Pcdh7 (protocadherin 7) - Rat Genome Database
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Gene: Pcdh7 (protocadherin 7) Rattus norvegicus
Analyze
Symbol: Pcdh7
Name: protocadherin 7
RGD ID: 1303209
Description: Predicted to have calcium ion binding activity. Predicted to be involved in cell adhesion. Predicted to localize to integral component of plasma membrane. Orthologous to human PCDH7 (protocadherin 7); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: protocadherin-7
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01454,649,054 - 55,081,632 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1455,072,200 - 55,081,551 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01454,783,951 - 55,216,900 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41456,609,036 - 57,323,892 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11456,611,426 - 57,326,283 (-)NCBI
Celera1451,655,345 - 52,076,631 (-)NCBICelera
Cytogenetic Map14q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-diaminotoluene  (ISO)
2-hydroxypropanoic acid  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrylamide  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
aflatoxin M1  (ISO)
all-trans-retinoic acid  (ISO)
amiodarone  (ISO)
antirheumatic drug  (ISO)
arsenite(3-)  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
cefaloridine  (EXP)
chloroprene  (ISO)
choline  (ISO)
cisplatin  (ISO)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
dexamethasone  (ISO)
diazinon  (ISO)
dibutyl phthalate  (ISO)
dorsomorphin  (ISO)
ethanol  (ISO)
ferric oxide  (ISO)
folic acid  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
leflunomide  (ISO)
levonorgestrel  (ISO)
maneb  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
methotrexate  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
nickel atom  (ISO)
NS-398  (ISO)
oxaliplatin  (EXP)
panobinostat  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
phenylmercury acetate  (ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
rac-lactic acid  (ISO)
raloxifene  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sulforaphane  (ISO)
tamoxifen  (ISO)
testosterone  (EXP)
testosterone undecanoate  (ISO)
tetrachloromethane  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
tunicamycin  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:30361391  


Genomics

Comparative Map Data
Pcdh7
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01454,649,054 - 55,081,632 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1455,072,200 - 55,081,551 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01454,783,951 - 55,216,900 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41456,609,036 - 57,323,892 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11456,611,426 - 57,326,283 (-)NCBI
Celera1451,655,345 - 52,076,631 (-)NCBICelera
Cytogenetic Map14q11NCBI
PCDH7
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl430,720,415 - 31,146,805 (+)EnsemblGRCh38hg38GRCh38
GRCh38430,719,861 - 31,146,800 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37430,721,951 - 31,148,423 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36430,331,135 - 30,757,519 (+)NCBINCBI36hg18NCBI36
Build 34430,398,305 - 30,821,017NCBI
Celera431,175,622 - 31,601,081 (+)NCBI
Cytogenetic Map4p15.1NCBI
HuRef430,065,600 - 30,492,188 (+)NCBIHuRef
CHM1_1430,723,442 - 31,149,754 (+)NCBICHM1_1
Pcdh7
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39557,873,487 - 58,290,578 (+)NCBIGRCm39mm39
GRCm38557,716,145 - 58,133,236 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl557,717,967 - 58,133,230 (+)EnsemblGRCm38mm10GRCm38
MGSCv37558,109,260 - 58,523,479 (+)NCBIGRCm37mm9NCBIm37
MGSCv36558,006,337 - 58,017,692 (+)NCBImm8
Celera555,089,145 - 55,508,003 (+)NCBICelera
Cytogenetic Map5C1NCBI
Pcdh7
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544314,769,879 - 15,160,377 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544314,765,994 - 15,160,377 (-)NCBIChiLan1.0ChiLan1.0
PCDH7
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1430,365,744 - 30,789,466 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl430,366,855 - 30,370,132 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0425,111,142 - 25,535,925 (+)NCBIMhudiblu_PPA_v0panPan3
PCDH7
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl379,976,541 - 80,388,896 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1379,973,680 - 80,388,896 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Pcdh7
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936482197,723 - 588,912 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PCDH7
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl823,459,475 - 23,872,006 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1823,459,475 - 23,872,204 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2824,323,016 - 24,732,096 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PCDH7
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12719,204,550 - 19,631,845 (-)NCBI
Pcdh7
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247551,575,466 - 1,985,757 (-)NCBI

Position Markers
D14Mit8  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01454,942,901 - 54,943,045NCBIRnor6.0
Rnor_5.01455,077,566 - 55,077,710UniSTSRnor5.0
RGSC_v3.41456,484,802 - 56,484,946UniSTSRGSC3.4
RGSC_v3.41457,187,009 - 57,187,154RGDRGSC3.4
RGSC_v3.41456,484,801 - 56,484,946RGDRGSC3.4
RGSC_v3.41457,187,010 - 57,187,154UniSTSRGSC3.4
RGSC_v3.11457,189,230 - 57,189,560RGD
Celera1451,941,915 - 51,942,059UniSTS
Cytogenetic Map14q11UniSTS
D14Got111  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01455,044,723 - 55,044,919NCBIRnor6.0
Rnor_5.01455,179,778 - 55,179,974UniSTSRnor5.0
RGSC_v3.41457,287,037 - 57,287,233UniSTSRGSC3.4
Celera1452,040,025 - 52,040,221UniSTS
Cytogenetic Map14q11UniSTS
D14Got110  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01455,044,819 - 55,044,933NCBIRnor6.0
Rnor_5.01455,179,874 - 55,179,988UniSTSRnor5.0
RGSC_v3.41457,287,133 - 57,287,247UniSTSRGSC3.4
Celera1452,040,121 - 52,040,235UniSTS
Cytogenetic Map14q11UniSTS
BE102626  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01454,965,318 - 54,965,467NCBIRnor6.0
Rnor_5.01455,100,373 - 55,100,522UniSTSRnor5.0
RGSC_v3.41457,212,040 - 57,212,189UniSTSRGSC3.4
Celera1451,965,030 - 51,965,179UniSTS
Cytogenetic Map14q11UniSTS
RH143022  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01455,071,360 - 55,071,524NCBIRnor6.0
Rnor_5.01455,206,634 - 55,206,798UniSTSRnor5.0
RGSC_v3.41457,313,701 - 57,313,865UniSTSRGSC3.4
Celera1452,066,440 - 52,066,604UniSTS
Cytogenetic Map14q11UniSTS
BE121006  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01454,713,963 - 54,714,122NCBIRnor6.0
Rnor_6.0X135,564,508 - 135,564,667NCBIRnor6.0
Rnor_5.01454,848,626 - 54,848,785UniSTSRnor5.0
Rnor_5.0X135,634,659 - 135,634,818UniSTSRnor5.0
RGSC_v3.41456,669,488 - 56,669,647UniSTSRGSC3.4
RGSC_v3.4X135,127,481 - 135,127,640UniSTSRGSC3.4
CeleraX126,849,765 - 126,849,924UniSTS
Celera1451,715,893 - 51,716,052UniSTS
Cytogenetic Map14q11UniSTS
PCDH7  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01455,082,149 - 55,082,342NCBIRnor6.0
Rnor_5.01455,217,423 - 55,217,616UniSTSRnor5.0
RGSC_v3.41457,324,490 - 57,324,683UniSTSRGSC3.4
Celera1452,077,229 - 52,077,422UniSTS
Cytogenetic Map14q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14975643572854397Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin141053997755539977Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)141053997755539977Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)141072926861873323Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1412680424106641756Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)142018938665189386Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)142145756566457565Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143259392686191589Rat
2324617Coatc2Coat color QTL 20.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)143303991261783215Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143316331673391571Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)144031561085315610Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)144031561085315610Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)144031561085315610Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)144031561085315610Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)144163756980841518Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1442442731108833671Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1443910761105074364Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1451818462105074364Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:42
Count of miRNA genes:34
Interacting mature miRNAs:41
Transcripts:ENSRNOT00000049245
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.


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 41 4 4 4 56 16 22 6
Low 3 2 51 35 19 35 8 9 18 19 17 5 8
Below cutoff 2 2 2 2 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001004087 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251022 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251023 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770189 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599291 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599292 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599293 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07015413 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07015414 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07015415 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01079929 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01079930 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01079931 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01079932 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01079933 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01079934 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01079935 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01079936 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01079937 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01079938 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01079939 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01079940 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY690613 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY690614 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY690615 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY690616 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226048 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000049245   ⟹   ENSRNOP00000045705
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1455,072,200 - 55,081,551 (-)Ensembl
RefSeq Acc Id: NM_001004087   ⟹   NP_001004087
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01454,652,957 - 55,081,551 (-)NCBI
Rnor_5.01454,783,951 - 55,216,900 (-)NCBI
RGSC_v3.41456,609,036 - 57,323,892 (-)RGD
Celera1451,655,345 - 52,076,631 (-)RGD
Sequence:
RefSeq Acc Id: XM_006251017   ⟹   XP_006251079
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01454,649,054 - 55,081,632 (-)NCBI
Rnor_5.01454,783,951 - 55,216,900 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251022   ⟹   XP_006251084
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01455,016,737 - 55,081,632 (-)NCBI
Rnor_5.01454,783,951 - 55,216,900 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251023   ⟹   XP_006251085
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01455,071,907 - 55,081,632 (-)NCBI
Rnor_5.01454,783,951 - 55,216,900 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008770189   ⟹   XP_008768411
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01454,837,220 - 55,081,632 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599291   ⟹   XP_017454780
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01454,653,266 - 55,081,632 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599292   ⟹   XP_017454781
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01454,837,220 - 55,081,632 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599293   ⟹   XP_017454782
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01454,653,217 - 55,081,632 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001004087   ⟸   NM_001004087
- Peptide Label: precursor
- UniProtKB: Q68HB5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251079   ⟸   XM_006251017
- Peptide Label: isoform X1
- UniProtKB: Q68HB6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251084   ⟸   XM_006251022
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006251085   ⟸   XM_006251023
- Peptide Label: isoform X5
- UniProtKB: Q68HB8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008768411   ⟸   XM_008770189
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017454782   ⟸   XM_017599293
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017454780   ⟸   XM_017599291
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017454781   ⟸   XM_017599292
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000045705   ⟸   ENSRNOT00000049245
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 (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)
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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
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/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 (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)
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
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
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/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
LE/Stm (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
LEW/Crl (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
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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
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 (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
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
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 (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 (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
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 (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 (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/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 (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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 55080595 55080596 G C snv WN/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303209 AgrOrtholog
Ensembl Genes ENSRNOG00000012367 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000045705 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000049245 ENTREZGENE, UniProtKB/TrEMBL
InterPro Cadherin UniProtKB/TrEMBL
  Cadherin-like UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
  Cadherin_N UniProtKB/TrEMBL
  Protocadherin UniProtKB/TrEMBL
KEGG Report rno:360942 UniProtKB/TrEMBL
NCBI Gene 360942 ENTREZGENE
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
  Protocadherin UniProtKB/TrEMBL
PhenoGen Pcdh7 PhenoGen
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin UniProtKB/TrEMBL
UniGene Rn.228266 ENTREZGENE
  Rn.230374 ENTREZGENE
UniProt Q68HB5 ENTREZGENE, UniProtKB/TrEMBL
  Q68HB6 ENTREZGENE, UniProtKB/TrEMBL
  Q68HB7_RAT UniProtKB/TrEMBL
  Q68HB8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-11-17 Pcdh7  protocadherin 7      Symbol and Name status set to approved 1299863 APPROVED
2005-07-14 Pcdh7  protocadherin 7      Symbol and Name status set to provisional 70820 PROVISIONAL