Shisa9 shisa family member 9 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Shisa9provided by MGI
Official Full Name: shisa family member 9provided by MGI
Primary source: MGI:MGI:1919805
See related: Ensembl:ENSMUSG00000022494 AllianceGenome:MGI:1919805
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Ckamp44; 2700045P11Rik
Summary: Enables PDZ domain binding activity. Involved in regulation of AMPA receptor activity; regulation of postsynaptic neurotransmitter receptor activity; and regulation of short-term neuronal synaptic plasticity. Located in glutamatergic synapse; postsynaptic density; and synaptic membrane. Part of AMPA glutamate receptor complex. Is integral component of postsynaptic density membrane. Is expressed in brain. Orthologous to human SHISA9 (shisa family member 9). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in frontal lobe adult (RPKM 7.4), CNS E18 (RPKM 4.4) and 6 other tissues See more
Orthologs: human all
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Genomic context

Location:: 16 A1; 16 6.89 cM

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	16	NC_000082.7 (11801457..12088768)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	16	NC_000082.6 (11983593..12270904)

Chromosome 16 - NC_000082.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Modulation of virus-induced neuroinflammation by the autophagy receptor SHISA9 in mice.
Title: Modulation of virus-induced neuroinflammation by the autophagy receptor SHISA9 in mice.
CKAMP44 controls synaptic function and strength of relay neurons during early development of the dorsal lateral geniculate nucleus.
Title: CKAMP44 controls synaptic function and strength of relay neurons during early development of the dorsal lateral geniculate nucleus.
Data indicate the importance of CKAMP44 for modulating synaptic short-term depression and visual input integration.
Title: CKAMP44 modulates integration of visual inputs in the lateral geniculate nucleus.
Ckamp44 expression is strongest in dentate gyrus granule cells and less abundant in the rest of the brain
Title: Facilitated c-Fos Induction in Mice Deficient for the AMPA Receptor-Associated Protein Ckamp44.
coexpression of both auxiliary subunits,CKAMP44 and TARP gamma-8 is necessary for the efficient targeting of AMPARs to the cell surface of dentate gyrus granule cells
Title: Coexpressed auxiliary subunits exhibit distinct modulatory profiles on AMPA receptor function.
Data show interaction partners of AMPA receptor auxiliary subunit Shisa9, and that the C-terminal interactions of Shisa9 through its PDZ domain interaction motif are important for AMPA receptor synaptic and network functions.
Title: C-terminal interactors of the AMPA receptor auxiliary subunit Shisa9.
CKAMP44 identified as a brain-specific type I transmembrane protein that associates with AMPA receptors in synaptic spines; findings show that CKAMP44 modulates short-term plasticity at specific excitatory synapses
Title: CKAMP44: a brain-specific protein attenuating short-term synaptic plasticity in the dentate gyrus.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (1)
Targeted (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:487948

D16Mit100 (e-PCR), detects polymorphism
- UniSTS:127727

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables PDZ domain binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in regulation of AMPA receptor activity	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of AMPA receptor activity	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of AMPA receptor activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of postsynaptic neurotransmitter receptor activity	IC Inferred by Curator more info	PubMed
involved_in regulation of postsynaptic neurotransmitter receptor activity	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of postsynaptic neurotransmitter receptor activity	IMP Inferred from Mutant Phenotype more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of AMPA glutamate receptor complex	IBA Inferred from Biological aspect of Ancestor more info
part_of AMPA glutamate receptor complex	IDA Inferred from Direct Assay more info	PubMed
located_in cell projection	IEA Inferred from Electronic Annotation more info
is_active_in dendritic spine membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in dendritic spine membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IEP Inferred from Expression Pattern more info	PubMed
is_active_in glutamatergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
part_of ionotropic glutamate receptor complex	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
is_active_in postsynaptic density	IBA Inferred from Biological aspect of Ancestor more info
located_in postsynaptic density	IDA Inferred from Direct Assay more info	PubMed
located_in postsynaptic density membrane	IC Inferred by Curator more info	PubMed
is_active_in postsynaptic density membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in postsynaptic density membrane	IEP Inferred from Expression Pattern more info	PubMed
is_active_in postsynaptic density membrane	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in postsynaptic membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in postsynaptic membrane	IDA Inferred from Direct Assay more info	PubMed
located_in synapse	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: protein shisa-9

Names: cystine-knot AMPAR modulating protein of 44 kDa; 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)

NM_001174086.1 → NP_001167557.1 protein shisa-9 isoform 2 precursor

Status: VALIDATED

Description

Transcript Variant: This variant (2, also known as CKAMP44b) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1. Isoform 2 contains an in-frame start site 41 codons upstream from the currently annotated site, but signal sequence considerations and orthology data support use of the downstream AUG.

Source sequence(s)

AC129020, AC154289, BC030884

Consensus CDS

CCDS49767.1

UniProtKB/TrEMBL

E9QN38

Related

ENSMUSP00000023138.7, ENSMUST00000023138.8

Conserved Domains (1) summary

pfam13908
Location:72 → 255

Shisa; Wnt and FGF inhibitory regulator
NM_028277.2 → NP_082553.2 protein shisa-9 isoform 1 precursor

See identical proteins and their annotated locations for NP_082553.2

Status: VALIDATED

Description

Transcript Variant: This variant (1, also known as CKAMP44a) represents the longer transcript and encodes the longer isoform (1). Isoform 1 contains an in-frame start site 41 codons upstream from the currently annotated site, but signal sequence considerations and orthology data support use of the downstream AUG.

Source sequence(s)

AC129020, AC154289, AK049860

Consensus CDS

CCDS49766.1

UniProtKB/Swiss-Prot

D4NZG2, D4NZG3, Q9CZN4

Related

ENSMUSP00000132646.2, ENSMUST00000170672.9

Conserved Domains (1) summary

pfam13908
Location:72 → 255

Shisa; Wnt and FGF inhibitory regulator

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000082.7 Reference GRCm39 C57BL/6J

Range

11801457..12088768

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030249286.1 → XP_030105146.1 protein shisa-9 isoform X2

Conserved Domains (1) summary

pfam13908
Location:113 → 222

Shisa; Wnt and FGF inhibitory regulator
XM_017317137.2 → XP_017172626.1 protein shisa-9 isoform X2

Conserved Domains (1) summary

pfam13908
Location:113 → 222

Shisa; Wnt and FGF inhibitory regulator
XM_036160140.1 → XP_036016033.1 protein shisa-9 isoform X1

Conserved Domains (1) summary

pfam13908
Location:113 → 296

Shisa; Wnt and FGF inhibitory regulator
XM_017317138.2 → XP_017172627.1 protein shisa-9 isoform X3

Conserved Domains (1) summary

pfam13908
Location:113 → 222

Shisa; Wnt and FGF inhibitory regulator