Pcdh8 (protocadherin 8) - Rat Genome Database

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Gene: Pcdh8 (protocadherin 8) Rattus norvegicus
Analyze
Symbol: Pcdh8
Name: protocadherin 8
RGD ID: 69350
Description: Predicted to enable calcium ion binding activity. Involved in chemical synaptic transmission; modulation of chemical synaptic transmission; and regulation of synaptic membrane adhesion. Is active in Schaffer collateral - CA1 synapse; glutamatergic synapse; and postsynaptic membrane. Orthologous to human PCDH8 (protocadherin 8); INTERACTS WITH 1,3-dinitrobenzene; 2,2',4,4'-Tetrabromodiphenyl ether; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: activity-regulated cadherin-like protein; Arcadlin; protocadherin-8
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81561,607,521 - 61,612,090 (-)NCBIGRCr8
mRatBN7.21555,198,470 - 55,203,039 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1555,198,459 - 55,205,872 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1559,313,542 - 59,317,323 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01560,431,918 - 60,435,699 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01557,256,791 - 57,260,575 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01562,196,469 - 62,201,498 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1562,197,060 - 62,200,837 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01565,856,803 - 65,861,374 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41561,056,994 - 61,060,741 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11561,072,773 - 61,076,521 (-)NCBI
Celera1554,773,168 - 54,776,945 (-)NCBICelera
Cytogenetic Map15q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
9. Arcadlin is a neural activity-regulated cadherin involved in long term potentiation. Yamagata K, etal., J Biol Chem 1999 Jul 2;274(27):19473-1979.
10. Activity-induced protocadherin arcadlin regulates dendritic spine number by triggering N-cadherin endocytosis via TAO2beta and p38 MAP kinases. Yasuda S, etal., Neuron. 2007 Nov 8;56(3):456-71. doi: 10.1016/j.neuron.2007.08.020.
Additional References at PubMed
PMID:12477932   PMID:12591245   PMID:31981722  


Genomics

Comparative Map Data
Pcdh8
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81561,607,521 - 61,612,090 (-)NCBIGRCr8
mRatBN7.21555,198,470 - 55,203,039 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1555,198,459 - 55,205,872 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1559,313,542 - 59,317,323 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01560,431,918 - 60,435,699 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01557,256,791 - 57,260,575 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01562,196,469 - 62,201,498 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1562,197,060 - 62,200,837 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01565,856,803 - 65,861,374 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41561,056,994 - 61,060,741 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11561,072,773 - 61,076,521 (-)NCBI
Celera1554,773,168 - 54,776,945 (-)NCBICelera
Cytogenetic Map15q12NCBI
PCDH8
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381352,842,889 - 52,848,640 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1352,842,889 - 52,848,641 (-)EnsemblGRCh38hg38GRCh38
GRCh371353,417,024 - 53,422,775 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361352,316,110 - 52,320,775 (-)NCBINCBI36Build 36hg18NCBI36
Build 341352,316,111 - 52,320,775NCBI
Celera1334,403,981 - 34,408,646 (-)NCBICelera
Cytogenetic Map13q14.3NCBI
HuRef1334,132,296 - 34,136,846 (-)NCBIHuRef
CHM1_11353,386,066 - 53,390,732 (-)NCBICHM1_1
T2T-CHM13v2.01352,058,334 - 52,064,085 (-)NCBIT2T-CHM13v2.0
Pcdh8
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391480,004,224 - 80,008,752 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1480,004,215 - 80,008,752 (-)EnsemblGRCm39 Ensembl
GRCm381479,766,772 - 79,771,312 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1479,766,775 - 79,771,312 (-)EnsemblGRCm38mm10GRCm38
MGSCv371480,166,582 - 80,171,119 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361478,500,948 - 78,505,388 (-)NCBIMGSCv36mm8
Celera1477,267,150 - 77,271,687 (-)NCBICelera
Cytogenetic Map14D3NCBI
cM Map1442.76NCBI
Pcdh8
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540450,403,752 - 50,413,264 (-)NCBIChiLan1.0ChiLan1.0
LOC100983617
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21454,183,685 - 54,188,750 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11352,827,777 - 52,833,666 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01333,880,543 - 33,886,243 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11352,687,943 - 52,692,601 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1352,688,522 - 52,692,399 (-)Ensemblpanpan1.1panPan2
PCDH8
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1229,860,590 - 9,865,298 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl229,860,827 - 9,865,412 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha229,857,555 - 9,862,239 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02210,085,702 - 10,090,390 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2210,085,937 - 10,090,183 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1229,782,421 - 9,787,104 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0229,832,472 - 9,837,157 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0229,847,219 - 9,851,906 (-)NCBIUU_Cfam_GSD_1.0
LOC101972150
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945151,178,242 - 151,182,890 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936667716,625 - 721,503 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936667716,802 - 721,441 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC100155738
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1126,127,401 - 26,132,123 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11126,127,398 - 26,133,481 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21126,882,342 - 26,887,069 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PCDH8
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1330,602,449 - 30,610,656 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl330,602,321 - 30,606,926 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605713,206,860 - 13,211,564 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pcdh8
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474814,285,475 - 14,290,166 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474814,285,553 - 14,290,236 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pcdh8
17 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:33
Count of miRNA genes:33
Interacting mature miRNAs:33
Transcripts:ENSRNOT00000017599
Prediction methods:Miranda, Rnahybrid
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
724545Niddm54Non-insulin dependent diabetes mellitus QTL 540.02blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)155079449473699215Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153361105871477291Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153361105871477291Rat
2317050Aia24Adjuvant induced arthritis QTL 242.06joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)155284790873690657Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)154063126898288169Rat
1576315Schws6Schwannoma susceptibility QTL 60.0069nervous system integrity trait (VT:0010566)post-insult time of death (CMO:0002005)155380615298806152Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
152025253Hrtrt24Heart rate QTL 243.82heart pumping trait (VT:2000009)152788577486257085Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)153405413979054139Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat

Markers in Region
42.MMHAP38FLF6.seq  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21555,199,005 - 55,199,187 (+)MAPPERmRatBN7.2
Rnor_6.01562,197,005 - 62,197,186NCBIRnor6.0
Rnor_5.01565,857,339 - 65,857,520UniSTSRnor5.0
RGSC_v3.41561,056,939 - 61,057,120UniSTSRGSC3.4
Celera1554,773,113 - 54,773,294UniSTS
Cytogenetic Map15q12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
7 3 12 109 42 25 22 8 22 2 112 35 93 45 54 3

Sequence


Ensembl Acc Id: ENSRNOT00000017599   ⟹   ENSRNOP00000017599
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1555,198,459 - 55,205,872 (-)Ensembl
Rnor_6.0 Ensembl1562,197,060 - 62,200,837 (-)Ensembl
RefSeq Acc Id: NM_001411975   ⟹   NP_001398904
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81561,607,521 - 61,612,090 (-)NCBI
mRatBN7.21555,198,470 - 55,203,039 (-)NCBI
RefSeq Acc Id: NM_022868   ⟹   NP_074059
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81561,607,521 - 61,612,090 (-)NCBI
mRatBN7.21555,198,470 - 55,203,039 (-)NCBI
Rnor_6.01562,197,060 - 62,200,837 (-)NCBI
Rnor_5.01565,856,803 - 65,861,374 (-)NCBI
RGSC_v3.41561,056,994 - 61,060,741 (-)RGD
Celera1554,773,168 - 54,776,945 (-)RGD
Sequence:
RefSeq Acc Id: NP_074059   ⟸   NM_022868
- Peptide Label: isoform 2 precursor
- UniProtKB: A6HU10 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000017599   ⟸   ENSRNOT00000017599
RefSeq Acc Id: NP_001398904   ⟸   NM_001411975
- Peptide Label: isoform 1 precursor
- UniProtKB: D3ZE55 (UniProtKB/Swiss-Prot),   A1A5N4 (UniProtKB/Swiss-Prot),   Q9WVR2 (UniProtKB/Swiss-Prot)
Protein Domains
Cadherin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZE55-F1-model_v2 AlphaFold D3ZE55 1-1069 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69350 AgrOrtholog
BioCyc Gene G2FUF-12983 BioCyc
Ensembl Genes ENSRNOG00000013101 Ensembl, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000017599.4 UniProtKB/Swiss-Prot
Gene3D-CATH Cadherins UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:8362872 IMAGE-MGC_LOAD
InterPro Cadherin-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Protocadherin/Cadherin-CA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:64865 UniProtKB/Swiss-Prot
MGC_CLONE MGC:156642 IMAGE-MGC_LOAD
NCBI Gene 64865 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTOCADHERIN-8 UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
Pfam Cadherin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pcdh8 PhenoGen
PRINTS CADHERIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000013101 RatGTEx
SMART SM00112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Cadherin-like UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
TIGR TC232455
UniProt A1A5N4 ENTREZGENE
  A6HU10 ENTREZGENE, UniProtKB/TrEMBL
  D3ZE55 ENTREZGENE, UniProtKB/Swiss-Prot
  Q9WVR2 ENTREZGENE
UniProt Secondary A1A5N4 UniProtKB/Swiss-Prot
  Q9WVR2 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Pcdh8  protocadherin 8      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains six cadherin repeats 68758
gene_expression expressed in synapses 68758
gene_protein 972 amino acids; 103.7 kDa, 68758
gene_regulation induced in hippocampal granule cells by seizures, and by N-methyl-D-aspartate-dependent synaptic activity in long term potentiation 68758