Pcdhb6 (protocadherin beta 6) - Rat Genome Database

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Gene: Pcdhb6 (protocadherin beta 6) Rattus norvegicus
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Symbol: Pcdhb6
Name: protocadherin beta 6
RGD ID: 1306123
Description: ENCODES a protein that exhibits calcium ion binding (ortholog); identical protein binding (ortholog); INVOLVED IN cell-cell recognition (ortholog); homophilic cell-cell adhesion (ortholog); FOUND IN plasma membrane (ortholog)
Type: protein-coding (Ensembl: pseudogene)
RefSeq Status: PROVISIONAL
Previously known as: LOC291653
RGD Orthologs
Mouse
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81829,320,391 - 29,323,753 (+)NCBIGRCr8GRCr8GRCr8
mRatBN7.21829,046,383 - 29,049,745 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1829,046,383 - 29,048,717 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1829,173,511 - 29,176,873 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01829,935,507 - 29,938,869 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01829,270,806 - 29,274,168 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01830,416,038 - 30,419,400 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1830,416,038 - 30,418,372 (+)Ensemblrn6Rnor6.0
Rnor_5.01830,123,238 - 30,126,600 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41830,150,687 - 30,154,049 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1828,742,187 - 28,745,549 (+)NCBICelera
RGSC_v3.11830,177,332 - 30,179,651 (+)NCBI
Cytogenetic Map18p11NCBI
JBrowse:




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 (+)NCBIGRCr8GRCr8GRCr8
mRatBN7.21829,046,383 - 29,049,745 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1829,046,383 - 29,048,717 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1829,173,511 - 29,176,873 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01829,935,507 - 29,938,869 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01829,270,806 - 29,274,168 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01830,416,038 - 30,419,400 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1830,416,038 - 30,418,372 (+)Ensemblrn6Rnor6.0
Rnor_5.01830,123,238 - 30,126,600 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41830,150,687 - 30,154,049 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1828,742,187 - 28,745,549 (+)NCBICelera
RGSC_v3.11830,177,332 - 30,179,651 (+)NCBI
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 EnsemblGRCm39
GRCm381837,333,860 - 37,337,438 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1837,333,921 - 37,337,674 (+)Ensemblmm10GRCm38
MGSCv371837,493,682 - 37,496,000 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361837,460,002 - 37,462,320 (+)NCBIMGSCv36mm8
Celera1838,681,808 - 38,709,360 (+)NCBICelera
Cytogenetic Map18B3NCBI
cM Map1819.47NCBI

Variants

.
Variants in Pcdhb6
29 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331733Bp233Blood pressure QTL 2333.97196arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182507112683910656Rat
2301409Cm70Cardiac mass QTL 700.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)18706572852065728Rat
1358358Sradr6Stress Responsive Adrenal Weight QTL 62.49adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)182201556261600538Rat
1331735Rf44Renal function QTL 442.981urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)181564228031610627Rat
61382Bp46Blood pressure QTL 4618.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181221668431644508Rat
2301413Bp318Blood pressure QTL 3180.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182682218671822186Rat
12904716Am21Aortic mass QTL 210.005aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)18706572852065728Rat
1331741Bp232Blood pressure QTL 2323.59112arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182349405785487725Rat
12904714Cm131Cardiac mass QTL 1310.002heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)18706572852065728Rat
12904715Cm132Cardiac mass QTL 1320.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)18706572852065728Rat
6903345Bp349Blood pressure QTL 3493.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)18391722648917226Rat
12904668Bw188Body weight QTL 1880.03body mass (VT:0001259)body weight (CMO:0000012)182682218671822186Rat
2313082Bss85Bone structure and strength QTL 850.80.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)181522610142690662Rat
12904669Cm125Cardiac mass QTL 1250.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)182682218671822186Rat
6903347Bp350Blood pressure QTL 3504.4arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)18131610627Rat
12904670Cm126Cardiac mass QTL 1260.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)182682218671822186Rat
2312568Glom21Glomerulus QTL 2120.005kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)18546045542690191Rat
6903349Bp351Blood pressure QTL 3513.5arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)18391722648917226Rat
631509Sald2Serum aldosterone level QTL 22.9blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)182641582171415821Rat
6903351Bp352Blood pressure QTL 3523.3arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)18391722648917226Rat
12904677Kidm72Kidney mass QTL 720.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)182682218671822186Rat
1331766Bp236Blood pressure QTL 2363.022arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)18131610627Rat
12904673Cm127Cardiac mass QTL 1270.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)182682218671822186Rat
12904675Am19Aortic mass QTL 190.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)182682218671822186Rat
631264Scl22Serum cholesterol level QTL 226.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)181221668431644508Rat
1331775Bp235Blood pressure QTL 2353.201arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181564228031610627Rat
2325839Bp348Blood pressure QTL 3480.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)18144930869Rat
1600373Mamtr6Mammary tumor resistance QTL 6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)181955353285493247Rat
2293708Bss46Bone structure and strength QTL 468.80.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)181206648257066482Rat
1578667Bss21Bone structure and strength QTL 213.5femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)181206648285493247Rat
2312598Bp340Blood pressure QTL 3400.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)18381190230809809Rat
2300180Bmd67Bone mineral density QTL 674.80.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)18134566578Rat
2299160Iddm35Insulin dependent diabetes mellitus QTL 352.79blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)18448264849482648Rat
1331753Bp231Blood pressure QTL 2313.643arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)18154490981Rat
1578661Bss20Bone structure and strength QTL 203.7femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)181206648285493247Rat
11565454Kidm59Kidney mass QTL 590.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)18706572852065728Rat
1331754Bp230Blood pressure QTL 2304.61609arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181564228086134022Rat
2293661Bss50Bone structure and strength QTL 504.640.0003lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)18134566578Rat
61375Bp41Blood pressure QTL 412.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)18430735449307354Rat

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

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
13 11 66 141 72 71 40 26 40 6 249 122 8 122 66 87 31 15 15

Sequence


Ensembl 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
  Protocadherin/Cadherin-CA 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