Pcdhgb1 (protocadherin gamma subfamily B, 1) - Rat Genome Database

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Gene: Pcdhgb1 (protocadherin gamma subfamily B, 1) Rattus norvegicus
Analyze
Symbol: Pcdhgb1
Name: protocadherin gamma subfamily B, 1
RGD ID: 1560482
Description: Predicted to be located in growth cone and membrane. Orthologous to human PCDHGB1 (protocadherin gamma subfamily B, 1); INTERACTS WITH paracetamol; aflatoxin B1 (ortholog); benzo[a]pyrene (ortholog).
Type: pseudo (Ensembl: protein-coding)
RefSeq Status: MODEL
Previously known as: LOC498848; protocadherin gamma subfamily B, 1-like; protocadherin gamma-B1-like; RGD1560482; similar to protocadherin gamma B1
RGD Orthologs
Human
Mouse
Pig
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81829,753,049 - 29,759,259 (+)NCBIGRCr8
mRatBN7.21829,501,739 - 29,508,024 (+)NCBImRatBN7.2mRatBN7.2
Rnor_6.01830,825,260 - 30,829,027 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1830,826,260 - 30,828,641 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01830,519,491 - 30,525,137 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41830,586,359 - 30,589,177 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1829,150,753 - 29,154,520 (+)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

Cellular Component
growth cone  (ISO)
membrane  (ISO)

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.
Additional References at PubMed
PMID:15347688   PMID:15581637  


Genomics

Comparative Map Data
Pcdhgb1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81829,753,049 - 29,759,259 (+)NCBIGRCr8
mRatBN7.21829,501,739 - 29,508,024 (+)NCBImRatBN7.2mRatBN7.2
Rnor_6.01830,825,260 - 30,829,027 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1830,826,260 - 30,828,641 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01830,519,491 - 30,525,137 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41830,586,359 - 30,589,177 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1829,150,753 - 29,154,520 (+)NCBICelera
Cytogenetic Map18p11NCBI
PCDHGB1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385141,350,099 - 141,512,975 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5141,350,099 - 141,512,975 (+)EnsemblGRCh38hg38GRCh38
GRCh375140,729,666 - 140,892,542 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,710,012 - 140,872,730 (+)NCBINCBI36Build 36hg18NCBI36
Build 345140,710,011 - 140,712,444NCBI
Celera5136,806,653 - 136,969,282 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5135,874,903 - 136,037,386 (+)NCBIHuRef
CHM1_15140,163,035 - 140,325,823 (+)NCBICHM1_1
T2T-CHM13v2.05141,875,723 - 142,038,959 (+)NCBIT2T-CHM13v2.0
Pcdhgb1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,813,325 - 37,974,923 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1837,813,286 - 37,974,923 (+)EnsemblGRCm39 Ensembl
GRCm381837,680,272 - 37,841,870 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1837,680,233 - 37,841,870 (+)EnsemblGRCm38mm10GRCm38
MGSCv371837,840,112 - 38,001,524 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361837,806,265 - 37,967,842 (+)NCBIMGSCv36mm8
MGSCv361837,867,198 - 38,028,845 (+)NCBIMGSCv36mm8
Celera1839,001,714 - 39,185,349 (+)NCBICelera
Cytogenetic Map18B3NCBI
cM Map1819.55NCBI
LOC106509585
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2142,989,140 - 142,991,824 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.12142,989,108 - 142,993,793 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22149,187,657 - 149,190,419 (+)NCBISscrofa10.2Sscrofa10.2susScr3

Variants

.
Variants in Pcdhgb1
40 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:13
Count of miRNA genes:12
Interacting mature miRNAs:12
Transcripts:ENSRNOT00000065235
Prediction methods:Miranda, Rnahybrid, Targetscan
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
BF403187  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21829,507,758 - 29,507,879 (+)MAPPERmRatBN7.2
Rnor_6.01830,828,762 - 30,828,882NCBIRnor6.0
Rnor_5.01830,522,989 - 30,523,109UniSTSRnor5.0
RGSC_v3.41830,588,912 - 30,589,032UniSTSRGSC3.4
Celera1829,154,255 - 29,154,375UniSTS
RH 3.4 Map18428.1UniSTS
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 2
Low 1 42 26 10 19 10 8 8 74 28 36 9 8
Below cutoff 2 1 26 26 26 3 6 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000065235   ⟹   ENSRNOP00000063269
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1830,826,260 - 30,828,641 (+)Ensembl
RefSeq Acc Id: XM_008772072   ⟹   XP_008770294
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01830,825,260 - 30,829,027 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008774114   ⟹   XP_008772336
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1829,150,753 - 29,154,520 (+)NCBI
Sequence:
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZUH3-F1-model_v2 AlphaFold D3ZUH3 1-681 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:1560482 AgrOrtholog
BioCyc Gene G2FUF-7809 BioCyc
Ensembl Genes ENSRNOG00000042264 Ensembl
NCBI Gene 498848 ENTREZGENE
PhenoGen Pcdhgb1 PhenoGen
RatGTEx ENSRNOG00000042264 RatGTEx


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-09-05 Pcdhgb1  protocadherin gamma subfamily B, 1  RGD1560482  similar to protocadherin gamma B1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-05-24 RGD1560482  similar to protocadherin gamma B1  LOC100363566  protocadherin gamma subfamily B, 1-like  Data merged from RGD:2322782 1643240 APPROVED
2010-05-06 LOC100363566  protocadherin gamma subfamily B, 1-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 RGD1560482  similar to protocadherin gamma B1   RGD1560482_predicted  similar to protocadherin gamma B1 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1560482_predicted  similar to protocadherin gamma B1 (predicted)  LOC498848  similar to protocadherin gamma B1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498848  similar to protocadherin gamma B1      Symbol and Name status set to provisional 70820 PROVISIONAL