Clstn2 (calsyntenin 2) - Rat Genome Database

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Gene: Clstn2 (calsyntenin 2) Rattus norvegicus
Analyze
Symbol: Clstn2
Name: calsyntenin 2
RGD ID: 621151
Description: Predicted to enable several functions, including X11-like protein binding activity; amyloid-beta binding activity; and kinesin binding activity. Predicted to be involved in positive regulation of synapse assembly and positive regulation of synaptic transmission. Located in postsynaptic membrane. Orthologous to human CLSTN2 (calsyntenin 2); INTERACTS WITH 17beta-estradiol; 6-propyl-2-thiouracil; benzo[a]pyrene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: alc-gamma; alcadein-gamma; calsyntenin-2; Cs2; Cstn2; LOC100359585
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2898,020,406 - 98,637,232 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl898,021,666 - 98,637,731 (-)Ensembl
Rnor_6.08105,322,577 - 106,036,821 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8105,323,837 - 105,462,168 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08104,768,386 - 104,906,597 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48102,614,117 - 103,214,037 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18102,633,571 - 103,233,492 (-)NCBI
Celera897,454,425 - 98,063,036 (-)NCBICelera
Cytogenetic Map8q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. The calsyntenins--a family of postsynaptic membrane proteins with distinct neuronal expression patterns. Hintsch G, etal., Mol Cell Neurosci 2002 Nov;21(3):393-409.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:24613359  


Genomics

Comparative Map Data
Clstn2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2898,020,406 - 98,637,232 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl898,021,666 - 98,637,731 (-)Ensembl
Rnor_6.08105,322,577 - 106,036,821 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8105,323,837 - 105,462,168 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08104,768,386 - 104,906,597 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48102,614,117 - 103,214,037 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18102,633,571 - 103,233,492 (-)NCBI
Celera897,454,425 - 98,063,036 (-)NCBICelera
Cytogenetic Map8q31NCBI
CLSTN2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383139,935,185 - 140,577,397 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl3139,935,185 - 140,577,397 (+)EnsemblGRCh38hg38GRCh38
GRCh373139,654,027 - 140,296,239 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363141,136,897 - 141,769,328 (+)NCBINCBI36hg18NCBI36
Build 343141,136,904 - 141,769,328NCBI
Celera3138,076,932 - 138,710,571 (+)NCBI
Cytogenetic Map3q23NCBI
HuRef3137,029,438 - 137,660,865 (+)NCBIHuRef
CHM1_13139,617,396 - 140,250,542 (+)NCBICHM1_1
T2T-CHM13v2.03142,682,539 - 143,324,729 (+)NCBI
Clstn2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39997,326,448 - 97,915,649 (-)NCBIGRCm39mm39
GRCm39 Ensembl997,326,448 - 97,915,234 (-)Ensembl
GRCm38997,444,395 - 98,033,373 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl997,444,395 - 98,033,181 (-)EnsemblGRCm38mm10GRCm38
MGSCv37997,344,814 - 97,933,586 (-)NCBIGRCm37mm9NCBIm37
MGSCv36997,253,747 - 97,842,519 (-)NCBImm8
Celera996,998,129 - 97,587,251 (-)NCBICelera
Cytogenetic Map9E3.3NCBI
Clstn2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555085,074,466 - 5,655,884 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555085,069,872 - 5,656,621 (-)NCBIChiLan1.0ChiLan1.0
CLSTN2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13144,571,574 - 145,201,588 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3144,571,706 - 145,199,768 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03136,971,615 - 137,612,365 (+)NCBIMhudiblu_PPA_v0panPan3
CLSTN2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12336,029,356 - 36,645,614 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2336,029,371 - 36,635,571 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2336,142,872 - 36,639,373 (+)NCBI
ROS_Cfam_1.02336,693,005 - 37,166,674 (+)NCBI
ROS_Cfam_1.0 Ensembl2336,566,381 - 37,166,639 (+)Ensembl
UMICH_Zoey_3.12336,374,497 - 36,857,999 (+)NCBI
UNSW_CanFamBas_1.02336,448,350 - 36,932,034 (+)NCBI
UU_Cfam_GSD_1.02336,690,788 - 37,174,298 (+)NCBI
Clstn2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560275,254,295 - 75,835,456 (+)NCBI
SpeTri2.0NW_0049365401,994,078 - 2,569,224 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLSTN2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1380,789,394 - 81,450,676 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11380,789,239 - 81,461,348 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21389,148,892 - 89,296,794 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CLSTN2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11549,996,144 - 50,622,454 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1549,999,908 - 50,151,120 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604122,955,556 - 23,588,228 (-)NCBIVero_WHO_p1.0
Clstn2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473016,568,556 - 17,176,251 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462473016,568,556 - 17,187,365 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D8Rat128  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2898,316,156 - 98,316,316 (+)MAPPERmRatBN7.2
Rnor_6.08105,697,532 - 105,697,691NCBIRnor6.0
Rnor_5.08105,141,903 - 105,142,062UniSTSRnor5.0
RGSC_v3.48102,883,462 - 102,883,622RGDRGSC3.4
RGSC_v3.48102,883,463 - 102,883,622UniSTSRGSC3.4
RGSC_v3.18102,902,666 - 102,903,146RGD
Celera897,741,865 - 97,742,024UniSTS
SHRSP x BN Map860.6299UniSTS
SHRSP x BN Map860.6299RGD
Cytogenetic Map8q31UniSTS
D8Rat127  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2898,275,437 - 98,275,613 (+)MAPPERmRatBN7.2
Rnor_6.08105,577,600 - 105,577,773NCBIRnor6.0
Rnor_5.08105,021,971 - 105,022,144UniSTSRnor5.0
RGSC_v3.48102,844,444 - 102,844,618RGDRGSC3.4
RGSC_v3.48102,844,445 - 102,844,618UniSTSRGSC3.4
RGSC_v3.18102,863,887 - 102,864,215RGD
Celera897,708,158 - 97,708,331UniSTS
SHRSP x BN Map860.6299UniSTS
SHRSP x BN Map860.6299RGD
Cytogenetic Map8q31UniSTS
D8Got157  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2898,029,909 - 98,030,129 (+)MAPPERmRatBN7.2
Rnor_6.08105,332,083 - 105,332,302NCBIRnor6.0
Rnor_5.08104,776,632 - 104,776,851UniSTSRnor5.0
RGSC_v3.48102,338,935 - 102,339,155RGDRGSC3.4
RGSC_v3.48102,338,936 - 102,339,155UniSTSRGSC3.4
RGSC_v3.18102,358,391 - 102,358,610RGD
Celera897,462,669 - 97,462,888UniSTS
RH 3.4 Map81077.59UniSTS
RH 3.4 Map81077.59RGD
RH 2.0 Map8859.9RGD
Cytogenetic Map8q31UniSTS
BI301360  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2898,453,829 - 98,453,982 (+)MAPPERmRatBN7.2
Rnor_6.08105,834,795 - 105,834,947NCBIRnor6.0
Rnor_5.08105,278,991 - 105,279,143UniSTSRnor5.0
RGSC_v3.48103,020,934 - 103,021,086UniSTSRGSC3.4
Celera897,879,580 - 97,879,732UniSTS
RH 3.4 Map81051.29UniSTS
Cytogenetic Map8q31UniSTS
BE097605  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2898,024,570 - 98,024,726 (+)MAPPERmRatBN7.2
Rnor_6.08105,326,742 - 105,326,897NCBIRnor6.0
Rnor_5.08104,771,291 - 104,771,446UniSTSRnor5.0
RGSC_v3.48102,344,344 - 102,344,499UniSTSRGSC3.4
Celera897,457,330 - 97,457,485UniSTS
RH 3.4 Map81080.3UniSTS
Cytogenetic Map8q31UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1358892Kidm26Kidney mass QTL 263.69kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)82720571599103503Rat
1358896Bp262Blood pressure QTL 2622.89arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)82720571599103503Rat
1358907Cm40Cardiac mass QTL 401.89heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)82720571599103503Rat
8662823Vetf5Vascular elastic tissue fragility QTL 51.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)82824291299525068Rat
1578755Pur5Proteinuria QTL 53.30.0001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)830848154101699754Rat
1578765Klgr1Kidney lesion grade QTL 13.30.0001kidney morphology trait (VT:0002135)organ lesion measurement (CMO:0000677)830848154101699754Rat
1578769Uae31Urinary albumin excretion QTL 313.30.001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)830848154101699754Rat
2316950Scl66Serum cholesterol level QTL 664.1blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)830848259105647037Rat
1331838Niddm61Non-insulin dependent diabetes mellitus QTL 613.530.0004blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83646953599083736Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
12879882Am8Aortic mass QTL 80.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)84329616998968765Rat
12879878Bw183Body weight QTL 1830.001body mass (VT:0001259)body weight (CMO:0000012)84329616998968765Rat
12879879Cm99Cardiac mass QTL 990.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)84329616998968765Rat
12879880Cm100Cardiac mass QTL 1000.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)84329616998968765Rat
12879881Cm101Cardiac mass QTL 1010.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)84329616998968765Rat
12879883Kidm65Kidney mass QTL 650.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)84329616998968765Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)846531639119088624Rat
1331837Bw23Body weight QTL 234.190.00007body mass (VT:0001259)body weight (CMO:0000012)84653172299083736Rat
1358912Bw51Body weight QTL 512.95body mass (VT:0001259)body weight (CMO:0000012)851351728107062046Rat
10402857Bp380Blood pressure QTL 3800.95arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)85396876598968765Rat
2301402Bp316Blood pressure QTL 3160.005arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)85396876598968765Rat
2293697Bmd39Bone mineral density QTL 39femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)85404374498968765Rat
631664Hcar3Hepatocarcinoma resistance QTL 32.90.0005liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)85423764499103503Rat
1300177Cm2Cardiac mass QTL 23.65heart mass (VT:0007028)heart weight (CMO:0000017)854259986100382532Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)861290298119084929Rat
631653Bp125Blood pressure QTL 1253.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)866142385111142385Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)869349194112783834Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)870513503118219066Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)871888757116888757Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)871888757116888757Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)871888757116888757Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)871888757116888757Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)873473045118473045Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat
2313400Anxrr25Anxiety related response QTL 25aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)889265192114019816Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:31
Count of miRNA genes:29
Interacting mature miRNAs:31
Transcripts:ENSRNOT00000066731
Prediction methods: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 60 2
Low 1 42 11 4 4 5 5 14 27 35 9 5
Below cutoff 2 1 20 13 16 13 3 6 8 6 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000066731   ⟹   ENSRNOP00000060748
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl898,021,666 - 98,637,731 (-)Ensembl
Rnor_6.0 Ensembl8105,323,859 - 105,462,141 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078760   ⟹   ENSRNOP00000070212
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl898,021,666 - 98,160,567 (-)Ensembl
Rnor_6.0 Ensembl8105,323,837 - 105,462,168 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118831   ⟹   ENSRNOP00000077209
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl898,029,699 - 98,637,731 (-)Ensembl
RefSeq Acc Id: NM_134377   ⟹   NP_599204
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2898,021,666 - 98,636,803 (-)NCBI
Rnor_6.08105,323,837 - 106,036,695 (-)NCBI
Rnor_5.08104,768,386 - 104,906,597 (-)NCBI
RGSC_v3.48102,614,117 - 103,214,037 (-)RGD
Celera897,454,425 - 98,063,036 (-)RGD
Sequence:
RefSeq Acc Id: XM_017595430   ⟹   XP_017450919
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2898,020,406 - 98,637,232 (-)NCBI
Rnor_6.08105,322,577 - 106,036,821 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_599204 (Get FASTA)   NCBI Sequence Viewer  
  XP_017450919 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAD20352 (Get FASTA)   NCBI Sequence Viewer  
  Q8VDA1 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_599204   ⟸   NM_134377
- Peptide Label: precursor
- UniProtKB: Q8VDA1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017450919   ⟸   XM_017595430
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000070212   ⟸   ENSRNOT00000078760
RefSeq Acc Id: ENSRNOP00000060748   ⟸   ENSRNOT00000066731
RefSeq Acc Id: ENSRNOP00000077209   ⟸   ENSRNOT00000118831
Protein Domains
Cadherin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8VDA1-F1-model_v2 AlphaFold Q8VDA1 1-965 view protein structure

Transcriptome

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


Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 105460919 105460920 G A snv GK/FarMcwi (2019), GK/Ox (RGD)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 98158739 98158740 G A snv GK/FarMcwi (2019)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621151 AgrOrtholog
BioCyc Gene G2FUF-29422 BioCyc
Ensembl Genes ENSRNOG00000043085 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000060748 ENTREZGENE
  ENSRNOP00000060748.4 UniProtKB/TrEMBL
  ENSRNOP00000070212.2 UniProtKB/TrEMBL
  ENSRNOP00000077209 ENTREZGENE
  ENSRNOP00000077209.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066731 ENTREZGENE
  ENSRNOT00000066731.4 UniProtKB/TrEMBL
  ENSRNOT00000078760.2 UniProtKB/TrEMBL
  ENSRNOT00000118831 ENTREZGENE
  ENSRNOT00000118831.1 UniProtKB/TrEMBL
InterPro Cadherin-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Calsyntenin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CLSTN_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ConA-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:171394 UniProtKB/Swiss-Prot
NCBI Gene 171394 ENTREZGENE
PANTHER PTHR14139 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CLSTN_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Clstn2 PhenoGen
PRINTS CADHERIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CADHERIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49313 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49899 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JXB8_RAT UniProtKB/TrEMBL
  A0A8I5XVW9_RAT UniProtKB/TrEMBL
  CSTN2_RAT UniProtKB/Swiss-Prot
  F1LMG0_RAT UniProtKB/TrEMBL
  Q8VDA1 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-04-17 Clstn2  calsyntenin 2  LOC100359585  calsyntenin 2  Data Merged 737654 PROVISIONAL
2010-05-06 LOC100359585  calsyntenin 2      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-20 Clstn2  calsyntenin 2  Cstn2    Symbol updated 1299863 APPROVED
2002-08-07 Cstn2  calsyntenin 2      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in excitatory central nervous system (CNS) synapses 632523