Cdh8 (cadherin 8) - Rat Genome Database

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Gene: Cdh8 (cadherin 8) Rattus norvegicus
Analyze
Symbol: Cdh8
Name: cadherin 8
RGD ID: 69286
Description: Predicted to have cadherin binding activity; calcium ion binding activity; and identical protein binding activity. Predicted to be involved in several processes, including calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules; cell-cell junction organization; and glutamatergic synaptic transmission. Predicted to localize to several cellular components, including catenin complex; glutamatergic synapse; and synaptic cleft. Orthologous to human CDH8 (cadherin 8); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3,4-methylenedioxymethamphetamine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: cadherin-8
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
mRatBN7.2195,494,038 - 5,901,810 (+)NCBI
Rnor_6.0 Ensembl196,046,665 - 6,426,216 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0196,031,654 - 6,431,502 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0196,024,414 - 6,424,501 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4195,685,862 - 6,014,208 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1195,690,687 - 6,019,033 (+)NCBI
Celera195,459,507 - 5,851,781 (+)NCBICelera
Cytogenetic Map19p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Additional References at PubMed
PMID:17392463   PMID:18064706   PMID:18682221   PMID:20848607   PMID:25126785   PMID:25158904  


Genomics

Comparative Map Data
Cdh8
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2195,494,038 - 5,901,810 (+)NCBI
Rnor_6.0 Ensembl196,046,665 - 6,426,216 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0196,031,654 - 6,431,502 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0196,024,414 - 6,424,501 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4195,685,862 - 6,014,208 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1195,690,687 - 6,019,033 (+)NCBI
Celera195,459,507 - 5,851,781 (+)NCBICelera
Cytogenetic Map19p13NCBI
CDH8
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1661,647,242 - 62,037,035 (-)EnsemblGRCh38hg38GRCh38
GRCh381661,640,398 - 62,036,446 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371661,681,154 - 62,070,342 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361660,244,736 - 60,627,537 (-)NCBINCBI36hg18NCBI36
Build 341660,244,735 - 60,627,537NCBI
Celera1646,191,618 - 46,573,463 (-)NCBI
Cytogenetic Map16q21NCBI
HuRef1647,554,742 - 47,940,223 (-)NCBIHuRef
CHM1_11663,092,871 - 63,477,579 (-)NCBICHM1_1
Cdh8
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39899,751,103 - 100,144,298 (-)NCBIGRCm39mm39
GRCm39 Ensembl899,751,103 - 100,143,103 (-)Ensembl
GRCm38899,024,471 - 99,417,666 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl899,024,471 - 99,416,471 (-)EnsemblGRCm38mm10GRCm38
MGSCv378101,552,669 - 101,940,357 (-)NCBIGRCm37mm9NCBIm37
MGSCv368101,917,898 - 102,305,586 (-)NCBImm8
Celera8103,311,393 - 103,701,585 (-)NCBICelera
Cytogenetic Map8D1NCBI
cM Map849.4NCBI
Cdh8
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543318,734,640 - 19,080,140 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543318,737,715 - 19,094,202 (-)NCBIChiLan1.0ChiLan1.0
CDH8
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11661,053,767 - 61,438,175 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1661,054,214 - 61,437,569 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01641,935,706 - 42,326,055 (-)NCBIMhudiblu_PPA_v0panPan3
CDH8
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1586,402,078 - 86,743,563 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl586,402,570 - 86,743,755 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha586,362,811 - 86,704,824 (+)NCBI
ROS_Cfam_1.0586,964,546 - 87,308,062 (+)NCBI
UMICH_Zoey_3.1586,701,569 - 87,060,354 (+)NCBI
UNSW_CanFamBas_1.0586,393,059 - 86,736,809 (+)NCBI
UU_Cfam_GSD_1.0587,027,257 - 87,369,201 (+)NCBI
Cdh8
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934946,467,163 - 46,806,813 (+)NCBI
SpeTri2.0NW_00493647512,784,997 - 13,121,912 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CDH8
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl622,923,140 - 23,279,296 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1622,922,965 - 23,644,501 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2621,405,526 - 21,523,536 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CDH8
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1547,450,781 - 47,853,805 (-)NCBI
ChlSab1.1 Ensembl547,465,277 - 47,853,706 (-)Ensembl
Cdh8
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474624,348,163 - 24,733,583 (+)NCBI

Position Markers
RH141996  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2195,863,486 - 5,863,676 (+)MAPPER
Rnor_6.0196,396,193 - 6,396,382NCBIRnor6.0
Rnor_5.0196,390,815 - 6,391,004UniSTSRnor5.0
RGSC_v3.4195,987,996 - 5,988,185UniSTSRGSC3.4
Celera195,825,570 - 5,825,759UniSTS
RH 3.4 Map190.0UniSTS
Cytogenetic Map19p13UniSTS
BE119945  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2195,783,208 - 5,783,406 (+)MAPPER
Rnor_6.0196,316,971 - 6,317,168NCBIRnor6.0
Rnor_5.0196,312,018 - 6,312,215UniSTSRnor5.0
RGSC_v3.4195,907,699 - 5,907,896UniSTSRGSC3.4
Celera195,745,284 - 5,745,481UniSTS
RH 3.4 Map190.0UniSTS
Cytogenetic Map19p13UniSTS
AW530740  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2195,663,850 - 5,664,009 (+)MAPPER
Rnor_6.0196,202,529 - 6,202,687NCBIRnor6.0
Rnor_5.0196,194,762 - 6,194,920UniSTSRnor5.0
Celera195,629,530 - 5,629,688UniSTS
RH 3.4 Map190.0UniSTS
Cytogenetic Map19p13UniSTS
CDH8_1919  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2195,889,202 - 5,889,993 (+)MAPPER
Rnor_6.0196,421,900 - 6,422,690NCBIRnor6.0
Rnor_5.0196,416,522 - 6,417,312UniSTSRnor5.0
RGSC_v3.4196,013,707 - 6,014,497UniSTSRGSC3.4
Celera195,851,280 - 5,852,070UniSTS
Cytogenetic Map19p13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411590Foco7Food consumption QTL 76.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)19124933090Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127635288Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19129558305Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19129558305Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19132379055Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19138221845Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19138221845Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19138221845Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19138221845Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19104464846044648Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19195770746957707Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19243296347217667Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)19370183548701835Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)19370183548701835Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19500757143907843Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:92
Count of miRNA genes:71
Interacting mature miRNAs:81
Transcripts:ENSRNOT00000067454
Prediction methods:Microtar, 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 64
Low 6 9 6 10 6 31
Below cutoff 3 18 16 9 7 9 5 5 14 10 7 5

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_053393 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601376 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601377 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601378 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601379 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601380 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098039 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098040 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098041 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AAHX01096923 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01096927 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01096928 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01096929 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01096931 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01096933 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01096934 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01096939 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF177679 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474006 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000303 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000084126   ⟹   ENSRNOP00000072182
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl196,046,665 - 6,426,216 (+)Ensembl
RefSeq Acc Id: NM_053393   ⟹   NP_445845
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2195,494,174 - 5,889,704 (+)NCBI
Rnor_6.0196,031,935 - 6,422,401 (+)NCBI
Rnor_5.0196,024,414 - 6,424,501 (+)NCBI
RGSC_v3.4195,685,862 - 6,014,208 (+)RGD
Celera195,459,507 - 5,851,781 (+)RGD
Sequence:
RefSeq Acc Id: XM_017601376   ⟹   XP_017456865
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0196,031,654 - 6,426,876 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601377   ⟹   XP_017456866
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2195,494,039 - 5,894,245 (+)NCBI
Rnor_6.0196,046,721 - 6,426,876 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601378   ⟹   XP_017456867
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2195,494,039 - 5,901,810 (+)NCBI
Rnor_6.0196,046,721 - 6,431,502 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601379   ⟹   XP_017456868
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0196,299,140 - 6,426,876 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601380   ⟹   XP_017456869
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2195,494,038 - 5,901,810 (+)NCBI
Rnor_6.0196,046,721 - 6,431,502 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039098039   ⟹   XP_038953967
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2195,494,041 - 5,822,671 (+)NCBI
RefSeq Acc Id: XM_039098040   ⟹   XP_038953968
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2195,494,038 - 5,810,719 (+)NCBI
RefSeq Acc Id: XM_039098041   ⟹   XP_038953969
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2195,494,038 - 5,813,828 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_445845   ⟸   NM_053393
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_017456865   ⟸   XM_017601376
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017456869   ⟸   XM_017601380
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017456867   ⟸   XM_017601378
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017456866   ⟸   XM_017601377
- Peptide Label: isoform X2
- UniProtKB: A0A0G2K2C1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456868   ⟸   XM_017601379
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000072182   ⟸   ENSRNOT00000084126
RefSeq Acc Id: XP_038953969   ⟸   XM_039098041
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038953968   ⟸   XM_039098040
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038953967   ⟸   XM_039098039
- Peptide Label: isoform X4
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)
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 (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
BBDP/Wor (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
BN/SsN (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
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)
Visual CSV TAB Printer
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)
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)
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
FHH/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)
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)
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)
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
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/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
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 (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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69286 AgrOrtholog
Ensembl Genes ENSRNOG00000056643 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000072182 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000084126 UniProtKB/TrEMBL
Gene3D-CATH 4.10.900.10 UniProtKB/Swiss-Prot
InterPro Cadherin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_cytoplasmic-dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Catenin_binding_dom_sf UniProtKB/Swiss-Prot
NCBI Gene 84408 ENTREZGENE
PANTHER PTHR24027 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cdh8 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 A0A0G2K2C1 ENTREZGENE, UniProtKB/TrEMBL
  CADH8_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O54801 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Cdh8  cadherin 8      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference