Cdh23 (cadherin-related 23) - Rat Genome Database

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Gene: Cdh23 (cadherin-related 23) Rattus norvegicus
Analyze
Symbol: Cdh23
Name: cadherin-related 23
RGD ID: 619760
Description: Enables protein N-terminus binding activity. Predicted to be involved in several processes, including equilibrioception; photoreceptor cell maintenance; and regulation of cytosolic calcium ion concentration. Predicted to act upstream of or within several processes, including animal organ morphogenesis; righting reflex; and sensory perception of sound. Located in apical part of cell. Human ortholog(s) of this gene implicated in Usher syndrome type 1D; autosomal recessive nonsyndromic deafness; autosomal recessive nonsyndromic deafness 12; and pituitary adenoma 5. Orthologous to human CDH23 (cadherin related 23); PARTICIPATES IN auditory mechanotransduction pathway; retinitis pigmentosa pathway; INTERACTS WITH 3,3',4,4',5-pentachlorobiphenyl; acrylamide; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: cadherin 23 (otocadherin); cadherin related 23; cadherin-23; cadherin-23-like; LOC103694885; otocadherin; W; Waltzing
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22028,240,643 - 28,622,490 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl2028,240,645 - 28,622,419 (-)Ensembl
Rnor_6.02029,857,018 - 30,263,758 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2029,857,637 - 29,990,111 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02031,668,747 - 32,073,985 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42027,622,049 - 28,016,145 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12027,635,850 - 28,029,945 (-)NCBI
Celera2029,678,961 - 30,059,893 (-)NCBICelera
Cytogenetic Map20q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Di Palma F, etal., Nat Genet. 2001 Jan;27(1):103-7.
2. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Gillespie PG and Muller U, Cell. 2009 Oct 2;139(1):33-44. doi: 10.1016/j.cell.2009.09.010.
4. GOA data from the GO Consortium
5. Hwang JH, etal., Otolaryngol Head Neck Surg. 2012 Sep;147(3):531-4. doi: 10.1177/0194599812446904. Epub 2012 May 11.
6. Kazmierczak P and Muller U, Trends Neurosci. 2012 Apr;35(4):220-9. doi: 10.1016/j.tins.2011.10.007. Epub 2011 Dec 15.
7. Libby RT, etal., Exp Eye Res. 2003 Dec;77(6):731-9.
8. MGD data from the GO Consortium
9. Michel V, etal., Dev Biol 2005 Apr 15;280(2):281-94.
10. Mouse Genome Database (MGD)
11. Nakajima D, etal., Brain Res Mol Brain Res 2001 Oct 19;94(1-2):85-95.
12. NCBI rat LocusLink and RefSeq merged data July 26, 2002
13. Noben-Trauth K, etal., Nat Genet 2003 Sep;35(1):21-3. Epub 2003 Aug 10.
14. OMIM Disease Annotation Pipeline
15. RGD automated data pipeline
16. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
17. RGD automated import pipeline for gene-chemical interactions
18. RGD comprehensive gene curation
19. Selvakumar D, etal., J Biol Chem. 2013 Mar 8;288(10):7215-29. doi: 10.1074/jbc.M112.443226. Epub 2013 Jan 17.
20. Wagatsuma M, etal., Clin Genet. 2007 Oct;72(4):339-44.
21. Wright AF, etal., Nat Rev Genet. 2010 Apr;11(4):273-84. doi: 10.1038/nrg2717.
22. Yang M, etal., Wei Sheng Yan Jiu. 2006 Jan;35(1):19-22.
Additional References at PubMed
PMID:7610888   PMID:8790740   PMID:9039475   PMID:9325047   PMID:9447922   PMID:10452381   PMID:11322776   PMID:11386759   PMID:12121736   PMID:12485990   PMID:13336002   PMID:14578428  
PMID:14759567   PMID:15537665   PMID:15820310   PMID:15882574   PMID:15925194   PMID:16481439   PMID:16679490   PMID:16962269   PMID:17050716   PMID:17234811   PMID:17329413   PMID:18339676  
PMID:19756182   PMID:23217710   PMID:24920589  


Genomics

Comparative Map Data
Cdh23
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22028,240,643 - 28,622,490 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl2028,240,645 - 28,622,419 (-)Ensembl
Rnor_6.02029,857,018 - 30,263,758 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2029,857,637 - 29,990,111 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02031,668,747 - 32,073,985 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42027,622,049 - 28,016,145 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12027,635,850 - 28,029,945 (-)NCBI
Celera2029,678,961 - 30,059,893 (-)NCBICelera
Cytogenetic Map20q11NCBI
CDH23
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1071,396,920 - 71,815,947 (+)EnsemblGRCh38hg38GRCh38
GRCh381071,396,920 - 71,815,947 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371073,156,677 - 73,575,704 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361072,826,697 - 73,245,710 (+)NCBINCBI36hg18NCBI36
Build 341072,826,696 - 73,076,543NCBI
Celera1066,439,492 - 66,858,274 (+)NCBI
Cytogenetic Map10q22.1NCBI
HuRef1067,150,783 - 67,156,961 (+)NCBIHuRef
CHM1_11073,439,263 - 73,857,682 (+)NCBICHM1_1
Cdh23
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391060,138,527 - 60,532,291 (-)NCBIGRCm39mm39
GRCm39 Ensembl1060,138,527 - 60,532,269 (-)Ensembl
GRCm381060,302,748 - 60,696,513 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1060,302,748 - 60,696,490 (-)EnsemblGRCm38mm10GRCm38
MGSCv371059,766,022 - 60,159,238 (-)NCBIGRCm37mm9NCBIm37
MGSCv361059,698,731 - 60,052,690 (-)NCBImm8
Celera1061,400,142 - 61,796,629 (-)NCBICelera
Cytogenetic Map10B4NCBI
cM Map1030.11NCBI
Cdh23
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543719,684,473 - 20,003,819 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543719,683,792 - 20,044,718 (-)NCBIChiLan1.0ChiLan1.0
CDH23
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11070,391,661 - 70,810,240 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1070,434,801 - 70,810,240 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01067,866,979 - 68,286,008 (+)NCBIMhudiblu_PPA_v0panPan3
CDH23
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1422,206,972 - 22,570,875 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl422,207,001 - 22,571,131 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha422,343,327 - 22,708,459 (+)NCBI
ROS_Cfam_1.0422,485,192 - 22,847,328 (+)NCBI
UMICH_Zoey_3.1422,382,421 - 22,753,409 (+)NCBI
UNSW_CanFamBas_1.0422,588,293 - 22,952,028 (+)NCBI
UU_Cfam_GSD_1.0422,941,027 - 23,306,533 (+)NCBI
LOC101969963
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721358,586,064 - 58,899,858 (-)NCBI
SpeTri2.0NW_0049365217,078,874 - 7,285,361 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CDH23
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1474,223,089 - 74,733,834 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11474,267,547 - 74,734,623 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21480,226,063 - 80,626,249 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103216037
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1959,475,126 - 59,893,824 (-)NCBI
Vero_WHO_p1.0NW_02366604820,118,874 - 20,208,512 (-)NCBI
Cdh23
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247545,356,006 - 5,725,774 (+)NCBI

Position Markers
D20Got108  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22028,540,995 - 28,541,219 (+)MAPPERmRatBN7.2
Rnor_6.02030,181,841 - 30,182,064NCBIRnor6.0
Rnor_5.02031,992,210 - 31,992,433UniSTSRnor5.0
RGSC_v3.42027,934,411 - 27,934,634UniSTSRGSC3.4
Celera2029,978,381 - 29,978,604UniSTS
Cytogenetic Map20q11UniSTS
RH128021  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22028,240,158 - 28,240,358 (+)MAPPERmRatBN7.2
Rnor_6.02029,856,534 - 29,856,733NCBIRnor6.0
Rnor_5.02031,668,263 - 31,668,462UniSTSRnor5.0
RGSC_v3.42027,621,565 - 27,621,764UniSTSRGSC3.4
Celera2029,678,477 - 29,678,676UniSTS
RH 3.4 Map21521.6UniSTS
Cytogenetic Map20q11UniSTS
RH131718  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22028,303,636 - 28,303,837 (+)MAPPERmRatBN7.2
Rnor_6.02029,919,756 - 29,919,956NCBIRnor6.0
Rnor_5.02031,731,221 - 31,731,421UniSTSRnor5.0
RGSC_v3.42027,684,647 - 27,684,847UniSTSRGSC3.4
Celera2029,741,790 - 29,741,990UniSTS
Cytogenetic Map20q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
4889870Pur30Proteinuria QTL 30190.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20804241029322208Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:140
Count of miRNA genes:116
Interacting mature miRNAs:123
Transcripts:ENSRNOT00000048029
Prediction methods:Microtar, Miranda, Rnahybrid
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 6
Low 2 43 17 2 19 2 8 10 72 24 35 11 8
Below cutoff 1 28 27 27 1 2 11

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_053644 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098361 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098362 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098363 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098364 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098366 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098367 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098368 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098369 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098370 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098371 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098372 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098373 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098374 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098375 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098376 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098377 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB053447 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000324 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000048029   ⟹   ENSRNOP00000048338
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2028,241,262 - 28,622,419 (-)Ensembl
Rnor_6.0 Ensembl2029,857,637 - 29,990,111 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100038   ⟹   ENSRNOP00000086738
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2028,240,645 - 28,622,419 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118579   ⟹   ENSRNOP00000096099
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2028,240,645 - 28,622,419 (-)Ensembl
RefSeq Acc Id: NM_053644   ⟹   NP_446096
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22028,240,643 - 28,622,419 (-)NCBI
Rnor_6.02029,857,018 - 30,263,758 (-)NCBI
Rnor_5.02031,668,747 - 32,073,985 (-)NCBI
RGSC_v3.42027,622,049 - 28,016,145 (-)RGD
Celera2029,678,961 - 30,059,893 (-)RGD
Sequence:
RefSeq Acc Id: XM_039098361   ⟹   XP_038954289
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22028,240,643 - 28,622,483 (-)NCBI
RefSeq Acc Id: XM_039098362   ⟹   XP_038954290
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22028,240,643 - 28,622,484 (-)NCBI
RefSeq Acc Id: XM_039098363   ⟹   XP_038954291
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22028,240,643 - 28,622,485 (-)NCBI
RefSeq Acc Id: XM_039098364   ⟹   XP_038954292
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22028,241,452 - 28,622,485 (-)NCBI
RefSeq Acc Id: XM_039098366   ⟹   XP_038954294
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22028,244,883 - 28,622,488 (-)NCBI
RefSeq Acc Id: XM_039098367   ⟹   XP_038954295
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22028,240,643 - 28,447,919 (-)NCBI
RefSeq Acc Id: XM_039098368   ⟹   XP_038954296
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22028,245,323 - 28,622,490 (-)NCBI
RefSeq Acc Id: XM_039098369   ⟹   XP_038954297
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22028,248,051 - 28,622,490 (-)NCBI
RefSeq Acc Id: XM_039098370   ⟹   XP_038954298
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22028,262,585 - 28,622,490 (-)NCBI
RefSeq Acc Id: XM_039098371   ⟹   XP_038954299
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22028,262,585 - 28,622,490 (-)NCBI
RefSeq Acc Id: XM_039098372   ⟹   XP_038954300
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22028,240,643 - 28,320,953 (-)NCBI
RefSeq Acc Id: XM_039098373   ⟹   XP_038954301
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22028,307,565 - 28,622,489 (-)NCBI
RefSeq Acc Id: XM_039098374   ⟹   XP_038954302
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22028,303,207 - 28,622,488 (-)NCBI
RefSeq Acc Id: XM_039098375   ⟹   XP_038954303
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22028,307,565 - 28,622,488 (-)NCBI
RefSeq Acc Id: XM_039098376   ⟹   XP_038954304
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22028,313,247 - 28,622,488 (-)NCBI
RefSeq Acc Id: XM_039098377   ⟹   XP_038954305
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22028,335,235 - 28,622,488 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_446096   ⟸   NM_053644
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000048338   ⟸   ENSRNOT00000048029
RefSeq Acc Id: XP_038954291   ⟸   XM_039098363
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038954290   ⟸   XM_039098362
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038954289   ⟸   XM_039098361
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038954295   ⟸   XM_039098367
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038954300   ⟸   XM_039098372
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038954292   ⟸   XM_039098364
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038954294   ⟸   XM_039098366
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038954296   ⟸   XM_039098368
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038954297   ⟸   XM_039098369
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038954299   ⟸   XM_039098371
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038954298   ⟸   XM_039098370
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038954302   ⟸   XM_039098374
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038954301   ⟸   XM_039098373
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038954303   ⟸   XM_039098375
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038954304   ⟸   XM_039098376
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038954305   ⟸   XM_039098377
- Peptide Label: isoform X15
RefSeq Acc Id: ENSRNOP00000096099   ⟸   ENSRNOT00000118579
RefSeq Acc Id: ENSRNOP00000086738   ⟸   ENSRNOT00000100038
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)
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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
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)
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
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)
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
F344/NCrl (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/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
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)
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
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)
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
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)
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
GH/OmrMcwi (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)
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)
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
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)
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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/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
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)
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: 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)
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
LEXF10A/StmMcwi (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: 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)
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
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)
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
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)
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
MNS/Gib (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
MR/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
MR/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
MWF/Hsd (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (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
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHR/OlalpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (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
SR/JrHsd (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WAG/RijCrl (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: 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)
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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 (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:619760 AgrOrtholog
Ensembl Genes ENSRNOG00000033087 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000048338 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000048029 UniProtKB/TrEMBL
InterPro Cadherin-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CDH23 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:114102 UniProtKB/Swiss-Prot
NCBI Gene 114102 ENTREZGENE
PANTHER PTHR24025:SF18 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cdh23 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 CAD23_RAT UniProtKB/Swiss-Prot
  F1LPE5_RAT UniProtKB/TrEMBL
  P58365 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Cdh23  cadherin-related 23  LOC103694885  cadherin-23-like  Data Merged 737654 PROVISIONAL
2014-08-25 LOC103694885  cadherin-23-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2012-01-06 Cdh23  cadherin-related 23  Cdh23  cadherin 23 (otocadherin)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Cdh23  cadherin 23 (otocadherin)    cadherin related 23  Name updated 1299863 APPROVED
2002-08-07 Cdh23  cadherin related 23      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression enriched in testis 633048