Pcdha4 (protocadherin alpha 4) - Rat Genome Database

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Gene: Pcdha4 (protocadherin alpha 4) Rattus norvegicus
Analyze
Symbol: Pcdha4 (Ensembl: Pcdha3)
Name: protocadherin alpha 4 (Ensembl:protocadherin alpha 3)
RGD ID: 620337
Description: Predicted to enable calcium ion binding activity; cell adhesion molecule binding activity; and identical protein binding activity. Predicted to be involved in cell adhesion. Predicted to be located in endoplasmic reticulum; membrane; and synapse. Predicted to be active in plasma membrane. Orthologous to human PCDHA4 (protocadherin alpha 4); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; acrolein.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cadherin-related neuronal receptor 1; cadherin-related neuronal receptor 10; cadherin-related neuronal receptor 11; cadherin-related neuronal receptor 12; cadherin-related neuronal receptor 13; cadherin-related neuronal receptor 2; cadherin-related neuronal receptor 3; cadherin-related neuronal receptor 4; cadherin-related neuronal receptor 5; cadherin-related neuronal receptor 6; cadherin-related neuronal receptor 7; cadherin-related neuronal receptor 8; cadherin-related neuronal receptor 9; cadherin-related neuronal receptor c1; cadherin-related neuronal receptor c2; Cnr1; cnr5; MGC93781; PCDH-alpha-4; Pcdha1; Pcdha10; Pcdha11; Pcdha12; Pcdha13; Pcdha2; Pcdha3; Pcdha5; Pcdha6; Pcdha7; Pcdha8; Pcdha9; Pcdhac1; Pcdhac2; protocadherin alpha 1; protocadherin alpha 10; protocadherin alpha 11; protocadherin alpha 12; protocadherin alpha 13; protocadherin alpha 2; protocadherin alpha 3; protocadherin alpha 5; protocadherin alpha 6; protocadherin alpha 7; protocadherin alpha 8; protocadherin alpha 9; protocadherin alpha c1; protocadherin alpha c2; protocadherin alpha-4; rCNRv01; rCNRv02; rCNRv03; rCNRv05; rCNRv06; rCNRv07; rCNRv08; rCNRv09; rCNRv10; rCNRv11; rCNRv12; rCNRv13; rCNRvc1; rCNRvc2
RGD Orthologs
Human
Mouse
Bonobo
Dog
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81828,688,274 - 29,120,227 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1828,855,256 - 29,120,227 (+)EnsemblGRCr8
mRatBN7.21828,581,040 - 28,846,214 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1828,581,225 - 28,846,211 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1828,730,299 - 28,973,352 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01829,492,377 - 29,735,418 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01828,827,594 - 29,070,639 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01829,950,217 - 30,215,901 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,972,808 - 29,975,192 (+)Ensemblrn6Rnor6.0
Rnor_6.0 Ensembl1829,966,245 - 29,968,614 (+)Ensemblrn6Rnor6.0
Rnor_6.0 Ensembl1829,987,206 - 30,215,897 (+)Ensemblrn6Rnor6.0
Rnor_5.01829,670,058 - 29,924,443 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41829,683,478 - 29,928,030 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1828,311,641 - 28,552,754 (+)NCBICelera
RGSC_v3.11829,710,123 - 29,954,676 (+)NCBI
Cytogenetic Map18p11NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
endoplasmic reticulum  (ISO)
membrane  (IEA,ISO)
plasma membrane  (IBA,IEA)
synapse  (ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Cadherin-related neuronal receptors in incisor development. Fukumoto E, etal., J Dent Res 2003 Jan;82(1):17-22.
2. 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.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Multiple cadherin superfamily members with unique expression profiles are produced in rat testis. Johnson KJ, etal., Endocrinology 2000 Feb;141(2):675-83.
5. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
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
8. Genomic sequence and organization of the family of CNR/Pcdhalpha genes in rat. Yanase H, etal., Genomics 2004 Apr;83(4):717-26.
Additional References at PubMed
PMID:9655502   PMID:11401448   PMID:12477932   PMID:14522826   PMID:14672974   PMID:15347688   PMID:15489334   PMID:15744052   PMID:17110050   PMID:27161523   PMID:31904090  


Genomics

Comparative Map Data
Pcdha4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81828,688,274 - 29,120,227 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1828,855,256 - 29,120,227 (+)EnsemblGRCr8
mRatBN7.21828,581,040 - 28,846,214 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1828,581,225 - 28,846,211 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1828,730,299 - 28,973,352 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01829,492,377 - 29,735,418 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01828,827,594 - 29,070,639 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01829,950,217 - 30,215,901 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,972,808 - 29,975,192 (+)Ensemblrn6Rnor6.0
Rnor_6.0 Ensembl1829,966,245 - 29,968,614 (+)Ensemblrn6Rnor6.0
Rnor_6.0 Ensembl1829,987,206 - 30,215,897 (+)Ensemblrn6Rnor6.0
Rnor_5.01829,670,058 - 29,924,443 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41829,683,478 - 29,928,030 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1828,311,641 - 28,552,754 (+)NCBICelera
RGSC_v3.11829,710,123 - 29,954,676 (+)NCBI
Cytogenetic Map18p11NCBI
PCDHA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385140,807,068 - 141,012,347 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5140,807,037 - 141,012,347 (+)Ensemblhg38GRCh38
GRCh375140,186,653 - 140,391,932 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,166,856 - 140,372,113 (+)NCBIBuild 36Build 36hg18NCBI36
Build 345140,166,855 - 140,169,353NCBI
Celera5136,263,450 - 136,468,708 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5135,331,387 - 135,536,628 (+)NCBIHuRef
CHM1_15139,619,864 - 139,825,092 (+)NCBICHM1_1
T2T-CHM13v2.05141,332,401 - 141,537,634 (+)NCBIT2T-CHM13v2.0
Pcdha4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,085,742 - 37,320,710 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1837,085,701 - 37,320,714 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381836,952,689 - 37,187,657 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1836,952,648 - 37,187,661 (+)Ensemblmm10GRCm38
MGSCv371837,112,343 - 37,347,311 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361837,078,663 - 37,313,631 (+)NCBIMGSCv36mm8
Celera1837,399,452 - 37,411,288 (+)NCBICelera
Cytogenetic Map18B2- B3NCBI
cM Map1819.46NCBI
PCDHA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1 Ensembl5142,286,433 - 142,289,088 (+)EnsemblpanPan2panpan1.1
PCDHA4
(Canis lupus familiaris - dog)		 No map positions available.

Variants

.
Variants in Pcdha4
1719 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:165
Count of miRNA genes:122
Interacting mature miRNAs:128
Transcripts:ENSRNOT00000074028, ENSRNOT00000074051
Prediction methods:Microtar, 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 (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)182479697779788953Rat
1358358Sradr6Stress Responsive Adrenal Weight QTL 62.49adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)181194429959330563Rat
1331735Rf44Renal function QTL 442.981urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)181823456431359530Rat
61382Bp46Blood pressure QTL 4618.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194179131393320Rat
2301413Bp318Blood pressure QTL 3180.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182654808246969551Rat
1331741Bp232Blood pressure QTL 2323.59112arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182137289383213037Rat
61388Bp2Blood pressure QTL 23.23arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)18135374722Rat
6903359Bp355Blood pressure QTL 3553.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194454459796478Rat
12904668Bw188Body weight QTL 1880.03body mass (VT:0001259)body weight (CMO:0000012)182654808246969551Rat
2313082Bss85Bone structure and strength QTL 850.80.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)181495133759951337Rat
12904669Cm125Cardiac mass QTL 1250.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)182654808246969551Rat
1641923Colcr8Colorectal carcinoma resistance QTL 83.10.0014intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)182206624252293055Rat
12904670Cm126Cardiac mass QTL 1260.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)182654808246969551Rat
2312568Glom21Glomerulus QTL 2120.005kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)18518585840503530Rat
12904677Kidm72Kidney mass QTL 720.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)182654808246969551Rat
1331766Bp236Blood pressure QTL 2363.022arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181194429931359530Rat
1358193Emca2Estrogen-induced mammary cancer QTL 21.6mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)181800759963571040Rat
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
631264Scl22Serum cholesterol level QTL 226.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)181194179131393320Rat
1331775Bp235Blood pressure QTL 2353.201arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181823456431359530Rat
2325839Bp348Blood pressure QTL 3480.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182557098570570985Rat
1600373Mamtr6Mammary tumor resistance QTL 6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)181927890183218561Rat
2293708Bss46Bone structure and strength QTL 468.80.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)181179151863636873Rat
9589153Insul31Insulin level QTL 317.150.05blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)18142547119Rat
1578667Bss21Bone structure and strength QTL 213.5femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)181179151883218561Rat
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
2299160Iddm35Insulin dependent diabetes mellitus QTL 352.79blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)18420794160377792Rat
1578661Bss20Bone structure and strength QTL 203.7femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)181179151883218561Rat
1331753Bp231Blood pressure QTL 2313.643arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194429952293055Rat
2293661Bss50Bone structure and strength QTL 504.640.0003lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)18134291613Rat
61375Bp41Blood pressure QTL 412.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)181194429941122201Rat

Markers in Region
WI-19540  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21828,845,892 - 28,846,156 (+)MAPPERmRatBN7.2
Rnor_6.01830,215,579 - 30,215,842NCBIRnor6.0
Rnor_5.01829,924,126 - 29,924,389UniSTSRnor5.0
RGSC_v3.41829,927,713 - 29,927,976UniSTSRGSC3.4
Celera1828,552,437 - 28,552,700UniSTS
Cytogenetic Map18p11UniSTS
RH65516  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21828,845,204 - 28,845,379 (+)MAPPERmRatBN7.2
Rnor_6.01830,214,891 - 30,215,065NCBIRnor6.0
Rnor_5.01829,923,438 - 29,923,612UniSTSRnor5.0
RGSC_v3.41829,927,025 - 29,927,199UniSTSRGSC3.4
Celera1828,551,749 - 28,551,923UniSTS
Cytogenetic Map18p11UniSTS
IB766  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21828,845,918 - 28,846,149 (+)MAPPERmRatBN7.2
Rnor_6.01830,215,605 - 30,215,835NCBIRnor6.0
Rnor_5.01829,924,152 - 29,924,382UniSTSRnor5.0
RGSC_v3.41829,927,739 - 29,927,969UniSTSRGSC3.4
Celera1828,552,463 - 28,552,693UniSTS
Cytogenetic Map18p11UniSTS
PMC311048P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21828,818,659 - 28,818,748 (+)MAPPERmRatBN7.2
Rnor_6.01830,188,352 - 30,188,440NCBIRnor6.0
Rnor_5.01829,896,899 - 29,896,987UniSTSRnor5.0
RGSC_v3.41829,900,486 - 29,900,574UniSTSRGSC3.4
Celera1828,525,314 - 28,525,402UniSTS
Cytogenetic Map18p11UniSTS
RH91795  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21828,843,505 - 28,843,650 (+)MAPPERmRatBN7.2
Rnor_6.01830,213,192 - 30,213,336NCBIRnor6.0
Rnor_5.01829,921,739 - 29,921,883UniSTSRnor5.0
RGSC_v3.41829,925,326 - 29,925,470UniSTSRGSC3.4
Celera1828,550,050 - 28,550,194UniSTS
Cytogenetic Map18p11UniSTS
BF389688  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21828,749,911 - 28,750,152 (+)MAPPERmRatBN7.2
Rnor_6.01830,119,568 - 30,119,808NCBIRnor6.0
Rnor_5.01829,815,629 - 29,815,869UniSTSRnor5.0
RGSC_v3.41829,831,514 - 29,831,754UniSTSRGSC3.4
Celera1828,458,199 - 28,458,439UniSTS
RH 3.4 Map18420.79UniSTS
Cytogenetic Map18p11UniSTS
PMC311048P3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21828,641,804 - 28,641,941 (+)MAPPERmRatBN7.2
Rnor_6.01830,011,467 - 30,011,603NCBIRnor6.0
Rnor_5.01829,708,717 - 29,708,853UniSTSRnor5.0
RGSC_v3.41829,722,152 - 29,722,288UniSTSRGSC3.4
Celera1828,350,300 - 28,350,436UniSTS
Cytogenetic Map18p11UniSTS
PMC312645P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21828,843,709 - 28,843,897 (+)MAPPERmRatBN7.2
Rnor_6.01830,213,396 - 30,213,583NCBIRnor6.0
Rnor_5.01829,921,943 - 29,922,130UniSTSRnor5.0
RGSC_v3.41829,925,530 - 29,925,717UniSTSRGSC3.4
Celera1828,550,254 - 28,550,441UniSTS
Cytogenetic Map18p11UniSTS
UniSTS:547524  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21828,843,567 - 28,844,209 (+)MAPPERmRatBN7.2
Rnor_6.01830,213,254 - 30,213,895NCBIRnor6.0
Rnor_5.01829,921,801 - 29,922,442UniSTSRnor5.0
Celera1828,550,112 - 28,550,753UniSTS
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
24 22 110 263 116 114 52 87 52 12 494 252 14 228 150 181 62 30 30

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_053933 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600813 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600814 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600815 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600816 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600817 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600818 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600819 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600820 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600821 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600822 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600823 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600824 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600825 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600826 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600827 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600828 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600829 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039096548 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063277056 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063277057 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063277059 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063277060 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063277061 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063277063 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063277064 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063277065 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063277066 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063277067 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063277068 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB113387 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC097339 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC103179 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF177687 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF539750 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY573978 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC085793 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473974 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000018 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000074028   ⟹   ENSRNOP00000066853
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1829,966,245 - 29,968,614 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000074051   ⟹   ENSRNOP00000067199
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1829,972,808 - 29,975,192 (+)Ensembl
RefSeq Acc Id: NM_053933   ⟹   NP_446385
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81828,877,169 - 29,120,223 (+)NCBI
mRatBN7.21828,603,160 - 28,846,210 (+)NCBI
Rnor_6.01829,972,808 - 30,215,896 (+)NCBI
Rnor_5.01829,670,058 - 29,924,443 (+)NCBI
RGSC_v3.41829,683,478 - 29,928,030 (+)RGD
Celera1828,311,641 - 28,552,754 (+)RGD
Sequence:
RefSeq Acc Id: XM_017600815   ⟹   XP_017456304
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81829,077,107 - 29,120,227 (+)NCBI
mRatBN7.21828,802,112 - 28,846,214 (+)NCBI
Rnor_6.01830,171,672 - 30,215,901 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600816   ⟹   XP_017456305
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81828,911,632 - 29,120,227 (+)NCBI
mRatBN7.21828,638,830 - 28,846,214 (+)NCBI
Rnor_6.01830,008,518 - 30,215,901 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600817   ⟹   XP_017456306
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81828,891,207 - 29,120,227 (+)NCBI
mRatBN7.21828,617,181 - 28,846,214 (+)NCBI
Rnor_6.01829,986,758 - 30,215,901 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600818   ⟹   XP_017456307
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81828,926,693 - 29,120,227 (+)NCBI
mRatBN7.21828,650,647 - 28,846,214 (+)NCBI
Rnor_6.01830,020,689 - 30,215,901 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600819   ⟹   XP_017456308
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81828,932,415 - 29,120,227 (+)NCBI
mRatBN7.21828,667,179 - 28,846,214 (+)NCBI
Rnor_6.01830,034,693 - 30,215,901 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600822   ⟹   XP_017456311
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81828,691,343 - 29,120,227 (+)NCBI
mRatBN7.21828,581,040 - 28,846,214 (+)NCBI
Rnor_6.01829,950,217 - 30,215,901 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600823   ⟹   XP_017456312
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81828,917,774 - 29,120,227 (+)NCBI
mRatBN7.21828,644,656 - 28,846,214 (+)NCBI
Rnor_6.01830,015,953 - 30,215,901 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600825   ⟹   XP_017456314
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81828,866,875 - 29,120,227 (+)NCBI
mRatBN7.21828,594,745 - 28,846,214 (+)NCBI
Rnor_6.01829,964,774 - 30,215,901 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600827   ⟹   XP_017456316
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81828,879,576 - 29,120,227 (+)NCBI
mRatBN7.21828,609,808 - 28,846,214 (+)NCBI
Rnor_6.01829,979,498 - 30,215,901 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039096548   ⟹   XP_038952476
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81828,932,415 - 29,120,227 (+)NCBI
mRatBN7.21828,667,179 - 28,846,214 (+)NCBI
RefSeq Acc Id: XM_063277056   ⟹   XP_063133126
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81829,018,529 - 29,120,227 (+)NCBI
RefSeq Acc Id: XM_063277057   ⟹   XP_063133127
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81829,018,529 - 29,120,227 (+)NCBI
RefSeq Acc Id: XM_063277059   ⟹   XP_063133129
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81829,077,107 - 29,120,227 (+)NCBI
RefSeq Acc Id: XM_063277060   ⟹   XP_063133130
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81828,900,092 - 29,120,227 (+)NCBI
RefSeq Acc Id: XM_063277061   ⟹   XP_063133131
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81828,858,055 - 29,120,227 (+)NCBI
RefSeq Acc Id: XM_063277063   ⟹   XP_063133133
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81828,906,078 - 29,120,227 (+)NCBI
RefSeq Acc Id: XM_063277064   ⟹   XP_063133134
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81828,894,075 - 29,120,227 (+)NCBI
RefSeq Acc Id: XM_063277065   ⟹   XP_063133135
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81828,891,162 - 29,120,227 (+)NCBI
RefSeq Acc Id: XM_063277066   ⟹   XP_063133136
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81828,932,415 - 29,120,227 (+)NCBI
RefSeq Acc Id: XM_063277067   ⟹   XP_063133137
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81828,858,055 - 29,120,227 (+)NCBI
RefSeq Acc Id: XM_063277068   ⟹   XP_063133138
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81828,688,274 - 29,120,227 (+)NCBI
Protein Sequences
Protein RefSeqs NP_446385 (Get FASTA)   NCBI Sequence Viewer  
  XP_017456304 (Get FASTA)   NCBI Sequence Viewer  
  XP_017456305 (Get FASTA)   NCBI Sequence Viewer  
  XP_017456306 (Get FASTA)   NCBI Sequence Viewer  
  XP_017456307 (Get FASTA)   NCBI Sequence Viewer  
  XP_017456308 (Get FASTA)   NCBI Sequence Viewer  
  XP_017456311 (Get FASTA)   NCBI Sequence Viewer  
  XP_017456312 (Get FASTA)   NCBI Sequence Viewer  
  XP_017456314 (Get FASTA)   NCBI Sequence Viewer  
  XP_017456316 (Get FASTA)   NCBI Sequence Viewer  
  XP_038952476 (Get FASTA)   NCBI Sequence Viewer  
  XP_063133126 (Get FASTA)   NCBI Sequence Viewer  
  XP_063133127 (Get FASTA)   NCBI Sequence Viewer  
  XP_063133129 (Get FASTA)   NCBI Sequence Viewer  
  XP_063133130 (Get FASTA)   NCBI Sequence Viewer  
  XP_063133131 (Get FASTA)   NCBI Sequence Viewer  
  XP_063133133 (Get FASTA)   NCBI Sequence Viewer  
  XP_063133134 (Get FASTA)   NCBI Sequence Viewer  
  XP_063133135 (Get FASTA)   NCBI Sequence Viewer  
  XP_063133136 (Get FASTA)   NCBI Sequence Viewer  
  XP_063133137 (Get FASTA)   NCBI Sequence Viewer  
  XP_063133138 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF87062 (Get FASTA)   NCBI Sequence Viewer  
  AAH85793 (Get FASTA)   NCBI Sequence Viewer  
  AAN31758 (Get FASTA)   NCBI Sequence Viewer  
  AAT77560 (Get FASTA)   NCBI Sequence Viewer  
  BAD06369 (Get FASTA)   NCBI Sequence Viewer  
  EDL76328 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000027340
  ENSRNOP00000027372
  ENSRNOP00000027383
  ENSRNOP00000027402
  ENSRNOP00000075260.2
GenBank Protein Q767I8 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_446385   ⟸   NM_053933
- Peptide Label: precursor
- UniProtKB: Q5U2Z9 (UniProtKB/Swiss-Prot),   Q8CJ01 (UniProtKB/Swiss-Prot),   Q767I8 (UniProtKB/Swiss-Prot),   Q593X7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456311   ⟸   XM_017600822
- Peptide Label: isoform X11
- UniProtKB: Q767J1 (UniProtKB/TrEMBL),   E9PSN7 (UniProtKB/TrEMBL),   A6J343 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456314   ⟸   XM_017600825
- Peptide Label: isoform X14
- UniProtKB: Q767I9 (UniProtKB/TrEMBL),   M0RBC1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456316   ⟸   XM_017600827
- Peptide Label: isoform X16
- UniProtKB: Q767I7 (UniProtKB/TrEMBL),   A6J347 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456306   ⟸   XM_017600817
- Peptide Label: isoform X5
- UniProtKB: Q767I6 (UniProtKB/TrEMBL),   F7F4E7 (UniProtKB/TrEMBL),   I6LBW5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456305   ⟸   XM_017600816
- Peptide Label: isoform X4
- UniProtKB: Q767I2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456312   ⟸   XM_017600823
- Peptide Label: isoform X12
- UniProtKB: Q767I1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456307   ⟸   XM_017600818
- Peptide Label: isoform X8
- UniProtKB: Q767I0 (UniProtKB/TrEMBL),   Q593Y1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456308   ⟸   XM_017600819
- Peptide Label: isoform X7
- UniProtKB: I6LBW4 (UniProtKB/TrEMBL),   A0A0G2K783 (UniProtKB/TrEMBL),   Q767H9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456304   ⟸   XM_017600815
- Peptide Label: isoform X3
- UniProtKB: Q767H7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000067199   ⟸   ENSRNOT00000074051
Ensembl Acc Id: ENSRNOP00000066853   ⟸   ENSRNOT00000074028
RefSeq Acc Id: XP_038952476   ⟸   XM_039096548
- Peptide Label: isoform X21
RefSeq Acc Id: XP_063133138   ⟸   XM_063277068
- Peptide Label: isoform X20
- UniProtKB: A6J343 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063133131   ⟸   XM_063277061
- Peptide Label: isoform X10
- UniProtKB: M0R8Z9 (UniProtKB/TrEMBL),   Q767J0 (UniProtKB/TrEMBL),   A0A8J8XGC7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063133137   ⟸   XM_063277067
- Peptide Label: isoform X19
- UniProtKB: A0A8J8XGC7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063133135   ⟸   XM_063277065
- Peptide Label: isoform X17
- UniProtKB: I6LBW5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063133134   ⟸   XM_063277064
- Peptide Label: isoform X15
- UniProtKB: M0RB51 (UniProtKB/TrEMBL),   Q767I5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063133130   ⟸   XM_063277060
- Peptide Label: isoform X9
- UniProtKB: F7F4G8 (UniProtKB/TrEMBL),   Q767I4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063133133   ⟸   XM_063277063
- Peptide Label: isoform X13
- UniProtKB: F1LM35 (UniProtKB/TrEMBL),   Q767I3 (UniProtKB/TrEMBL),   A6J351 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063133136   ⟸   XM_063277066
- Peptide Label: isoform X18
- UniProtKB: Q767H9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063133126   ⟸   XM_063277056
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063133127   ⟸   XM_063277057
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063133129   ⟸   XM_063277059
- Peptide Label: isoform X6
Protein Domains
Cadherin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-E9PSN7-F1-model_v2 AlphaFold E9PSN7 1-796 view protein structure
AF-Q767I8-F1-model_v2 AlphaFold Q767I8 1-947 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:620337 AgrOrtholog
BioCyc Gene G2FUF-7852 BioCyc
Ensembl Genes ENSRNOG00000020119 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00000047174 Ensembl
  ENSRNOG00000050378 Ensembl
Ensembl Transcript ENSRNOT00000027340 ENTREZGENE
  ENSRNOT00000027372 ENTREZGENE
  ENSRNOT00000027383 ENTREZGENE
  ENSRNOT00000027402 ENTREZGENE
  ENSRNOT00000079794.2 UniProtKB/Swiss-Prot
Gene3D-CATH Cadherins UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7109469 IMAGE-MGC_LOAD
InterPro Cadherin-like_dom UniProtKB/Swiss-Prot
  Cadherin-like_sf UniProtKB/Swiss-Prot
  Cadherin_CBD UniProtKB/Swiss-Prot
  Cadherin_CS UniProtKB/Swiss-Prot
  Cadherin_N UniProtKB/Swiss-Prot
  Protocadherin/Cadherin-CA UniProtKB/Swiss-Prot
KEGG Report rno:116741 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93781 IMAGE-MGC_LOAD
NCBI Gene 116741 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/Swiss-Prot
  PROTOCADHERIN ALPHA-4 UniProtKB/Swiss-Prot
Pfam Cadherin UniProtKB/Swiss-Prot
  Cadherin_2 UniProtKB/Swiss-Prot
  Cadherin_tail UniProtKB/Swiss-Prot
PhenoGen Pcdha4 PhenoGen
PRINTS CADHERIN UniProtKB/Swiss-Prot
PROSITE CADHERIN_1 UniProtKB/Swiss-Prot
  CADHERIN_2 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000020119 RatGTEx
  ENSRNOG00000047174 RatGTEx
  ENSRNOG00000050378 RatGTEx
SMART SM00112 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49313 UniProtKB/Swiss-Prot
UniProt A0A0G2K783 ENTREZGENE, UniProtKB/TrEMBL
  A0A8J8XGC7 ENTREZGENE, UniProtKB/TrEMBL
  A6J343 ENTREZGENE, UniProtKB/TrEMBL
  A6J347 ENTREZGENE, UniProtKB/TrEMBL
  A6J351 ENTREZGENE, UniProtKB/TrEMBL
  E9PSN7 ENTREZGENE
  F1LM35 ENTREZGENE
  F7F4E7 ENTREZGENE
  F7F4G8 ENTREZGENE
  I6LBW4 ENTREZGENE, UniProtKB/TrEMBL
  I6LBW5 ENTREZGENE, UniProtKB/TrEMBL
  M0R8Z9 ENTREZGENE
  M0RB51 ENTREZGENE
  M0RBC1 ENTREZGENE
  PCDA4_RAT UniProtKB/Swiss-Prot
  Q593X7 ENTREZGENE, UniProtKB/TrEMBL
  Q593Y1 ENTREZGENE, UniProtKB/TrEMBL
  Q5U2Z9 ENTREZGENE
  Q767H7 ENTREZGENE, UniProtKB/TrEMBL
  Q767H9 ENTREZGENE, UniProtKB/TrEMBL
  Q767I0 ENTREZGENE, UniProtKB/TrEMBL
  Q767I1 ENTREZGENE, UniProtKB/TrEMBL
  Q767I2 ENTREZGENE, UniProtKB/TrEMBL
  Q767I3 ENTREZGENE
  Q767I4 ENTREZGENE
  Q767I5 ENTREZGENE
  Q767I6 ENTREZGENE, UniProtKB/TrEMBL
  Q767I7 ENTREZGENE, UniProtKB/TrEMBL
  Q767I8 ENTREZGENE
  Q767I9 ENTREZGENE, UniProtKB/TrEMBL
  Q767J0 ENTREZGENE
  Q767J1 ENTREZGENE, UniProtKB/TrEMBL
  Q8CJ01 ENTREZGENE
UniProt Secondary Q5U2Z9 UniProtKB/Swiss-Prot
  Q8CJ01 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Pcdha4  protocadherin alpha 4      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Pcdha4  protocadherin alpha 4      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in the secretory stage of incisor development 633554