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

Gene ID: 729993, updated on 12-Oct-2019

Summary

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
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
Expression
Biased expression in brain (RPKM 3.5), prostate (RPKM 1.1) and 3 other tissues See more
Orthologs

Genomic context

See SHISA9 in Genome Data Viewer
Location:
16p13.12
Exon count:
9
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (12901598..13563427)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (12995477..13334273)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371089 Neighboring gene calcineurin like phosphoesterase domain containing 1 Neighboring gene ribosomal protein L35a pseudogene 34 Neighboring gene uncharacterized LOC105371092 Neighboring gene uncharacterized LOC105371091 Neighboring gene uncharacterized LOC107984137 Neighboring gene TATA element modulatory factor 1 pseudogene 1 Neighboring gene putative uncharacterized protein encoded by LINC00596 Neighboring gene uncharacterized LOC105371093

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
PDZ domain binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
regulation of AMPA receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of postsynaptic neurotransmitter receptor activity IEA
Inferred from Electronic Annotation
more info
 
regulation of short-term neuronal synaptic plasticity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of short-term neuronal synaptic plasticity ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
AMPA glutamate receptor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell junction IEA
Inferred from Electronic Annotation
more info
 
dendritic spine membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
dendritic spine membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
integral component of postsynaptic density membrane IEA
Inferred from Electronic Annotation
more info
 
ionotropic glutamate receptor complex ISS
Inferred from Sequence or Structural Similarity
more info
 
postsynaptic density IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
postsynaptic membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
synapse IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
synapse ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

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

NCBI Reference Sequences (RefSeq)

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_001145204.3NP_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
    Related
    ENSP00000454014.2, ENST00000558583.3
    Conserved Domains (1) summary
    pfam13908
    Location:72255
    Shisa; Wnt and FGF inhibitory regulator
  2. NM_001145205.2NP_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
    UniProtKB/Swiss-Prot
    B4DS77
    Related
    ENSP00000395245.2, ENST00000423335.2
    Conserved Domains (1) summary
    pfam13908
    Location:72188
    Shisa; Wnt and FGF inhibitory regulator

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    12901598..13563427
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011522642.2XP_011520944.1  protein shisa-9 isoform X2

    Conserved Domains (1) summary
    pfam13908
    Location:113296
    Shisa; Wnt and FGF inhibitory regulator
  2. XM_005255539.3XP_005255596.2  protein shisa-9 isoform X1

    Conserved Domains (1) summary
    pfam13908
    Location:113296
    Shisa; Wnt and FGF inhibitory regulator

RNA

  1. XR_001751976.1 RNA Sequence

  2. XR_932915.2 RNA Sequence

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