Pcdhb17 (protocadherin beta 17) - Rat Genome Database

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Gene: Pcdhb17 (protocadherin beta 17) Rattus norvegicus
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Symbol: Pcdhb17
Name: protocadherin beta 17
RGD ID: 1549775
Description: Predicted to enable calcium ion binding activity. Predicted to be involved in homophilic cell adhesion via plasma membrane adhesion molecules.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: protocadherin beta-16; protocadherin beta-18
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81829,470,868 - 29,475,832 (+)NCBIGRCr8
mRatBN7.21829,196,858 - 29,201,822 (+)NCBImRatBN7.2mRatBN7.2
Rnor_6.01830,565,817 - 30,570,184 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01830,267,062 - 30,278,519 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41830,296,770 - 30,299,187 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1828,891,967 - 28,896,334 (+)NCBICelera
Cytogenetic Map18p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model



Biological Process

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Pcdhb17Ratcell adhesion involved_inIBAMGI:106671 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033
Pcdhb17Ratcell adhesion involved_inIEAInterPro:IPR0208941600115GO_REF:0000002InterProGO_REF:0000002
Pcdhb17Ratcell adhesion involved_inIEAUniProtKB-KW:KW-01301600115GO_REF:0000043UniProtGO_REF:0000043
Pcdhb17Rathomophilic cell adhesion via plasma membrane adhesion molecules involved_inIEAInterPro:IPR0021261600115GO_REF:0000002InterProGO_REF:0000002

Cellular Component

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Pcdhb17Ratmembrane located_inIEAUniProtKB-SubCell:SL-01621600115GO_REF:0000044UniProtGO_REF:0000044
Pcdhb17Ratmembrane located_inIEAInterPro:IPR002126 and InterPro:IPR0159191600115GO_REF:0000002InterProGO_REF:0000002
Pcdhb17Ratmembrane located_inIEAUniProtKB-KW:KW-04721600115GO_REF:0000043UniProtGO_REF:0000043
Pcdhb17Ratplasma membrane located_inIEAInterPro:IPR0208941600115GO_REF:0000002InterProGO_REF:0000002
Pcdhb17Ratplasma membrane is_active_inIBAMGI:106671 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033
Pcdhb17Ratplasma membrane located_inIEAUniProtKB-KW:KW-10031600115GO_REF:0000043UniProtGO_REF:0000043

Molecular Function

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Pcdhb17Ratcalcium ion binding enablesIEAUniRule:UR0004134501600115GO_REF:0000104UniProtGO_REF:0000104
Pcdhb17Ratcalcium ion binding enablesIEAInterPro:IPR002126 and InterPro:IPR0159191600115GO_REF:0000002InterProGO_REF:0000002


#
Reference Title
Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
3. Multiple variable first exons: a mechanism for cell- and tissue-specific gene regulation. Zhang T, etal., Genome Res 2004 Jan;14(1):79-89. Epub 2003 Dec 12.
PMID:10650949   PMID:15744052   PMID:21873635  



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Variants in Pcdhb17
29 total Variants

Predicted Target Of
Summary Value
Count of predictions:117
Count of miRNA genes:108
Interacting mature miRNAs:113
Transcripts:ENSRNOT00000040998
Prediction methods:Microtar, 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.


1 to 10 of 36 rows
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
1331733Bp233Blood pressure QTL 2333.97196arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182479697779788953Rat
1358358Sradr6Stress Responsive Adrenal Weight QTL 62.49adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)181194429959330563Rat
1331735Rf44Renal function QTL 442.981urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)181823456431359530Rat
61382Bp46Blood pressure QTL 4618.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194179131393320Rat
2301413Bp318Blood pressure QTL 3180.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182654808246969551Rat
1331741Bp232Blood pressure QTL 2323.59112arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182137289383213037Rat
61388Bp2Blood pressure QTL 23.23arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)18135374722Rat
6903359Bp355Blood pressure QTL 3553.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194454459796478Rat
12904668Bw188Body weight QTL 1880.03body mass (VT:0001259)body weight (CMO:0000012)182654808246969551Rat
2313082Bss85Bone structure and strength QTL 850.80.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)181495133759951337Rat

1 to 10 of 36 rows
PMC311048P5  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81829,466,547 - 29,466,663 (+)Marker Load Pipeline
mRatBN7.21829,192,537 - 29,192,652 (+)MAPPERmRatBN7.2
Rnor_6.01830,562,185 - 30,562,299NCBIRnor6.0
Rnor_5.01830,269,380 - 30,269,494UniSTSRnor5.0
RGSC_v3.41830,296,777 - 30,296,891UniSTSRGSC3.4
Celera1828,888,335 - 28,888,449UniSTS
Cytogenetic Map18p11UniSTS







RefSeq Acc Id: NM_001408905   ⟹   NP_001395834
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81829,470,868 - 29,475,832 (+)NCBI
mRatBN7.21829,196,858 - 29,201,822 (+)NCBI
Protein RefSeqs NP_001395834 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL76355 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000083136.1
RefSeq Acc Id: NP_001395834   ⟸   NM_001408905
- Peptide Label: precursor
- UniProtKB: A6J374 (UniProtKB/TrEMBL),   A0A8I5ZYQ9 (UniProtKB/TrEMBL)
Cadherin


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



1 to 25 of 25 rows
Database
Acc Id
Source(s)
BioCyc Gene G2FUF-7824 BioCyc
Ensembl Genes ENSRNOG00000039470 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000060486.3 UniProtKB/TrEMBL
Gene3D-CATH Cadherins UniProtKB/TrEMBL
InterPro Cadherin-like_dom UniProtKB/TrEMBL
  Cadherin-like_sf UniProtKB/TrEMBL
  Cadherin_C UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
  Cadherin_N UniProtKB/TrEMBL
  Protocadherin/Cadherin-CA UniProtKB/TrEMBL
NCBI Gene 548104 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/TrEMBL
  PROTOCADHERIN BETA-10 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
  Cadherin_C_2 UniProtKB/TrEMBL
PhenoGen Pcdhb17 PhenoGen
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000039470 RatGTEx
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin-like UniProtKB/TrEMBL
UniProt A0A8I5ZYQ9 ENTREZGENE, UniProtKB/TrEMBL
  A6J374 ENTREZGENE, UniProtKB/TrEMBL
1 to 25 of 25 rows


Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-09-15 Pcdhb17  protocadherin beta 17      Symbol and Name status set to provisional 70820 PROVISIONAL