Pcdhgc4 MGI Mouse Gene Detail - MGI:1935203 - protocadherin gamma subfamily C, 4

Symbol

Pcdhgc4
Name

protocadherin gamma subfamily C, 4

Feature Type

protein coding gene
IDs

MGI:1935203
NCBI Gene: 93707
Member of

Pcdhg cluster
Alliance

gene page
Transcription Start Sites

4 TSS
Regulated by

Rr72, Rr73, Rr74 ... (4 regulatory regions)

Sequence Map

Chr18:37948132-37974926 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 18, 19.68 cM
Mapping Data

2 experiments

SNPs within 2kb

562 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1935203	protein coding gene	Chr18:37948132-37974926 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0024352	protein coding gene	Chr18:36232308-36259977 (+)
A/J	MGP_AJ_G0024319	protein coding gene	Chr18:34984401-35011794 (+)
AKR/J	MGP_AKRJ_G0024288	protein coding gene	Chr18:35942912-35972570 (+)
BALB/cJ	MGP_BALBcJ_G0024319	protein coding gene	Chr18:35050604-35077409 (+)
C3H/HeJ	MGP_C3HHeJ_G0024085	protein coding gene	Chr18:36011413-36038769 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0024761	protein coding gene	Chr18:37529759-37559702 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0022200	protein coding gene	Chr18:35001720-35028291 (+)
CAST/EiJ	MGP_CASTEiJ_G0023560	protein coding gene	Chr18:35949782-35977834 (+)
CBA/J	MGP_CBAJ_G0024055	protein coding gene	Chr18:38638546-38667943 (+)
DBA/2J	MGP_DBA2J_G0024185	protein coding gene	Chr18:34583842-34611340 (+)
FVB/NJ	MGP_FVBNJ_G0024151	protein coding gene	Chr18:34294352-34321591 (+)
LP/J	MGP_LPJ_G0024269	protein coding gene	Chr18:36293384-36321813 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0024182	protein coding gene	Chr18:39899558-39929365 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0024810	protein coding gene	Chr18:35804977-35837204 (+)
PWK/PhJ	MGP_PWKPhJ_G0023304	protein coding gene	Chr18:34790413-34819114 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0023109	protein coding gene	Chr18:36025899-36054330 (+)
WSB/EiJ	MGP_WSBEiJ_G0023623	protein coding gene	Chr18:35706881-35737854 (+)

Human Ortholog

PCDHGC4, protocadherin gamma subfamily C, 4

Vertebrate Orthologs

10

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

PCDHGC4, protocadherin gamma subfamily C, 4
Synonyms

NEDGS, PCDH-GAMMA-C4
Links

HGNC:8717

NCBI Gene ID: 56098

neXtProt AC: NX_Q9Y5F7

UniProt: Q9Y5F7
Chr Location

5q31.3; chr5:141484997-141512975 (+) GRCh38

MGI Vertebrate Homology

Pcdhgc4 stringent orthology
1 human;1 mouse;9 zebrafish
HCOP

vertebrate homology predictions: PCDHGC4
Gene Tree

Pcdhgc4

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Phenotype Summary

6 phenotype references

All Mutations and Alleles

6
Endonuclease-mediated

2
Targeted

4
Genomic Mutations

6 involving Pcdhgc4
Incidental Mutations

CvDC
Find Mice (IMSR)

53 strains or lines available

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All GO Annotations

9
GO References

4

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 differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	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	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	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

730
Tissues

12
cDNA Data

7
Literature Summary

10

Images

Tissue x Stage Matrix

Other Mouse Links

Allen Institute

GEO

Expression Atlas

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All Sequences

38
RefSeq

2
UniProt

4
CCDS

CCDS29193.1

Ensembl

ENSMUSG00000023036 (Evidence)
NCBI Gene

93707

			Length	Strain/Species	Flank
genomic	93707	NCBI Gene Model \| MGI Sequence Detail	26795	C57BL/6J	± kb
transcript	NM_033582	RefSeq \| MGI Sequence Detail	5047	C57BL/6
polypeptide	NP_291060	RefSeq \| MGI Sequence Detail	941	C57BL/6

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UniProt

4 Sequences
PDB

7JGZ, 7RGF
InterPro Domains

IPR020894 Cadherin conserved site

IPR031904 Cadherin, C-terminal catenin-binding domain

IPR002126 Cadherin-like

IPR015919 Cadherin-like superfamily

IPR013164 Cadherin, N-terminal

IPR050174 Protocadherin/Cadherin-related Cell Adhesion
GlyGen

Q91XX0 3 sites, 1 N-linked glycan (1 site)

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All nucleic 14

Genomic 2

cDNA 8

Primer pair 4

Summaries

All 30

Developmental Gene Expression 10

Gene Ontology 4

Phenotypes 6
Earliest

J:67989 Wu Q, et al., Comparative dna sequence analysis of mouse and human protocadherin gene clusters. Genome Res. 2001 Mar;11(3):389-404
Latest

J:358998 Leon WRM, et al., The clustered gamma protocadherin PcdhgammaC4 isoform regulates cortical interneuron programmed cell death in the mouse cortex. Proc Natl Acad Sci U S A. 2024 Feb 6;121(6):e2313596120

Pcdhgc4 expression regulated by:

Feature	Feature Type	Location	Reference
Rr72, regulatory region 72	unclassified other genome feature	Chr18, Syntenic	J:277249
Rr73, regulatory region 73	unclassified other genome feature	Chr18, Syntenic	J:277249
Rr74, regulatory region 74	unclassified other genome feature	Chr18, Syntenic	J:277249
Rr75, regulatory region 75	unclassified other genome feature	Chr18, Syntenic	J:277249

TSS for Pcdhgc4:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr150750	Chr18:37946227-37946287 (+)	-1,875 bp
Tssr150751	Chr18:37946422-37946438 (+)	-1,702 bp
Tssr150752	Chr18:37948443-37948490 (+)	335 bp
Tssr150753	Chr18:37948497-37948520 (+)	377 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)
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