Shank3 (SH3 and multiple ankyrin repeat domains 3) - Rat Genome Database

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Gene: Shank3 (SH3 and multiple ankyrin repeat domains 3) Rattus norvegicus
Analyze
Symbol: Shank3
Name: SH3 and multiple ankyrin repeat domains 3
RGD ID: 69264
Description: Exhibits several functions, including SH3 domain binding activity; protein C-terminus binding activity; and scaffold protein binding activity. A structural constituent of postsynaptic density. Involved in positive regulation of glutamate receptor signaling pathway and regulation of synapse organization. Localizes to ciliary membrane; glutamatergic synapse; and postsynaptic density, intracellular component. Predicted to colocalize with ionotropic glutamate receptor complex and postsynaptic membrane. Human ortholog(s) of this gene implicated in Phelan-McDermid syndrome and schizophrenia 15. Orthologous to human SHANK3 (SH3 and multiple ankyrin repeat domains 3); PARTICIPATES IN glutamate signaling pathway; INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,5-hexanedione.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: proline rich synapse associated protein 2; proline-rich synapse-associated protein 2; Prosap2; SH3 and multiple ankyrin repeat domains protein 3; SH3/ankyrin domain gene 3; Shank postsynaptic density protein 3a; SPANK-2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Shank3em1Bux  
Genetic Models: SD-Shank3em1Bux
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27120,568,707 - 120,630,796 (+)NCBI
Rnor_6.0 Ensembl7130,474,279 - 130,534,679 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07130,474,278 - 130,534,679 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07130,159,246 - 130,220,171 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47127,817,026 - 127,877,875 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17127,851,199 - 127,912,102 (+)NCBI
Celera7117,042,941 - 117,102,379 (+)NCBICelera
Cytogenetic Map7q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,5-hexanedione  (EXP)
2,6-dinitrotoluene  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP)
bisphenol F  (ISO)
Butylparaben  (EXP)
C60 fullerene  (EXP)
cadmium dichloride  (EXP)
carbendazim  (EXP)
chloroacetaldehyde  (ISO)
cidofovir anhydrous  (ISO)
clodronic acid  (ISO)
cobalt dichloride  (EXP)
cocaine  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) chloride  (EXP)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
enzacamene  (EXP)
ethanol  (ISO)
furan  (EXP)
glyphosate  (EXP)
L-methionine  (EXP)
lipopolysaccharide  (EXP)
methapyrilene  (ISO)
methoxychlor  (EXP)
Methylazoxymethanol acetate  (EXP)
N-methyl-4-phenylpyridinium  (ISO)
N1'-[2-[[5-[(dimethylamino)methyl]-2-furanyl]methylthio]ethyl]-N1-methyl-2-nitroethene-1,1-diamine  (EXP)
orphenadrine  (EXP)
phenylmercury acetate  (ISO)
phosgene  (ISO)
potassium atom  (EXP)
potassium dichromate  (ISO)
ranitidine  (EXP)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
SB 431542  (ISO)
serpentine asbestos  (ISO)
testosterone  (EXP)
triptonide  (ISO)
valproic acid  (EXP,ISO)
vorinostat  (ISO)
zinc atom  (EXP)
zinc dichloride  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adult behavior  (ISO)
AMPA glutamate receptor clustering  (IEA,ISO,ISS)
brain morphogenesis  (IEA,ISO,ISS)
dendritic spine morphogenesis  (IEA,ISO,ISS)
embryonic epithelial tube formation  (IEA,ISO)
exploration behavior  (ISO)
guanylate kinase-associated protein clustering  (IEA,ISO,ISS)
learning  (IEA,ISO,ISS)
learning or memory  (ISO)
locomotion  (IEA,ISO)
locomotory behavior  (ISO)
locomotory exploration behavior  (IEA,ISO,ISS)
long-term synaptic depression  (IEA,ISO)
long-term synaptic potentiation  (IEA,ISO)
maintenance of postsynaptic density structure  (IC,IEA)
MAPK cascade  (IEA,ISO,ISS)
memory  (IEA,ISO,ISS)
negative regulation of actin filament bundle assembly  (IEA,ISO,ISS)
negative regulation of cell volume  (IEA,ISO,ISS)
neuromuscular process controlling balance  (IEA,ISO,ISS)
NMDA glutamate receptor clustering  (IEA,ISO,ISS)
positive regulation of AMPA receptor activity  (IEA,ISO,ISS)
positive regulation of dendritic spine development  (IEA,ISO,ISS)
positive regulation of excitatory postsynaptic potential  (IEA,ISO,ISS)
positive regulation of glutamate receptor signaling pathway  (IEA,IMP,ISO,ISS)
positive regulation of long-term neuronal synaptic plasticity  (IEA,ISO,ISS)
positive regulation of long-term synaptic potentiation  (IEA,ISO,ISS)
positive regulation of synapse structural plasticity  (IEA,ISO,ISS)
positive regulation of synaptic transmission, glutamatergic  (IEA,ISO,ISS)
postsynaptic density assembly  (IEA,ISO,ISS)
regulation of AMPA glutamate receptor clustering  (IEA,ISO)
regulation of behavioral fear response  (IEA,ISO,ISS)
regulation of dendritic spine morphogenesis  (IEA,ISO,ISS)
regulation of grooming behavior  (IEA,ISO,ISS)
regulation of long-term synaptic depression  (IEA,ISO,ISS)
regulation of long-term synaptic potentiation  (ISO,ISS)
regulation of synapse organization  (IDA,IMP)
regulation of synaptic plasticity  (ISO)
social behavior  (IEA,ISO,ISS)
striatal medium spiny neuron differentiation  (IEA,ISO,ISS)
synapse assembly  (ISO,ISS)
vocal learning  (ISO)
vocalization behavior  (IEA,ISO,ISS)

Cellular Component

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. Bockers TM, etal., J Biol Chem 2001 Oct 26;276(43):40104-12.
3. Bockmann J, etal., J Neurochem. 2002 Nov;83(4):1013-7.
4. Boeckers TM, etal., J Neurosci 1999 Aug 1;19(15):6506-18.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. Grabrucker AM, etal., EMBO J. 2011 Feb 2;30(3):569-81. doi: 10.1038/emboj.2010.336. Epub 2011 Jan 7.
7. Harony-Nicolas H, etal., Elife. 2017 Jan 31;6. doi: 10.7554/eLife.18904.
8. MacGillavry HD, etal., Neuron. 2013 May 22;78(4):615-22. doi: 10.1016/j.neuron.2013.03.009.
9. MGD data from the GO Consortium
10. Naisbitt S, etal., Neuron 1999 Jul;23(3):569-82.
11. NCBI rat LocusLink and RefSeq merged data July 26, 2002
12. OMIM Disease Annotation Pipeline
13. Park E, etal., J Biol Chem. 2003 May 23;278(21):19220-9. Epub 2003 Mar 7.
14. Petralia RS, etal., Mol Cell Neurosci. 2005 Jul;29(3):436-52.
15. Pipeline to import KEGG annotations from KEGG into RGD
16. Proepper C, etal., EMBO J. 2007 Mar 7;26(5):1397-409. Epub 2007 Feb 15.
17. Qualmann B, etal., J Neurosci. 2004 Mar 10;24(10):2481-95.
18. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. RGD automated import pipeline for gene-chemical interactions
20. Saavedra MV, etal., Neuroreport. 2008 Jul 16;19(11):1123-6. doi: 10.1097/WNR.0b013e3283086797.
21. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
22. Thomas GM, etal., Proc Natl Acad Sci U S A. 2005 Oct 18;102(42):15006-11. Epub 2005 Oct 10.
23. Tobaben S, etal., J Biol Chem 2000 Nov 17;275(46):36204-10.
24. Tu JC, etal., Neuron. 1999 Jul;23(3):583-92.
25. Verpelli C, etal., J Biol Chem. 2011 Oct 7;286(40):34839-50. doi: 10.1074/jbc.M111.258384. Epub 2011 Jul 27.
26. Wendholt D, etal., J Biol Chem. 2006 May 12;281(19):13805-16. Epub 2006 Mar 7.
27. Wilson HL, etal., J Med Genet. 2003 Aug;40(8):575-84.
Additional References at PubMed
PMID:10527873   PMID:10806096   PMID:15207857   PMID:15458844   PMID:15569713   PMID:15689539   PMID:16606358   PMID:17173049   PMID:19208628   PMID:19481056   PMID:20800661   PMID:21148417  
PMID:21167025   PMID:21378602   PMID:21423165   PMID:21558424   PMID:23897824   PMID:24211303   PMID:26627310   PMID:26725465   PMID:27144302   PMID:27161151   PMID:27581454   PMID:27592227  
PMID:28263956   PMID:28647360   PMID:29250591   PMID:29377611   PMID:29473168   PMID:29476059   PMID:29735556   PMID:30868621   PMID:31983435   PMID:32199104  


Genomics

Comparative Map Data
Shank3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27120,568,707 - 120,630,796 (+)NCBI
Rnor_6.0 Ensembl7130,474,279 - 130,534,679 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07130,474,278 - 130,534,679 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07130,159,246 - 130,220,171 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47127,817,026 - 127,877,875 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17127,851,199 - 127,912,102 (+)NCBI
Celera7117,042,941 - 117,102,379 (+)NCBICelera
Cytogenetic Map7q34NCBI
SHANK3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2250,674,415 - 50,733,298 (+)EnsemblGRCh38hg38GRCh38
GRCh382250,672,823 - 50,733,212 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372251,111,251 - 51,171,640 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362249,459,936 - 49,518,507 (+)NCBINCBI36hg18NCBI36
Build 342249,449,206 - 49,461,782NCBI
Celera2234,989,101 - 35,047,689 (+)NCBI
Cytogenetic Map22q13.33NCBI
HuRef2234,005,374 - 34,064,052 (+)NCBIHuRef
CHM1_12251,072,241 - 51,130,430 (+)NCBICHM1_1
Shank3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391589,376,929 - 89,444,464 (+)NCBIGRCm39mm39
GRCm39 Ensembl1589,383,826 - 89,444,464 (+)Ensembl
GRCm381589,493,013 - 89,560,261 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1589,499,623 - 89,560,261 (+)EnsemblGRCm38mm10GRCm38
MGSCv371589,330,288 - 89,390,692 (+)NCBIGRCm37mm9NCBIm37
MGSCv361589,327,624 - 89,386,090 (+)NCBImm8
Celera1591,629,363 - 91,689,694 (+)NCBICelera
Cytogenetic Map15E3NCBI
Shank3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541333,660,022 - 33,712,796 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541333,660,025 - 33,714,649 (+)NCBIChiLan1.0ChiLan1.0
SHANK3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12250,026,620 - 50,071,446 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v02230,951,866 - 30,973,608 (+)NCBIMhudiblu_PPA_v0panPan3
SHANK3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11016,621,445 - 16,665,366 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1016,599,507 - 16,646,609 (-)NCBI
ROS_Cfam_1.01017,348,145 - 17,395,273 (-)NCBI
UMICH_Zoey_3.11017,072,629 - 17,119,713 (-)NCBI
UNSW_CanFamBas_1.01017,395,724 - 17,442,764 (-)NCBI
UU_Cfam_GSD_1.01017,527,515 - 17,574,624 (-)NCBI
Shank3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945114,175 - 167,562 (-)NCBI
SpeTri2.0NW_004936629114,175 - 168,697 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SHANK3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl541,786 - 93,177 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1541,376 - 93,033 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SHANK3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11933,155,695 - 33,209,679 (+)NCBI
ChlSab1.1 Ensembl1933,155,770 - 33,208,224 (+)Ensembl
Shank3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475272,545 - 127,321 (-)NCBI

Position Markers
D7Got127  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27120,589,606 - 120,589,895 (+)MAPPER
Rnor_6.07130,493,475 - 130,493,763NCBIRnor6.0
Rnor_5.07130,178,453 - 130,178,741UniSTSRnor5.0
RGSC_v3.47127,836,249 - 127,836,538RGDRGSC3.4
RGSC_v3.47127,836,250 - 127,836,538UniSTSRGSC3.4
RGSC_v3.17127,870,479 - 127,870,768RGD
Celera7117,061,748 - 117,062,036UniSTS
RH 3.4 Map7959.0UniSTS
RH 3.4 Map7959.0RGD
RH 2.0 Map7711.2RGD
Cytogenetic Map7q34UniSTS
D7Wox53  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27120,630,286 - 120,630,485 (+)MAPPER
Rnor_6.07130,534,170 - 130,534,368NCBIRnor6.0
Rnor_5.07130,219,662 - 130,219,860UniSTSRnor5.0
RGSC_v3.47127,877,366 - 127,877,564UniSTSRGSC3.4
Celera7117,101,870 - 117,102,068UniSTS
Cytogenetic Map7q34UniSTS
RH143496  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27120,600,500 - 120,600,646 (+)MAPPER
Rnor_6.07130,504,368 - 130,504,513NCBIRnor6.0
Rnor_5.07130,189,345 - 130,189,490UniSTSRnor5.0
RGSC_v3.47127,847,049 - 127,847,194UniSTSRGSC3.4
Celera7117,072,085 - 117,072,230UniSTS
RH 3.4 Map7958.9UniSTS
Cytogenetic Map7q34UniSTS
BE108630  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27120,590,475 - 120,590,627 (+)MAPPER
Rnor_6.07130,494,344 - 130,494,495NCBIRnor6.0
Rnor_5.07130,179,322 - 130,179,473UniSTSRnor5.0
RGSC_v3.47127,837,119 - 127,837,270UniSTSRGSC3.4
Celera7117,062,617 - 117,062,768UniSTS
RH 3.4 Map7959.3UniSTS
Cytogenetic Map7q34UniSTS
BF405313  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27120,590,605 - 120,590,788 (+)MAPPER
Rnor_6.07130,494,474 - 130,494,656NCBIRnor6.0
Rnor_5.07130,179,452 - 130,179,634UniSTSRnor5.0
RGSC_v3.47127,837,249 - 127,837,431UniSTSRGSC3.4
Celera7117,062,747 - 117,062,929UniSTS
RH 3.4 Map7958.2UniSTS
Cytogenetic Map7q34UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)751251919145729302Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)771448715145729302Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)781645773140745067Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)785595369130595369Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)785595369130595369Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)788365265133365265Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)788365265134673427Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)791018361136018361Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)793726906138726906Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)793726906138726906Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)796630946141630946Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)7100028953145729302Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)7100160423140335001Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)7100192194145192194Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)7106564316145729302Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7111519266143965591Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7114825174145729302Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7115922628145729302Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7120746024145692398Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7121654760145729302Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7121986439143965591Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7122421276143965415Rat
1582240Sffal1Serum free fatty acids level QTL 13.40.0021blood free fatty acid amount (VT:0001553)serum free fatty acids level (CMO:0000547)7126463649134098026Rat
631201Panci1Pancreas inflammation QTL 100.001pancreas integrity trait (VT:0010560)percentage of study population displaying chronic pancreatitis at a point in time (CMO:0001214)7126463827137325116Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7129412003145729302Rat


Genetic Models
This gene Shank3 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:302
Count of miRNA genes:109
Interacting mature miRNAs:113
Transcripts:ENSRNOT00000045913, ENSRNOT00000047960
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 33 6 6 5 6 71 23 26 11
Low 3 10 51 35 14 35 8 11 3 12 15 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_021676 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079817 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079818 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079820 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079821 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079822 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079823 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079824 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079825 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079826 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005486713 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC125982 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF133301 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF159047 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ133120 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CS301518 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000187 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000085191   ⟹   ENSRNOP00000071295
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7130,474,508 - 130,532,758 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092299
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7130,532,435 - 130,533,587 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092388   ⟹   ENSRNOP00000075892
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7130,474,279 - 130,532,234 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092413
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7130,475,972 - 130,532,234 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092431   ⟹   ENSRNOP00000075760
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7130,498,199 - 130,532,234 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092535   ⟹   ENSRNOP00000075887
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7130,532,435 - 130,534,679 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092672   ⟹   ENSRNOP00000075813
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7130,532,435 - 130,532,758 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092684   ⟹   ENSRNOP00000075759
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7130,498,199 - 130,532,179 (+)Ensembl
RefSeq Acc Id: NM_021676   ⟹   NP_067708
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,570,402 - 120,629,247 (+)NCBI
Rnor_6.07130,474,278 - 130,534,679 (+)NCBI
Rnor_5.07130,159,246 - 130,220,171 (+)NCBI
RGSC_v3.47127,817,026 - 127,877,875 (+)RGD
Celera7117,042,941 - 117,102,379 (+)RGD
Sequence:
RefSeq Acc Id: XM_039079817   ⟹   XP_038935745
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,568,717 - 120,630,796 (+)NCBI
RefSeq Acc Id: XM_039079818   ⟹   XP_038935746
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,568,717 - 120,630,796 (+)NCBI
RefSeq Acc Id: XM_039079820   ⟹   XP_038935748
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,568,717 - 120,628,429 (+)NCBI
RefSeq Acc Id: XM_039079821   ⟹   XP_038935749
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,568,717 - 120,628,716 (+)NCBI
RefSeq Acc Id: XM_039079822   ⟹   XP_038935750
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,568,717 - 120,630,796 (+)NCBI
RefSeq Acc Id: XM_039079823   ⟹   XP_038935751
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,613,763 - 120,630,796 (+)NCBI
RefSeq Acc Id: XM_039079824   ⟹   XP_038935752
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,568,708 - 120,618,300 (+)NCBI
RefSeq Acc Id: XM_039079825   ⟹   XP_038935753
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,568,707 - 120,628,423 (+)NCBI
RefSeq Acc Id: XM_039079826   ⟹   XP_038935754
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,568,711 - 120,630,796 (+)NCBI
RefSeq Acc Id: XR_005486713
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,568,712 - 120,613,847 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_067708   ⟸   NM_021676
- Sequence:
RefSeq Acc Id: ENSRNOP00000075892   ⟸   ENSRNOT00000092388
RefSeq Acc Id: ENSRNOP00000075759   ⟸   ENSRNOT00000092684
RefSeq Acc Id: ENSRNOP00000075813   ⟸   ENSRNOT00000092672
RefSeq Acc Id: ENSRNOP00000075887   ⟸   ENSRNOT00000092535
RefSeq Acc Id: ENSRNOP00000075760   ⟸   ENSRNOT00000092431
RefSeq Acc Id: ENSRNOP00000071295   ⟸   ENSRNOT00000085191
RefSeq Acc Id: XP_038935753   ⟸   XM_039079825
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038935752   ⟸   XM_039079824
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038935754   ⟸   XM_039079826
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038935750   ⟸   XM_039079822
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038935745   ⟸   XM_039079817
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038935746   ⟸   XM_039079818
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038935749   ⟸   XM_039079821
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038935748   ⟸   XM_039079820
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038935751   ⟸   XM_039079823
- Peptide Label: isoform X6
Protein Domains
ANK_REP_REGION   PDZ   SAM   SH3

Transcriptome

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

Promoters
RGD ID:13695606
Promoter ID:EPDNEW_R6116
Type:single initiation site
Name:Shank3_1
Description:SH3 and multiple ankyrin repeat domains 3
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_6.07130,474,449 - 130,474,509EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (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/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 (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)
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
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
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/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
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 (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69264 AgrOrtholog
Ensembl Genes ENSRNOG00000052296 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000071295 UniProtKB/TrEMBL
  ENSRNOP00000075759 UniProtKB/TrEMBL
  ENSRNOP00000075760 UniProtKB/TrEMBL
  ENSRNOP00000075813 UniProtKB/TrEMBL
  ENSRNOP00000075887 UniProtKB/TrEMBL
  ENSRNOP00000075892 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000085191 UniProtKB/TrEMBL
  ENSRNOT00000092388 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000092431 UniProtKB/TrEMBL
  ENSRNOT00000092535 UniProtKB/TrEMBL
  ENSRNOT00000092672 UniProtKB/TrEMBL
  ENSRNOT00000092684 UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.50 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  1.25.40.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.30.42.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Ankyrin_rpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ankyrin_rpt-contain_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ankyrin_rpt-contain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ_6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM/pointed_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:59312 UniProtKB/Swiss-Prot
NCBI Gene 59312 ENTREZGENE
Pfam Ank_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ_6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Shank3 PhenoGen
PROSITE ANK_REP_REGION UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ANK_REPEAT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM_DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART ANK UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47769 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF48403 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF50044 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF50156 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC204614
UniProt A0A0G2K042_RAT UniProtKB/TrEMBL
  A0A0U1RRP4_RAT UniProtKB/TrEMBL
  A0A0U1RRP5_RAT UniProtKB/TrEMBL
  A0A0U1RS08_RAT UniProtKB/TrEMBL
  A0A0U1RS13_RAT UniProtKB/TrEMBL
  Q9JLU4 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q9WUY7 UniProtKB/Swiss-Prot
  Q9WV47 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-11-04 Shank3  SH3 and multiple ankyrin repeat domains 3  Shank3  SH3/ankyrin domain gene 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Shank3  SH3/ankyrin domain gene 3      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains ankyrin repeats, an Src homology 3 (SH3) domain, a PSD-95/discs large/ZO-1 (PDZ) domain, several proline-rich regions, and a C-terminal sterile alpha-motif (SAM) domain 628460
gene_expression expressed in the brain 628460
gene_function master scaffold for glutamate receptor complexes in postsynaptic specialization 628460
gene_physical_interaction binds to the cytoskeletal protein Spna2 (alpha-fodrin) 628460
gene_process mediates organization of the subsynaptic scaffold by interacting with several synaptic proteins including the glutamate receptors 628460
gene_protein ankyrin repeats are responsible for the binding to Spna2 628460