2 BMI1 DPF2 TBX21 SHISA9 LOC105371092 GC16P013153
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SHISA9 on UCSC Golden Path with GeneCards custom track

Promoters for SHISA9 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000083562 80 601 CTCF MXI1 HDAC6 SUZ12 CHD1 SIN3A RAD21 E2F1 CTBP1 POLR2A

Genomic Location for SHISA9 Gene

12,901,620 bp from pter
13,562,919 bp from pter
661,300 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 Asn45, Asn89, and Asn116
  • 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

Protein Domains for SHISA9 Gene


Suggested Antigen Peptide Sequences for SHISA9 Gene

GenScript: Design optimal peptide antigens:

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).

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

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

Animal Model Products

CRISPR Products

miRNA for SHISA9 Gene

miRTarBase miRNAs that target SHISA9

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , 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 5
mitochondrion 2
nucleus 1
cytosol 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for SHISA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008328 ionotropic glutamate receptor complex ISS --
GO:0014069 postsynaptic density IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030054 cell junction IEA --
genes like me logo Genes that share ontologies with SHISA9: view

Pathways & Interactions for SHISA9 Gene

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:2000311 regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity IEA --
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

(4) REFSEQ mRNAs :
(9) Additional mRNA sequences :
(5) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SHISA9 Gene

Shisa homolog 9 (Xenopus laevis):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

No ASD Table

Relevant External Links for SHISA9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SHISA9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, and MOPED for SHISA9 Gene

Protein tissue co-expression partners for SHISA9 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SHISA9 Gene:


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

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 34 35
  • 99.44 (n)
(Bos Taurus)
Mammalia SHISA9 35
  • 97 (a)
(Canis familiaris)
Mammalia SHISA9 34 35
  • 93.63 (n)
(Mus musculus)
Mammalia Shisa9 34 16 35
  • 90.88 (n)
(Rattus norvegicus)
Mammalia Shisa9 34
  • 89.47 (n)
(Monodelphis domestica)
Mammalia SHISA9 35
  • 65 (a)
(Gallus gallus)
Aves SHISA9 34
  • 71.25 (n)
(Anolis carolinensis)
Reptilia -- 35
  • 23 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia shisa9 34
  • 68 (n)
(Danio rerio)
Actinopterygii shisa9a 34 35
  • 63.43 (n)
shisa9b 35
  • 42 (a)
Species where no ortholog for SHISA9 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)
  • 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 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)
  • worm (Caenorhabditis elegans)

Evolution for SHISA9 Gene

Gene Tree for SHISA9 (if available)
Gene Tree for SHISA9 (if available)

Paralogs for SHISA9 Gene

Paralogs for SHISA9 Gene

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

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

Variants for SHISA9 Gene

Sequence variations from dbSNP and Humsavar for SHISA9 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
rs1000002012 -- 13,514,252(+) CCTCC(C/T)GAAGT intron-variant
rs1000005778 -- 13,115,777(+) GTTCA(C/T)ACCAG intron-variant
rs1000014117 -- 12,945,835(+) TCACA(C/T)ATCCT intron-variant
rs1000015305 -- 13,346,367(+) GGAAG(G/T)TCTCA intron-variant
rs1000016337 -- 13,202,924(+) ATTGC(A/G)TGTCC intron-variant

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)

Relevant External Links for SHISA9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SHISA9 Gene

Disorders for SHISA9 Gene

Relevant External Links for SHISA9

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for SHISA9 Gene.

No data available for MalaCards , 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 D.E. … van den Oord E.J. (Mol. Psychiatry 2011) 3 46 64
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  3. Identification of loci associated with schizophrenia by genome-wide association and follow-up. (PMID: 18677311) O'Donovan M.C. … Cloninger C.R. (Nat. Genet. 2008) 3 46 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. Genome-wide association study identifies novel loci associated with concentrations of four plasma phospholipid fatty acids in the de novo lipogenesis pathway: results from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium. (PMID: 23362303) Wu J.H. … Mozaffarian D. (Circ Cardiovasc Genet 2013) 3 64

Products for SHISA9 Gene

Sources for SHISA9 Gene

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