Pcdh9 MGI Mouse Gene Detail - MGI:1306801

Symbol

Pcdh9
Name

protocadherin 9
Synonyms

1500001L12Rik, A730003J17Rik, C530050I23Rik, C630029H24Rik, LOC382930

Feature Type

protein coding gene
IDs

MGI:1306801
NCBI Gene: 211712
Alliance

gene page
Transcription Start Sites

2 TSS

Sequence Map

Chr14:93013410-93890679 bp, - strand
From Ensembl annotation of GRCm38

View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 14, 45.80 cM
Mapping Data

4 experiments

SNPs within 2kb

9487 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1306801	protein coding gene	Chr14:93013410-93892834 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0021610	protein coding gene	Chr14:88874903-89814765 (-)
A/J	MGP_AJ_G0021568	protein coding gene	Chr14:86304495-87162946 (-)
AKR/J	MGP_AKRJ_G0021544	protein coding gene	Chr14:88857081-89742657 (-)
BALB/cJ	MGP_BALBcJ_G0021574	protein coding gene	Chr14:86441814-87322365 (-)
C3H/HeJ	MGP_C3HHeJ_G0021352	protein coding gene	Chr14:88642437-89546593 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0022014	protein coding gene	Chr14:92569227-93533240 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0019554	protein coding gene	Chr14:83572750-84417095 (-)
CAST/EiJ	MGP_CASTEiJ_G0020869	protein coding gene	Chr14:85757361-86690274 (-)
CBA/J	MGP_CBAJ_G0021320	protein coding gene	Chr14:95790788-96805134 (-)
DBA/2J	MGP_DBA2J_G0021444	protein coding gene	Chr14:85712955-86599263 (-)
FVB/NJ	MGP_FVBNJ_G0021420	protein coding gene	Chr14:84812718-85682919 (-)
LP/J	MGP_LPJ_G0021512	protein coding gene	Chr14:89756767-90699919 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0021448	protein coding gene	Chr14:97172865-98456400 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0022037	protein coding gene	Chr14:88252475-89167594 (-)
PWK/PhJ	MGP_PWKPhJ_G0020612	protein coding gene	Chr14:82568617-83466678 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0020450	protein coding gene	Chr14:84161957-85064127 (-)
WSB/EiJ	MGP_WSBEiJ_G0020922	protein coding gene	Chr14:88773480-89693792 (-)

Human Ortholog

PCDH9, protocadherin 9

Vertebrate Orthologs

10

Human Ortholog

PCDH9, protocadherin 9
Orthology source: HomoloGene, HGNC
Links

HGNC:8661

NCBI Gene ID: 5101

neXtProt AC: NX_Q9HC56

UniProt: Q9HC56
Chr Location

13q21.32; chr13:66302834-67230336 (-) GRCh38.p7

HomoloGene

Vertebrate Homology Class 10698
1 human;1 mouse;1 rat;1 chimpanzee;1 cattle;1 dog;1 chicken;1 zebrafish;1 frog, western clawed;1 macaque, rhesus
HCOP

human homology predictions: PCDH9
Gene Tree

Pcdh9

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Phenotype Summary

16 phenotypes from 2 alleles in 2 genetic backgrounds
7 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	immune system	integument	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	neoplasm	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	vision/eye

Click cells to view annotations.

All Mutations and Alleles

5
Chemically induced (other)

1
Gene trapped

1
Targeted

3
Genomic Mutations

1 involving Pcdh9
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

1 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit impaired long-term social and bject recognition and sensorimotor development.

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All GO Annotations

6
GO References

4

External Resources

FuncBase

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell death	cell differentiation	cell population proliferation	cellular component organization	establishment of localization	homeostatic process	immune system process	lipid metabolic process	nucleic acid-templated transcription	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	non-membrane-bounded organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

775
Tissues

121
cDNA Data

22
Literature Summary

14

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GENSAT

GEO

Expression Atlas
Other Vertebrate Links

GEISHA PCDH9

Xenbase pcdh9

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Pcdh9 interacts with 134 markers (Mir7-1, Mir7-2, Mir7b, ...) View All

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All Sequences

89
RefSeq

17
UniProt

15
CCDS

CCDS36992.1, CCDS79350.1, CCDS79352.1, CCDS84156.1

Ensembl

ENSMUSG00000055421 (Evidence)
NCBI Gene

211712

			Length	Strain/Species	Flank
genomic	ENSMUSG00000055421	Ensembl Gene Model \| MGI Sequence Detail	877270	C57BL/6J	± kb
transcript	ENSMUST00000068992	Ensembl \| MGI Sequence Detail	3714	Not Applicable
polypeptide	ENSMUSP00000070935	Ensembl \| MGI Sequence Detail	1237	Not Applicable

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UniProt

15 Sequences
InterPro Domains

IPR020894 Cadherin conserved site

IPR002126 Cadherin-like

IPR015919 Cadherin-like superfamily

IPR013164 Cadherin, N-terminal

IPR013585 Protocadherin

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All nucleic 28

cDNA 25

Primer pair 1

Other 2

Microarray probesets 9

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MGI:1916209, MGI:2444471, MGI:2685143, MGI:2686059, MGI:3510991

Summaries

All 38

Developmental Gene Expression 14

Gene Ontology 4

Phenotypes 7
Earliest

J:50455 Strehl S, et al., Characterization of two novel protocadherins (PCDH8 and PCDH9) localized on human chromosome 13 and mouse chromosome 14. Genomics. 1998 Oct 1;53(1):81-9
Latest

J:288805 Pensold D, et al., Single-Cell Transcriptomics Reveals Regulators of Neuronal Migration and Maturation During Brain Development. J Exp Neurosci. 2018;12:1179069518760783

TSS for Pcdh9:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr129977	Chr14:93890692-93890716 (-)	-25 bp
Tssr129976	Chr14:93890674-93890689 (-)	-3 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer & Copyright Notice Send questions and comments to User Support.	last database update 10/13/2020 MGI 6.16