Pcdhgc5 (protocadherin gamma subfamily C, 5) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Pcdhgc5 (protocadherin gamma subfamily C, 5) Mus musculus
Analyze
Symbol: Pcdhgc5
Name: protocadherin gamma subfamily C, 5
RGD ID: 1623077
MGI Page MGI
Description: Acts upstream of or within negative regulation of neuron apoptotic process and synapse organization. Located in membrane. Is expressed in brain and cerebellum. Orthologous to human PCDHGC5 (protocadherin gamma subfamily C, 5).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: protocadherin gamma-C5
RGD Orthologs
Human
Rat
Dog
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,952,599 - 37,974,926 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1837,952,566 - 37,974,926 (+)EnsemblGRCm39 Ensembl
GRCm381837,819,546 - 37,841,873 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1837,819,513 - 37,841,873 (+)EnsemblGRCm38mm10GRCm38
MGSCv371837,979,200 - 38,001,527 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361837,945,520 - 37,967,847 (+)NCBIMGSCv36mm8
Celera1839,163,021 - 39,185,352 (+)NCBICelera
Cytogenetic Map18B3NCBI
cM Map1819.69NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10380929   PMID:10716726   PMID:11230163   PMID:12154121   PMID:12477932   PMID:15347688   PMID:15964765   PMID:19029045   PMID:19843561   PMID:21873635   PMID:22884324   PMID:23515096  
PMID:26386307   PMID:30377227   PMID:32633719   PMID:33653874  


Genomics

Comparative Map Data
Pcdhgc5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,952,599 - 37,974,926 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1837,952,566 - 37,974,926 (+)EnsemblGRCm39 Ensembl
GRCm381837,819,546 - 37,841,873 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1837,819,513 - 37,841,873 (+)EnsemblGRCm38mm10GRCm38
MGSCv371837,979,200 - 38,001,527 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361837,945,520 - 37,967,847 (+)NCBIMGSCv36mm8
Celera1839,163,021 - 39,185,352 (+)NCBICelera
Cytogenetic Map18B3NCBI
cM Map1819.69NCBI
PCDHGC5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385141,489,081 - 141,512,975 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5141,489,081 - 141,512,975 (+)EnsemblGRCh38hg38GRCh38
GRCh375140,868,648 - 140,892,542 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,848,992 - 140,872,730 (+)NCBINCBI36Build 36hg18NCBI36
Build 345140,848,991 - 140,851,628NCBI
Celera5136,945,627 - 136,969,282 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5136,013,646 - 136,037,386 (+)NCBIHuRef
CHM1_15140,302,073 - 140,325,823 (+)NCBICHM1_1
T2T-CHM13v2.05142,015,052 - 142,038,959 (+)NCBIT2T-CHM13v2.0
Pcdhgc5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81829,898,430 - 29,917,566 (+)NCBIGRCr8
mRatBN7.21829,647,201 - 29,666,336 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1829,493,954 - 29,667,868 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1829,751,531 - 29,770,661 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01830,513,479 - 30,532,641 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01829,848,818 - 29,867,982 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01830,964,402 - 30,969,584 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01830,660,087 - 30,660,536 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41830,752,227 - 30,752,676 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1829,291,177 - 29,310,425 (+)NCBICelera
Cytogenetic Map18p11NCBI
LOC478038
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1236,297,841 - 36,481,900 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl236,316,678 - 36,480,278 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha233,339,711 - 33,533,913 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0236,742,430 - 36,935,809 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl236,832,245 - 36,838,095 (+)EnsemblROS_Cfam_1.0 Ensembl
ROS_Cfam_1.0 Ensembl236,761,461 - 36,935,806 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1233,816,473 - 34,010,677 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0234,627,480 - 34,822,204 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0235,435,129 - 35,629,409 (+)NCBIUU_Cfam_GSD_1.0

Variants

.
Variants in Pcdhgc5
560 total Variants

QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
27226723Tibw9_mtibia width 9, proximal, 16 week (mouse)18320000060933072Mouse
1558849W3q15_mweight 3 weeks QTL 15 (mouse)Not determined18504111961272643Mouse
1558873Hrtfm7_mheart failure modifier 7 (mouse)Not determined18808696442087106Mouse
13504732Cath6_mcarotid atherosclerosis 6 (mouse)181363712647637126Mouse
1357603Mom3_mmodifier of Min 3 (mouse)Not determined181403002367098962Mouse
1300994Pvcan3_mprotection against vaginal candidiasis 3 (mouse)Not determined181619964050199776Mouse
1301307Phospq1_mphospholipid QTL 1 (mouse)Not determined181813970452139859Mouse
1300638Im7_mimmunoregulatory 7 (mouse)Not determined181901887453018992Mouse
1558743Kcal1_mkilocalorie 1 (mouse)Not determined181901887453018992Mouse
11532709Sluc41_msusceptibility to lung cancer 41 (mouse)182095369457590708Mouse
13463476Hctq8_mhematocrit QTL 8 (mouse)182121758055217727Mouse
1300877Adip8_madiposity 8 (mouse)Not determined182261991456620127Mouse
11532710Sluc41a_msusceptibility to lung cancer 41a (mouse)182261991456620127Mouse
11532715Sluc41b_msusceptibility to lung cancer 41b (mouse)182261991456620127Mouse
11532716Sluc41c_msusceptibility to lung cancer 41c (mouse)182261991456620127Mouse
1301570Sluc14_msusceptibility to lung cancer 14 (mouse)Not determined182261991456620127Mouse
4142031Moen1_mmodifier of engrailed QTL 1 (mouse)Not determined182411556058115730Mouse
25823173Hrsq12_mhost response to SARS QTL 12, hemorrhage (mouse)182489588178339555Mouse
12904950Smmq3_msoleus muscle mass QTL 3 (mouse)182605687560056875Mouse
25823167Hrsq5_mhost response to SARS QTL 5, D3% weight (mouse)182724111558827077Mouse
25823171Hrsq10_mhost response to SARS QTL 10, D4% weight (mouse)182724111558827077Mouse
25823174Hrsq11_mhost response to SARS QTL 11, log titer (mouse)182724111558827077Mouse
1301400Lmr13_mleishmaniasis resistance 13 (mouse)Not determined182810938062109518Mouse
4141857Mhysq5_mmale hybrid sterility QTL 5 (mouse)Not determined2813060462130739Mouse
1302163Bmd16_mbone mineral density 16 (mouse)Not determined182966791463668060Mouse
12880412V125Dq12_mvitamin D active form serum level QTL 12 (mouse)183023306764233067Mouse
1300685Scc5_mcolon tumor susceptibility 5 (mouse)Not determined183198848065988629Mouse
1357690Vtbt19_mvertebral trabecular bone trait 19 (mouse)Not determined183309104367091221Mouse
1301771Pcyts6_mplasmacytoma susceptibility 6 (mouse)Not determined183565863269658851Mouse
11041903Lmr27_mleishmaniasis resistance 27 (mouse)183618756745109518Mouse
4142366Chlq10_mcirculating hormone level QTL 10 (mouse)Not determined183629102270291180Mouse

Markers in Region
RH136252  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381837,818,336 - 37,818,532UniSTSGRCm38
MGSCv371837,977,990 - 37,978,186UniSTSGRCm37
Celera1839,161,811 - 39,162,007UniSTS
Cytogenetic Map18CUniSTS
Cytogenetic Map18B3UniSTS
cM Map1818.0UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000055935   ⟹   ENSMUSP00000060949
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1837,952,566 - 37,974,926 (+)Ensembl
GRCm38.p6 Ensembl1837,819,513 - 37,841,873 (+)Ensembl
RefSeq Acc Id: ENSMUST00000192875
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1837,952,707 - 37,973,217 (+)Ensembl
GRCm38.p6 Ensembl1837,819,654 - 37,840,164 (+)Ensembl
RefSeq Acc Id: ENSMUST00000193890   ⟹   ENSMUSP00000142214
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1837,952,605 - 37,973,104 (+)Ensembl
GRCm38.p6 Ensembl1837,819,552 - 37,840,051 (+)Ensembl
RefSeq Acc Id: ENSMUST00000193941   ⟹   ENSMUSP00000141256
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1837,952,619 - 37,973,253 (+)Ensembl
GRCm38.p6 Ensembl1837,819,566 - 37,840,200 (+)Ensembl
RefSeq Acc Id: NM_033583   ⟹   NP_291061
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391837,952,599 - 37,974,926 (+)NCBI
GRCm381837,819,546 - 37,841,873 (+)ENTREZGENE
MGSCv371837,979,200 - 38,001,527 (+)RGD
Celera1839,163,021 - 39,185,352 (+)RGD
cM Map18 ENTREZGENE
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_291061   ⟸   NM_033583
- Peptide Label: precursor
- UniProtKB: Q91XW9 (UniProtKB/TrEMBL),   Q8K4A2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000142214   ⟸   ENSMUST00000193890
RefSeq Acc Id: ENSMUSP00000141256   ⟸   ENSMUST00000193941
RefSeq Acc Id: ENSMUSP00000060949   ⟸   ENSMUST00000055935
Protein Domains
Cadherin   Cadherin C-terminal catenin-binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q91XW9-F1-model_v2 AlphaFold Q91XW9 1-944 view protein structure

Promoters
RGD ID:13677598
Promoter ID:EPDNEW_M22948
Type:initiation region
Name:Pcdhgc5_1
Description:Mus musculus protocadherin gamma subfamily C, 5 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381837,819,551 - 37,819,611EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1935205 AgrOrtholog
Ensembl Genes ENSMUSG00000102543 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000055935 ENTREZGENE
  ENSMUST00000055935.11 UniProtKB/TrEMBL
  ENSMUST00000193890.2 UniProtKB/TrEMBL
  ENSMUST00000193941.2 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
KEGG Report mmu:93708 UniProtKB/TrEMBL
MGD MGI:1935205 ENTREZGENE
NCBI Gene 93708 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/TrEMBL
  PROTOCADHERIN GAMMA-C5 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
  Cadherin_C_2 UniProtKB/TrEMBL
  Cadherin_tail UniProtKB/TrEMBL
PhenoGen Pcdhgc5 PhenoGen
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin UniProtKB/TrEMBL
UniProt A0A0A6YVT4_MOUSE UniProtKB/TrEMBL
  A0A0A6YXZ9_MOUSE UniProtKB/TrEMBL
  Q8K4A2 ENTREZGENE, UniProtKB/TrEMBL
  Q91XW9 ENTREZGENE, UniProtKB/TrEMBL