Itsn2 (intersectin 2) - Rat Genome Database
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Gene: Itsn2 (intersectin 2) Rattus norvegicus
Analyze
Symbol: Itsn2
Name: intersectin 2
RGD ID: 1590890
Description: Predicted to have molecular adaptor activity. Predicted to be involved in clathrin-dependent synaptic vesicle endocytosis and positive regulation of dendrite extension. Predicted to localize to several cellular components, including centrosome; clathrin-coated pit; and presynaptic membrane. Orthologous to human ITSN2 (intersectin 2); INTERACTS WITH bisphenol A; chloroprene; finasteride.
Type: protein-coding
RefSeq Status: MODEL
Also known as: intersectin-2; LOC313934; similar to Intersectin-2 (SH3 domain-containing protein 1B) (SH3P18) (SH3P18-like WASP-associated protein)
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
Rnor_6.0630,098,378 - 30,208,694 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl630,098,380 - 30,187,337 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0639,701,659 - 39,790,623 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera627,085,036 - 27,196,783 (+)NCBICelera
Cytogenetic Map6q14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:16903783   PMID:19056867   PMID:20448150   PMID:20479469   PMID:23999003  


Genomics

Comparative Map Data
Itsn2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0630,098,378 - 30,208,694 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl630,098,380 - 30,187,337 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0639,701,659 - 39,790,623 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera627,085,036 - 27,196,783 (+)NCBICelera
Cytogenetic Map6q14NCBI
ITSN2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl224,202,864 - 24,360,714 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl224,202,864 - 24,360,536 (-)EnsemblGRCh38hg38GRCh38
GRCh38224,202,864 - 24,360,538 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37224,425,733 - 24,583,647 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36224,279,239 - 24,436,881 (-)NCBINCBI36hg18NCBI36
Build 34224,354,843 - 24,495,028NCBI
Celera224,266,029 - 24,423,608 (-)NCBI
Cytogenetic Map2p23.3NCBI
HuRef224,164,460 - 24,322,301 (-)NCBIHuRef
CHM1_1224,355,106 - 24,512,765 (-)NCBICHM1_1
Itsn2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39124,642,792 - 4,763,952 (+)NCBIGRCm39mm39
GRCm38124,592,643 - 4,713,952 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl124,592,638 - 4,713,962 (+)EnsemblGRCm38mm10GRCm38
MGSCv37124,599,814 - 4,720,758 (+)NCBIGRCm37mm9NCBIm37
MGSCv36124,606,965 - 4,727,848 (+)NCBImm8
Celera124,524,713 - 4,645,575 (+)NCBICelera
Cytogenetic Map12A1.1NCBI
Itsn2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554696,358,131 - 6,493,956 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554696,358,131 - 6,493,956 (-)NCBIChiLan1.0ChiLan1.0
ITSN2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A24,296,617 - 24,451,013 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A24,297,373 - 24,419,593 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A24,199,600 - 24,354,314 (-)NCBIMhudiblu_PPA_v0panPan3
ITSN2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1718,627,935 - 18,756,114 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11718,627,543 - 18,756,669 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Itsn2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364937,716,424 - 7,842,818 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ITSN2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3114,363,528 - 114,508,445 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13114,363,319 - 114,508,447 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23121,628,711 - 121,773,090 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ITSN2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl1483,297,259 - 83,453,335 (+)Ensembl
ChlSab1.11483,297,061 - 83,452,784 (+)NCBI
Itsn2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247386,480,203 - 6,637,713 (-)NCBI

Position Markers
D6Got197  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0630,172,059 - 30,172,184NCBIRnor6.0
Rnor_5.0639,716,817 - 39,716,942UniSTSRnor5.0
Celera627,122,727 - 27,122,870UniSTS
Cytogenetic Map6q12UniSTS
RH 3.4 Map6115.4UniSTS
RH 3.4 Map6115.4RGD
RH 2.0 Map6229.6RGD
RH128822  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0630,098,405 - 30,098,584NCBIRnor6.0
Rnor_5.0639,790,417 - 39,790,596UniSTSRnor5.0
Celera627,196,577 - 27,196,756UniSTS
Cytogenetic Map6q12UniSTS
RH 3.4 Map6117.3UniSTS
AA850325  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0630,129,456 - 30,129,636NCBIRnor6.0
Rnor_5.0639,759,365 - 39,759,545UniSTSRnor5.0
Celera627,164,556 - 27,164,736UniSTS
Cytogenetic Map6q12UniSTS
RH 3.4 Map6117.6UniSTS
RH138620  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0630,161,693 - 30,161,892NCBIRnor6.0
Rnor_5.0639,727,109 - 39,727,308UniSTSRnor5.0
Celera627,132,720 - 27,132,919UniSTS
Cytogenetic Map6q12UniSTS
RH 3.4 Map6116.49UniSTS
BM386909  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0630,131,621 - 30,131,823NCBIRnor6.0
Rnor_5.0639,757,178 - 39,757,380UniSTSRnor5.0
Celera627,162,369 - 27,162,571UniSTS
Cytogenetic Map6q12UniSTS
RH 3.4 Map6116.49UniSTS
AL033711  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01125,674,523 - 25,674,645NCBIRnor6.0
Rnor_6.0630,151,960 - 30,152,082NCBIRnor6.0
Rnor_5.01129,298,025 - 29,298,147UniSTSRnor5.0
Rnor_5.0639,736,919 - 39,737,041UniSTSRnor5.0
RGSC_v3.41125,761,857 - 25,761,979UniSTSRGSC3.4
Celera1125,055,477 - 25,055,599UniSTS
Celera627,142,530 - 27,142,652UniSTS
Cytogenetic Map6q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738023Alc17Alcohol consumption QTL 173.10.003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)6135623029Rat
1354616Despr12Despair related QTL 120.0012locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)6135623029Rat
1549905Stresp10Stress response QTL 106.830.0066stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)6135623029Rat
2300176Bmd51Bone mineral density QTL 5111.70.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)6135623029Rat
2300190Bmd52Bone mineral density QTL 5211.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)6135623029Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6141917988Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6142388212Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6142388212Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142388212Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6142388212Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6142388212Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6143665660Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6143665660Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6143665660Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6144015370Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6144570292Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6175623393Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6112039346120393Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)6112039375023446Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)6616172276002731Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6616172276002731Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)71017386255173862Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)61312295834367603Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)61312295857516539Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
8552910Pigfal5Plasma insulin-like growth factor 1 level QTL 54.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)61941788764417887Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62151530265784818Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:145
Count of miRNA genes:79
Interacting mature miRNAs:85
Transcripts:ENSRNOT00000073870, ENSRNOT00000074150
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 3 43 52 36 19 36 8 8 62 35 36 11 8
Low 5 5 5 3 12 5
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_001067254 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_003750126 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_003754161 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225721 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006239863 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764569 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008776199 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594422 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017603210 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_233945 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07063359 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01042447 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01042448 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01042449 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01042450 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473947 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000074150   ⟹   ENSRNOP00000065329
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl630,098,380 - 30,187,337 (-)Ensembl
RefSeq Acc Id: XM_001067254   ⟹   XP_001067254
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera627,106,744 - 27,196,783 (+)NCBI
Sequence:
RefSeq Acc Id: XM_003750126   ⟹   XP_003750174
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0630,098,378 - 30,188,201 (-)NCBI
Rnor_5.0639,701,659 - 39,790,623 (+)NCBI
Sequence:
RefSeq Acc Id: XM_003754161   ⟹   XP_003754209
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera627,106,744 - 27,196,783 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006225721   ⟹   XP_006225783
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera627,106,744 - 27,196,783 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006239863   ⟹   XP_006239925
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0630,098,378 - 30,188,201 (-)NCBI
Rnor_5.0639,701,659 - 39,790,623 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008764569   ⟹   XP_008762791
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0630,098,378 - 30,208,694 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008776199   ⟹   XP_008774421
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera627,085,036 - 27,196,783 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594422   ⟹   XP_017449911
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0630,100,302 - 30,188,201 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017603210   ⟹   XP_017458699
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera627,106,744 - 27,194,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_233945   ⟹   XP_233945
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0630,098,378 - 30,188,201 (-)NCBI
Rnor_5.0639,701,659 - 39,790,623 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: XP_001067254   ⟸   XM_001067254
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_003750174   ⟸   XM_003750126
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_233945   ⟸   XM_233945
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_003754209   ⟸   XM_003754161
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_006225783   ⟸   XM_006225721
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_006239925   ⟸   XM_006239863
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008774421   ⟸   XM_008776199
- Peptide Label: isoform X6
- UniProtKB: M0R7A6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008762791   ⟸   XM_008764569
- Peptide Label: isoform X1
- UniProtKB: M0R7A6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017458699   ⟸   XM_017603210
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_017449911   ⟸   XM_017594422
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000065329   ⟸   ENSRNOT00000074150
Protein Domains
C2   DH   EF-hand   EH   PH   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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
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:1590890 AgrOrtholog
Ensembl Genes ENSRNOG00000046741 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000065329 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000074150 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.20.900.10 UniProtKB/TrEMBL
  2.30.29.30 UniProtKB/TrEMBL
  2.60.40.150 UniProtKB/TrEMBL
InterPro C2_Ca-dep UniProtKB/TrEMBL
  C2_domain_sf UniProtKB/TrEMBL
  DBL_dom_sf UniProtKB/TrEMBL
  DH-domain UniProtKB/TrEMBL
  EF-hand-like_dom UniProtKB/TrEMBL
  EF_Hand_1_Ca_BS UniProtKB/TrEMBL
  EF_hand_dom UniProtKB/TrEMBL
  EPS15_homology UniProtKB/TrEMBL
  Intersectin-2 UniProtKB/TrEMBL
  Intersectin-2_SH3_1 UniProtKB/TrEMBL
  Intersectin-2_SH3_2 UniProtKB/TrEMBL
  Intersectin-2_SH3_3 UniProtKB/TrEMBL
  Intersectin-2_SH3_4 UniProtKB/TrEMBL
  Intersectin-2_SH3_5 UniProtKB/TrEMBL
  PH_like_dom UniProtKB/TrEMBL
  Pleckstrin_homology UniProtKB/TrEMBL
  SH3-like_dom UniProtKB/TrEMBL
  SH3_domain UniProtKB/TrEMBL
NCBI Gene 313934 ENTREZGENE
PANTHER PTHR11216:SF29 UniProtKB/TrEMBL
Pfam EF-hand_4 UniProtKB/TrEMBL
  PF00168 UniProtKB/TrEMBL
  PH_13 UniProtKB/TrEMBL
  RhoGEF UniProtKB/TrEMBL
  SH3_1 UniProtKB/TrEMBL
  SH3_2 UniProtKB/TrEMBL
  SH3_9 UniProtKB/TrEMBL
PhenoGen Itsn2 PhenoGen
PRINTS SH3DOMAIN UniProtKB/TrEMBL
PROSITE DH_2 UniProtKB/TrEMBL
  EF_HAND_1 UniProtKB/TrEMBL
  EF_HAND_2 UniProtKB/TrEMBL
  PH_DOMAIN UniProtKB/TrEMBL
  PS50004 UniProtKB/TrEMBL
  PS50031 UniProtKB/TrEMBL
  SH3 UniProtKB/TrEMBL
SMART EFh UniProtKB/TrEMBL
  RhoGEF UniProtKB/TrEMBL
  SH3 UniProtKB/TrEMBL
  SM00027 UniProtKB/TrEMBL
  SM00233 UniProtKB/TrEMBL
  SM00239 UniProtKB/TrEMBL
Superfamily-SCOP DH-domain UniProtKB/TrEMBL
  SH3 UniProtKB/TrEMBL
  SSF47473 UniProtKB/TrEMBL
UniProt M0R7A6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-05 Itsn2  intersectin 2  LOC313934  similar to Intersectin-2 (SH3 domain-containing protein 1B) (SH3P18) (SH3P18-like WASP-associated protein)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC313934  similar to Intersectin-2 (SH3 domain-containing protein 1B) (SH3P18) (SH3P18-like WASP-associated protein)      Symbol and Name status set to provisional 70820 PROVISIONAL