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Gene: Pcdhac2 (protocadherin alpha subfamily C, 2) Rattus norvegicus

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Symbol:

Pcdhac2 (Ensembl: Pcdha3)

Name:

protocadherin alpha subfamily C, 2 (Ensembl:protocadherin alpha 3)

RGD ID:

735216

Description:

Predicted to enable calcium ion binding activity. Predicted to be involved in homophilic cell adhesion via plasma membrane adhesion molecules. Predicted to act upstream of or within serotonergic neuron axon guidance. Predicted to be located in plasma membrane. Orthologous to human PCDHAC2 (protocadherin alpha subfamily C, 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3,4-methylenedioxymethamphetamine; 6-propyl-2-thiouracil.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

cadherin-related neuronal receptor c2; protocadherin alpha c2; protocadherin alpha subfamily C 2; protocadherin alpha-C2; rCNRvc2

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Latest Assembly:

GRCr8 - GRCr8 Assembly

NCBI Annotation Information:

Genome Annotation Status: not in current annotation release

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8 Ensembl	18	28,855,256 - 29,120,227 (+)	Ensembl				GRCr8
mRatBN7.2 Ensembl	18	28,581,225 - 28,846,211 (+)	Ensembl				mRatBN7.2
Rnor_6.0	18	30,172,740 - 30,215,896 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	18	29,987,206 - 30,215,897 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	18	29,881,386 - 29,924,443 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	18	29,884,685 - 29,928,030 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	18	28,509,807 - 28,552,754 (+)	NCBI		Celera
RGSC_v3.1	18	29,911,330 - 29,954,676 (+)	NCBI
Cytogenetic Map	18	p11	NCBI

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autosomal dominant intellectual developmental disorder 31 (ISO)

familial adenomatous polyposis 1 (ISO)

Hereditary Neoplastic Syndromes (ISO)

Hirschsprung's disease (ISO)

Neurodevelopmental Disorders (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP)

3,4-methylenedioxymethamphetamine (EXP)

4,4'-sulfonyldiphenol (ISO)

6-propyl-2-thiouracil (EXP)

amiodarone (ISO)

amitrole (EXP)

ammonium chloride (EXP)

amosite asbestos (ISO)

arsenite(3-) (ISO)

benzo[a]pyrene (ISO)

benzo[b]fluoranthene (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

carbon nanotube (ISO)

CGP 52608 (ISO)

choline (ISO)

chrysene (ISO)

copper(II) sulfate (ISO)

crocidolite asbestos (ISO)

cyclosporin A (ISO)

dibenz[a,h]anthracene (ISO)

dioxygen (ISO)

ethanol (ISO)

ethylparaben (ISO)

folic acid (ISO)

furan (EXP)

gentamycin (EXP)

glyphosate (ISO)

L-methionine (ISO)

lead(0) (ISO)

lipopolysaccharide (ISO)

methimazole (EXP)

methylmercury chloride (ISO)

N-Nitrosopyrrolidine (ISO)

O-methyleugenol (ISO)

ozone (ISO)

paracetamol (EXP)

perfluorononanoic acid (ISO)

phenylmercury acetate (ISO)

serpentine asbestos (ISO)

sulfadimethoxine (EXP)

sunitinib (ISO)

tetrachloromethane (EXP)

tetraphene (ISO)

titanium dioxide (ISO)

tunicamycin (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cell adhesion (IEA)

homophilic cell adhesion via plasma membrane adhesion molecules (IEA)

serotonergic neuron axon guidance (ISO)

Cellular Component

membrane (IEA)

plasma membrane (IEA)

Molecular Function

calcium ion binding (IEA)

References

References - curated

#	Reference Title	Reference Citation
1.	GOA pipeline	RGD automated data pipeline
2.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
4.	Genomic sequence and organization of the family of CNR/Pcdhalpha genes in rat.	Yanase H, etal., Genomics 2004 Apr;83(4):717-26.

Additional References at PubMed

PMID:12508039	PMID:14672974	PMID:15744052	PMID:17110050

Genomics

Comparative Map Data

Pcdhac2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8 Ensembl	18	28,855,256 - 29,120,227 (+)	Ensembl				GRCr8
mRatBN7.2 Ensembl	18	28,581,225 - 28,846,211 (+)	Ensembl				mRatBN7.2
Rnor_6.0	18	30,172,740 - 30,215,896 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	18	29,987,206 - 30,215,897 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	18	29,881,386 - 29,924,443 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	18	29,884,685 - 29,928,030 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	18	28,509,807 - 28,552,754 (+)	NCBI		Celera
RGSC_v3.1	18	29,911,330 - 29,954,676 (+)	NCBI
Cytogenetic Map	18	p11	NCBI

PCDHAC2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	5	140,966,476 - 141,012,347 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	5	140,966,470 - 141,012,347 (+)	Ensembl			hg38	GRCh38
GRCh37	5	140,346,061 - 140,391,932 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	5	140,326,536 - 140,372,113 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	5	140,326,535 - 140,329,190	NCBI
Celera	5	136,422,531 - 136,468,708 (+)	NCBI		Celera
Cytogenetic Map	5	q31.3	NCBI
HuRef	5	135,490,462 - 135,536,628 (+)	NCBI		HuRef
CHM1_1	5	139,778,941 - 139,825,092 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	5	141,491,769 - 141,537,634 (+)	NCBI		T2T-CHM13v2.0

Pcdhac2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	18	37,276,731 - 37,320,716 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	18	37,276,556 - 37,320,710 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	18	37,143,678 - 37,187,663 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	18	37,143,503 - 37,187,657 (+)	Ensembl			mm10	GRCm38
MGSCv37	18	37,303,623 - 37,347,311 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	18	37,269,943 - 37,313,631 (+)	NCBI		MGSCv36	mm8
MGSCv36	18	37,331,075 - 37,374,763 (+)	NCBI		MGSCv36	mm8
Cytogenetic Map	18	B3	NCBI
cM Map	18	19.46	NCBI

PCDHAC2
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	5	142,445,483 - 142,448,709 (+)	NCBI	PanPan1.1	PanPan1.1	panPan2

LOC111089960
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	2	35,954,126 - 36,096,661 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	2	35,910,402 - 36,095,110 (+)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	2	32,989,113 - 33,114,899 (+)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha

LOC100621701
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	2	142,460,178 - 142,688,089 (+)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	2	142,477,627 - 142,687,684 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	2	148,423,053 - 148,427,771 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	1000
Count of miRNA genes:	249
Interacting mature miRNAs:	325
Transcripts:	ENSRNOT00000027340, ENSRNOT00000027343
Prediction methods:	Microtar, Miranda, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Markers in Region

WI-19540

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	18	28,845,892 - 28,846,156 (+)	MAPPER	mRatBN7.2
Rnor_6.0	18	30,215,579 - 30,215,842	NCBI	Rnor6.0
Rnor_5.0	18	29,924,126 - 29,924,389	UniSTS	Rnor5.0
RGSC_v3.4	18	29,927,713 - 29,927,976	UniSTS	RGSC3.4
Celera	18	28,552,437 - 28,552,700	UniSTS
Cytogenetic Map	18	p11	UniSTS

RH65516

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	18	28,845,204 - 28,845,379 (+)	MAPPER	mRatBN7.2
Rnor_6.0	18	30,214,891 - 30,215,065	NCBI	Rnor6.0
Rnor_5.0	18	29,923,438 - 29,923,612	UniSTS	Rnor5.0
RGSC_v3.4	18	29,927,025 - 29,927,199	UniSTS	RGSC3.4
Celera	18	28,551,749 - 28,551,923	UniSTS
Cytogenetic Map	18	p11	UniSTS

IB766

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	18	28,845,918 - 28,846,149 (+)	MAPPER	mRatBN7.2
Rnor_6.0	18	30,215,605 - 30,215,835	NCBI	Rnor6.0
Rnor_5.0	18	29,924,152 - 29,924,382	UniSTS	Rnor5.0
RGSC_v3.4	18	29,927,739 - 29,927,969	UniSTS	RGSC3.4
Celera	18	28,552,463 - 28,552,693	UniSTS
Cytogenetic Map	18	p11	UniSTS

PMC311048P1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	18	28,818,659 - 28,818,748 (+)	MAPPER	mRatBN7.2
Rnor_6.0	18	30,188,352 - 30,188,440	NCBI	Rnor6.0
Rnor_5.0	18	29,896,899 - 29,896,987	UniSTS	Rnor5.0
RGSC_v3.4	18	29,900,486 - 29,900,574	UniSTS	RGSC3.4
Celera	18	28,525,314 - 28,525,402	UniSTS
Cytogenetic Map	18	p11	UniSTS

RH91795

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	18	28,843,505 - 28,843,650 (+)	MAPPER	mRatBN7.2
Rnor_6.0	18	30,213,192 - 30,213,336	NCBI	Rnor6.0
Rnor_5.0	18	29,921,739 - 29,921,883	UniSTS	Rnor5.0
RGSC_v3.4	18	29,925,326 - 29,925,470	UniSTS	RGSC3.4
Celera	18	28,550,050 - 28,550,194	UniSTS
Cytogenetic Map	18	p11	UniSTS

PMC312645P1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	18	28,843,709 - 28,843,897 (+)	MAPPER	mRatBN7.2
Rnor_6.0	18	30,213,396 - 30,213,583	NCBI	Rnor6.0
Rnor_5.0	18	29,921,943 - 29,922,130	UniSTS	Rnor5.0
RGSC_v3.4	18	29,925,530 - 29,925,717	UniSTS	RGSC3.4
Celera	18	28,550,254 - 28,550,441	UniSTS
Cytogenetic Map	18	p11	UniSTS

UniSTS:547524

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	18	28,843,567 - 28,844,209 (+)	MAPPER	mRatBN7.2
Rnor_6.0	18	30,213,254 - 30,213,895	NCBI	Rnor6.0
Rnor_5.0	18	29,921,801 - 29,922,442	UniSTS	Rnor5.0
Celera	18	28,550,112 - 28,550,753	UniSTS
Cytogenetic Map	18	p11	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_201422	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AB113398	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC097339	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY573985	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000018	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

NM_201422 ⟹ NP_958825

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	18	30,172,740 - 30,215,896 (+)	NCBI
Rnor_5.0	18	29,881,386 - 29,924,443 (+)	NCBI
RGSC_v3.4	18	29,884,685 - 29,928,030 (+)	RGD
Celera	18	28,509,807 - 28,552,754 (+)	RGD

Protein Sequences


Protein RefSeqs	NP_958825	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAT77567	(Get FASTA)	NCBI Sequence Viewer
	BAD06380	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000027340.3

RefSeq Acc Id:	NP_958825 ⟸ NM_201422
- Peptide Label:	precursor
- UniProtKB:	Q767H7 (UniProtKB/TrEMBL)

Protein Domains

Cadherin

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:735216	AgrOrtholog
Ensembl Genes	ENSRNOG00000020119	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000027340.6	UniProtKB/TrEMBL
Gene3D-CATH	Cadherins	UniProtKB/TrEMBL
InterPro	Cadherin	UniProtKB/TrEMBL
	Cadherin-like	UniProtKB/TrEMBL
	Cadherin_C	UniProtKB/TrEMBL
	Cadherin_CBD	UniProtKB/TrEMBL
	Cadherin_CS	UniProtKB/TrEMBL
	Cadherin_N	UniProtKB/TrEMBL
	Protocadherin/Cadherin-CA	UniProtKB/TrEMBL
NCBI Gene	393092	ENTREZGENE
PANTHER	CADHERIN-87A	UniProtKB/TrEMBL
	PTHR24028:SF119	UniProtKB/TrEMBL
Pfam	Cadherin	UniProtKB/TrEMBL
	Cadherin_2	UniProtKB/TrEMBL
	Cadherin_C_2	UniProtKB/TrEMBL
	Cadherin_tail	UniProtKB/TrEMBL
PhenoGen	Pcdhac2	PhenoGen
PRINTS	CADHERIN	UniProtKB/TrEMBL
PROSITE	CADHERIN_1	UniProtKB/TrEMBL
	CADHERIN_2	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000020119	RatGTEx
SMART	SM00112	UniProtKB/TrEMBL
Superfamily-SCOP	Cadherin	UniProtKB/TrEMBL
UniProt	Q767H7	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2005-10-12	Pcdhac2				Symbol and Name status set to provisional	70820	PROVISIONAL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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