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

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; 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

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_000016.10 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: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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 EBI GWAS CatalogPubMed
Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects. EBI GWAS Catalog EBI GWAS CatalogPubMed
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 EBI GWAS CatalogPubMed
Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of loci associated with schizophrenia by genome-wide association and follow-up. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D16S3062 (e-PCR)
- UniSTS:13331

A115XE1 (e-PCR)
- UniSTS:14867

RH78567 (e-PCR)
- UniSTS:67357

L17953 (e-PCR)
- UniSTS:74788

D8S2279 (e-PCR)
- UniSTS:473907

D11S3014 (e-PCR)
- UniSTS:152118

D16S2828 (e-PCR)
- UniSTS:153398

SHGC-2863 (e-PCR)
- UniSTS:45899

D16S2852 (e-PCR)
- UniSTS:153422

D16S292 (e-PCR)
- UniSTS:52825

SHGC-60505 (e-PCR)
- UniSTS:32096

RH123156 (e-PCR)
- UniSTS:135537

D16S2893 (e-PCR)
- UniSTS:153463

D16S3288 (e-PCR)
- UniSTS:3459

G02304 (e-PCR)
- UniSTS:4742

SHGC-60526 (e-PCR)
- UniSTS:57993

D11S2766 (e-PCR)
- UniSTS:151969

NoName (e-PCR)
- UniSTS:62643

SHGC-17618 (e-PCR)
- UniSTS:75445

D16S741 (e-PCR)
- UniSTS:68044

D16S2746 (e-PCR)
- UniSTS:153316

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)

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
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

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

12901598..13563017

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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