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SHISA9 Gene

protein-coding   GIFtS: 42
GCID: GC16P012995

Shisa Family Member 9

(Previous name: shisa homolog 9 (Xenopus laevis))
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Shisa Family Member 91 2
CKAMP442 5
Shisa Homolog 9 (Xenopus Laevis)1
Cystine-Knot AMPAR Modulating Protein2
Protein Shisa-92
Shisa Homolog 92

External Ids:    HGNC: 372311   Entrez Gene: 7299932   Ensembl: ENSG000002375157   OMIM: 6133465   UniProtKB: B4DS773   

Export aliases for SHISA9 gene to outside databases

Previous GC identifer: GC16P012912


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for SHISA9 Gene:
SHISA9 (shisa family member 9) is a protein-coding gene. Diseases associated with SHISA9 include schizophrenia, and neuronitis. An important paralog of this gene is SHISA6.

UniProtKB/Swiss-Prot: SHSA9_HUMAN, B4DS77
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)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000016.10  NT_010393.17  NC_018927.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for SHISA9
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for SHISA9

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SHISA9


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 16p13.12   Ensembl cytogenetic band:  16p13.12   HGNC cytogenetic band: 16p13.12

SHISA9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SHISA9 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16P012995:  view genomic region     (about GC identifiers)

Start:
12,995,477 bp from pter      End:
13,334,273 bp from pter
Size:
338,797 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: SHSA9_HUMAN, B4DS77 (See protein sequence)
Recommended Name: Protein shisa-9 precursor  
Size: 424 amino acids; 46925 Da
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)
Secondary accessions: C9J314 C9JCE9
Alternative splicing: 3 isoforms:  B4DS77-1   B4DS77-2   B4DS77-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SHISA9: NX_B4DS77

Explore proteomics data for SHISA9 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn45, Asn89, Asn116
  • Modification sites at PhosphoSitePlus

  • See SHISA9 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001138676.2  NP_001138677.2  

    ENSEMBL proteins: 
     ENSP00000407958   ENSP00000395245   ENSP00000454014   ENSP00000453410  

    SHISA9 Human Recombinant Protein Products:

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    Novus Biologicals SHISA9 Protein
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    Cloud-Clone Corp. Proteins for SHISA9

    SHISA9 Antibody Products:

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    SHISA9 Assay Products:

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    Cloud-Clone Corp. CLIAs for SHISA9


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    SHISA: Shisa homologs

    1 InterPro protein domain:
     IPR026910 Shisa

    Graphical View of Domain Structure for InterPro Entry B4DS77

    ProtoNet protein and cluster: B4DS77

    UniProtKB/Swiss-Prot: SHSA9_HUMAN, B4DS77
    Similarity: Belongs to the shisa family. SHISA9 subfamily


    SHISA9 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SHSA9_HUMAN, B4DS77
    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)

    Animal Models:

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    hsa-miR-3678-3p hsa-miR-193a-3p hsa-miR-1258 hsa-miR-890 hsa-miR-298 hsa-miR-4325 hsa-miR-3613-3p hsa-miR-3612
    Browse SwitchGear 3'UTR luciferase reporter plasmids
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    Gene Editing
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    Browse Sino Biological Human cDNA Clones
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    SHSA9_HUMAN, B4DS77: Cell projection, dendritic spine membrane; Single-pass type I membrane protein (By
    similarity). Cell junction, synapse (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5
    mitochondrion2
    cytosol1
    golgi apparatus1
    lysosome1
    nucleus1

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008328ionotropic glutamate receptor complex ISS--
    GO:0030054cell junction IEA--
    GO:0032281alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex IEA--
    GO:0032591dendritic spine membrane ISS--
    GO:0045202synapse ISS--

    SHISA9 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SHISA9
    Interactions:

        Search GeneGlobe Interaction Network for SHISA9

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0048172regulation of short-term neuronal synaptic plasticity ISS--

    SHISA9 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SHISA9 (SHSA9)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for SHISA9 gene (2 alternative transcripts): 
    NM_001145204.2  NM_001145205.1  

    Unigene Cluster for SHISA9:

    Shisa homolog 9 (Xenopus laevis)
    Hs.130661  [show with all ESTs]
    Unigene Representative Sequence: NM_001145204
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000424107 ENST00000423335 ENST00000482916 ENST00000566106 ENST00000558583(uc010uyy.2)
    ENST00000558318(uc002dcd.2)
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate SHISA9 (see all 90):
    hsa-miR-3678-3p hsa-miR-193a-3p hsa-miR-1258 hsa-miR-890 hsa-miR-298 hsa-miR-4325 hsa-miR-3613-3p hsa-miR-3612
    Browse SwitchGear 3'UTR luciferase reporter plasmids
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    Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat SHISA9
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      QuantiTect SYBR Green Assays in human, mouse, rat SHISA9
      QuantiFast Probe-based Assays in human, mouse, rat SHISA9

    Additional mRNA sequence: 

    AJ002784.1 AK000877.1 AK026131.1 AK094972.1 AK299610.1 AK309038.1 AK309193.1 CR627300.1 
    CR749545.1 

    6 DOTS entries:

    DT.75170453  DT.407673  DT.427514  DT.92032947  DT.95247377  DT.120680728 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    SHISA9 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CCCTGACATC
    SHISA9 Expression
    About this image


    SHISA9 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 7) fully expand
     
     Inner Cell Mass (Early Embryonic Tissues)    fully expand to see all 2 entries
             Human embryonic stem cells (family)
     
     Neurons
             Glycinergic Amacrine Cells Inner Nuclear Layer
     
     Bone (Muscoskeletal System)
             Zeugopod Epiphyseal End
     
     Blood (Hematopoietic System)
             Hematopoietic Stem Cells Hematopoietic Bone Marrow
     
     Neural Tube (Nervous System)
             Mesencephalic Floor Plate
    SHISA9 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SHISA9 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.130661
        Custom PCR Arrays for SHISA9
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SHISA9

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for SHISA9 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Shisa91 , 5 shisa homolog 9 (Xenopus laevis)1, 5 90.88(n)1
    93.63(a)1
      16 (6.89 cM)5
    725551  NM_028277.21  NP_082553.21 
     119841135 
    chicken
    (Gallus gallus)
    Aves SHISA91 shisa homolog 9 (Xenopus laevis) 71.25(n)
    74.45(a)
      416419  XM_414733.4  XP_414733.4 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    23(a)
    many ↔ many
    2(104475197-104495089)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia shisa91 shisa family member 9 68(n)
    71.69(a)
      100127547  NM_001112925.1  NP_001106396.1 
    zebrafish
    (Danio rerio)
    Actinopterygii shisa9a1 shisa homolog 9a (Xenopus laevis) 63.43(n)
    61.52(a)
      541382  NM_001013509.1  NP_001013527.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SHISA9 gene
    SHISA62  SHISA82  SHISA72  
    2 SIMAP similar genes for SHISA9 using alignment to 3 protein entries:     SHSA9_HUMAN (see all proteins):
    SHISA8    SHISA6

    SHISA9 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SHISA9 (see all 8226)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1389580061,2
    --12993891(+) CTATTA/GTAATG 2 -- us2k10--------
    rs1172532541,2
    C,F--12993981(+) CAATGT/CCTTGC 2 -- us2k11Minor allele frequency- C:0.01NA 120
    rs1158722481,2
    C,F--12994050(+) GGGGCG/AATTAG 2 -- us2k11Minor allele frequency- A:0.02WA 118
    rs116443621,2
    C,F,A,H--12994097(+) CCCAAT/CAAATC 2 -- us2k127Minor allele frequency- C:0.42NS EA NA WA CSA 2770
    rs1855948221,2
    --12994465(+) GAAACA/TCAGAG 2 -- us2k10--------
    rs1901247841,2
    --12994596(+) GGTCCC/GGGAGG 2 -- us2k10--------
    rs360562521,2
    C,F--12994672(+) GGTGTG/TCCCTC 2 -- us2k19Minor allele frequency- T:0.45NA WA CSA EA 369
    rs1502878781,2
    --12994686(+) TGGAGC/GGCAGA 2 -- us2k10--------
    rs1930369031,2
    --12994725(+) AAGCGG/TCAGGT 2 -- us2k10--------
    rs727826251,2
    C,F--12994942(+) AGCCAT/CGCGGG 2 -- us2k13Minor allele frequency- C:0.11NA CSA 124

    HapMap Linkage Disequilibrium report for SHISA9 (12995477 - 13245477 bp, first 250kb of SHISA9)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for SHISA9 (see all 25):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2713993CNV Deletion23290073
    esv2665133CNV Deletion23128226
    esv2713995CNV Deletion23290073
    esv2365778CNV Deletion18987734
    esv2713990CNV Deletion23290073
    esv1009468CNV Deletion20482838
    esv2713991CNV Deletion23290073
    esv2453404CNV Deletion19546169
    esv2713992CNV Deletion23290073
    esv1005806CNV Deletion20482838

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 613346    OMIM disorders: --

    2 diseases for SHISA9:    
    About MalaCards
    schizophrenia    neuronitis


    SHISA9 for disorders           About GeneDecksing

    Genetic Association Database (GAD): SHISA9
    Human Genome Epidemiology (HuGE) Navigator: SHISA9 (1 document)

    Export disorders for SHISA9 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for SHISA9 gene, integrated from 10 sources (see all 11):
    (articles sorted by number of sources associating them with SHISA9)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs. (PubMed id 20195266)1, 4 Adkins D.E....van den Oord E.J. (Mol. Psychiatry 2011)
    2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    3. Identification of loci associated with schizophrenia by genome-wide association and follow-up. (PubMed id 18677311)1, 4 O'Donovan M.C....Cloninger C.R. (Nat. Genet. 2008)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    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. (PubMed id 23362303)1 Wu J.H....Mozaffarian D. (Circ Cardiovasc Genet 2013)
    6. Gene network analysis in a pediatric cohort identifies novel lung function genes. (PubMed id 24023788)1 Ong B.A....Hakonarson H. (PLoS ONE 2013)
    7. A genome-wide association study of the metabolic syndrome in Indian Asian men. (PubMed id 20694148)4 Zabaneh D. and Balding D.J. (PLoS ONE 2010)
    8. CKAMP44: a brain-specific protein attenuating short-term synaptic plasticity in the dentate gyrus. (PubMed id 20185686)1 von Engelhardt J....Monyer H. (Science 2010)
    9. Genome-wide association with bone mass and geometry in the Framingham Heart Study. (PubMed id 17903296)4 Kiel D.P....Karasik D. (BMC Med. Genet. 2007)
    10. A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. (PubMed id 17463248)4 Scott L.J....Boehnke M. (Science 2007)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 729993 HGNC: 37231 Ensembl:ENSG00000237515 euGenes: HUgn729993 ECgene: SHISA9
    H-InvDB: SHISA9

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for SHISA9 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SHISA9 gene:
    Search GeneIP for patents involving SHISA9

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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