Pcdhb6 (protocadherin beta 6) - Rat Genome Database

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Gene: Pcdhb6 (protocadherin beta 6) Rattus norvegicus
Analyze
Symbol: Pcdhb6
Name: protocadherin beta 6
RGD ID: 1306123
Description: Predicted to enable calcium ion binding activity and identical protein binding activity. Predicted to be involved in cell-cell recognition and homophilic cell adhesion via plasma membrane adhesion molecules. Predicted to be located in plasma membrane.
Type: protein-coding (Ensembl: pseudogene)
RefSeq Status: PROVISIONAL
Previously known as: LOC291653
RGD Orthologs
Mouse
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81829,320,391 - 29,323,753 (+)NCBIGRCr8
mRatBN7.21829,046,383 - 29,049,745 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1829,046,383 - 29,048,717 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1829,173,511 - 29,176,873 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01829,935,507 - 29,938,869 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01829,270,806 - 29,274,168 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01830,416,038 - 30,419,400 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1830,416,038 - 30,418,372 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01830,123,238 - 30,126,600 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41830,150,687 - 30,154,049 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11830,177,332 - 30,179,651 (+)NCBI
Celera1828,742,187 - 28,745,549 (+)NCBICelera
Cytogenetic Map18p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. Comprehensive gene review and curation RGD comprehensive gene curation
5. 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.
Additional References at PubMed
PMID:15744052  


Genomics

Comparative Map Data
Pcdhb6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81829,320,391 - 29,323,753 (+)NCBIGRCr8
mRatBN7.21829,046,383 - 29,049,745 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1829,046,383 - 29,048,717 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1829,173,511 - 29,176,873 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01829,935,507 - 29,938,869 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01829,270,806 - 29,274,168 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01830,416,038 - 30,419,400 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1830,416,038 - 30,418,372 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01830,123,238 - 30,126,600 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41830,150,687 - 30,154,049 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11830,177,332 - 30,179,651 (+)NCBI
Celera1828,742,187 - 28,745,549 (+)NCBICelera
Cytogenetic Map18p11NCBI
Pcdhb6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,466,913 - 37,470,491 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1837,466,974 - 37,470,727 (+)EnsemblGRCm39 Ensembl
GRCm381837,333,860 - 37,337,438 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1837,333,921 - 37,337,674 (+)EnsemblGRCm38mm10GRCm38
MGSCv371837,493,682 - 37,496,000 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361837,460,002 - 37,462,320 (+)NCBIMGSCv36mm8
Celera1838,681,808 - 38,709,360 (+)NCBICelera
Cytogenetic Map18B3NCBI
cM Map1819.47NCBI

Variants

.
Variants in Pcdhb6
5 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:118
Count of miRNA genes:93
Interacting mature miRNAs:95
Transcripts:ENSRNOT00000073425
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

Markers in Region
BF406179  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21829,049,250 - 29,049,421 (+)MAPPERmRatBN7.2
Rnor_6.01830,418,906 - 30,419,076NCBIRnor6.0
Rnor_5.01830,126,106 - 30,126,276UniSTSRnor5.0
RGSC_v3.41830,153,555 - 30,153,725UniSTSRGSC3.4
Celera1828,745,055 - 28,745,225UniSTS
RH 3.4 Map18418.89UniSTS
Cytogenetic Map18p11UniSTS


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 3 7 11 1 1 68 29 32 10 1
Below cutoff 1 40 32 23 8 23 7 9 6 5 7 1 7

Sequence


RefSeq Acc Id: ENSRNOT00000080650
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1829,046,383 - 29,048,717 (+)Ensembl
Rnor_6.0 Ensembl1830,416,038 - 30,418,372 (+)Ensembl
RefSeq Acc Id: NM_001014780   ⟹   NP_001014780
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81829,320,391 - 29,323,753 (+)NCBI
mRatBN7.21829,046,383 - 29,049,745 (+)NCBI
Rnor_6.01830,416,038 - 30,419,400 (+)NCBI
Rnor_5.01830,123,238 - 30,126,600 (+)NCBI
RGSC_v3.41830,150,687 - 30,154,049 (+)RGD
Celera1828,742,187 - 28,745,549 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001014780 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001014780   ⟸   NM_001014780
- Peptide Label: precursor
- UniProtKB: A6J362 (UniProtKB/TrEMBL)
- Sequence:
Protein Domains
Cadherin

Transcriptome

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


Additional Information

Database Acc Id Source(s)
BioCyc Gene G2FUF-7838 BioCyc
Ensembl Genes ENSRNOG00000054953 Ensembl
Gene3D-CATH Cadherins UniProtKB/TrEMBL
InterPro Cadherin-like_dom UniProtKB/TrEMBL
  Cadherin-like_sf UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
  Cadherin_N UniProtKB/TrEMBL
NCBI Gene 291653 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/TrEMBL
  PROTOCADHERIN BETA-6-RELATED UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
PhenoGen Pcdhb6 PhenoGen
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000054953 RatGTEx
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin-like UniProtKB/TrEMBL
UniProt A6J362 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Pcdhb6  protocadherin beta 6   Pcdhb6_predicted  protocadherin beta 6 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Pcdhb6_predicted  protocadherin beta 6 (predicted)      Symbol and Name status set to approved 70820 APPROVED