Ctnna1 (catenin alpha 1) - Rat Genome Database

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Gene: Ctnna1 (catenin alpha 1) Rattus norvegicus
Analyze
Symbol: Ctnna1
Name: catenin alpha 1
RGD ID: 1359485
Description: Predicted to enable several functions, including beta-catenin binding activity; cytoskeletal protein binding activity; and gamma-catenin binding activity. Involved in several processes, including gap junction assembly; gonad development; and response to estrogen. Located in acrosomal vesicle; adherens junction; and plasma membrane. Biomarker of esophageal cancer and lung carcinoma. Human ortholog(s) of this gene implicated in patterned macular dystrophy 2. Orthologous to human CTNNA1 (catenin alpha 1); PARTICIPATES IN E-cadherin signaling pathway; N-cadherin signaling pathway; vascular endothelial growth factor signaling pathway; INTERACTS WITH 1,3-dinitrobenzene; 5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: catenin (cadherin associated protein), alpha 1; catenin (cadherin-associated protein), alpha 1; catenin (cadherin-associated protein), alpha 1, 102kDa; catenin alpha-1; catenin alpha-1-like; catenin, alpha 1; Catna1; LOC100911326; MGC93767; uncharacterized LOC100911326
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
mRatBN7.21826,728,246 - 26,860,911 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1826,728,485 - 26,860,910 (+)Ensembl
Rnor_6.01827,923,229 - 28,055,972 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1827,923,572 - 28,055,960 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01827,633,009 - 27,766,069 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41827,629,915 - 27,769,360 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11827,656,560 - 27,796,004 (+)NCBI
Celera1826,463,736 - 26,596,152 (+)NCBICelera
Cytogenetic Map18p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
1-chloro-2,4-dinitrobenzene  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-methylcholanthrene  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP)
6-propyl-2-thiouracil  (EXP)
acrolein  (ISO)
acrylamide  (EXP)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
amiodarone  (EXP)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzbromarone  (EXP)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
calcitriol  (ISO)
cisplatin  (EXP)
clofibrate  (EXP)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
corticosterone  (ISO)
cyclosporin A  (ISO)
deoxynivalenol  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
ethanol  (ISO)
fenamidone  (ISO)
folic acid  (ISO)
fumonisin B1  (ISO)
geldanamycin  (ISO)
glafenine  (EXP)
hydrogen peroxide  (ISO)
ivermectin  (ISO)
jaspamide  (EXP)
L-ethionine  (EXP)
latrunculin A  (EXP)
lead nitrate  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
methotrexate  (ISO)
methylazoxymethanol  (ISO)
methylmercury(1+)  (ISO)
mitomycin C  (ISO)
N-ethyl-N-nitrosourea  (ISO)
ochratoxin A  (EXP,ISO)
omeprazole  (EXP)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (ISO)
phenobarbital  (EXP,ISO)
pirinixic acid  (EXP,ISO)
quercetin  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
sodium dichromate  (ISO)
sodium fluoride  (ISO)
Soman  (EXP)
sulfur dioxide  (ISO)
sunitinib  (ISO)
tert-butyl hydroperoxide  (ISO)
thimerosal  (ISO)
thioacetamide  (EXP)
topotecan  (EXP)
tributylstannane  (ISO)
Tributyltin oxide  (ISO)
trimellitic anhydride  (ISO)
tungsten  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
1. Aaltomaa S, etal., Anticancer Res. 2005 Nov-Dec;25(6C):4707-12.
2. Blanco D, etal., Lab Invest. 2004 Aug;84(8):999-1012.
3. Byers SW, etal., Endocrinology. 1994 Feb;134(2):630-9.
4. Carico E, etal., Gynecol Oncol. 2001 Feb;80(2):156-61.
5. Davies BR, etal., Histopathology. 1998 Jan;32(1):69-80.
6. Fasen K, etal., J Neuropathol Exp Neurol 2002 Oct;61(10):903-13.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Hertig CM, etal., J Cell Sci. 1996 Jan;109 ( Pt 1):11-20.
9. Higashi N, etal., Cell Tissue Res. 2004 Jul;317(1):35-43. Epub 2004 Jun 10.
10. Jung KY, etal., Mech Ageing Dev. 2004 Jun;125(6):445-53.
11. Kashibuchi K, etal., Eur Urol. 2006 May;49(5):839-45; discussion 845. Epub 2006 Jan 6.
12. Kashibuchi K, etal., Int J Urol. 2007 Sep;14(9):789-94.
13. Khare L, etal., Int J Oncol. 1999 Jan;14(1):33-40.
14. MGD data from the GO Consortium
15. Nakopoulou L, etal., Histopathology. 2002 Jun;40(6):536-46.
16. Park D, etal., APMIS. 2007 Jan;115(1):52-65.
17. Piedra J, etal., Mol Cell Biol. 2003 Apr;23(7):2287-97.
18. Pipeline to import KEGG annotations from KEGG into RGD
19. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
20. RGD automated data pipeline
21. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
22. RGD automated import pipeline for gene-chemical interactions
23. Scholten AN, etal., Int J Gynecol Cancer. 2006 May-Jun;16(3):1379-85.
24. Shimazui T, etal., Int J Cancer. 1997 Oct 21;74(5):523-8.
25. Sobarzo CM, etal., Reprod Toxicol. 2006 Jul;22(1):77-86. Epub 2006 May 5.
26. Sorkin BC, etal., J Histochem Cytochem. 2000 Mar;48(3):397-406.
27. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
28. Sundfeldt K, etal., J Reprod Fertil. 2000 Mar;118(2):375-85.
29. Tomlinson JS, etal., Cancer Res. 2001 Jul 1;61(13):5231-41.
30. Uehara K and Uehara A, Histochem Cell Biol. 2008 Jan;129(1):95-103. Epub 2007 Sep 25.
31. van Oort IM, etal., Prostate. 2007 Sep 15;67(13):1432-8.
32. Wu JC, etal., J Cell Biochem. 2003 Mar 1;88(4):823-35.
33. Zhang RD, etal., Zhonghua Nan Ke Xue. 2006 May;12(5):394-6, 400.
Additional References at PubMed
PMID:7650039   PMID:7890674   PMID:8853988   PMID:9700171   PMID:10460003   PMID:10868478   PMID:11025210   PMID:11795944   PMID:12695331   PMID:12734196   PMID:14657280   PMID:15775979  
PMID:16510873   PMID:16543460   PMID:17535849   PMID:17989230   PMID:18195371   PMID:19129494   PMID:19805073   PMID:21399649   PMID:21423176   PMID:22411810   PMID:22658674   PMID:23292143  
PMID:23417122   PMID:24046456   PMID:24973089   PMID:25468996   PMID:25931508   PMID:26377600   PMID:26514267   PMID:27782092   PMID:28051089   PMID:30361391  


Genomics

Comparative Map Data
Ctnna1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21826,728,246 - 26,860,911 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1826,728,485 - 26,860,910 (+)Ensembl
Rnor_6.01827,923,229 - 28,055,972 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1827,923,572 - 28,055,960 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01827,633,009 - 27,766,069 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41827,629,915 - 27,769,360 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11827,656,560 - 27,796,004 (+)NCBI
Celera1826,463,736 - 26,596,152 (+)NCBICelera
Cytogenetic Map18p11NCBI
CTNNA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5138,610,967 - 138,935,034 (+)EnsemblGRCh38hg38GRCh38
GRCh385138,753,425 - 138,935,034 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh375138,089,114 - 138,270,723 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365138,117,006 - 138,298,622 (+)NCBINCBI36hg18NCBI36
Build 345138,117,005 - 138,298,621NCBI
Celera5134,210,957 - 134,392,494 (+)NCBI
Cytogenetic Map5q31.2NCBI
HuRef5133,278,985 - 133,460,517 (+)NCBIHuRef
CHM1_15137,521,762 - 137,703,280 (+)NCBICHM1_1
Ctnna1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391835,251,955 - 35,387,829 (+)NCBIGRCm39mm39
GRCm39 Ensembl1835,251,912 - 35,387,832 (+)Ensembl
GRCm381835,118,902 - 35,254,776 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1835,118,859 - 35,254,779 (+)EnsemblGRCm38mm10GRCm38
MGSCv371835,278,566 - 35,414,429 (+)NCBIGRCm37mm9NCBIm37
MGSCv361835,244,886 - 35,380,749 (+)NCBImm8
Celera1835,608,364 - 35,710,407 (+)NCBICelera
Cytogenetic Map18B1NCBI
cM Map1818.89NCBI
Ctnna1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554181,592,229 - 1,754,689 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554181,592,555 - 1,754,423 (-)NCBIChiLan1.0ChiLan1.0
CTNNA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15140,261,883 - 140,438,854 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5140,261,883 - 140,438,547 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05134,134,944 - 134,313,239 (+)NCBIMhudiblu_PPA_v0panPan3
CTNNA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11126,273,322 - 26,459,497 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1126,143,013 - 26,459,091 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1125,040,958 - 25,226,366 (+)NCBI
ROS_Cfam_1.01127,129,159 - 27,315,090 (+)NCBI
UMICH_Zoey_3.11125,836,828 - 26,022,382 (+)NCBI
UNSW_CanFamBas_1.01125,658,855 - 25,844,720 (+)NCBI
UU_Cfam_GSD_1.01126,323,192 - 26,509,271 (+)NCBI
Ctnna1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213153,575,485 - 153,790,091 (-)NCBI
SpeTri2.0NW_0049365317,865,907 - 8,036,020 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CTNNA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2140,682,371 - 140,871,334 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.12140,682,776 - 140,869,828 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22146,440,632 - 146,624,719 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CTNNA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12341,423,504 - 41,599,458 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2341,447,675 - 41,600,190 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603436,284,586 - 36,461,261 (-)NCBIVero_WHO_p1.0
Ctnna1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474331,512,481 - 31,700,340 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D18Got111  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21826,802,654 - 26,802,812 (+)MAPPERmRatBN7.2
Rnor_6.01827,997,695 - 27,997,852NCBIRnor6.0
Rnor_5.01827,707,131 - 27,707,288UniSTSRnor5.0
RGSC_v3.41827,706,319 - 27,706,476UniSTSRGSC3.4
Celera1826,537,814 - 26,537,971UniSTS
Cytogenetic Map18p11UniSTS
BB129880  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21826,819,936 - 26,820,027 (+)MAPPERmRatBN7.2
Rnor_6.01828,014,998 - 28,015,088NCBIRnor6.0
Rnor_5.01827,724,807 - 27,724,897UniSTSRnor5.0
RGSC_v3.41827,724,838 - 27,724,928UniSTSRGSC3.4
Celera1826,555,095 - 26,555,185UniSTS
Cytogenetic Map18p11UniSTS
RH127326  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2468,141,841 - 68,142,025 (+)MAPPERmRatBN7.2
mRatBN7.21826,859,830 - 26,860,014 (+)MAPPERmRatBN7.2
Rnor_6.01828,054,887 - 28,055,070NCBIRnor6.0
Rnor_6.0467,151,096 - 67,151,279NCBIRnor6.0
Rnor_5.01827,764,990 - 27,765,173UniSTSRnor5.0
RGSC_v3.4466,874,130 - 66,874,313UniSTSRGSC3.4
RGSC_v3.41827,768,281 - 27,768,464UniSTSRGSC3.4
Celera1826,595,073 - 26,595,256UniSTS
Cytogenetic Map4q22UniSTS
Cytogenetic Map18p11UniSTS
RH129529  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21826,860,469 - 26,860,666 (+)MAPPERmRatBN7.2
mRatBN7.2468,142,479 - 68,142,676 (+)MAPPERmRatBN7.2
Rnor_6.01828,055,526 - 28,055,722NCBIRnor6.0
Rnor_6.0467,151,734 - 67,151,930NCBIRnor6.0
Rnor_5.0466,958,195 - 66,958,391UniSTSRnor5.0
Rnor_5.01827,765,629 - 27,765,825UniSTSRnor5.0
RGSC_v3.41827,768,920 - 27,769,116UniSTSRGSC3.4
RGSC_v3.4466,874,768 - 66,874,964UniSTSRGSC3.4
Celera1826,595,712 - 26,595,908UniSTS
Cytogenetic Map4q22UniSTS
Cytogenetic Map18p11UniSTS
RH132461  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21826,817,053 - 26,817,235 (+)MAPPERmRatBN7.2
Rnor_6.01828,012,115 - 28,012,296NCBIRnor6.0
Rnor_5.01827,721,874 - 27,722,055UniSTSRnor5.0
RGSC_v3.41827,721,955 - 27,722,136UniSTSRGSC3.4
Celera1826,552,212 - 26,552,393UniSTS
RH 3.4 Map18372.8UniSTS
Cytogenetic Map18p11UniSTS
RH135258  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21826,800,545 - 26,800,748 (+)MAPPERmRatBN7.2
Rnor_6.01827,995,586 - 27,995,788NCBIRnor6.0
Rnor_5.01827,705,022 - 27,705,224UniSTSRnor5.0
RGSC_v3.41827,704,210 - 27,704,412UniSTSRGSC3.4
Celera1826,535,705 - 26,535,907UniSTS
RH 3.4 Map18366.7UniSTS
Cytogenetic Map18p11UniSTS
AI230960  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21826,804,183 - 26,804,400 (+)MAPPERmRatBN7.2
Rnor_6.01827,999,225 - 27,999,441NCBIRnor6.0
Rnor_5.01827,708,661 - 27,708,877UniSTSRnor5.0
RGSC_v3.41827,707,849 - 27,708,065UniSTSRGSC3.4
Celera1826,539,344 - 26,539,560UniSTS
RH 3.4 Map18372.9UniSTS
Cytogenetic Map18p11UniSTS
AI851755  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21826,817,980 - 26,818,087 (+)MAPPERmRatBN7.2
Rnor_6.01828,013,042 - 28,013,148NCBIRnor6.0
Rnor_5.01827,722,851 - 27,722,957UniSTSRnor5.0
RGSC_v3.41827,722,882 - 27,722,988UniSTSRGSC3.4
Celera1826,553,139 - 26,553,245UniSTS
Cytogenetic Map18p11UniSTS
Lrrtm2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21826,821,028 - 26,821,665 (+)MAPPERmRatBN7.2
Rnor_6.01828,016,090 - 28,016,726NCBIRnor6.0
Rnor_5.01827,725,899 - 27,726,535UniSTSRnor5.0
RGSC_v3.41827,725,930 - 27,726,566UniSTSRGSC3.4
Celera1826,556,187 - 26,556,823UniSTS
Cytogenetic Map18p11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2312598Bp340Blood pressure QTL 3400.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)18130558703Rat
2300180Bmd67Bone mineral density QTL 674.80.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)18134291613Rat
2293661Bss50Bone structure and strength QTL 504.640.0003lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)18134291613Rat
61388Bp2Blood pressure QTL 23.23arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)18135374722Rat
9589153Insul31Insulin level QTL 317.150.05blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)18142547119Rat
2299160Iddm35Insulin dependent diabetes mellitus QTL 352.79blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)18420794160377792Rat
2312568Glom21Glomerulus QTL 2120.005kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)18518585840503530Rat
2293708Bss46Bone structure and strength QTL 468.80.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)181179151863636873Rat
1578661Bss20Bone structure and strength QTL 203.7femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)181179151883218561Rat
1578667Bss21Bone structure and strength QTL 213.5femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)181179151883218561Rat
61382Bp46Blood pressure QTL 4618.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194179131393320Rat
631264Scl22Serum cholesterol level QTL 226.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)181194179131393320Rat
1331766Bp236Blood pressure QTL 2363.022arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181194429931359530Rat
61375Bp41Blood pressure QTL 412.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)181194429941122201Rat
1331753Bp231Blood pressure QTL 2313.643arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194429952293055Rat
1358358Sradr6Stress Responsive Adrenal Weight QTL 62.49adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)181194429959330563Rat
6903359Bp355Blood pressure QTL 3553.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194454459796478Rat
2313082Bss85Bone structure and strength QTL 850.80.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)181495133759951337Rat
1358193Emca2Estrogen-induced mammary cancer QTL 21.6mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)181800759963571040Rat
1331735Rf44Renal function QTL 442.981total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)181823456431359530Rat
1331775Bp235Blood pressure QTL 2353.201arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181823456431359530Rat
1600373Mamtr6Mammary tumor resistance QTL 6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)181927890183218561Rat
1331741Bp232Blood pressure QTL 2323.59112arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182137289383213037Rat
1641923Colcr8Colorectal carcinoma resistance QTL 83.10.0014intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)182206624252293055Rat
1331733Bp233Blood pressure QTL 2333.97196arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182479697779788953Rat
2325839Bp348Blood pressure QTL 3480.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182557098570570985Rat
12904673Cm127Cardiac mass QTL 1270.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)182654808246969551Rat
12904675Am19Aortic mass QTL 190.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)182654808246969551Rat
12904677Kidm72Kidney mass QTL 720.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)182654808246969551Rat
12904668Bw188Body weight QTL 1880.03body mass (VT:0001259)body weight (CMO:0000012)182654808246969551Rat
12904669Cm125Cardiac mass QTL 1250.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)182654808246969551Rat
12904670Cm126Cardiac mass QTL 1260.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)182654808246969551Rat
2301413Bp318Blood pressure QTL 3180.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182654808246969551Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:325
Count of miRNA genes:203
Interacting mature miRNAs:228
Transcripts:ENSRNOT00000008041
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 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008041   ⟹   ENSRNOP00000008041
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1826,728,485 - 26,860,910 (+)Ensembl
Rnor_6.0 Ensembl1827,923,572 - 28,055,960 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000080999   ⟹   ENSRNOP00000070637
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1827,956,429 - 28,054,203 (+)Ensembl
RefSeq Acc Id: NM_001007145   ⟹   NP_001007146
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21826,728,518 - 26,860,910 (+)NCBI
Rnor_6.01827,923,572 - 28,055,966 (+)NCBI
Rnor_5.01827,633,009 - 27,766,069 (+)NCBI
RGSC_v3.41827,629,915 - 27,769,360 (+)RGD
Celera1826,463,736 - 26,596,152 (+)RGD
Sequence:
RefSeq Acc Id: XM_008772037   ⟹   XP_008770259
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21826,823,011 - 26,860,911 (+)NCBI
Rnor_6.01828,018,122 - 28,055,972 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600964   ⟹   XP_017456453
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21826,728,246 - 26,860,911 (+)NCBI
Rnor_6.01827,923,229 - 28,055,972 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600965   ⟹   XP_017456454
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21826,831,911 - 26,860,911 (+)NCBI
Rnor_6.01828,026,935 - 28,055,972 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039096868   ⟹   XP_038952796
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21826,729,071 - 26,860,911 (+)NCBI
RefSeq Acc Id: XM_039096869   ⟹   XP_038952797
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21826,843,222 - 26,860,911 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001007146   ⟸   NM_001007145
- UniProtKB: Q5U302 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008770259   ⟸   XM_008772037
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017456453   ⟸   XM_017600964
- Peptide Label: isoform X1
- UniProtKB: Q5U302 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456454   ⟸   XM_017600965
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000008041   ⟸   ENSRNOT00000008041
RefSeq Acc Id: ENSRNOP00000070637   ⟸   ENSRNOT00000080999
RefSeq Acc Id: XP_038952796   ⟸   XM_039096868
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038952797   ⟸   XM_039096869
- Peptide Label: isoform X4

Transcriptome

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

Promoters
RGD ID:13700706
Promoter ID:EPDNEW_R11229
Type:single initiation site
Name:Ctnna1_1
Description:catenin alpha 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01827,923,534 - 27,923,594EPDNEW

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)
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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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
18 27726672 27726673 T C snv Crl:SD (UDEL), IS/Kyo (KyushuU), KFRS3B/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), DOB/Oda (KyushuU), RCS/Kyo (KyushuU)


Assembly: RGSC_v3.4
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
18 27666608 27666609 G T snv SHRSP/Gcrc (MDC)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359485 AgrOrtholog
Ensembl Genes ENSRNOG00000005796 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000008041 UniProtKB/TrEMBL
  ENSRNOP00000070637 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008041 UniProtKB/TrEMBL
  ENSRNOT00000080999 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7108824 IMAGE-MGC_LOAD
InterPro Alpha-catenin/vinculin-like_sf UniProtKB/TrEMBL
  Alpha_catenin UniProtKB/TrEMBL
  CTNNA1/CTNNA3 UniProtKB/TrEMBL
  Vinculin/catenin UniProtKB/TrEMBL
  Vinculin_CS UniProtKB/TrEMBL
KEGG Report rno:307505 UniProtKB/TrEMBL
MGC_CLONE MGC:93767 IMAGE-MGC_LOAD
NCBI Gene 307505 ENTREZGENE
PANTHER PTHR18914:SF24 UniProtKB/TrEMBL
Pfam Vinculin UniProtKB/TrEMBL
PhenoGen Ctnna1 PhenoGen
PRINTS ALPHACATENIN UniProtKB/TrEMBL
PROSITE VINCULIN_1 UniProtKB/TrEMBL
Superfamily-SCOP Vinculin/catenin UniProtKB/TrEMBL
UniProt A0A0G2JYF7_RAT UniProtKB/TrEMBL
  Q5U302 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Ctnna1  catenin alpha 1  LOC100911326  uncharacterized LOC100911326  Data Merged 737654 PROVISIONAL
2015-11-25 Ctnna1  catenin alpha 1  Ctnna1  catenin (cadherin-associated protein), alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-19 Ctnna1  catenin (cadherin-associated protein), alpha 1  Ctnna1  catenin (cadherin-associated protein), alpha 1, 102kDa  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-05 LOC100911326  uncharacterized LOC100911326      Symbol and Name status set to provisional 70820 PROVISIONAL
2012-01-10 Ctnna1  catenin (cadherin-associated protein), alpha 1, 102kDa  Ctnna1  catenin (cadherin associated protein), alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-11 Ctnna1  catenin (cadherin associated protein), alpha 1  Catna1  catenin (cadherin-associated protein), alpha 1  Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2006-03-30 Catna1  catenin (cadherin-associated protein), alpha 1    catenin (cadherin-associated protein), alpha 1, 102kDa  Name updated 1299863 APPROVED
2005-07-29 Catna1  catenin (cadherin-associated protein), alpha 1, 102kDa      Symbol and Name status set to provisional 70820 PROVISIONAL