Pcdhga9 (protocadherin gamma subfamily A, 9) - Rat Genome Database

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Gene: Pcdhga9 (protocadherin gamma subfamily A, 9) Rattus norvegicus
Analyze
Symbol: Pcdhga9
Name: protocadherin gamma subfamily A, 9
RGD ID: 620729
Description: Involved in spermatogenesis. Predicted to be located in membrane. Orthologous to human PCDHGA9 (protocadherin gamma subfamily A, 9); INTERACTS WITH bisphenol A; furan; glycidol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: protocadherin gamma-A9
RGD Orthologs
Human
Mouse
Pig
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
NCBI Annotation Information: Annotation category: suggests misassembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81829,815,845 - 29,919,095 (+)NCBIGRCr8
mRatBN7.21829,564,614 - 29,667,865 (+)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx1829,668,952 - 29,772,190 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01830,430,903 - 30,534,170 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01829,766,226 - 29,869,511 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01830,885,605 - 30,971,113 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1830,885,789 - 30,888,209 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01830,579,832 - 30,662,065 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41830,645,765 - 30,754,205 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11830,674,162 - 30,674,259 (+)NCBI
Celera1829,211,103 - 29,311,954 (+)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
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.
2. Multiple cadherin superfamily members with unique expression profiles are produced in rat testis. Johnson KJ, etal., Endocrinology 2000 Feb;141(2):675-83.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14672974   PMID:15347688   PMID:15744052   PMID:17110050   PMID:22681889  


Genomics

Comparative Map Data
Pcdhga9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81829,815,845 - 29,919,095 (+)NCBIGRCr8
mRatBN7.21829,564,614 - 29,667,865 (+)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx1829,668,952 - 29,772,190 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01830,430,903 - 30,534,170 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01829,766,226 - 29,869,511 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01830,885,605 - 30,971,113 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1830,885,789 - 30,888,209 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01830,579,832 - 30,662,065 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41830,645,765 - 30,754,205 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11830,674,162 - 30,674,259 (+)NCBI
Celera1829,211,103 - 29,311,954 (+)NCBICelera
Cytogenetic Map18p11NCBI
PCDHGA9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385141,402,778 - 141,512,975 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5141,402,778 - 141,512,975 (+)EnsemblGRCh38hg38GRCh38
GRCh375140,782,345 - 140,892,542 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,762,704 - 140,872,730 (+)NCBINCBI36Build 36hg18NCBI36
Build 345140,762,703 - 140,765,190NCBI
Celera5136,859,342 - 136,969,282 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5135,927,540 - 136,037,386 (+)NCBIHuRef
CHM1_15140,215,743 - 140,325,823 (+)NCBICHM1_1
T2T-CHM13v2.05141,928,414 - 142,038,959 (+)NCBIT2T-CHM13v2.0
Pcdhga9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,869,989 - 37,974,916 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1837,869,989 - 37,974,923 (+)EnsemblGRCm39 Ensembl
GRCm381837,736,936 - 37,841,863 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1837,736,936 - 37,841,870 (+)EnsemblGRCm38mm10GRCm38
MGSCv371837,896,590 - 38,001,517 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361837,862,910 - 37,967,837 (+)NCBIMGSCv36mm8
Celera1839,069,999 - 39,185,342 (+)NCBICelera
Cytogenetic Map18B3NCBI
cM Map1819.6NCBI
LOC110259670
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.12143,041,492 - 143,046,022 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1

Variants

.
Variants in Pcdhga9
665 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:20
Count of miRNA genes:18
Interacting mature miRNAs:20
Transcripts:ENSRNOT00000044434
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
2325839Bp348Blood pressure QTL 3480.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182557098570570985Rat
6903359Bp355Blood pressure QTL 3553.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194454459796478Rat
9589153Insul31Insulin level QTL 317.150.05blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)18142547119Rat
1358358Sradr6Stress Responsive Adrenal Weight QTL 62.49adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)181194429959330563Rat
1331733Bp233Blood pressure QTL 2333.97196arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182479697779788953Rat
1331735Rf44Renal function QTL 442.981urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)181823456431359530Rat
1331741Bp232Blood pressure QTL 2323.59112arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182137289383213037Rat
1331753Bp231Blood pressure QTL 2313.643arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194429952293055Rat
1331766Bp236Blood pressure QTL 2363.022arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181194429931359530Rat
1331775Bp235Blood pressure QTL 2353.201arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181823456431359530Rat
1358193Emca2Estrogen-induced mammary cancer QTL 21.6mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)181800759963571040Rat
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
61388Bp2Blood pressure QTL 23.23arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)18135374722Rat
631264Scl22Serum cholesterol level QTL 226.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)181194179131393320Rat
2301413Bp318Blood pressure QTL 3180.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182654808246969551Rat
2299160Iddm35Insulin dependent diabetes mellitus QTL 352.79blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)18420794160377792Rat
2312598Bp340Blood pressure QTL 3400.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)18130558703Rat
2293661Bss50Bone structure and strength QTL 504.640.0003lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)18134291613Rat
2312568Glom21Glomerulus QTL 2120.005kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)18518585840503530Rat
12904670Cm126Cardiac mass QTL 1260.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)182654808246969551Rat
2300177Bmd65Bone mineral density QTL 6519.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)182896485373964853Rat
1641923Colcr8Colorectal carcinoma resistance QTL 83.10.0014intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)182206624252293055Rat
12904675Am19Aortic mass QTL 190.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)182654808246969551Rat
12904669Cm125Cardiac mass QTL 1250.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)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
61382Bp46Blood pressure QTL 4618.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194179131393320Rat
2313082Bss85Bone structure and strength QTL 850.80.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)181495133759951337Rat
1600373Mamtr6Mammary tumor resistance QTL 6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)181927890183218561Rat
2293704Bss35Bone structure and strength QTL 354.590.0002femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)182896485373964853Rat
2293708Bss46Bone structure and strength QTL 468.80.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)181179151863636873Rat
2300157Bmd66Bone mineral density QTL 6613.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)182896485373964853Rat
2300180Bmd67Bone mineral density QTL 674.80.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)18134291613Rat
12904673Cm127Cardiac mass QTL 1270.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)182654808246969551Rat
61375Bp41Blood pressure QTL 412.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)181194429941122201Rat

Markers in Region
D18Rat100  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21829,607,001 - 29,607,214 (+)MAPPERmRatBN7.2
Rnor_6.01830,928,541 - 30,928,753NCBIRnor6.0
Rnor_5.01830,622,699 - 30,622,911UniSTSRnor5.0
RGSC_v3.41830,688,754 - 30,688,967RGDRGSC3.4
RGSC_v3.41830,688,755 - 30,688,967UniSTSRGSC3.4
RGSC_v3.11830,715,400 - 30,715,613RGD
Celera1829,253,446 - 29,253,658UniSTS
SHRSP x BN Map1813.7599RGD
SHRSP x BN Map1813.7599UniSTS
Cytogenetic Map18p11UniSTS
D18Wox21  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21829,666,368 - 29,666,447 (+)MAPPERmRatBN7.2
Rnor_6.01830,969,617 - 30,969,695NCBIRnor6.0
Rnor_5.01830,660,569 - 30,660,647UniSTSRnor5.0
RGSC_v3.41830,752,709 - 30,752,787UniSTSRGSC3.4
Celera1829,310,458 - 29,310,536UniSTS
Cytogenetic Map18p11UniSTS
RH129840  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21829,632,404 - 29,632,572 (+)MAPPERmRatBN7.2
Rnor_6.01830,953,941 - 30,954,108NCBIRnor6.0
Rnor_5.01830,648,099 - 30,648,266UniSTSRnor5.0
RGSC_v3.41830,713,933 - 30,714,100UniSTSRGSC3.4
Celera1829,279,250 - 29,279,417UniSTS
Cytogenetic Map18p11UniSTS
BF398325  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21829,579,114 - 29,579,264 (+)MAPPERmRatBN7.2
Rnor_6.01830,900,106 - 30,900,255NCBIRnor6.0
Rnor_5.01830,594,333 - 30,594,482UniSTSRnor5.0
RGSC_v3.41830,660,266 - 30,660,415UniSTSRGSC3.4
Celera1829,225,604 - 29,225,753UniSTS
RH 3.4 Map8610.9UniSTS
Cytogenetic Map18p11UniSTS
RH138098  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21829,586,544 - 29,586,696 (+)MAPPERmRatBN7.2
Rnor_6.01830,907,536 - 30,907,687NCBIRnor6.0
Rnor_5.01830,601,763 - 30,601,914UniSTSRnor5.0
RGSC_v3.41830,667,696 - 30,667,847UniSTSRGSC3.4
Celera1829,233,034 - 29,233,185UniSTS
RH 3.4 Map18426.4UniSTS
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 7
Low 37 30 14 18 14 8 8 74 30 39 4 8
Below cutoff 3 6 16 16 1 16 3 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000044434   ⟹   ENSRNOP00000047881
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1830,885,789 - 30,888,209 (+)Ensembl
RefSeq Acc Id: NM_001037158   ⟹   NP_001032235
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81829,815,845 - 29,919,095 (+)NCBI
mRatBN7.21829,564,614 - 29,667,865 (+)NCBI
Rnor_6.01830,885,605 - 30,971,113 (+)NCBI
Rnor_5.01830,579,832 - 30,662,065 (+)NCBI
RGSC_v3.41830,645,765 - 30,754,205 (+)RGD
Celera1829,211,103 - 29,311,954 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001032235 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF87069 (Get FASTA)   NCBI Sequence Viewer  
  AAT77602 (Get FASTA)   NCBI Sequence Viewer  
  EDL76387 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001032235   ⟸   NM_001037158
- Peptide Label: precursor
- UniProtKB: I6LBX6 (UniProtKB/TrEMBL),   A6J3A5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000047881   ⟸   ENSRNOT00000044434
Protein Domains
Cadherin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-E9PT60-F1-model_v2 AlphaFold E9PT60 1-807 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:620729 AgrOrtholog
BioCyc Gene G2FUF-7800 BioCyc
Ensembl Genes ENSRNOG00000030352 Ensembl
Gene3D-CATH Cadherins UniProtKB/TrEMBL
InterPro Cadherin UniProtKB/TrEMBL
  Cadherin-like UniProtKB/TrEMBL
  Cadherin_C UniProtKB/TrEMBL
  Cadherin_CBD UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
  Cadherin_N UniProtKB/TrEMBL
KEGG Report rno:252895 UniProtKB/TrEMBL
NCBI Gene 252895 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/TrEMBL
  PROTOCADHERIN GAMMA-A9 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
  Cadherin_C_2 UniProtKB/TrEMBL
  Cadherin_tail UniProtKB/TrEMBL
PhenoGen Pcdhga9 PhenoGen
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000030352 RatGTEx
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin UniProtKB/TrEMBL
UniProt A6J3A5 ENTREZGENE, UniProtKB/TrEMBL
  I6LBX6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Pcdhga9  protocadherin gamma subfamily A, 9      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Pcdhga9  protocadherin gamma subfamily A, 9      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in testis 68759