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    SHISA6 shisa family member 6 [ Homo sapiens (human) ]

    Gene ID: 388336, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SHISA6provided by HGNC
    Official Full Name
    shisa family member 6provided by HGNC
    Primary source
    HGNC:HGNC:34491
    See related
    Ensembl:ENSG00000188803 MIM:617327; AllianceGenome:HGNC:34491
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Predicted to enable ionotropic glutamate receptor binding activity. Predicted to be involved in several processes, including excitatory chemical synaptic transmission; modulation of chemical synaptic transmission; and negative regulation of canonical Wnt signaling pathway. Predicted to be located in asymmetric, glutamatergic, excitatory synapse. Predicted to be part of AMPA glutamate receptor complex. Predicted to be active in dendritic spine membrane; glutamatergic synapse; and postsynaptic density membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in brain (RPKM 3.7), endometrium (RPKM 2.0) and 9 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SHISA6 in Genome Data Viewer
    Location:
    17p12
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (11241213..11564063)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (11149418..11472179)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (11144530..11467380)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:10829767-10830266 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:11053466-11054665 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:11102854-11104053 Neighboring gene RNA, 7SL, cytoplasmic 601, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:11148155-11148656 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:11161596-11161784 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:11177103-11177604 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:11200213-11200381 Neighboring gene uncharacterized LOC124903929 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:11397143-11397680 Neighboring gene NANOG hESC enhancer GRCh37_chr17:11406563-11407064 Neighboring gene MPRA-validated peak2723 silencer Neighboring gene MPRA-validated peak2724 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:11540697-11541896 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:11571267-11572208 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:11572478-11573677 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:11602804-11604003 Neighboring gene dynein axonemal heavy chain 9 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:11639660-11640859 Neighboring gene uncharacterized LOC101928350 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:11812057-11812249 Neighboring gene NANOG hESC enhancer GRCh37_chr17:11831780-11832352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:11851561-11852062 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:11852063-11852562 Neighboring gene uncharacterized LOC124903928

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Genetic variants in the SHISA6 gene are associated with delayed cognitive impairment in two family datasets. Ramos J, et al. Alzheimers Dement, 2023 Feb. PMID 35490390, Free PMC Article
    2. Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia. Verhoeven VJ, et al. Nat Genet, 2013 Mar. PMID 23396134, Free PMC Article
    3. Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants. Dichgans M, et al. Stroke, 2014 Jan. PMID 24262325, Free PMC Article
    4. Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. Lauc G, et al. PLoS Genet, 2013. PMID 23382691, Free PMC Article
    5. Assessment of community efforts to advance network-based prediction of protein-protein interactions. Wang XW, et al. Nat Commun, 2023 Mar 22. PMID 36949045, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Genetic variants in the SHISA6 gene are associated with delayed cognitive impairment in two family datasets.
      Title: Genetic variants in the SHISA6 gene are associated with delayed cognitive impairment in two family datasets.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia.
    EBI GWAS Catalog
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog
    Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ37030, FLJ37733, FLJ45455

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables PDZ domain binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ionotropic glutamate receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ionotropic glutamate receptor binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in excitatory chemical synaptic transmission ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of canonical Wnt signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in postsynaptic neurotransmitter receptor diffusion trapping IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of AMPA glutamate receptor clustering ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of postsynaptic neurotransmitter receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of short-term neuronal synaptic plasticity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spermatogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    part_of AMPA glutamate receptor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in asymmetric, glutamatergic, excitatory synapse ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in dendritic spine membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in postsynaptic density IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in postsynaptic density ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in postsynaptic density membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in postsynaptic membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    protein shisa-6
    Names
    protein shisa-6 homolog
    shisa homolog 6

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001173461.2 → NP_001166932.1  protein shisa-6 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001166932.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AC005725, AC007510
      Consensus CDS
      CCDS54090.1
      UniProtKB/Swiss-Prot
      B3KXV5, Q4PL63, Q6ZSJ9
      Related
      ENSP00000387157.3, ENST00000409168.7
      Conserved Domains (1) summary
      pfam13908
      Location:92 → 273
      Shisa; Wnt and FGF inhibitory regulator

    2. NM_001173462.2 → NP_001166933.1  protein shisa-6 isoform 3 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate exon in the coding region, compared to variant 1. The resulting isoform (3) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AC005725, AC007510
      Consensus CDS
      CCDS54089.1
      UniProtKB/Swiss-Prot
      Q6ZSJ9
      Related
      ENSP00000388659.3, ENST00000432116.7

    3. NM_207386.4 → NP_997269.2  protein shisa-6 isoform 1 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC005725, AC007510, AK128003, DA362563
      Consensus CDS
      CCDS45615.1
      UniProtKB/Swiss-Prot
      Q6ZSJ9
      Related
      ENSP00000390084.3, ENST00000441885.8
      Conserved Domains (1) summary
      pfam13908
      Location:91 → 258
      Shisa; Wnt and FGF inhibitory regulator

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      11241213..11564063
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      11149418..11472179
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_175903.2: Suppressed sequence

      Description
      NM_175903.2: This RefSeq was permanently suppressed because it is primarily UTR sequence.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZSJ9.2 GenPept UniProtKB/Swiss-Prot:Q6ZSJ9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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