Shank1 (SH3 and multiple ankyrin repeat domains 1) - Rat Genome Database
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Gene: Shank1 (SH3 and multiple ankyrin repeat domains 1) Rattus norvegicus
Analyze
Symbol: Shank1
Name: SH3 and multiple ankyrin repeat domains 1
RGD ID: 621011
Description: Exhibits several functions, including protein C-terminus binding activity; protein domain specific binding activity; and signaling receptor binding activity. Involved in positive regulation of dendritic spine development; protein-containing complex assembly; and synapse maturation. Localizes to dendritic spine and postsynaptic membrane. Colocalizes with NMDA selective glutamate receptor complex. Orthologous to human SHANK1 (SH3 and multiple ankyrin repeat domains 1); PARTICIPATES IN glutamate signaling pathway; INTERACTS WITH ammonium chloride; androgen antagonist; atrazine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: GKAP/SAPAP interacting protein; GKAP/SAPAP-interacting protein; SAPAP-interacting protein synamon; SH3 and multiple ankyrin repeat domains protein 1; SH3/ankyrin domain gene 1; Shank1a; somatostatin receptor-interacting protein; SPANK-1; Spank1; SSTR-interacting protein; Sstrip; synamon
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2194,807,879 - 94,857,356 (+)NCBI
Rnor_6.0 Ensembl1100,297,152 - 100,344,377 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01100,297,137 - 100,344,377 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01101,362,243 - 101,410,338 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4194,791,887 - 94,840,584 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1194,872,463 - 94,918,294 (+)NCBI
Celera189,071,051 - 89,118,344 (+)NCBICelera
Cytogenetic Map1q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Arstikaitis P, etal., Mol Biol Cell. 2008 May;19(5):2026-38. doi: 10.1091/mbc.E07-08-0802. Epub 2008 Feb 20.
2. Bockers TM, etal., J Biol Chem 2001 Oct 26;276(43):40104-12.
3. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. GOA data from the GO Consortium
5. Hayashi MK, etal., Cell. 2009 Apr 3;137(1):159-71. doi: 10.1016/j.cell.2009.01.050.
6. Lim S, etal., J Biol Chem 1999 Oct 8;274(41):29510-8.
7. Lim S, etal., Mol Cell Neurosci 2001 Feb;17(2):385-97.
8. Miletic G, etal., Pain. 2010 Apr;149(1):152-9. Epub 2010 Feb 18.
9. Naisbitt S, etal., Neuron 1999 Jul;23(3):569-82.
10. NCBI rat LocusLink and RefSeq merged data July 26, 2002
11. Okamoto PM, etal., J Biol Chem 2001 Dec 21;276(51):48458-65.
12. Park E, etal., J Biol Chem. 2003 May 23;278(21):19220-9. Epub 2003 Mar 7.
13. Park SH, etal., Acta Crystallogr D Biol Crystallogr 2002 Aug;58(Pt 8):1353-5.
14. Pipeline to import KEGG annotations from KEGG into RGD
15. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
16. RGD automated import pipeline for gene-chemical interactions
17. Romorini S, etal., J Neurosci. 2004 Oct 20;24(42):9391-404.
18. Thomas GM, etal., Proc Natl Acad Sci U S A. 2005 Oct 18;102(42):15006-11. Epub 2005 Oct 10.
19. Tobaben S, etal., J Biol Chem 2000 Nov 17;275(46):36204-10.
20. Tu JC, etal., Neuron. 1999 Jul;23(3):583-92.
21. Yao I, etal., J Biol Chem 1999 Sep 24;274(39):27463-6.
22. Zitzer H, etal., J Biol Chem. 1999 Nov 12;274(46):32997-3001.
Additional References at PubMed
PMID:10806096   PMID:11498055   PMID:12954649   PMID:15121189   PMID:15207857   PMID:15458844   PMID:15689539   PMID:15950311   PMID:16002212   PMID:16606358   PMID:18272690   PMID:19208628  
PMID:19416473   PMID:19547699   PMID:20117114   PMID:20868654   PMID:21144999   PMID:21376703   PMID:21695253   PMID:21795692   PMID:21940441   PMID:22503632   PMID:24298140   PMID:25775468  
PMID:28263956   PMID:29250591   PMID:29476059  


Genomics

Comparative Map Data
Shank1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2194,807,879 - 94,857,356 (+)NCBI
Rnor_6.0 Ensembl1100,297,152 - 100,344,377 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01100,297,137 - 100,344,377 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01101,362,243 - 101,410,338 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4194,791,887 - 94,840,584 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1194,872,463 - 94,918,294 (+)NCBI
Celera189,071,051 - 89,118,344 (+)NCBICelera
Cytogenetic Map1q22NCBI
SHANK1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1950,659,255 - 50,719,802 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1950,661,827 - 50,719,450 (-)EnsemblGRCh38hg38GRCh38
GRCh381950,659,255 - 50,719,802 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371951,162,512 - 51,223,059 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361955,856,896 - 55,912,007 (-)NCBINCBI36hg18NCBI36
Build 341955,856,895 - 55,912,007NCBI
Celera1948,216,374 - 48,271,323 (-)NCBI
Cytogenetic Map19q13.33NCBI
HuRef1947,499,910 - 47,555,290 (-)NCBIHuRef
CHM1_11951,164,298 - 51,221,938 (-)NCBICHM1_1
Shank1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39743,958,343 - 44,009,518 (+)NCBIGRCm39mm39
GRCm39 Ensembl743,959,677 - 44,009,996 (+)Ensembl
GRCm38744,308,916 - 44,360,094 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl744,310,253 - 44,360,572 (+)EnsemblGRCm38mm10GRCm38
MGSCv37751,565,634 - 51,613,723 (+)NCBIGRCm37mm9NCBIm37
MGSCv36744,178,306 - 44,225,515 (+)NCBImm8
Celera739,770,665 - 39,816,636 (+)NCBICelera
Cytogenetic Map7B3NCBI
Shank1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955559523,765 - 564,472 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955559522,466 - 566,275 (+)NCBIChiLan1.0ChiLan1.0
SHANK1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11956,526,557 - 56,580,516 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1956,526,577 - 56,580,442 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01947,623,474 - 47,684,476 (-)NCBIMhudiblu_PPA_v0panPan3
SHANK1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1106,097,048 - 106,114,673 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11106,086,094 - 106,128,700 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Shank1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936889428,404 - 470,161 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SHANK1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1655,452,095 - 55,496,304 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2651,348,953 - 51,395,795 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SHANK1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1643,718,904 - 43,776,814 (-)NCBI
ChlSab1.1 Ensembl643,716,714 - 43,773,945 (-)Ensembl
Shank1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248323,934,525 - 3,978,607 (+)NCBI

Position Markers
BE101668  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01100,338,049 - 100,338,248NCBIRnor6.0
Rnor_5.01101,403,160 - 101,403,359UniSTSRnor5.0
RGSC_v3.4194,833,470 - 94,833,669UniSTSRGSC3.4
Celera189,112,016 - 89,112,215UniSTS
RH 3.4 Map1907.0UniSTS
Cytogenetic Map1q22UniSTS
RH137039  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01100,320,670 - 100,320,851NCBIRnor6.0
Rnor_5.01101,385,781 - 101,385,962UniSTSRnor5.0
RGSC_v3.4194,815,397 - 94,815,578UniSTSRGSC3.4
Celera189,094,525 - 89,094,706UniSTS
RH 3.4 Map1904.1UniSTS
Cytogenetic Map1q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15655769122614963Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123406428108057505Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)125951907130917265Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134993530173445086Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135377692217372257Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143579208126240667Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143579208126240667Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143579208126240667Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143579208126240667Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143579208126240667Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)149147799156446783Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149578577169852184Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149578693217054291Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)157761301104391981Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)158209327103209327Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)158354072161711996Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)164588516125875986Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)166113339122614963Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)179134941113593716Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)179689548124689548Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)182788437239853971Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)183502376128502376Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)183656882126240667Rat
61344Bp29Blood pressure QTL 297.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)185779320130779320Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)185917265130917265Rat
4889494Scort2Serum corticosterone level QTL 24.2blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)186776571131776571Rat
2300324Fetw1Fetal weight QTL 112.10.005fetal growth trait (VT:0004201)fetal body weight (CMO:0002080)188634585106002500Rat
724529Cm16Cardiac mass QTL 162.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)190804143161321256Rat
738022Anxrr13Anxiety related response QTL 134.60.00039locomotor behavior trait (VT:0001392)number of 20 x 20 cm floor squares crossed into, out of or within a discrete space in an experimental apparatus (CMO:0001514)191093646136093646Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)194201400184846632Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)194201400197187904Rat
1302788Scl19Serum cholesterol QTL 194.60.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)194225372130917265Rat
1300153Bp171Blood pressure QTL 1713.37arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)194364073153076991Rat
724567Tcas6Tongue tumor susceptibility QTL 66.85tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)195304961156446783Rat
1331800Scl25Serum cholesterol level QTL 253.013blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)199983293127203999Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)199983293188289386Rat
1331751Bp199Blood pressure QTL 1993.60022arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)199983293198656062Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)199983293216213510Rat
70209Niddm23Non-insulin dependent diabetes mellitus QTL 232.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)199983293216325819Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1100131562236763528Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1314
Count of miRNA genes:189
Interacting mature miRNAs:230
Transcripts:ENSRNOT00000026100, ENSRNOT00000044257, ENSRNOT00000046418, ENSRNOT00000048805, ENSRNOT00000049346
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 58 2
Low 1 24 6 6 6 16 21 32
Below cutoff 2 18 25 10 16 10 6 6 12 7 5 6

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_031751 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008759416 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017589760 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017589761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091739 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091745 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091758 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091766 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF102855 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF131951 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF141902 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF141904 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF159046 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY461452 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473979 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000033 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000026100   ⟹   ENSRNOP00000026100
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1100,297,152 - 100,344,377 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000044257   ⟹   ENSRNOP00000039860
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1100,299,635 - 100,343,385 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092327   ⟹   ENSRNOP00000075838
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1100,299,626 - 100,343,976 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092351
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1100,322,102 - 100,329,623 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092528
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1100,322,102 - 100,330,237 (+)Ensembl
RefSeq Acc Id: NM_031751   ⟹   NP_113939
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2194,808,282 - 94,855,824 (+)NCBI
Rnor_6.01100,297,157 - 100,344,377 (+)NCBI
Rnor_5.01101,362,243 - 101,410,338 (+)NCBI
RGSC_v3.4194,791,887 - 94,840,584 (+)RGD
Celera189,071,051 - 89,118,344 (+)RGD
Sequence:
RefSeq Acc Id: XM_008759416   ⟹   XP_008757638
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2194,807,879 - 94,852,298 (+)NCBI
Rnor_6.01100,297,137 - 100,342,197 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017589758   ⟹   XP_017445247
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01100,299,430 - 100,343,978 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017589759   ⟹   XP_017445248
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01100,297,137 - 100,343,978 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017589760   ⟹   XP_017445249
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2194,807,880 - 94,857,356 (+)NCBI
Rnor_6.01100,297,137 - 100,343,978 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017589761   ⟹   XP_017445250
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2194,807,879 - 94,854,248 (+)NCBI
Rnor_6.01100,297,137 - 100,342,750 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039091739   ⟹   XP_038947667
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2194,810,759 - 94,855,100 (+)NCBI
RefSeq Acc Id: XM_039091745   ⟹   XP_038947673
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2194,807,880 - 94,857,356 (+)NCBI
RefSeq Acc Id: XM_039091758   ⟹   XP_038947686
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2194,824,401 - 94,857,356 (+)NCBI
RefSeq Acc Id: XM_039091761   ⟹   XP_038947689
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2194,834,841 - 94,857,356 (+)NCBI
RefSeq Acc Id: XM_039091766   ⟹   XP_038947694
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2194,833,053 - 94,857,356 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_113939   ⟸   NM_031751
- UniProtKB: Q9WV48 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008757638   ⟸   XM_008759416
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017445248   ⟸   XM_017589759
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017445249   ⟸   XM_017589760
- Peptide Label: isoform X2
- UniProtKB: Q9WV48 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017445250   ⟸   XM_017589761
- Peptide Label: isoform X5
- UniProtKB: Q9WV48 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017445247   ⟸   XM_017589758
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000075838   ⟸   ENSRNOT00000092327
RefSeq Acc Id: ENSRNOP00000026100   ⟸   ENSRNOT00000026100
RefSeq Acc Id: ENSRNOP00000039860   ⟸   ENSRNOT00000044257
RefSeq Acc Id: XP_038947673   ⟸   XM_039091745
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038947667   ⟸   XM_039091739
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947686   ⟸   XM_039091758
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038947694   ⟸   XM_039091766
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038947689   ⟸   XM_039091761
- Peptide Label: isoform X7
Protein Domains
PDZ   SAM   SH3

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (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
Damaging Variants


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 100337642 100337643 C T snv WKY/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621011 AgrOrtholog
Ensembl Genes ENSRNOG00000019207 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000026100 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000039860 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000075838 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000026100 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000044257 UniProtKB/Swiss-Prot
  ENSRNOT00000092327 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.150.50 UniProtKB/Swiss-Prot
  1.25.40.20 UniProtKB/Swiss-Prot
  2.30.42.10 UniProtKB/Swiss-Prot
InterPro Ankyrin_rpt UniProtKB/Swiss-Prot
  Ankyrin_rpt-contain_dom UniProtKB/Swiss-Prot
  Ankyrin_rpt-contain_sf UniProtKB/Swiss-Prot
  PDZ UniProtKB/Swiss-Prot
  PDZ_6 UniProtKB/Swiss-Prot
  PDZ_sf UniProtKB/Swiss-Prot
  SAM UniProtKB/Swiss-Prot
  SAM/pointed_sf UniProtKB/Swiss-Prot
  SH3-like_dom_sf UniProtKB/Swiss-Prot
  SH3_domain UniProtKB/Swiss-Prot
KEGG Report rno:78957 UniProtKB/Swiss-Prot
NCBI Gene 78957 ENTREZGENE
Pfam Ank_2 UniProtKB/Swiss-Prot
  PDZ_6 UniProtKB/Swiss-Prot
  SAM_1 UniProtKB/Swiss-Prot
  SH3_2 UniProtKB/Swiss-Prot
PhenoGen Shank1 PhenoGen
PROSITE ANK_REP_REGION UniProtKB/Swiss-Prot
  ANK_REPEAT UniProtKB/Swiss-Prot
  PDZ UniProtKB/Swiss-Prot
  SAM_DOMAIN UniProtKB/Swiss-Prot
  SH3 UniProtKB/Swiss-Prot
SMART ANK UniProtKB/Swiss-Prot
  PDZ UniProtKB/Swiss-Prot
  SAM UniProtKB/Swiss-Prot
  SH3 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47769 UniProtKB/Swiss-Prot
  SSF48403 UniProtKB/Swiss-Prot
  SSF50044 UniProtKB/Swiss-Prot
  SSF50156 UniProtKB/Swiss-Prot
UniProt Q9WV48 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q9QZZ8 UniProtKB/Swiss-Prot
  Q9WU13 UniProtKB/Swiss-Prot
  Q9WUE8 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-11-04 Shank1  SH3 and multiple ankyrin repeat domains 1  Shank1  SH3/ankyrin domain gene 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-22 Shank1  SH3/ankyrin domain gene 1  Shank1  SH3 and multiple ankyrin repeat domains 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Shank1  SH3 and multiple ankyrin repeat domains 1    Shank1  Name updated 1299863 APPROVED
2002-08-07 Shank1  Shank1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains contains ankyrin repeats, an SH3 domain, a PDZ domain, a long proline-rich region and an SAM domain 633974