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SHISA9 shisa family member 9 [ Homo sapiens (human) ]

Gene ID: 729993, updated on 5-Mar-2024

Summary

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Official Symbol
SHISA9provided by HGNC
Official Full Name
shisa family member 9provided by HGNC
Primary source
HGNC:HGNC:37231
See related
Ensembl:ENSG00000237515 MIM:613346; AllianceGenome:HGNC:37231
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
Also known as
CKAMP44
Summary
Predicted to enable PDZ domain binding activity. Predicted to be involved in regulation of AMPA receptor activity and regulation of short-term neuronal synaptic plasticity. Predicted to be located in synapse. Predicted to be part of AMPA glutamate receptor complex. Predicted to be active in glutamatergic synapse; postsynaptic density; and synaptic membrane. Predicted to be integral component of postsynaptic density membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in brain (RPKM 3.5), prostate (RPKM 1.1) and 3 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
16p13.12
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (12901598..13563017)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (12938717..13600679)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (12995455..13334273)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA27 Neighboring gene ribosomal protein L35a pseudogene 34 Neighboring gene uncharacterized LOC105371092 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:13033541-13034740 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:13105885-13106658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:13106659-13107432 Neighboring gene MPRA-validated peak2503 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:13163591-13164125 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:13164126-13164659 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:13186399-13186558 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:13195592-13196122 Neighboring gene NANOG hESC enhancer GRCh37_chr16:13261801-13262350 Neighboring gene uncharacterized LOC105371091 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:13324393-13325128 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:13325129-13325863 Neighboring gene uncharacterized LOC107984137 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:13400658-13401857 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:13445515-13446114 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:13446115-13446714 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:13446715-13447314 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:13451262-13452208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:13461095-13461596 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10481 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10482 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10483 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10484 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7222 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:13546486-13547685 Neighboring gene NANOG hESC enhancer GRCh37_chr16:13553376-13553877 Neighboring gene TATA element modulatory factor 1 pseudogene 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:13677141-13677699 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:13689018-13689951 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:13700037-13700536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:13701935-13702436 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:13702437-13702936 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:13850765-13851964 Neighboring gene uncharacterized LOC124903645 Neighboring gene uncharacterized LOC124903646

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
  • 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. Identification of loci associated with schizophrenia by genome-wide association and follow-up. O'Donovan MC, et al. Nat Genet, 2008 Sep. PMID 18677311
  2. CKAMP44: a brain-specific protein attenuating short-term synaptic plasticity in the dentate gyrus. von Engelhardt J, et al. Science, 2010 Mar 19. PMID 20185686
  3. Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs. Adkins DE, et al. Mol Psychiatry, 2011 Mar. PMID 20195266, Free PMC Article
  4. Gene network analysis in a pediatric cohort identifies novel lung function genes. Ong BA, et al. PLoS One, 2013. PMID 24023788, Free PMC Article
  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. Wu JH, et al. Circ Cardiovasc Genet, 2013 Apr. PMID 23362303, Free PMC Article

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. Functionally characterizes the homologous mouse gene.
    Title: CKAMP44: a brain-specific protein attenuating short-term synaptic plasticity in the dentate gyrus.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Gene network analysis in a pediatric cohort identifies novel lung function genes.
EBI GWAS Catalog
Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
EBI GWAS Catalog
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) consortiu
EBI GWAS Catalog
Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs.
EBI GWAS Catalog
Identification of loci associated with schizophrenia by genome-wide association and follow-up.
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

  • FLJ10015, FLJ37653, FLJ58277, FLJ99079, FLJ99234, DKFZp686D24206, DKFZp686E24206

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables PDZ domain binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in regulation of AMPA 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 regulation of short-term neuronal synaptic plasticity 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
  
is_active_in dendritic spine membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in dendritic spine membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
  
part_of ionotropic glutamate receptor complex ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in postsynaptic density IBA
Inferred from Biological aspect of Ancestor
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
  
located_in synapse ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
protein shisa-9
Names
cystine-knot AMPAR modulating protein
shisa homolog 9

NCBI Reference Sequences (RefSeq)

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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_001145204.3 → NP_001138676.2  protein shisa-9 isoform 1 precursor

    See identical proteins and their annotated locations for NP_001138676.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1). This RefSeq contains an in-frame start site 41 codons upstream from the currently annotated site but is not being annotated as a start site since it is in a weak Kozak sequence context. Also, use of the upstream AUG would eliminate the signal peptide.
    Source sequence(s)
    AC009134, AC092324, AK299610, DC375222, H20826
    Consensus CDS
    CCDS45417.2
    UniProtKB/Swiss-Prot
    B4DS77, C9J314, C9JCE9
    Related
    ENSP00000454014.2, ENST00000558583.3
    Conserved Domains (1) summary
    pfam13908
    Location:72 → 255
    Shisa; Wnt and FGF inhibitory regulator

  2. NM_001145205.2 → NP_001138677.2  protein shisa-9 isoform 2 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate terminal exon, compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus, compared to isoform 1. This RefSeq contains an in-frame start site 41 codons upstream from the currently annotated site but is not being annotated as a start site since it is in a weak Kozak sequence context. Also, use of the upstream AUG would eliminate the signal peptide.
    Source sequence(s)
    AC092324, AK299610, AK309038, CR627300
    Consensus CDS
    CCDS45418.2
    Related
    ENSP00000395245.2, ENST00000423335.2
    Conserved Domains (1) summary
    pfam13908
    Location:72 → 188
    Shisa; Wnt and FGF inhibitory regulator

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    12901598..13563017
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011522642.3 → XP_011520944.1  protein shisa-9 isoform X3

    Conserved Domains (1) summary
    pfam13908
    Location:113 → 296
    Shisa; Wnt and FGF inhibitory regulator

  2. XM_047434582.1 → XP_047290538.1  protein shisa-9 isoform X1

  3. XM_005255539.4 → XP_005255596.2  protein shisa-9 isoform X2

    Conserved Domains (1) summary
    pfam13908
    Location:113 → 296
    Shisa; Wnt and FGF inhibitory regulator

RNA

  1. XR_932915.3 RNA Sequence

  2. XR_007064905.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    12938717..13600679
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054313826.1 → XP_054169801.1  protein shisa-9 isoform X3

  2. XM_054313824.1 → XP_054169799.1  protein shisa-9 isoform X1

  3. XM_054313825.1 → XP_054169800.1  protein shisa-9 isoform X2

RNA

  1. XR_008484731.1 RNA Sequence

  2. XR_008484732.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
B4DS77.3 GenPept UniProtKB/Swiss-Prot:B4DS77

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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