PCDH9 protocadherin 9 [Homo sapiens] - Gene

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Summary

Official Symbol: PCDH9provided by HGNC
Official Full Name: protocadherin 9provided by HGNC
Primary source: HGNC:8661
Locus tag: RP11-335P18.3
See related: Ensembl:ENSG00000184226; HPRD:04661; MIM:603581; Vega:OTTHUMG00000017040
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. The mRNA encodes a cadherin-related neuronal receptor that localizes to synaptic junctions and is putatively involved in specific neuronal connections and signal transduction. Sharing a characteristic with other protocadherin genes, this gene has a notably large exon that encodes six cadherin domains and a transmembrane region. Two alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Feb 2009]

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Genomic context

Location :: 13q21.32

Sequence :: Chromosome: 13; NC_000013.10 (66876966..67804468, complement)

See PCDH9 in Epigenomics, MapViewer

Chromosome 13 - NC_000013.10 Genomic Context describing neighboring genes

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Genomic regions, transcripts, and products

Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

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Bibliography

GeneRIFs: Gene References Into Functions What's a GeneRIF?

Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
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

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Phenotypes

Review eQTL and phenotype association data in this region using PheGenI

A genome-wide association study on obesity and obesity-related traits.

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description
BioGRID:111134	BioGRID:107076	BCL6		BioGRID	PubMed	Affinity Capture-MS
BioGRID:111134	BioGRID:112171	RYK		BioGRID	PubMed	Affinity Capture-MS

Function	Evidence Code	Pubs
calcium ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
cell adhesion	IEA Inferred from Electronic Annotation more info
homophilic cell adhesion	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
integral to membrane	IEA Inferred from Electronic Annotation more info
plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

Preferred Names: protocadherin-9

Names: protocadherin-9; cadherin superfamily protein VR4-11

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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.

Genomic

NG_011876.1 RefSeqGene

Range

5001..932503

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_020403.4 → NP_065136.1 protocadherin-9 isoform 2 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, as compared to variant 1. It encodes the shorter isoform (2) which is missing an internal segment, as compared to isoform 1.

Source sequence(s)

AI300218, AK054661, AL603863, AL834258, BC136627, BX537422

Consensus CDS

CCDS9443.1

UniProtKB/Swiss-Prot

Q9HC56

Related

ENSP00000401699, OTTHUMP00000018490, ENST00000456367, OTTHUMT00000045214

Conserved Domains (2) summary

pfam08374
Location:777 – 1002
Blast Score: 643

Protocadherin; Protocadherin

cd11304
Location:576 – 671
Blast Score: 295

Cadherin_repeat; Cadherin tandem repeat domain.
NM_203487.2 → NP_982354.1 protocadherin-9 isoform 1 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AI300218, AK054661, AL834258, BX537422, DA278856

Consensus CDS

CCDS9444.1

UniProtKB/Swiss-Prot

Q9HC56

Related

ENSP00000442186, ENST00000544246

Conserved Domains (2) summary

pfam08374
Location:777 – 1002
Blast Score: 641

Protocadherin; Protocadherin

cd11304
Location:576 – 671
Blast Score: 296

Cadherin_repeat; Cadherin tandem repeat domain.

RefSeqs of Annotated Genomes: Build 37.3

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

Reference GRCh37.p5 Primary Assembly

Genomic

NC_000013.10 Reference GRCh37.p5 Primary Assembly

Range

66876966..67804468, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000145.1 Alternate HuRef

Range

47575260..48502804, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

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Related Sequences

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	AL136999.26	CAI12502.1
		CAM13771.1
genomic	AL138682.13 (100..164603)	None
genomic	AL138814.13	CAM13066.1
genomic	AL160254.10 (100..139880)	None
genomic	AL355173.25	CAH72612.1
		CAM17290.1
genomic	AL356305.11 (1995..132435)	None
genomic	AL450107.11 (100..50885)	None
genomic	AL603863.7	CAH72758.1
		CAH72759.1
		CAM17491.1
genomic	AL603863.7	CAH72758.1
		CAH72759.1
		CAM17491.1
genomic	CH471093.1	EAW80499.1
mRNA	AB114416.1	None
mRNA	AF169692.2	AAF89689.2
mRNA	AI300218.1	None
mRNA	AK054661.1	None
mRNA	AK057768.1	None
mRNA	AL834258.1	CAD38933.1
mRNA	BC136626.1	AAI36627.1
mRNA	BC136627.1	AAI36628.1
mRNA	BC144321.1	AAI44322.1
mRNA	BC150296.1	AAI50297.1
mRNA	BX537422.1	CAD97664.1
mRNA	DA278856.1	None
mRNA	R38168.1	None