Ctnnd2 (catenin delta 2) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Ctnnd2 (catenin delta 2) Rattus norvegicus
Analyze
Symbol: Ctnnd2
Name: catenin delta 2
RGD ID: 620734
Description: Predicted to enable beta-catenin binding activity and cadherin binding activity. Predicted to be involved in several processes, including cell-cell junction assembly; dendritic spine morphogenesis; and regulation of canonical Wnt signaling pathway. Predicted to act upstream of or within learning; morphogenesis of a branching structure; and regulation of synaptic plasticity. Located in neuron projection; nucleus; and postsynaptic density. Human ortholog(s) of this gene implicated in anxiety disorder; major depressive disorder; and schizophrenia. Orthologous to human CTNND2 (catenin delta 2); INTERACTS WITH 1,3,5-trinitro-1,3,5-triazinane; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: catenin (cadherin-associated protein), delta 2; catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein); catenin delta-2
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
mRatBN7.2281,168,976 - 82,016,495 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl283,393,282 - 84,094,315 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0283,227,247 - 84,094,315 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02103,069,807 - 103,768,936 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4282,238,091 - 83,088,901 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1282,788,377 - 82,926,463 (+)NCBI
Celera276,879,503 - 77,545,735 (+)NCBICelera
Cytogenetic Map2q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
adherens junction  (IBA)
cell junction  (IEA)
cytoplasm  (IBA)
dendrite  (IEA)
neuron projection  (IDA)
nucleus  (IBA,IDA)
perikaryon  (IEA,ISO,ISS)
plasma membrane  (IBA)
postsynaptic density  (IBA,IDA,ISO)

Molecular Function

References

Additional References at PubMed
PMID:15380068   PMID:17097608   PMID:17114649   PMID:20623542   PMID:22022388   PMID:25724647   PMID:25807484  


Genomics

Comparative Map Data
Ctnnd2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2281,168,976 - 82,016,495 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl283,393,282 - 84,094,315 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0283,227,247 - 84,094,315 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02103,069,807 - 103,768,936 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4282,238,091 - 83,088,901 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1282,788,377 - 82,926,463 (+)NCBI
Celera276,879,503 - 77,545,735 (+)NCBICelera
Cytogenetic Map2q22NCBI
CTNND2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl510,971,836 - 11,904,446 (-)EnsemblGRCh38hg38GRCh38
GRCh38510,971,836 - 11,904,446 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37510,971,948 - 11,904,558 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36511,024,952 - 11,957,110 (-)NCBINCBI36hg18NCBI36
Build 34511,024,951 - 11,957,110NCBI
Celera511,009,117 - 11,940,384 (-)NCBI
Cytogenetic Map5p15.2NCBI
HuRef510,955,380 - 11,886,519 (-)NCBIHuRef
CHM1_1510,971,878 - 11,903,969 (-)NCBICHM1_1
Ctnnd2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391530,172,680 - 31,029,490 (+)NCBIGRCm39mm39
GRCm39 Ensembl1530,172,739 - 31,029,487 (+)Ensembl
GRCm381530,172,534 - 31,029,344 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1530,172,593 - 31,029,341 (+)EnsemblGRCm38mm10GRCm38
MGSCv371530,102,348 - 30,959,099 (+)NCBIGRCm37mm9NCBIm37
MGSCv361530,117,182 - 30,972,978 (+)NCBImm8
Celera1530,892,803 - 31,737,347 (+)NCBICelera
Cytogenetic Map15B2NCBI
Ctnnd2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955426636,225 - 1,350,784 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955426635,287 - 1,007,389 (-)NCBIChiLan1.0ChiLan1.0
CTNND2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1511,137,843 - 11,553,313 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0511,288,652 - 12,227,569 (-)NCBIMhudiblu_PPA_v0panPan3
CTNND2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1342,521,730 - 3,438,218 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl342,521,724 - 3,437,292 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha347,025,336 - 7,942,431 (+)NCBI
ROS_Cfam_1.0342,424,759 - 3,340,469 (+)NCBI
UMICH_Zoey_3.1342,482,252 - 3,394,692 (+)NCBI
UNSW_CanFamBas_1.0342,452,724 - 3,371,552 (+)NCBI
UU_Cfam_GSD_1.0342,689,314 - 3,602,824 (+)NCBI
Ctnnd2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213235,603,479 - 236,456,778 (+)NCBI
SpeTri2.0NW_0049366432,945,994 - 3,799,321 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CTNND2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl16508,634 - 1,521,611 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.116508,630 - 1,521,773 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.216241,808 - 523,553 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CTNND2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1410,499,822 - 11,426,432 (-)NCBI
ChlSab1.1 Ensembl410,500,761 - 10,762,677 (-)Ensembl
Vero_WHO_p1.0NW_02366606417,117,009 - 18,045,253 (+)NCBI
Ctnnd2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247518,160,520 - 9,049,871 (-)NCBI

Position Markers
D2Rat212  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2281,689,826 - 81,689,944 (+)MAPPERmRatBN7.2
Rnor_6.0283,754,907 - 83,755,024NCBIRnor6.0
Rnor_5.02103,429,722 - 103,429,839UniSTSRnor5.0
RGSC_v3.4282,761,368 - 82,761,486RGDRGSC3.4
RGSC_v3.4282,761,369 - 82,761,486UniSTSRGSC3.4
RGSC_v3.1282,706,236 - 82,706,562RGD
Celera277,224,707 - 77,224,820UniSTS
SHRSP x BN Map233.1798RGD
SHRSP x BN Map233.1798UniSTS
Cytogenetic Map2q22UniSTS
D2Rat211  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2281,829,923 - 81,830,126 (+)MAPPERmRatBN7.2
Rnor_6.0283,908,790 - 83,908,992NCBIRnor6.0
Rnor_5.02103,583,241 - 103,583,443UniSTSRnor5.0
RGSC_v3.4282,901,477 - 82,901,680RGDRGSC3.4
RGSC_v3.4282,901,478 - 82,901,680UniSTSRGSC3.4
RGSC_v3.1282,846,433 - 82,846,743RGD
Celera277,362,615 - 77,362,817UniSTS
SHRSP x BN Map233.0998RGD
SHRSP x BN Map233.0998UniSTS
Cytogenetic Map2q22UniSTS
D2Rat275  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2281,754,530 - 81,754,745 (+)MAPPERmRatBN7.2
Rnor_6.0283,819,608 - 83,819,822NCBIRnor6.0
Rnor_5.02103,494,092 - 103,494,306UniSTSRnor5.0
RGSC_v3.4282,826,122 - 82,826,336RGDRGSC3.4
RGSC_v3.4282,826,123 - 82,826,337UniSTSRGSC3.4
RGSC_v3.1282,771,084 - 82,771,298RGD
Celera277,289,347 - 77,289,561UniSTS
RH 3.4 Map11611.2UniSTS
RH 3.4 Map11611.2RGD
SHRSP x BN Map233.0998UniSTS
SHRSP x BN Map233.0998RGD
Cytogenetic Map2q22UniSTS
D2Rat324  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2281,974,206 - 81,974,307 (+)MAPPERmRatBN7.2
Rnor_6.0284,052,777 - 84,052,877NCBIRnor6.0
Rnor_5.02103,727,228 - 103,727,328UniSTSRnor5.0
RGSC_v3.4283,047,313 - 83,047,414RGDRGSC3.4
RGSC_v3.4283,047,314 - 83,047,414UniSTSRGSC3.4
RGSC_v3.1282,992,275 - 82,992,376RGD
Celera277,504,145 - 77,504,245UniSTS
SHRSP x BN Map233.1798RGD
SHRSP x BN Map233.1798UniSTS
Cytogenetic Map2q22UniSTS
D2Got33  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2281,956,908 - 81,957,137 (+)MAPPERmRatBN7.2
Rnor_6.0284,035,480 - 84,035,708NCBIRnor6.0
Rnor_5.02103,709,931 - 103,710,159UniSTSRnor5.0
RGSC_v3.4283,030,015 - 83,030,244RGDRGSC3.4
RGSC_v3.4283,030,016 - 83,030,244UniSTSRGSC3.4
RGSC_v3.1282,974,978 - 82,975,206RGD
RH 3.4 Map2516.2UniSTS
RH 3.4 Map2516.2RGD
RH 2.0 Map2417.8RGD
Cytogenetic Map2q22UniSTS
D2Got41  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2281,891,408 - 81,891,603 (+)MAPPERmRatBN7.2
Rnor_6.0283,970,452 - 83,970,646NCBIRnor6.0
Rnor_5.02103,644,903 - 103,645,097UniSTSRnor5.0
RGSC_v3.4282,963,910 - 82,964,103RGDRGSC3.4
RGSC_v3.4282,963,909 - 82,964,103UniSTSRGSC3.4
RGSC_v3.1282,908,872 - 82,909,065RGD
Celera277,421,814 - 77,422,008UniSTS
RH 3.4 Map2517.0UniSTS
RH 3.4 Map2517.0RGD
RH 2.0 Map2420.2RGD
Cytogenetic Map2q22UniSTS
BE120970  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2281,515,921 - 81,516,071 (+)MAPPERmRatBN7.2
Rnor_6.0283,580,909 - 83,581,058NCBIRnor6.0
Rnor_5.02103,256,372 - 103,256,521UniSTSRnor5.0
RGSC_v3.4282,586,977 - 82,587,126UniSTSRGSC3.4
Celera277,054,180 - 77,054,329UniSTS
RH 3.4 Map2368.7UniSTS
Cytogenetic Map2q22UniSTS
D5S2317  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2282,015,560 - 82,015,659 (+)MAPPERmRatBN7.2
Rnor_6.0284,094,112 - 84,094,210NCBIRnor6.0
Rnor_5.02103,768,733 - 103,768,831UniSTSRnor5.0
RGSC_v3.4283,088,702 - 83,088,800UniSTSRGSC3.4
Celera277,545,532 - 77,545,630UniSTS
Cytogenetic Map2q22UniSTS
RH128575  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2282,015,402 - 82,015,613 (+)MAPPERmRatBN7.2
Rnor_6.0284,093,954 - 84,094,164NCBIRnor6.0
Rnor_5.02103,768,575 - 103,768,785UniSTSRnor5.0
RGSC_v3.4283,088,544 - 83,088,754UniSTSRGSC3.4
Celera277,545,374 - 77,545,584UniSTS
RH 3.4 Map2516.3UniSTS
Cytogenetic Map2q22UniSTS
BE101962  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2281,648,475 - 81,648,661 (+)MAPPERmRatBN7.2
Rnor_6.0283,713,554 - 83,713,739NCBIRnor6.0
Rnor_5.02103,388,391 - 103,388,576UniSTSRnor5.0
RGSC_v3.4282,719,534 - 82,719,719UniSTSRGSC3.4
Celera277,183,426 - 77,183,611UniSTS
RH 3.4 Map2370.1UniSTS
Cytogenetic Map2q22UniSTS
BF386798  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2281,498,993 - 81,499,191 (+)MAPPERmRatBN7.2
Rnor_6.0283,564,032 - 83,564,229NCBIRnor6.0
Rnor_5.02103,240,459 - 103,240,656UniSTSRnor5.0
RGSC_v3.4282,570,000 - 82,570,197UniSTSRGSC3.4
Celera277,043,701 - 77,043,898UniSTS
RH 3.4 Map2364.82UniSTS
Cytogenetic Map2q22UniSTS
BE102128  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2281,611,488 - 81,611,670 (+)MAPPERmRatBN7.2
Rnor_6.0283,676,910 - 83,677,091NCBIRnor6.0
Rnor_5.02103,351,747 - 103,351,928UniSTSRnor5.0
RGSC_v3.4282,682,642 - 82,682,823UniSTSRGSC3.4
Celera277,148,452 - 77,148,633UniSTS
RH 3.4 Map2370.3UniSTS
Cytogenetic Map2q22UniSTS
AU047732  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2281,414,906 - 81,415,196 (+)MAPPERmRatBN7.2
Rnor_6.0283,479,816 - 83,480,105NCBIRnor6.0
Rnor_5.02103,156,342 - 103,156,631UniSTSRnor5.0
RGSC_v3.4282,485,588 - 82,485,877UniSTSRGSC3.4
Celera276,960,645 - 76,960,934UniSTS
Cytogenetic Map2q22UniSTS
RH137492  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2282,010,892 - 82,011,104 (+)MAPPERmRatBN7.2
Rnor_6.0284,089,476 - 84,089,687NCBIRnor6.0
Rnor_5.02103,763,884 - 103,764,095UniSTSRnor5.0
RGSC_v3.4283,084,000 - 83,084,211UniSTSRGSC3.4
Celera277,540,941 - 77,541,152UniSTS
Cytogenetic Map2q22UniSTS
AU049514  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2281,825,575 - 81,825,865 (+)MAPPERmRatBN7.2
Rnor_6.0283,904,444 - 83,904,731NCBIRnor6.0
Rnor_5.02103,578,895 - 103,579,182UniSTSRnor5.0
RGSC_v3.4282,897,132 - 82,897,419UniSTSRGSC3.4
Celera277,358,269 - 77,358,556UniSTS
Cytogenetic Map2q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)225413423143657569Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)22691781781754745Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226917817127469484Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226917817136917119Rat
61371Edpm1Estrogen-dependent pituitary mass QTL 140.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)23513484188029593Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)240067944102785628Rat
2293835Kiddil5Kidney dilation QTL 53.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607157142209Rat
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607182042367Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243154682202446871Rat
2293676Bmd19Bone mineral density QTL 1910.70.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)243162366111362592Rat
2293682Bmd24Bone mineral density QTL 248.90.0001femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)243162366111362592Rat
2293671Bss44Bone structure and strength QTL 4410.970.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)243162366148478373Rat
631208Bw1Body weight QTL15.09mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)24317101783575226Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243171017184114403Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256043031202447032Rat
1558648Smcn1Smooth muscle cell number QTL 10.039blood vessel smooth muscle cell quantity (VT:0010525)aorta smooth muscle cell count per unit vessel length (CMO:0001646)259134147127460910Rat
5684990Bmd82Bone mineral density QTL 822.8tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)259324377103795077Rat
5684996Bmd85Bone mineral density QTL 854.70.024tibia mineral mass (VT:1000283)bone mineral density (CMO:0001226)259324377103795077Rat
61438Cia7Collagen induced arthritis QTL 74.60.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)259324377141596857Rat
631500Bp99Blood pressure QTL 992.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)259324719102755241Rat
1578777Stresp15Stress response QTL 1520.05blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)259846005104846005Rat
2306903Bp336Blood pressure QTL 3360.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)264366971109366971Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118275202447032Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
7411551Bw131Body weight QTL 13129.60.001body mass (VT:0001259)body weight gain (CMO:0000420)267942638112942638Rat
1558653Prcr1Prostate cancer resistance QTL 15prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)272532993157142209Rat
1359034Bp274Blood pressure QTL 274arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)27478666494359546Rat
1359034Bp274Blood pressure QTL 274arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)27478666494359546Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)274786664206665859Rat
61465Bp13Blood pressure QTL 133.3blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)276539322102785628Rat
61465Bp13Blood pressure QTL 133.3blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)276539322102785628Rat
631198Cm22Cardiac mass QTL 224.30.0008heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)276539322150540526Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)276539322202447032Rat
2299162Iddm32Insulin dependent diabetes mellitus QTL 322.36blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)278665616143657569Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
61392Bp6Blood pressure QTL 67arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)280270434125270434Rat
1598865Bp296Blood pressure QTL 2962.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)281018907126018907Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)281689826221035911Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:20
Count of miRNA genes:17
Interacting mature miRNAs:20
Transcripts:ENSRNOT00000044871
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 74 2
Low 3 20 20 4 12 4 21 38 10
Below cutoff 16 18 18 7 18 4 6 14 1 1 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000044871   ⟹   ENSRNOP00000045121
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl283,393,282 - 84,094,315 (+)Ensembl
RefSeq Acc Id: NM_001271502   ⟹   NP_001258431
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2281,329,654 - 82,015,764 (+)NCBI
Rnor_6.0283,393,282 - 84,094,315 (+)NCBI
Rnor_5.02103,069,807 - 103,768,936 (+)NCBI
Celera276,879,503 - 77,545,735 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006232094   ⟹   XP_006232156
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2281,168,976 - 82,016,495 (+)NCBI
Rnor_6.0283,227,247 - 84,094,311 (+)NCBI
Rnor_5.02103,069,807 - 103,768,936 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017590573   ⟹   XP_017446062
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2281,168,976 - 82,016,495 (+)NCBI
Rnor_6.0283,227,247 - 84,094,311 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039101549   ⟹   XP_038957477
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2281,456,559 - 82,016,495 (+)NCBI
RefSeq Acc Id: XM_039101550   ⟹   XP_038957478
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2281,329,687 - 82,016,495 (+)NCBI
RefSeq Acc Id: XM_039101551   ⟹   XP_038957479
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2281,456,239 - 82,016,495 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001258431   ⟸   NM_001271502
- UniProtKB: F1M787 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006232156   ⟸   XM_006232094
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017446062   ⟸   XM_017590573
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000045121   ⟸   ENSRNOT00000044871
RefSeq Acc Id: XP_038957478   ⟸   XM_039101550
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038957479   ⟸   XM_039101551
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038957477   ⟸   XM_039101549
- Peptide Label: isoform X3

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)
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
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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-Lx/CubMcwi (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
BN/NHsdMcwi (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
BN/NHsdMcwi (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
BN/SsN (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
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 (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
BXH2/CubMcwi (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
BXH3/CubMcwi (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
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)
DA/OlaHsd (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (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/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)
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
F344/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
FHH/EurMcwi (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
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
FXLE16/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
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)
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
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)
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
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)
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
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)
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
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/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
WKY/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
WKY/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
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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
WN/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
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:620734 AgrOrtholog
Ensembl Genes ENSRNOG00000010649 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000045121 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000044871 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.25.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro ARM-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Armadillo UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Plakophilin/d_Catenin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:114028 UniProtKB/TrEMBL
NCBI Gene 114028 ENTREZGENE
PANTHER PTHR10372 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Arm UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ctnnd2 PhenoGen
PROSITE ARM_REPEAT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART ARM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48371 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt CTND2_RAT UniProtKB/Swiss-Prot
  F1M787 ENTREZGENE, UniProtKB/TrEMBL
  O35116 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-25 Ctnnd2  catenin delta 2  Ctnnd2  catenin (cadherin-associated protein), delta 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-08-22 Ctnnd2  catenin (cadherin-associated protein), delta 2  Ctnnd2  catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-26 Ctnnd2  catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)  Ctnnd2  catenin (cadherin-associated protein), delta 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Ctnnd2  catenin (cadherin-associated protein), delta 2    catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)  Name updated 1299863 APPROVED
2002-08-07 Ctnnd2  catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)      Symbol and Name status set to provisional 70820 PROVISIONAL