Magi2 (membrane associated guanylate kinase, WW and PDZ domain containing 2) - Rat Genome Database

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Gene: Magi2 (membrane associated guanylate kinase, WW and PDZ domain containing 2) Rattus norvegicus
Analyze
Symbol: Magi2
Name: membrane associated guanylate kinase, WW and PDZ domain containing 2
RGD ID: 621855
Description: Enables kinesin binding activity. A structural constituent of postsynaptic density. Involved in several processes, including nerve growth factor signaling pathway; regulation of neurotransmitter receptor localization to postsynaptic specialization membrane; and regulation of synaptic membrane adhesion. Located in several cellular components, including glutamatergic synapse; postsynaptic density; and slit diaphragm. Part of protein-containing complex. Is active in GABA-ergic synapse. Is extrinsic component of postsynaptic membrane. Human ortholog(s) of this gene implicated in nephrotic syndrome type 15. Orthologous to human MAGI2 (membrane associated guanylate kinase, WW and PDZ domain containing 2); INTERACTS WITH 2,2',5,5'-tetrachlorobiphenyl; 2,3,7,8-tetrachlorodibenzodioxine; 3,4-methylenedioxymethamphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: activin receptor interacting protein 1; Acvrinp1; Acvrip1; AIP-1; atrophin-1-interacting protein 1; MAGI-2; membrane-associated guanylate kinase inverted 2; membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2; S-SCAM; synaptic-scaffolding molecule
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
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2414,388,322 - 15,870,036 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl414,386,399 - 15,870,240 (-)Ensembl
Rnor_6.0410,995,241 - 12,472,423 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl410,995,234 - 11,610,518 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0410,987,831 - 12,456,502 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.449,909,448 - 11,441,301 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1410,054,955 - 11,441,302 (-)NCBI
Celera49,948,183 - 11,419,535 (-)NCBICelera
Cytogenetic Map4q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
3,4-methylenedioxymethamphetamine  (EXP,ISO)
5-aza-2'-deoxycytidine  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
androgen antagonist  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
butanal  (ISO)
Butylparaben  (EXP)
cadmium dichloride  (EXP)
cobalt atom  (ISO)
cobalt dichloride  (EXP,ISO)
DDE  (EXP)
dibutyl phthalate  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
enzacamene  (EXP)
epoxiconazole  (EXP)
ethanol  (ISO)
furan  (EXP)
hexane  (EXP)
L-ascorbic acid  (ISO)
linuron  (EXP)
methapyrilene  (ISO)
methoxychlor  (EXP)
methylmercury chloride  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-acetyl-1,4-benzoquinone imine  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nickel atom  (ISO)
panobinostat  (ISO)
paracetamol  (EXP,ISO)
PCB138  (EXP)
permethrin  (EXP)
phenylmercury acetate  (ISO)
prochloraz  (EXP)
procymidone  (EXP)
quercetin  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
sodium arsenite  (ISO)
succimer  (ISO)
thimerosal  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
Tungsten carbide  (ISO)
valproic acid  (ISO)
venlafaxine hydrochloride  (EXP)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
1. Babayeva S, etal., Am J Physiol Renal Physiol. 2011 Feb;300(2):F549-60. doi: 10.1152/ajprenal.00566.2009. Epub 2010 Jun 9.
2. Bender J, etal., PLoS One. 2015 Sep 9;10(9):e0136768. doi: 10.1371/journal.pone.0136768. eCollection 2015.
3. Danielson E, etal., J Neurosci. 2012 May 16;32(20):6967-80. doi: 10.1523/JNEUROSCI.0025-12.2012.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Hirabayashi S, etal., J Neurochem 2004 Jul;90(2):332-9.
6. Hirao K, etal., J Biol Chem 1998 Aug 14;273(33):21105-10.
7. Hirao K, etal., J Biol Chem 2000 Jan 28;275(4):2966-72.
8. Hisata S, etal., J Cell Biol. 2007 Aug 27;178(5):843-60.
9. Hu Y, etal., Arch Biochem Biophys. 2007 Nov 1;467(1):1-9. Epub 2007 Aug 22.
10. Ide N, etal., Biochem Biophys Res Commun. 1999 Mar 24;256(3):456-61.
11. Kawata A, etal., J Biochem. 2006 May;139(5):931-9.
12. Kitano J, etal., J Biol Chem 2003 Apr 25;278(17):14762-8. Epub 2003 Feb 13.
13. Lehtonen S, etal., Am J Pathol. 2004 Sep;165(3):923-36.
14. Lehtonen S, etal., Proc Natl Acad Sci U S A. 2005 Jul 12;102(28):9814-9. Epub 2005 Jul 1.
15. MGD data from the GO Consortium
16. Mok H, etal., J Neurosci. 2002 Jul 1;22(13):5253-8.
17. NCBI rat LocusLink and RefSeq merged data July 26, 2002
18. Nishimura W, etal., J Neurosci 2002 Feb 1;22(3):757-65.
19. Ohtsuka T, etal., Biochem Biophys Res Commun. 1999 Nov;265(1):38-44.
20. Rehbein M, etal., J Neurochem 2002 Sep;82(5):1039-46.
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. Shoji H, etal., J Biol Chem. 2000 Feb 25;275(8):5485-92.
24. Sugi T, etal., EMBO J. 2007 Apr 18;26(8):2192-205. Epub 2007 Mar 29.
25. Sumita K, etal., J Neurochem. 2007 Jan;100(1):154-66. doi: 10.1111/j.1471-4159.2006.04170.x. Epub 2006 Oct 24.
26. Tobaben S, etal., J Biol Chem 2000 Nov 17;275(46):36204-10.
27. Valiente M, etal., J Biol Chem. 2005 Aug 12;280(32):28936-43. Epub 2005 Jun 10.
28. Woo J, etal., J Cell Biol. 2013 Jun 10;201(6):929-44. doi: 10.1083/jcb.201209132.
29. Yao I, etal., J Biol Chem 1999 Apr 23;274(17):11889-96.
30. Yap CC, etal., Biochem Biophys Res Commun 2003 Feb 21;301(4):1122-8.
Additional References at PubMed
PMID:10760291   PMID:11526121   PMID:14596909   PMID:15458844   PMID:16648306   PMID:16870733   PMID:20534458   PMID:22128856   PMID:22871113  


Genomics

Comparative Map Data
Magi2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2414,388,322 - 15,870,036 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl414,386,399 - 15,870,240 (-)Ensembl
Rnor_6.0410,995,241 - 12,472,423 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl410,995,234 - 11,610,518 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0410,987,831 - 12,456,502 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.449,909,448 - 11,441,301 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1410,054,955 - 11,441,302 (-)NCBI
Celera49,948,183 - 11,419,535 (-)NCBICelera
Cytogenetic Map4q11NCBI
MAGI2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl778,017,055 - 79,453,667 (-)EnsemblGRCh38hg38GRCh38
GRCh38778,017,055 - 79,453,667 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37777,646,372 - 79,082,983 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36777,484,310 - 78,920,826 (-)NCBINCBI36hg18NCBI36
Build 34777,291,048 - 78,727,541NCBI
Celera772,346,978 - 73,783,869 (-)NCBI
Cytogenetic Map7q21.11NCBI
HuRef772,249,405 - 73,685,020 (-)NCBIHuRef
CHM1_1777,576,560 - 79,013,089 (-)NCBICHM1_1
CRA_TCAGchr7v2776,978,436 - 78,414,480 (-)NCBI
Magi2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39519,431,787 - 20,909,790 (+)NCBIGRCm39mm39
GRCm39 Ensembl519,432,034 - 20,909,790 (+)Ensembl
GRCm38519,219,387 - 20,704,792 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl519,227,036 - 20,704,792 (+)EnsemblGRCm38mm10GRCm38
MGSCv37518,732,864 - 20,210,610 (+)NCBIGRCm37mm9NCBIm37
MGSCv36518,738,799 - 20,216,616 (+)NCBImm8
Celera516,180,595 - 17,665,978 (+)NCBICelera
Cytogenetic Map5A3NCBI
Magi2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554106,400,242 - 7,294,924 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554106,739,115 - 7,295,027 (+)NCBIChiLan1.0ChiLan1.0
MAGI2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1783,759,307 - 84,511,987 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl783,758,512 - 84,760,872 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0769,943,704 - 71,395,176 (-)NCBIMhudiblu_PPA_v0panPan3
MAGI2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11817,973,058 - 19,098,785 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1817,918,928 - 18,930,059 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1817,565,936 - 18,971,443 (-)NCBI
ROS_Cfam_1.01818,307,564 - 19,031,590 (-)NCBI
UMICH_Zoey_3.11818,054,185 - 19,371,256 (-)NCBI
UNSW_CanFamBas_1.01817,997,659 - 18,302,395 (-)NCBI
UU_Cfam_GSD_1.01818,251,940 - 19,581,985 (-)NCBI
Magi2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511860,250,078 - 60,938,785 (-)NCBI
SpeTri2.0NW_00493647921,373,917 - 22,062,498 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MAGI2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9100,847,212 - 102,169,003 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.19100,846,693 - 102,171,199 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29112,312,166 - 112,574,012 (+)NCBISscrofa10.2Sscrofa10.2susScr3
MAGI2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12169,460,345 - 70,916,684 (+)NCBI
Vero_WHO_p1.0NW_02366604233,007,517 - 34,474,279 (-)NCBI
Magi2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473927,132,533 - 28,430,765 (-)NCBI

Position Markers
D4Rat6  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2414,770,630 - 14,770,800 (+)MAPPERmRatBN7.2
Rnor_6.0411,381,746 - 11,381,915NCBIRnor6.0
Rnor_5.0411,368,225 - 11,368,394UniSTSRnor5.0
RGSC_v3.4410,298,231 - 10,298,400UniSTSRGSC3.4
RGSC_v3.4410,298,194 - 10,298,520RGDRGSC3.4
RGSC_v3.1410,298,194 - 10,298,520RGD
Celera410,327,416 - 10,327,585UniSTS
RH 3.4 Map455.7RGD
RH 3.4 Map455.7UniSTS
RH 2.0 Map481.2RGD
SHRSP x BN Map45.5999RGD
Cytogenetic Map4q11UniSTS
D4Got18  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2414,886,312 - 14,886,475 (+)MAPPERmRatBN7.2
Rnor_6.0411,495,960 - 11,496,122NCBIRnor6.0
Rnor_5.0411,481,773 - 11,481,935UniSTSRnor5.0
RGSC_v3.4410,418,029 - 10,418,192RGDRGSC3.4
RGSC_v3.4410,418,030 - 10,418,192UniSTSRGSC3.4
RGSC_v3.1410,418,030 - 10,418,192RGD
Celera410,441,826 - 10,441,988UniSTS
RH 3.4 Map456.8UniSTS
RH 3.4 Map456.8RGD
RH 2.0 Map483.5RGD
Cytogenetic Map4q11UniSTS
D4Wox26  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2415,583,060 - 15,583,255 (+)MAPPERmRatBN7.2
Rnor_6.0412,186,517 - 12,186,711NCBIRnor6.0
Rnor_5.0412,171,476 - 12,171,670UniSTSRnor5.0
RGSC_v3.4411,143,530 - 11,143,725RGDRGSC3.4
RGSC_v3.4411,143,531 - 11,143,725UniSTSRGSC3.4
RGSC_v3.1411,143,530 - 11,143,725RGD
Celera411,132,622 - 11,132,816UniSTS
RH 3.4 Map461.2UniSTS
RH 3.4 Map461.2RGD
RH 2.0 Map4101.0RGD
Cytogenetic Map4q11UniSTS
D4Uwm4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2414,808,285 - 14,808,493 (+)MAPPERmRatBN7.2
Rnor_6.0411,419,429 - 11,419,636NCBIRnor6.0
Rnor_5.0411,405,721 - 11,405,928UniSTSRnor5.0
RGSC_v3.4410,336,506 - 10,336,713UniSTSRGSC3.4
Celera410,364,840 - 10,365,047UniSTS
Cytogenetic Map4q11UniSTS
BF388517  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2415,298,656 - 15,298,791 (+)MAPPERmRatBN7.2
Rnor_6.0411,905,884 - 11,906,018NCBIRnor6.0
Rnor_5.0411,889,656 - 11,889,790UniSTSRnor5.0
RGSC_v3.4410,849,959 - 10,850,093UniSTSRGSC3.4
Celera410,846,344 - 10,846,478UniSTS
RH 3.4 Map4510.5UniSTS
Cytogenetic Map4q11UniSTS
RH141994  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2415,483,019 - 15,483,223 (+)MAPPERmRatBN7.2
Rnor_6.0412,088,254 - 12,088,457NCBIRnor6.0
Rnor_5.0412,073,213 - 12,073,416UniSTSRnor5.0
RGSC_v3.4411,041,195 - 11,041,398UniSTSRGSC3.4
Celera411,031,414 - 11,031,617UniSTS
RH 3.4 Map461.3UniSTS
Cytogenetic Map4q11UniSTS
BE106713  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2414,429,794 - 14,429,946 (+)MAPPERmRatBN7.2
Rnor_6.0411,044,930 - 11,045,081NCBIRnor6.0
Rnor_5.0411,032,438 - 11,032,589UniSTSRnor5.0
RGSC_v3.449,950,497 - 9,950,648UniSTSRGSC3.4
Celera49,989,547 - 9,989,698UniSTS
RH 3.4 Map454.5UniSTS
Cytogenetic Map4q11UniSTS
BI301779  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2414,929,662 - 14,929,889 (+)MAPPERmRatBN7.2
Rnor_6.0411,538,966 - 11,539,192NCBIRnor6.0
Rnor_5.0411,524,161 - 11,524,387UniSTSRnor5.0
RGSC_v3.4410,473,309 - 10,473,535UniSTSRGSC3.4
Celera410,485,158 - 10,485,384UniSTS
RH 3.4 Map457.0UniSTS
Cytogenetic Map4q11UniSTS
BF399248  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2415,702,894 - 15,703,041 (+)MAPPERmRatBN7.2
Rnor_6.0412,305,500 - 12,305,646NCBIRnor6.0
Rnor_5.0412,290,340 - 12,290,486UniSTSRnor5.0
Celera411,252,454 - 11,252,600UniSTS
RH 3.4 Map460.8UniSTS
Cytogenetic Map4q11UniSTS
AU046470  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2414,533,648 - 14,533,793 (+)MAPPERmRatBN7.2
Rnor_6.0411,148,190 - 11,148,334NCBIRnor6.0
Rnor_5.0411,135,100 - 11,135,244UniSTSRnor5.0
RGSC_v3.4410,056,962 - 10,057,107UniSTSRGSC3.4
Celera410,094,121 - 10,094,261UniSTS
Cytogenetic Map4q11UniSTS
AU049234  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2414,657,394 - 14,657,933 (+)MAPPERmRatBN7.2
mRatBN7.2414,657,715 - 14,657,933 (+)MAPPERmRatBN7.2
Rnor_6.0411,270,518 - 11,271,107NCBIRnor6.0
Rnor_6.0411,270,888 - 11,271,107NCBIRnor6.0
Rnor_5.0411,257,798 - 11,258,017UniSTSRnor5.0
Rnor_5.0411,257,428 - 11,258,017UniSTSRnor5.0
RGSC_v3.4410,181,964 - 10,182,183UniSTSRGSC3.4
Celera410,219,001 - 10,219,220UniSTS
Cytogenetic Map4q11UniSTS
AU049610  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2414,470,612 - 14,470,791 (+)MAPPERmRatBN7.2
Rnor_6.0411,085,573 - 11,085,751NCBIRnor6.0
Rnor_5.0411,072,435 - 11,072,613UniSTSRnor5.0
RGSC_v3.449,992,756 - 9,992,934UniSTSRGSC3.4
Celera410,030,355 - 10,030,533UniSTS
Cytogenetic Map4q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61351Bp33Blood pressure QTL 330.0018arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4127716890Rat
61408Scl23Serum cholesterol level QTL 230.0005blood HDL phospholipid amount (VT:0010504)serum high density lipoprotein phospholipid level (CMO:0001567)4127716890Rat
724557Plsm1Polydactyly-luxate syndrome (PLS) morphotypes QTL 10.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)4127716890Rat
1641905Colcr1Colorectal carcinoma resistance QTL 14.30.0003intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)4129494328Rat
61333Gluco16Glucose level QTL 164.30.00001adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)4130372989Rat
9589097Slep11Serum leptin concentration QTL 115.090.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)4131934116Rat
8552903Pigfal2Plasma insulin-like growth factor 1 level QTL 27.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)4131934116Rat
9589046Scfw2Subcutaneous fat weight QTL 25.540.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)4131934116Rat
9590100Sffal4Serum free fatty acids level QTL 47.360.05blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)4131934116Rat
738021Hcar13Hepatocarcinoma resistance QTL 134.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)4132584199Rat
1357341Gluco5Glucose level QTL 56.4adipocyte free fatty acid secretion trait (VT:0010465)absolute change in adipocyte free fatty acid secretion per unit volume (CMO:0001446)4133250345Rat
1357343Gluco4Glucose level QTL 40.00002adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)4133250345Rat
61415Eae11Experimental allergic encephalomyelitis QTL 112.9nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)4139505420Rat
634323Hc2Hypercalciuria QTL 22.15urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)421079645210796Rat
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829457114705Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
1358201Gluco12Glucose level QTL121.6adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake (CMO:0000870)4521839229593287Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521917856647776Rat
631209Bw2Body weight QTL24.2retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)4994088544463908Rat
1300141Bp178Blood pressure QTL 178arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)41002490139524530Rat
6478724Anxrr35Anxiety related response QTL 350.00449defecation behavior trait (VT:0010462)defecation measurement (CMO:0000997)41008408955084089Rat
6478766Anxrr47Anxiety related response QTL 470.09637locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)41008408955084089Rat
6478769Anxrr48Anxiety related response QTL 480.02514locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)41008408955084089Rat
8694374Bw155Body weight QTL 1553.390.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)41008408955084089Rat
9590304Scort17Serum corticosterone level QTL 174.960.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)41008408955084089Rat
8552906Pigfal3Plasma insulin-like growth factor 1 level QTL 3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)41008408955084089Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2303585Bw86Body weight QTL 864body mass (VT:0001259)body weight (CMO:0000012)41467806559678065Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:150
Count of miRNA genes:107
Interacting mature miRNAs:125
Transcripts:ENSRNOT00000066643
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 64 7
Low 7 9 11 6 6 10 35 31 11 6
Below cutoff 3 36 27 20 8 20 2 4 3 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000066643   ⟹   ENSRNOP00000059912
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl414,388,323 - 15,155,328 (-)Ensembl
Rnor_6.0 Ensembl410,995,234 - 11,610,518 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078799   ⟹   ENSRNOP00000070380
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl414,428,358 - 15,001,949 (-)Ensembl
Rnor_6.0 Ensembl411,044,326 - 11,497,531 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000094238   ⟹   ENSRNOP00000090186
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl414,386,399 - 15,870,240 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000095227   ⟹   ENSRNOP00000095318
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl414,388,315 - 15,870,240 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115899   ⟹   ENSRNOP00000091952
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl414,386,399 - 15,870,240 (-)Ensembl
RefSeq Acc Id: NM_053621   ⟹   NP_446073
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2414,388,322 - 15,870,036 (-)NCBI
Rnor_6.0410,995,241 - 12,472,423 (-)NCBI
Rnor_5.0410,987,831 - 12,456,502 (-)NCBI
RGSC_v3.449,909,448 - 11,441,301 (-)RGD
Celera49,948,183 - 11,419,535 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_446073 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAC31124 (Get FASTA)   NCBI Sequence Viewer  
  AAD31015 (Get FASTA)   NCBI Sequence Viewer  
  EDL99441 (Get FASTA)   NCBI Sequence Viewer  
  EDL99442 (Get FASTA)   NCBI Sequence Viewer  
  O88382 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_446073   ⟸   NM_053621
- Sequence:
RefSeq Acc Id: ENSRNOP00000059912   ⟸   ENSRNOT00000066643
RefSeq Acc Id: ENSRNOP00000070380   ⟸   ENSRNOT00000078799
RefSeq Acc Id: ENSRNOP00000095318   ⟸   ENSRNOT00000095227
RefSeq Acc Id: ENSRNOP00000091952   ⟸   ENSRNOT00000115899
RefSeq Acc Id: ENSRNOP00000090186   ⟸   ENSRNOT00000094238
Protein Domains
Guanylate kinase-like   PDZ   WW

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)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621855 AgrOrtholog
Ensembl Genes ENSRNOG00000013962 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000059912 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070380 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066643 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000078799 UniProtKB/TrEMBL
Gene3D-CATH 2.30.42.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro GK/Ca_channel_bsu UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Guanylate_kin-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Guanylate_kinase_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MAGI2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WW_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WW_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:113970 UniProtKB/Swiss-Prot
NCBI Gene 113970 ENTREZGENE
PANTHER PTHR10316:SF27 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Guanylate_kin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PF00397 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Magi2 PhenoGen
PROSITE GUANYLATE_KINASE_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GUANYLATE_KINASE_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WW_DOMAIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WW_DOMAIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART GuKc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00456 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50156 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF51045 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52540 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JXR9_RAT UniProtKB/TrEMBL
  D3ZY03_RAT UniProtKB/TrEMBL
  MAGI2_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary D3ZRR9 UniProtKB/TrEMBL
  Q9R271 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Magi2  membrane associated guanylate kinase, WW and PDZ domain containing 2  Acvrinp1  activin receptor interacting protein 1  Symbol and Name updated 1299863 APPROVED
2005-01-20 Acvrinp1  activin receptor interacting protein 1  Acvrip1    Symbol updated 1299863 APPROVED
2002-08-07 Acvrip1        Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains contains six PDZ, two WW, and one guanylate kinase (GK) domains 632272
gene_function interacts with N-methyl-d-aspartate receptor subunits, neuroligin, and beta-catenin 1304344
gene_physical_interaction interacts with N-methyl-D-aspartate receptors and neuronal cell adhesion proteins 632272
gene_physical_interaction interacts with N-methyl-D-aspartate receptors and neuronal cell adhesion proteins 632273