Shank2 (SH3 and multiple ankyrin repeat domains 2) - Rat Genome Database

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Gene: Shank2 (SH3 and multiple ankyrin repeat domains 2) Rattus norvegicus
Analyze
Symbol: Shank2
Name: SH3 and multiple ankyrin repeat domains 2
RGD ID: 628772
Description: Enables SH3 domain binding activity and protein C-terminus binding activity. A structural constituent of postsynaptic density. Involved in several processes, including adult locomotory behavior; associative learning; and social behavior. Located in several cellular components, including apical plasma membrane; cell projection membrane; and growth cone. Is active in glutamatergic synapse; hippocampal mossy fiber to CA3 synapse; and postsynaptic density. Used to study autism spectrum disorder. Human ortholog(s) of this gene implicated in autistic disorder. Orthologous to human SHANK2 (SH3 and multiple ankyrin repeat domains 2); PARTICIPATES IN glutamate signaling pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: cortactin-binding protein 1; CortBP1; GKAP/SAPAP-interacting protein; LOC103690160; proline rich synapse associated protein 1; proline-rich synapse-associated protein 1; ProSAP1; SH3 and multiple ankyrin repeat domains protein 2; SH3 and multiple ankyrin repeat domains protein 2-like; SH3/ankyrin domain gene 2; Spank-3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Shank2em13Sage  
Genetic Models: SD-Shank2em13Sage
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21199,146,210 - 199,590,962 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1199,169,429 - 199,589,394 (+)Ensembl
Rnor_6.01217,149,156 - 217,593,950 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1217,151,166 - 217,592,763 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01222,118,530 - 222,150,341 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01224,028,791 - 224,450,737 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41204,399,856 - 204,855,474 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11204,553,308 - 205,005,561 (+)NCBI
Celera1196,732,183 - 197,149,084 (+)NCBICelera
Cytogenetic Map1q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
androgen antagonist  (EXP)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (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)
Butylparaben  (EXP)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chlorpyrifos  (ISO)
cisplatin  (EXP,ISO)
cobalt dichloride  (EXP)
cocaine  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) chloride  (EXP)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
DDE  (EXP)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dichloroacetic acid  (ISO)
dicrotophos  (ISO)
dorsomorphin  (ISO)
elemental selenium  (ISO)
enzacamene  (EXP)
epoxiconazole  (EXP)
ethanol  (ISO)
fipronil  (EXP)
GW 4064  (ISO)
hydralazine  (ISO)
hydrogen peroxide  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
linuron  (EXP)
melphalan  (ISO)
menadione  (ISO)
methapyrilene  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
N-Nitrosopyrrolidine  (ISO)
nickel atom  (ISO)
nickel sulfate  (ISO)
nitroglycerin  (EXP)
Nor-9-carboxy-delta9-THC  (ISO)
O-methyleugenol  (ISO)
paracetamol  (EXP,ISO)
PCB138  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
potassium atom  (EXP)
prochloraz  (EXP)
procymidone  (EXP)
propanal  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium dichromate  (EXP)
tetrachloromethane  (EXP)
tributylstannane  (EXP)
trichostatin A  (ISO)
triptonide  (ISO)
urethane  (ISO)
valproic acid  (EXP,ISO)
venlafaxine hydrochloride  (EXP)
vinclozolin  (EXP)
vitamin E  (ISO)
vorinostat  (ISO)
zinc atom  (ISO)
zinc dichloride  (EXP)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Baron MK, etal., Science. 2006 Jan 27;311(5760):531-5.
2. Boeckers TM, etal., J Neurosci 1999 Aug 1;19(15):6506-18.
3. Du Y, etal., Mol Cell Biol 1998 Oct;18(10):5838-51.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Grabrucker AM, etal., EMBO J. 2011 Feb 2;30(3):569-81. doi: 10.1038/emboj.2010.336. Epub 2011 Jan 7.
6. Han W, etal., J Biol Chem. 2006 Jan 20;281(3):1461-9. Epub 2005 Nov 17.
7. Hwang JI, etal., J Biol Chem. 2005 Apr 1;280(13):12467-73. Epub 2005 Jan 4.
8. Ishida H, etal., FEBS Lett. 2018 Aug;592(16):2786-2797. doi: 10.1002/1873-3468.13209. Epub 2018 Aug 12.
9. Kreienkamp HJ, etal., J Biol Chem. 2000 Oct 20;275(42):32387-90.
10. Kreienkamp HJ, etal., J Physiol Paris. 2000 May-Aug;94(3-4):193-8.
11. Lee JH, etal., J Biol Chem. 2007 Apr 6;282(14):10414-22. Epub 2007 Jan 23.
12. Lim S, etal., J Biol Chem 1999 Oct 8;274(41):29510-8.
13. McWilliams RR, etal., Am J Physiol Cell Physiol. 2005 Oct;289(4):C1042-51. Epub 2005 May 25.
14. Modi ME, etal., Front Mol Neurosci. 2018 Jun 19;11:107. doi: 10.3389/fnmol.2018.00107. eCollection 2018.
15. OMIM Disease Annotation Pipeline
16. Park E, etal., J Biol Chem. 2003 May 23;278(21):19220-9. Epub 2003 Mar 7.
17. Pipeline to import KEGG annotations from KEGG into RGD
18. Qualmann B, etal., J Neurosci. 2004 Mar 10;24(10):2481-95.
19. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
20. RGD automated import pipeline for gene-chemical interactions
21. Saavedra MV, etal., Neuroreport. 2008 Jul 16;19(11):1123-6. doi: 10.1097/WNR.0b013e3283086797.
22. Tobaben S, etal., J Biol Chem 2000 Nov 17;275(46):36204-10.
23. Yang J, etal., EMBO J. 2011 Jan 5;30(1):165-80. doi: 10.1038/emboj.2010.286. Epub 2010 Nov 30.
Additional References at PubMed
PMID:10373412   PMID:10527873   PMID:10806096   PMID:11583995   PMID:14679199   PMID:14977424   PMID:15207857   PMID:15458844   PMID:16606358   PMID:16758162   PMID:17120053   PMID:19299912  
PMID:20131911   PMID:20473310   PMID:20800661   PMID:20810910   PMID:21795692   PMID:22699619   PMID:22699620   PMID:25775468   PMID:26627310   PMID:27890541   PMID:29250591   PMID:29476059  
PMID:32564287  


Genomics

Comparative Map Data
Shank2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21199,146,210 - 199,590,962 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1199,169,429 - 199,589,394 (+)Ensembl
Rnor_6.01217,149,156 - 217,593,950 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1217,151,166 - 217,592,763 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01222,118,530 - 222,150,341 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01224,028,791 - 224,450,737 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41204,399,856 - 204,855,474 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11204,553,308 - 205,005,561 (+)NCBI
Celera1196,732,183 - 197,149,084 (+)NCBICelera
Cytogenetic Map1q42NCBI
SHANK2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1170,467,854 - 71,252,577 (-)EnsemblGRCh38hg38GRCh38
GRCh381170,467,854 - 71,252,724 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371170,313,959 - 70,963,623 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361169,991,609 - 70,185,520 (-)NCBINCBI36hg18NCBI36
Build 341170,012,765 - 70,185,520NCBI
Celera1167,575,145 - 68,227,408 (-)NCBI
Cytogenetic Map11q13.3-q13.4NCBI
HuRef1166,575,130 - 67,004,438 (-)NCBIHuRef
HuRef1167,062,872 - 67,229,732 (-)NCBIHuRef
CHM1_11170,197,402 - 70,819,749 (-)NCBICHM1_1
Shank2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm397143,531,819 - 143,979,780 (+)NCBIGRCm39mm39
GRCm39 Ensembl7143,555,665 - 143,978,231 (+)Ensembl
GRCm387143,978,077 - 144,426,043 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl7144,001,928 - 144,424,494 (+)EnsemblGRCm38mm10GRCm38
MGSCv377151,361,425 - 151,608,580 (+)NCBIGRCm37mm9NCBIm37
MGSCv367143,840,654 - 144,232,065 (+)NCBImm8
Celera7143,939,514 - 144,185,177 (+)NCBICelera
Cytogenetic Map7F5NCBI
Shank2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542215,295,772 - 15,814,711 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542215,295,800 - 15,818,067 (+)NCBIChiLan1.0ChiLan1.0
SHANK2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11168,857,186 - 69,495,237 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1168,860,606 - 69,437,925 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01165,570,677 - 66,268,139 (-)NCBIMhudiblu_PPA_v0panPan3
SHANK2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11847,477,625 - 47,915,557 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1847,635,788 - 47,912,117 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1846,010,915 - 46,522,454 (+)NCBI
ROS_Cfam_1.01848,113,005 - 48,589,823 (+)NCBI
UMICH_Zoey_3.11847,525,882 - 48,036,670 (+)NCBI
UNSW_CanFamBas_1.01847,111,601 - 47,622,440 (+)NCBI
UU_Cfam_GSD_1.01847,858,659 - 48,368,562 (+)NCBI
Shank2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049473,637,810 - 4,021,398 (+)NCBI
SpeTri2.0NW_004936599196,512 - 463,749 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SHANK2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl22,503,181 - 3,016,433 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.122,517,853 - 3,016,959 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22924,313 - 1,073,976 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SHANK2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.113,453,268 - 4,104,515 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666038100,644,177 - 101,362,369 (+)NCBIVero_WHO_p1.0
Shank2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476716,296,053 - 16,828,714 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D1Rat168  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21199,368,955 - 199,369,166 (+)MAPPERmRatBN7.2
Rnor_6.01217,372,257 - 217,372,467NCBIRnor6.0
Rnor_5.01224,224,750 - 224,224,960UniSTSRnor5.0
RGSC_v3.41204,621,918 - 204,622,129RGDRGSC3.4
RGSC_v3.41204,621,919 - 204,622,129UniSTSRGSC3.4
RGSC_v3.11204,775,371 - 204,775,582RGD
Celera1196,929,409 - 196,929,619UniSTS
RH 2.0 Map11104.7RGD
SHRSP x BN Map1104.5599RGD
Cytogenetic Map1q41UniSTS
D1Got184  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21199,463,338 - 199,463,553 (+)MAPPERmRatBN7.2
Rnor_6.01217,466,279 - 217,466,493NCBIRnor6.0
Rnor_5.01224,319,717 - 224,319,931UniSTSRnor5.0
Rnor_5.01224,808,843 - 224,809,057UniSTSRnor5.0
RGSC_v3.41204,729,897 - 204,730,112RGDRGSC3.4
RGSC_v3.41204,729,898 - 204,730,112UniSTSRGSC3.4
RGSC_v3.11204,883,350 - 204,883,565RGD
Celera1197,023,455 - 197,023,669UniSTS
RH 2.0 Map11103.1RGD
Cytogenetic Map1q41UniSTS
D1Wox81  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21199,587,887 - 199,588,094 (+)MAPPERmRatBN7.2
Rnor_6.01217,590,876 - 217,591,082NCBIRnor6.0
Rnor_6.01215,243,564 - 215,243,770NCBIRnor6.0
Rnor_5.01222,147,267 - 222,147,473UniSTSRnor5.0
Rnor_5.01224,447,663 - 224,447,869UniSTSRnor5.0
RGSC_v3.41204,853,947 - 204,854,153UniSTSRGSC3.4
Celera1197,147,557 - 197,147,763UniSTS
Cytogenetic Map1q41UniSTS
RH138116  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21199,341,510 - 199,341,650 (+)MAPPERmRatBN7.2
Rnor_6.01217,344,812 - 217,344,951NCBIRnor6.0
Rnor_5.01224,196,988 - 224,197,127UniSTSRnor5.0
RGSC_v3.41204,586,021 - 204,586,160UniSTSRGSC3.4
RH 3.4 Map11561.9UniSTS
Cytogenetic Map1q41UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2292218Kidm35Kidney mass QTL 35kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1199368955224569684Rat
619613Bp77Blood pressure QTL 770.01arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1164747424209747424Rat
619613Bp77Blood pressure QTL 770.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1164747424209747424Rat
631214Bw61Body weight QTL613.40.0001intramuscular adipose amount (VT:0010044)intramuscular fat area (CMO:0001162)1173108781218108781Rat
2302375Bw83Body weight QTL 834.870.0002body mass (VT:0001259)body weight (CMO:0000012)1197697768242697768Rat
2302378Insul11Insulin level QTL 113.25blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1144267353251128347Rat
70163Bw20Body weight QTL 205.1body mass (VT:0001259)body weight (CMO:0000012)1174133260219133260Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1150700142252085212Rat
724559Pancm1Pancreatic morphology QTL 17.1islet of Langerhans morphology trait (VT:0005215)pancreatic islet damage composite score (CMO:0001156)1181759564214537555Rat
724562Rends1Renal damage susceptibility QTL 10.05kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)1169537671214537671Rat
737828Hcas3Hepatocarcinoma susceptibility QTL 34.9liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)1144267353222987745Rat
1298084Thym4Thymus enlargement QTL 410.68thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1197814409242814409Rat
631658Cm7Cardiac mass QTL 75.320.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)1196248093241248093Rat
737977Bp160Blood pressure QTL 1600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1181133855226133855Rat
1331790Bp201Blood pressure QTL 2013.127arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1198211513225126682Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1156677124256448636Rat
1582206Kidm33Kidney mass QTL 336.9kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1188377360224054420Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)194642722214537671Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1176426412257976495Rat
631549Bp89Blood pressure QTL 895.7arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1123350581201284552Rat
1302787Stl25Serum triglyceride level QTL 252.70.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)1180359209210702199Rat
1641926Teswt2Testicular weight QTL 22.82testis mass (VT:1000644)both testes wet weight (CMO:0000175)1197697768238755659Rat
1598853Memor3Memory QTL 34.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)1143506580212458660Rat
2300161Bmd43Bone mineral density QTL 438.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1171629477216629477Rat
2300174Bmd42Bone mineral density QTL 428.40.0001lumbar vertebra mineral mass (VT:0010511)bone mineral density (CMO:0001226)1171629477216629477Rat
2300187Bmd41Bone mineral density QTL 418.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1171629477216629477Rat
2293654Bss30Bone structure and strength QTL 3032.650.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1171629477216629477Rat
2293673Bss27Bone structure and strength QTL 2718.630.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)1171629477216629477Rat
2293677Bss41Bone structure and strength QTL 419.380.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1171629477216629477Rat
2293689Bss47Bone structure and strength QTL 477.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)1171629477216629477Rat
2293693Bss22Bone structure and strength QTL 2233.520.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1171629477216629477Rat
631838Niddm36Non-insulin dependent diabetes mellitus QTL 360.01insulin secretion trait (VT:0003564)calculated pancreatic islet insulin release measurement (CMO:0001217)1184550676229550676Rat
634312Bp143Blood pressure QTL 14330.0002arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1182623426219932796Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1199050459259647894Rat
634321Hc1Hypercalciuria QTL 12.91urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1178810256240830002Rat
634338Hcar4Hepatocarcinoma resistance QTL 44.6liver integrity trait (VT:0010547)liver tumorous lesion number to liver area ratio (CMO:0001210)1193422268214537671Rat
1357335Bw39Body weight QTL 393.3body mass (VT:0001259)body weight (CMO:0000012)1197814409242814409Rat
1600374Mcs17Mammary carcinoma susceptibility QTL 173mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1197670404242670404Rat
1600380Niddm70Non-insulin dependent diabetes mellitus QTL 703.10.0008blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1176550523221550523Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1195804352257091168Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1150700247252085048Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1179567751260522016Rat
1578778Pur4Proteinuria QTL 43.30.003total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1150700247252085048Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)181591954219808434Rat
1300145Rf7Renal function QTL 72.96urine creatinine amount (VT:0010540)urine creatinine level (CMO:0000125)1185145134221264292Rat
1354591Cm36Cardiac mass QTL 364.1heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1102813953201278233Rat
1354602Bw35Body weight QTL 3512.2body mass (VT:0001259)body weight (CMO:0000012)1151162512201278233Rat
1354606Bp246Blood pressure QTL 2463.6arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)1102813953218753816Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1354615Cm32Cardiac mass QTL 325.2heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1102813953201278233Rat
1354618Kidm15Kidney mass QTL 155kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)1156677124201278233Rat
1354620Kidm19Kidney mass QTL 194kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1151162512201278233Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1177227632256448636Rat
1354634Kidm12Kidney mass QTL 123.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)1151162512201278233Rat
1354636Lmblg1Limb length QTL 16.4tibia length (VT:0004357)tibia length (CMO:0000450)1151162512201278233Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1151162512256448636Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1177227632256448636Rat
1354653Despr9Despair related QTL 90.00019locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1167909849212909849Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1359018Hrtrt20Heart rate QTL 203.08heart pumping trait (VT:2000009)heart rate (CMO:0000002)1185356336202902618Rat
1558658Bw59Body weight QTL 593.50.0003body mass (VT:0001259)body weight (CMO:0000012)1178784622223784622Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1153136852260522016Rat
1358191Ept10Estrogen-induced pituitary tumorigenesis QTL 103.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)1192825253243914732Rat
2292220Bp306Blood pressure QTL 3063.470.00087arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1164310393243914901Rat
2292222Bp307Blood pressure QTL 3073.060.0014arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1164310393213533942Rat
2293083Iddm25Insulin dependent diabetes mellitus QTL 254.18blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1181829673224569684Rat
2312420Pur17Proteinuria QTL 177.10.0001urine protein amount (VT:0005160)urine total protein excretion rate (CMO:0000756)1156677124218753816Rat
2312564Glom18Glomerulus QTL 182.40.003kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)1185356336231689108Rat
2303622Vencon6Ventilatory control QTL 60.001respiration trait (VT:0001943)respiration rate (CMO:0000289)1154561505199561505Rat
1358886Bp260Blood pressure QTL 2603.67arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1151162766225824951Rat
1358898Bp255Blood pressure QTL 2553.6arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1191019702246062233Rat
1549830Bss1Bone structure and strength QTL 14.8femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)1172609619217609619Rat
1358292Cm37Cardiac mass QTL 376.20.00000081heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1196248093241248093Rat
1358294Bw37Body weight QTL 3750.000011body mass (VT:0001259)body weight (CMO:0000012)1171310381216310381Rat
61341Bp26Blood pressure QTL 26arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1169537671214537671Rat
61347Bp197Blood pressure QTL 1974.2arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)1158633083203633083Rat
61376Bp42Blood pressure QTL 4223.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1197814409242814409Rat
4889428Stresp24Stress response QTL 240.05heart pumping trait (VT:2000009)absolute change in electrocardiographic low frequency R-R spectral component to high frequency R-R spectral component ratio (CMO:0002162)1155866514200866514Rat
6480773Gluco64Glucose level QTL 645.09blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1199050459200611765Rat
6480780Insul18Insulin level QTL 184.11blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1189607473200611765Rat
6480783Insul19Insulin level QTL 194.33blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1197489281200611765Rat
6903303Scl34Serum cholesterol QTL 342.50.0033blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)1180359209218108781Rat
8655655Arrd2Age-related retinal degeneration QTL 27.79retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1183970203243914901Rat
7794788Mcs32Mammary carcinoma susceptibility QTL 322.61mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)1115540693238914717Rat
7771612Cm80Cardiac mass QTL 808.4heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)1149448574221264292Rat
7421630Bp362Blood pressure QTL 3620.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1118608292241799120Rat
8552891Epfw5Epididymal fat weight QTL 54.4epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1193113876238113876Rat
8655855Arrd3Age-related retinal degeneration QTL 33.07lens clarity trait (VT:0001304)cataract incidence/prevalence measurement (CMO:0001585)1183970203243914901Rat
10059590Kidm44Kidney mass QTL 443.420.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1191033875236033875Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
10059600Bp378Blood pressure QTL 3783.080.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1176869060221869060Rat


Genetic Models
This gene Shank2 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:264
Count of miRNA genes:92
Interacting mature miRNAs:105
Transcripts:ENSRNOT00000071484, ENSRNOT00000071741, ENSRNOT00000075078
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 50 6
Low 3 12 51 41 4 41 24 29 39 11
Below cutoff 29 6 15 7 8 2 7

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001004133 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_133440 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_133441 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_201350 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760068 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588715 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588716 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588717 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588718 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588719 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588720 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588721 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588722 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588723 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588724 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588725 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588726 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588727 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087343 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087361 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087396 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087434 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087471 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005490582 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC125304 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC131216 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF060116 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF141903 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF159048 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ131899 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ249562 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY298755 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000044 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000071235   ⟹   ENSRNOP00000065594
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1215,214,853 - 215,241,723 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000071484   ⟹   ENSRNOP00000064763
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1199,345,799 - 199,589,394 (+)Ensembl
Rnor_6.0 Ensembl1217,151,166 - 217,592,763 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000071741   ⟹   ENSRNOP00000067841
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1199,169,429 - 199,586,049 (+)Ensembl
Rnor_6.0 Ensembl1217,345,545 - 217,589,035 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000075078   ⟹   ENSRNOP00000065891
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1199,169,429 - 199,586,049 (+)Ensembl
Rnor_6.0 Ensembl1217,173,199 - 217,589,037 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000080442   ⟹   ENSRNOP00000074205
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1215,214,853 - 215,241,723 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092278   ⟹   ENSRNOP00000075778
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1217,349,493 - 217,566,581 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092357   ⟹   ENSRNOP00000075800
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1199,407,033 - 199,589,394 (+)Ensembl
Rnor_6.0 Ensembl1217,459,321 - 217,589,488 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092386   ⟹   ENSRNOP00000075919
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1199,456,274 - 199,589,394 (+)Ensembl
Rnor_6.0 Ensembl1217,459,215 - 217,592,403 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092516   ⟹   ENSRNOP00000075839
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1199,341,853 - 199,589,394 (+)Ensembl
Rnor_6.0 Ensembl1217,345,154 - 217,592,403 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092579   ⟹   ENSRNOP00000075896
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1217,349,497 - 217,577,938 (+)Ensembl
RefSeq Acc Id: NM_001004133   ⟹   NP_001004133
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21199,456,380 - 199,586,500 (+)NCBI
Rnor_6.01217,459,321 - 217,589,488 (+)NCBI
Rnor_5.01224,028,791 - 224,450,737 (+)NCBI
RGSC_v3.41204,399,856 - 204,855,474 (+)RGD
Celera1197,016,496 - 197,146,169 (+)NCBI
Sequence:
RefSeq Acc Id: NM_133440   ⟹   NP_597684
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21199,456,274 - 199,589,415 (+)NCBI
Rnor_6.01217,459,215 - 217,592,403 (+)NCBI
Rnor_5.01224,028,791 - 224,450,737 (+)NCBI
RGSC_v3.41204,399,856 - 204,855,474 (+)RGD
Celera1197,016,390 - 197,149,084 (+)NCBI
Sequence:
RefSeq Acc Id: NM_133441   ⟹   NP_597685
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21199,341,853 - 199,589,415 (+)NCBI
Rnor_6.01217,345,154 - 217,592,403 (+)NCBI
Rnor_5.01224,028,791 - 224,450,737 (+)NCBI
RGSC_v3.41204,399,856 - 204,855,474 (+)RGD
Celera1196,902,548 - 197,149,084 (+)NCBI
Sequence:
RefSeq Acc Id: NM_201350   ⟹   NP_958738
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21199,169,429 - 199,586,049 (+)NCBI
Rnor_6.01217,173,199 - 217,589,037 (+)NCBI
Rnor_5.01224,028,791 - 224,450,737 (+)NCBI
RGSC_v3.41204,399,856 - 204,855,474 (+)RGD
Celera1196,732,183 - 197,145,718 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008760068   ⟹   XP_008758290
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21199,147,005 - 199,586,047 (+)NCBI
Rnor_6.01217,150,473 - 217,593,950 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588715   ⟹   XP_017444204
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21199,147,005 - 199,590,962 (+)NCBI
Rnor_6.01217,150,473 - 217,593,950 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588716   ⟹   XP_017444205
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21199,146,210 - 199,586,047 (+)NCBI
Rnor_6.01217,149,795 - 217,593,950 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588718   ⟹   XP_017444207
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21199,147,005 - 199,586,047 (+)NCBI
Rnor_6.01217,150,473 - 217,593,950 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588719   ⟹   XP_017444208
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21199,146,664 - 199,586,047 (+)NCBI
Rnor_6.01217,150,298 - 217,593,950 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588720   ⟹   XP_017444209
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21199,147,005 - 199,590,962 (+)NCBI
Rnor_6.01217,150,473 - 217,593,950 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588721   ⟹   XP_017444210
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21199,147,005 - 199,590,962 (+)NCBI
Rnor_6.01217,150,473 - 217,593,950 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588722   ⟹   XP_017444211
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21199,147,005 - 199,590,962 (+)NCBI
Rnor_6.01217,150,473 - 217,593,950 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588723   ⟹   XP_017444212
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21199,147,006 - 199,590,962 (+)NCBI
Rnor_6.01217,150,473 - 217,593,950 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588725   ⟹   XP_017444214
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21199,147,005 - 199,590,962 (+)NCBI
Rnor_6.01217,150,473 - 217,593,950 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588726   ⟹   XP_017444215
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21199,147,005 - 199,590,962 (+)NCBI
Rnor_6.01217,150,473 - 217,593,950 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588727   ⟹   XP_017444216
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21199,147,005 - 199,590,962 (+)NCBI
Rnor_6.01217,150,473 - 217,593,950 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039087343   ⟹   XP_038943271
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21199,340,330 - 199,586,047 (+)NCBI
RefSeq Acc Id: XM_039087361   ⟹   XP_038943289
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21199,406,529 - 199,586,047 (+)NCBI
RefSeq Acc Id: XM_039087396   ⟹   XP_038943324
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21199,456,804 - 199,586,047 (+)NCBI
RefSeq Acc Id: XM_039087434   ⟹   XP_038943362
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21199,455,952 - 199,590,962 (+)NCBI
RefSeq Acc Id: XM_039087471   ⟹   XP_038943399
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21199,455,691 - 199,586,047 (+)NCBI
RefSeq Acc Id: XR_005490582
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21199,146,990 - 199,572,198 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001004133 (Get FASTA)   NCBI Sequence Viewer  
  NP_597684 (Get FASTA)   NCBI Sequence Viewer  
  NP_597685 (Get FASTA)   NCBI Sequence Viewer  
  NP_958738 (Get FASTA)   NCBI Sequence Viewer  
  XP_008758290 (Get FASTA)   NCBI Sequence Viewer  
  XP_017444204 (Get FASTA)   NCBI Sequence Viewer  
  XP_017444205 (Get FASTA)   NCBI Sequence Viewer  
  XP_017444207 (Get FASTA)   NCBI Sequence Viewer  
  XP_017444208 (Get FASTA)   NCBI Sequence Viewer  
  XP_017444209 (Get FASTA)   NCBI Sequence Viewer  
  XP_017444210 (Get FASTA)   NCBI Sequence Viewer  
  XP_017444211 (Get FASTA)   NCBI Sequence Viewer  
  XP_017444212 (Get FASTA)   NCBI Sequence Viewer  
  XP_017444214 (Get FASTA)   NCBI Sequence Viewer  
  XP_017444215 (Get FASTA)   NCBI Sequence Viewer  
  XP_017444216 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943271 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943289 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943324 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943362 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943399 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAC62226 (Get FASTA)   NCBI Sequence Viewer  
  AAD42977 (Get FASTA)   NCBI Sequence Viewer  
  AAF02497 (Get FASTA)   NCBI Sequence Viewer  
  AAP85236 (Get FASTA)   NCBI Sequence Viewer  
  CAB44312 (Get FASTA)   NCBI Sequence Viewer  
  CAB44313 (Get FASTA)   NCBI Sequence Viewer  
  CAB44314 (Get FASTA)   NCBI Sequence Viewer  
  CAB56522 (Get FASTA)   NCBI Sequence Viewer  
  Q9QX74 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_958738   ⟸   NM_201350
- Peptide Label: isoform a
- UniProtKB: Q9QX74 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_597685   ⟸   NM_133441
- Peptide Label: isoform d
- UniProtKB: Q9QX74 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_597684   ⟸   NM_133440
- Peptide Label: isoform c
- UniProtKB: Q9QX74 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001004133   ⟸   NM_001004133
- Peptide Label: isoform b
- UniProtKB: Q9QX74 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008758290   ⟸   XM_008760068
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017444205   ⟸   XM_017588716
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017444208   ⟸   XM_017588719
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017444204   ⟸   XM_017588715
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017444209   ⟸   XM_017588720
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017444211   ⟸   XM_017588722
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017444214   ⟸   XM_017588725
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017444210   ⟸   XM_017588721
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017444212   ⟸   XM_017588723
- Peptide Label: isoform X6
- UniProtKB: M0R5T5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017444215   ⟸   XM_017588726
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017444216   ⟸   XM_017588727
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_017444207   ⟸   XM_017588718
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000075778   ⟸   ENSRNOT00000092278
RefSeq Acc Id: ENSRNOP00000075919   ⟸   ENSRNOT00000092386
RefSeq Acc Id: ENSRNOP00000075800   ⟸   ENSRNOT00000092357
RefSeq Acc Id: ENSRNOP00000075839   ⟸   ENSRNOT00000092516
RefSeq Acc Id: ENSRNOP00000075896   ⟸   ENSRNOT00000092579
RefSeq Acc Id: ENSRNOP00000065891   ⟸   ENSRNOT00000075078
RefSeq Acc Id: ENSRNOP00000064763   ⟸   ENSRNOT00000071484
RefSeq Acc Id: ENSRNOP00000067841   ⟸   ENSRNOT00000071741
RefSeq Acc Id: XP_038943271   ⟸   XM_039087343
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038943289   ⟸   XM_039087361
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038943399   ⟸   XM_039087471
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038943362   ⟸   XM_039087434
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038943324   ⟸   XM_039087396
- Peptide Label: isoform X12
RefSeq Acc Id: ENSRNOP00000065594   ⟸   ENSRNOT00000071235
RefSeq Acc Id: ENSRNOP00000074205   ⟸   ENSRNOT00000080442
Protein Domains
PDZ   SAM   SH3

Transcriptome

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

Promoters
RGD ID:13690583
Promoter ID:EPDNEW_R1107
Type:single initiation site
Name:Shank2_1
Description:SH3 and multiple ankyrin repeat domains 2
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_6.01217,459,268 - 217,459,328EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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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)
ACI/EurMcwi (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
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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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
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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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
F344/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
F344/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
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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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
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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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
GH/OmrMcwi (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)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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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
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (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
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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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
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/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
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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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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:628772 AgrOrtholog
Ensembl Genes ENSRNOG00000047651 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000050206 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000064763 UniProtKB/TrEMBL
  ENSRNOP00000065594 UniProtKB/TrEMBL
  ENSRNOP00000065891 UniProtKB/Swiss-Prot
  ENSRNOP00000067841 UniProtKB/Swiss-Prot
  ENSRNOP00000074205 UniProtKB/TrEMBL
  ENSRNOP00000075778 UniProtKB/TrEMBL
  ENSRNOP00000075800 UniProtKB/Swiss-Prot
  ENSRNOP00000075839 UniProtKB/Swiss-Prot
  ENSRNOP00000075896 UniProtKB/TrEMBL
  ENSRNOP00000075919 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000071235 UniProtKB/TrEMBL
  ENSRNOT00000071484 UniProtKB/TrEMBL
  ENSRNOT00000071741 UniProtKB/Swiss-Prot
  ENSRNOT00000075078 UniProtKB/Swiss-Prot
  ENSRNOT00000080442 UniProtKB/TrEMBL
  ENSRNOT00000092278 UniProtKB/TrEMBL
  ENSRNOT00000092357 UniProtKB/Swiss-Prot
  ENSRNOT00000092386 UniProtKB/Swiss-Prot
  ENSRNOT00000092516 UniProtKB/Swiss-Prot
  ENSRNOT00000092579 UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.50 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  1.25.40.20 UniProtKB/TrEMBL