Pcdhb2 (protocadherin beta 2) - Rat Genome Database

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Gene: Pcdhb2 (protocadherin beta 2) Rattus norvegicus
Analyze
Symbol: Pcdhb2
Name: protocadherin beta 2
RGD ID: 1563132
Description: Predicted to enable calcium ion binding activity. Predicted to be involved in cell adhesion. Predicted to be located in plasma membrane. Orthologous to human PCDHB2 (protocadherin beta 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; copper atom.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC498843; protocadherin beta-2; RGD1563132; similar to protocadherin beta 2
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81829,280,004 - 29,282,790 (+)NCBIGRCr8
mRatBN7.21829,005,996 - 29,008,782 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1829,005,996 - 29,008,782 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1829,133,124 - 29,135,910 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01829,895,186 - 29,897,972 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01829,230,419 - 29,233,205 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01830,375,798 - 30,378,194 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1830,375,798 - 30,378,194 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01830,083,426 - 30,085,822 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41830,104,780 - 30,107,179 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1828,708,489 - 28,710,888 (+)NCBICelera
Cytogenetic Map18p11NCBI
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. 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. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Pcdhb2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81829,280,004 - 29,282,790 (+)NCBIGRCr8
mRatBN7.21829,005,996 - 29,008,782 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1829,005,996 - 29,008,782 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1829,133,124 - 29,135,910 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01829,895,186 - 29,897,972 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01829,230,419 - 29,233,205 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01830,375,798 - 30,378,194 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1830,375,798 - 30,378,194 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01830,083,426 - 30,085,822 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41830,104,780 - 30,107,179 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1828,708,489 - 28,710,888 (+)NCBICelera
Cytogenetic Map18p11NCBI
PCDHB2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385141,094,615 - 141,098,703 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5141,094,606 - 141,098,703 (+)EnsemblGRCh38hg38GRCh38
GRCh375140,474,199 - 140,478,287 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,454,421 - 140,457,148 (+)NCBINCBI36Build 36hg18NCBI36
Build 345140,454,420 - 140,457,146NCBI
Celera5136,551,049 - 136,553,776 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5135,618,927 - 135,621,654 (+)NCBIHuRef
CHM1_15139,907,425 - 139,910,152 (+)NCBICHM1_1
T2T-CHM13v2.05141,619,933 - 141,624,021 (+)NCBIT2T-CHM13v2.0
Pcdhb2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,427,893 - 37,430,667 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1837,427,865 - 37,430,677 (+)EnsemblGRCm39 Ensembl
GRCm381837,294,840 - 37,297,614 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1837,294,812 - 37,297,624 (+)EnsemblGRCm38mm10GRCm38
MGSCv371837,454,494 - 37,457,268 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361837,420,950 - 37,423,349 (+)NCBIMGSCv36mm8
Celera1838,640,177 - 38,642,951 (+)NCBICelera
Cytogenetic Map18B3NCBI
cM Map1819.46NCBI
PCDHB2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v24136,346,100 - 136,356,554 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan15134,485,646 - 134,496,106 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v05136,458,253 - 136,463,369 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15142,572,502 - 142,575,025 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5142,572,690 - 142,574,838 (+)Ensemblpanpan1.1panPan2
LOC106557817
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1236,157,839 - 36,161,560 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha233,210,137 - 33,213,518 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0236,612,776 - 36,616,157 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1233,687,167 - 33,690,547 (+)NCBIUMICH_Zoey_3.1
UU_Cfam_GSD_1.0235,305,504 - 35,308,914 (+)NCBIUU_Cfam_GSD_1.0
Pcdhb2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213151,500,823 - 151,504,890 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493650413,076,299 - 13,078,692 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493650413,076,176 - 13,078,824 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
Pcdhb2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624774377,247 - 382,096 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pcdhb2
6 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:105
Count of miRNA genes:94
Interacting mature miRNAs:96
Transcripts:ENSRNOT00000060497
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2312598Bp340Blood pressure QTL 3400.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)18130558703Rat
2300180Bmd67Bone mineral density QTL 674.80.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)18134291613Rat
2293661Bss50Bone structure and strength QTL 504.640.0003lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)18134291613Rat
61388Bp2Blood pressure QTL 23.23arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)18135374722Rat
9589153Insul31Insulin level QTL 317.150.05blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)18142547119Rat
2299160Iddm35Insulin dependent diabetes mellitus QTL 352.79blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)18420794160377792Rat
2312568Glom21Glomerulus QTL 2120.005kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)18518585840503530Rat
2293708Bss46Bone structure and strength QTL 468.80.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)181179151863636873Rat
1578661Bss20Bone structure and strength QTL 203.7femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)181179151883218561Rat
1578667Bss21Bone structure and strength QTL 213.5femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)181179151883218561Rat
61382Bp46Blood pressure QTL 4618.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194179131393320Rat
631264Scl22Serum cholesterol level QTL 226.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)181194179131393320Rat
1331766Bp236Blood pressure QTL 2363.022arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181194429931359530Rat
61375Bp41Blood pressure QTL 412.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)181194429941122201Rat
1331753Bp231Blood pressure QTL 2313.643arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194429952293055Rat
1358358Sradr6Stress Responsive Adrenal Weight QTL 62.49adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)181194429959330563Rat
6903359Bp355Blood pressure QTL 3553.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194454459796478Rat
2313082Bss85Bone structure and strength QTL 850.80.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)181495133759951337Rat
1358193Emca2Estrogen-induced mammary cancer QTL 21.6mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)181800759963571040Rat
1331735Rf44Renal function QTL 442.981urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)181823456431359530Rat
1331775Bp235Blood pressure QTL 2353.201arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181823456431359530Rat
1600373Mamtr6Mammary tumor resistance QTL 6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)181927890183218561Rat
1331741Bp232Blood pressure QTL 2323.59112arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182137289383213037Rat
1641923Colcr8Colorectal carcinoma resistance QTL 83.10.0014intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)182206624252293055Rat
1331733Bp233Blood pressure QTL 2333.97196arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182479697779788953Rat
2325839Bp348Blood pressure QTL 3480.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182557098570570985Rat
12904673Cm127Cardiac mass QTL 1270.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)182654808246969551Rat
12904675Am19Aortic mass QTL 190.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)182654808246969551Rat
12904677Kidm72Kidney mass QTL 720.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)182654808246969551Rat
12904668Bw188Body weight QTL 1880.03body mass (VT:0001259)body weight (CMO:0000012)182654808246969551Rat
12904669Cm125Cardiac mass QTL 1250.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)182654808246969551Rat
12904670Cm126Cardiac mass QTL 1260.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)182654808246969551Rat
2301413Bp318Blood pressure QTL 3180.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182654808246969551Rat
2293704Bss35Bone structure and strength QTL 354.590.0002femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)182896485373964853Rat
2300157Bmd66Bone mineral density QTL 6613.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)182896485373964853Rat
2300177Bmd65Bone mineral density QTL 6519.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)182896485373964853Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium
Low 17 2 8 6 7 66 28 33 10 6
Below cutoff 3 25 35 23 9 23 2 4 6 6 3 1 2

Sequence


RefSeq Acc Id: ENSRNOT00000060497   ⟹   ENSRNOP00000057239
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1829,005,996 - 29,008,782 (+)Ensembl
Rnor_6.0 Ensembl1830,375,798 - 30,378,194 (+)Ensembl
RefSeq Acc Id: NM_001109123   ⟹   NP_001102593
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81829,280,004 - 29,282,790 (+)NCBI
mRatBN7.21829,005,996 - 29,008,782 (+)NCBI
Rnor_6.01830,375,798 - 30,378,194 (+)NCBI
Rnor_5.01830,083,426 - 30,085,822 (+)NCBI
RGSC_v3.41830,104,780 - 30,107,179 (+)RGD
Celera1828,708,489 - 28,710,888 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102593 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL76340 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000057239
  ENSRNOP00000057239.3
RefSeq Acc Id: NP_001102593   ⟸   NM_001109123
- Peptide Label: precursor
- UniProtKB: F1M7D0 (UniProtKB/TrEMBL),   A6J358 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000057239   ⟸   ENSRNOT00000060497
Protein Domains
Cadherin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M7D0-F1-model_v2 AlphaFold F1M7D0 1-798 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:1563132 AgrOrtholog
BioCyc Gene G2FUF-7842 BioCyc
Ensembl Genes ENSRNOG00000039476 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000060497 ENTREZGENE
  ENSRNOT00000060497.3 UniProtKB/TrEMBL
Gene3D-CATH Cadherins UniProtKB/TrEMBL
InterPro Cadherin UniProtKB/TrEMBL
  Cadherin-like UniProtKB/TrEMBL
  Cadherin_C UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
  Cadherin_N UniProtKB/TrEMBL
KEGG Report rno:498843 UniProtKB/TrEMBL
NCBI Gene 498843 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/TrEMBL
  PTHR24028:SF281 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
  Cadherin_C_2 UniProtKB/TrEMBL
PhenoGen Pcdhb2 PhenoGen
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000039476 RatGTEx
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin UniProtKB/TrEMBL
UniProt A6J358 ENTREZGENE, UniProtKB/TrEMBL
  F1M7D0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-19 Pcdhb2  protocadherin beta 2  RGD1563132_predicted  similar to protocadherin beta 2 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1563132_predicted  similar to protocadherin beta 2 (predicted)  LOC498843  similar to protocadherin beta 2  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498843  similar to protocadherin beta 2      Symbol and Name status set to provisional 70820 PROVISIONAL