Pcdha4 (protocadherin alpha 4) - Rat Genome Database

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Gene: Pcdha4 (protocadherin alpha 4) Rattus norvegicus
Analyze
Symbol: Pcdha4
Name: protocadherin alpha 4
RGD ID: 620337
Description: Predicted to enable calcium ion 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 integral component of plasma membrane. Orthologous to several human genes including PCDHA4 (protocadherin alpha 4); INTERACTS WITH 17alpha-ethynylestradiol; ammonium chloride; beta-naphthoflavone.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also 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 Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21828,581,040 - 28,846,214 (+)NCBImRatBN7.2
Rnor_6.01829,950,217 - 30,215,901 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,966,245 - 29,968,614 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,972,808 - 29,975,192 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,987,206 - 30,215,897 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01829,670,058 - 29,924,443 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41829,683,478 - 29,928,030 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11829,710,123 - 29,954,676 (+)NCBI
Celera1828,311,641 - 28,552,754 (+)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

Molecular Function

References

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
mRatBN7.21828,581,040 - 28,846,214 (+)NCBImRatBN7.2
Rnor_6.01829,950,217 - 30,215,901 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,966,245 - 29,968,614 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,972,808 - 29,975,192 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,987,206 - 30,215,897 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01829,670,058 - 29,924,443 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41829,683,478 - 29,928,030 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11829,710,123 - 29,954,676 (+)NCBI
Celera1828,311,641 - 28,552,754 (+)NCBICelera
Cytogenetic Map18p11NCBI
PCDHA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5140,806,929 - 141,012,347 (+)EnsemblGRCh38hg38GRCh38
GRCh385140,807,068 - 141,012,347 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh375140,186,653 - 140,391,932 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,166,856 - 140,372,113 (+)NCBINCBI36hg18NCBI36
Build 345140,166,855 - 140,169,353NCBI
Celera5136,263,450 - 136,468,708 (+)NCBI
Cytogenetic Map5q31.3NCBI
HuRef5135,331,387 - 135,536,628 (+)NCBIHuRef
CHM1_15139,619,864 - 139,825,092 (+)NCBICHM1_1
Pcdha4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,085,742 - 37,320,710 (+)NCBIGRCm39mm39
GRCm39 Ensembl1837,085,701 - 37,320,714 (+)Ensembl
GRCm381836,952,689 - 37,187,657 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1836,952,648 - 37,187,661 (+)EnsemblGRCm38mm10GRCm38
MGSCv371837,112,343 - 37,347,311 (+)NCBIGRCm37mm9NCBIm37
MGSCv361837,078,663 - 37,313,631 (+)NCBImm8
Celera1837,399,452 - 37,411,288 (+)NCBICelera
Cytogenetic Map18B2- B3NCBI
PCDHA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1 Ensembl5142,286,433 - 142,289,088 (+)Ensemblpanpan1.1panPan2
PCDHA4
(Canis lupus familiaris - dog)
No map positions available.

Position Markers
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


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 442.981total urine 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

miRNA Target Status

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.


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 25 1
Low 16 23 4 19 4 7 7 89 45 60 20 7
Below cutoff 5 53 36 23 18 23 9 14 6 25 19 2 9

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
GenBank Nucleotide AB045585 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB045586 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB113384 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB113385 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB113386 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB113387 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB113388 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB113389 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB113390 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB113391 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB113392 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB113393 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB113394 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB113395 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB113396 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB113397 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB113398 (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
  AF539749 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF539750 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY573971 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY573972 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY573973 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY573974 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY573975 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY573976 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY573977 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY573978 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY573979 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY573980 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY573981 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY573982 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY573983 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY573984 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY573985 (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
  JACYVU010000299 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000074028   ⟹   ENSRNOP00000066853
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1829,966,245 - 29,968,614 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000074051   ⟹   ENSRNOP00000067199
RefSeq Status:
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: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21828,667,179 - 28,846,214 (+)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  
GenBank Protein AAF87062 (Get FASTA)   NCBI Sequence Viewer  
  AAH85793 (Get FASTA)   NCBI Sequence Viewer  
  AAN31757 (Get FASTA)   NCBI Sequence Viewer  
  AAN31758 (Get FASTA)   NCBI Sequence Viewer  
  AAT77553 (Get FASTA)   NCBI Sequence Viewer  
  AAT77554 (Get FASTA)   NCBI Sequence Viewer  
  AAT77555 (Get FASTA)   NCBI Sequence Viewer  
  AAT77556 (Get FASTA)   NCBI Sequence Viewer  
  AAT77557 (Get FASTA)   NCBI Sequence Viewer  
  AAT77558 (Get FASTA)   NCBI Sequence Viewer  
  AAT77559 (Get FASTA)   NCBI Sequence Viewer  
  AAT77560 (Get FASTA)   NCBI Sequence Viewer  
  AAT77561 (Get FASTA)   NCBI Sequence Viewer  
  AAT77562 (Get FASTA)   NCBI Sequence Viewer  
  AAT77563 (Get FASTA)   NCBI Sequence Viewer  
  AAT77564 (Get FASTA)   NCBI Sequence Viewer  
  AAT77565 (Get FASTA)   NCBI Sequence Viewer  
  AAT77566 (Get FASTA)   NCBI Sequence Viewer  
  AAT77567 (Get FASTA)   NCBI Sequence Viewer  
  BAB61763 (Get FASTA)   NCBI Sequence Viewer  
  BAB61764 (Get FASTA)   NCBI Sequence Viewer  
  BAD06366 (Get FASTA)   NCBI Sequence Viewer  
  BAD06367 (Get FASTA)   NCBI Sequence Viewer  
  BAD06368 (Get FASTA)   NCBI Sequence Viewer  
  BAD06369 (Get FASTA)   NCBI Sequence Viewer  
  BAD06370 (Get FASTA)   NCBI Sequence Viewer  
  BAD06371 (Get FASTA)   NCBI Sequence Viewer  
  BAD06372 (Get FASTA)   NCBI Sequence Viewer  
  BAD06373 (Get FASTA)   NCBI Sequence Viewer  
  BAD06374 (Get FASTA)   NCBI Sequence Viewer  
  BAD06375 (Get FASTA)   NCBI Sequence Viewer  
  BAD06376 (Get FASTA)   NCBI Sequence Viewer  
  BAD06377 (Get FASTA)   NCBI Sequence Viewer  
  BAD06378 (Get FASTA)   NCBI Sequence Viewer  
  BAD06379 (Get FASTA)   NCBI Sequence Viewer  
  BAD06380 (Get FASTA)   NCBI Sequence Viewer  
  EDL76328 (Get FASTA)   NCBI Sequence Viewer  
  Q767I8 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_446385   ⟸   NM_053933
- Peptide Label: precursor
- UniProtKB: Q767I8 (UniProtKB/Swiss-Prot),   Q593X7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456311   ⟸   XM_017600822
- Peptide Label: isoform X6
- UniProtKB: Q767J1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456314   ⟸   XM_017600825
- Peptide Label: isoform X8
- UniProtKB: Q767I9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456316   ⟸   XM_017600827
- Peptide Label: isoform X9
- UniProtKB: Q767I7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456306   ⟸   XM_017600817
- Peptide Label: isoform X3
- UniProtKB: Q767I6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456305   ⟸   XM_017600816
- Peptide Label: isoform X2
- UniProtKB: Q767I2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456312   ⟸   XM_017600823
- Peptide Label: isoform X7
- UniProtKB: Q767I1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456307   ⟸   XM_017600818
- Peptide Label: isoform X4
- UniProtKB: Q767I0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456308   ⟸   XM_017600819
- Peptide Label: isoform X5
- UniProtKB: I6LBW4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456304   ⟸   XM_017600815
- Peptide Label: isoform X1
- UniProtKB: Q767H7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000067199   ⟸   ENSRNOT00000074051
RefSeq Acc Id: ENSRNOP00000066853   ⟸   ENSRNOT00000074028
RefSeq Acc Id: XP_038952476   ⟸   XM_039096548
- Peptide Label: isoform X10
Protein Domains
Cadherin

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620337 AgrOrtholog
Ensembl Genes ENSRNOG00000020119 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000047174 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000050378 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000027340 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000027372 UniProtKB/TrEMBL
  ENSRNOP00000027383 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000027393 UniProtKB/TrEMBL
  ENSRNOP00000066774 UniProtKB/TrEMBL
  ENSRNOP00000066853 UniProtKB/TrEMBL
  ENSRNOP00000067199 UniProtKB/TrEMBL
  ENSRNOP00000069635 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000074100 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000074164 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000075260 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027340 UniProtKB/TrEMBL
  ENSRNOT00000027372 UniProtKB/TrEMBL
  ENSRNOT00000027383 UniProtKB/TrEMBL
  ENSRNOT00000027393 UniProtKB/TrEMBL
  ENSRNOT00000074028 UniProtKB/TrEMBL
  ENSRNOT00000074051 UniProtKB/TrEMBL
  ENSRNOT00000075810 UniProtKB/TrEMBL
  ENSRNOT00000077824 UniProtKB/TrEMBL
  ENSRNOT00000079008 UniProtKB/TrEMBL
  ENSRNOT00000079794 UniProtKB/TrEMBL
  ENSRNOT00000084132 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7109469 IMAGE-MGC_LOAD
InterPro Cadherin-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_C UniProtKB/TrEMBL
  Cadherin_CBD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PCDHA1 UniProtKB/TrEMBL
  PCDHAC2 UniProtKB/TrEMBL
KEGG Report rno:116741 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:93781 IMAGE-MGC_LOAD
NCBI Gene 116741 ENTREZGENE
PANTHER PTHR24028:SF119 UniProtKB/TrEMBL
  PTHR24028:SF92 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_C_2 UniProtKB/TrEMBL
  Cadherin_tail UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pcdha4 PhenoGen
PRINTS CADHERIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49313 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt I6LBW4 ENTREZGENE, UniProtKB/TrEMBL
  M0RBC1_RAT UniProtKB/TrEMBL
  M0RC89_RAT UniProtKB/TrEMBL
  PCDA4_RAT UniProtKB/Swiss-Prot
  Q593X7 ENTREZGENE, UniProtKB/TrEMBL
  Q767H7 ENTREZGENE, UniProtKB/TrEMBL
  Q767I0 ENTREZGENE, UniProtKB/TrEMBL
  Q767I1 ENTREZGENE, UniProtKB/TrEMBL
  Q767I2 ENTREZGENE, UniProtKB/TrEMBL
  Q767I3_RAT UniProtKB/TrEMBL
  Q767I4_RAT UniProtKB/TrEMBL
  Q767I5_RAT UniProtKB/TrEMBL
  Q767I6 ENTREZGENE, UniProtKB/TrEMBL
  Q767I7 ENTREZGENE, UniProtKB/TrEMBL
  Q767I8 ENTREZGENE
  Q767I9 ENTREZGENE, UniProtKB/TrEMBL
  Q767J0_RAT UniProtKB/TrEMBL
  Q767J1 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary F1LM35 UniProtKB/TrEMBL
  F7F4E7 UniProtKB/TrEMBL
  F7F4G8 UniProtKB/TrEMBL
  M0RB51 UniProtKB/TrEMBL
  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