Clstn3 (calsyntenin 3) - Rat Genome Database

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Gene: Clstn3 (calsyntenin 3) Rattus norvegicus
Analyze
Symbol: Clstn3
Name: calsyntenin 3
RGD ID: 621153
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; positive regulation of synaptic transmission; and regulation of presynapse assembly. Predicted to act upstream of or within several processes, including chemical synaptic transmission; positive regulation of protein localization to synapse; and synapse assembly. Located in postsynaptic membrane. Orthologous to human CLSTN3 (calsyntenin 3); INTERACTS WITH 1-naphthyl isothiocyanate; 2,2',4,4'-Tetrabromodiphenyl ether; 2,2',5,5'-tetrachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: alc-beta; alcadein-beta; calsyntenin-3; Cs3; Cstn3
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
mRatBN7.24157,331,494 - 157,364,769 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4157,331,494 - 157,364,769 (-)Ensembl
Rnor_6.04157,044,736 - 157,078,013 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4157,043,925 - 157,078,130 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04224,064,529 - 224,097,591 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44160,631,047 - 160,665,193 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14160,875,982 - 160,910,129 (-)NCBI
Celera4146,072,428 - 146,105,625 (-)NCBICelera
Cytogenetic Map4q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1-naphthyl isothiocyanate  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,2',5,5'-tetrachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
7,12-dimethyltetraphene  (ISO)
acetamide  (EXP)
acrylamide  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
Butylbenzyl phthalate  (EXP)
cadmium dichloride  (EXP)
carbon nanotube  (ISO)
CGP 52608  (ISO)
clofibrate  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
dexamethasone  (ISO)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (EXP)
dichloroacetic acid  (ISO)
diethyl phthalate  (EXP)
diisobutyl phthalate  (EXP)
diisononyl phthalate  (EXP)
ethanol  (ISO)
fenamidone  (ISO)
gentamycin  (EXP)
isotretinoin  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
monosodium L-glutamate  (ISO)
paracetamol  (EXP,ISO)
pentachlorophenol  (ISO)
permethrin  (ISO)
pioglitazone  (ISO)
pirinixic acid  (ISO)
pravastatin  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
selenomethionine  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sunitinib  (ISO)
tetrachloromethane  (EXP)
titanium dioxide  (ISO)
tributylstannane  (ISO)
trichloroethene  (EXP,ISO)
triptonide  (ISO)
troglitazone  (ISO)
uranium atom  (ISO)
valproic acid  (ISO)
zaragozic acid A  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:18158283   PMID:23376485   PMID:24094106   PMID:24613359  


Genomics

Comparative Map Data
Clstn3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24157,331,494 - 157,364,769 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4157,331,494 - 157,364,769 (-)Ensembl
Rnor_6.04157,044,736 - 157,078,013 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4157,043,925 - 157,078,130 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04224,064,529 - 224,097,591 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44160,631,047 - 160,665,193 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14160,875,982 - 160,910,129 (-)NCBI
Celera4146,072,428 - 146,105,625 (-)NCBICelera
Cytogenetic Map4q42NCBI
CLSTN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38127,129,093 - 7,158,945 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl127,129,698 - 7,158,945 (+)EnsemblGRCh38hg38GRCh38
GRCh37127,282,967 - 7,311,541 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36127,174,234 - 7,202,808 (+)NCBINCBI36hg18NCBI36
Build 34127,174,236 - 7,201,985NCBI
Celera128,859,131 - 8,887,704 (+)NCBI
Cytogenetic Map12p13.31NCBI
HuRef127,095,705 - 7,124,262 (+)NCBIHuRef
CHM1_1127,281,942 - 7,310,507 (+)NCBICHM1_1
T2T-CHM13v2.0127,143,523 - 7,172,097 (+)NCBI
Clstn3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396124,407,715 - 124,441,743 (-)NCBIGRCm39mm39
GRCm39 Ensembl6124,407,540 - 124,441,753 (-)Ensembl
GRCm386124,430,756 - 124,464,784 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6124,430,581 - 124,464,794 (-)EnsemblGRCm38mm10GRCm38
MGSCv376124,380,774 - 124,414,802 (-)NCBIGRCm37mm9NCBIm37
MGSCv366124,396,386 - 124,430,343 (-)NCBImm8
Celera6126,121,281 - 126,154,711 (-)NCBICelera
Cytogenetic Map6F2NCBI
Clstn3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554134,690,637 - 4,719,929 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554134,690,637 - 4,719,929 (+)NCBIChiLan1.0ChiLan1.0
CLSTN3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1127,175,951 - 7,204,526 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl127,175,951 - 7,204,526 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0127,260,361 - 7,288,903 (+)NCBIMhudiblu_PPA_v0panPan3
CLSTN3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12737,879,047 - 37,913,317 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2737,879,269 - 37,913,281 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha278,703,426 - 8,737,782 (+)NCBI
ROS_Cfam_1.02738,232,299 - 38,265,672 (-)NCBI
ROS_Cfam_1.0 Ensembl2738,232,319 - 38,258,846 (-)Ensembl
UMICH_Zoey_3.12738,106,420 - 38,140,738 (-)NCBI
UNSW_CanFamBas_1.02738,147,404 - 38,181,685 (-)NCBI
UU_Cfam_GSD_1.0278,181,467 - 8,215,782 (+)NCBI
Clstn3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945101,963,756 - 102,005,760 (-)NCBI
SpeTri2.0NW_004936709641,615 - 673,309 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLSTN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl563,572,065 - 63,599,525 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1563,572,062 - 63,612,177 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2565,899,699 - 65,927,179 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CLSTN3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1117,197,725 - 7,226,479 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl117,197,539 - 7,226,651 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666063984,091 - 1,012,812 (-)NCBIVero_WHO_p1.0
Clstn3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248603,709,139 - 3,738,221 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046248603,710,121 - 3,737,617 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D4Cebr1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24157,347,999 - 157,348,138 (+)MAPPERmRatBN7.2
Rnor_6.04157,061,242 - 157,061,380NCBIRnor6.0
Rnor_5.04224,081,035 - 224,081,173UniSTSRnor5.0
RGSC_v3.44160,647,603 - 160,647,741UniSTSRGSC3.4
Celera4146,088,912 - 146,089,050UniSTS
Cytogenetic Map4q42UniSTS
BE101768  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24157,361,438 - 157,361,602 (+)MAPPERmRatBN7.2
Rnor_6.04157,074,683 - 157,074,846NCBIRnor6.0
Rnor_5.04224,094,261 - 224,094,424UniSTSRnor5.0
RGSC_v3.44160,661,863 - 160,662,026UniSTSRGSC3.4
Celera4146,102,295 - 146,102,458UniSTS
RH 3.4 Map41000.8UniSTS
Cytogenetic Map4q42UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)464528739157573521Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)493308457167139447Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4109866907167139601Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
12798519Anxrr54Anxiety related response QTL 542.540.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4114627026159627026Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4118856416163856416Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4119428175157578333Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4124778595169778595Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4126395976167139601Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132642577167139601Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4146565735175236377Rat
12798525Anxrr57Anxiety related response QTL 573.210.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4147278504167139601Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4148090542168069246Rat
61446Coreg2Compensatory renal growth QTL 23.5kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)4148423102157580971Rat
1581574Eae20Experimental allergic encephalomyelitis QTL 207.8nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)4153031106158841762Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:93
Count of miRNA genes:81
Interacting mature miRNAs:85
Transcripts:ENSRNOT00000015570
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 7 1 68
Low 3 20 22 13 15 13 3 3 6 25 40 8 3
Below cutoff 21 24 24 3 24 5 6 9 1 3 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000015570   ⟹   ENSRNOP00000015570
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4157,331,494 - 157,364,769 (-)Ensembl
Rnor_6.0 Ensembl4157,043,925 - 157,078,130 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096523   ⟹   ENSRNOP00000083803
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4157,331,494 - 157,333,687 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102207   ⟹   ENSRNOP00000076723
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4157,331,494 - 157,362,920 (-)Ensembl
RefSeq Acc Id: NM_134376   ⟹   NP_599203
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24157,331,494 - 157,364,769 (-)NCBI
Rnor_6.04157,044,736 - 157,078,013 (-)NCBI
Rnor_5.04224,064,529 - 224,097,591 (-)NCBI
RGSC_v3.44160,631,047 - 160,665,193 (-)RGD
Celera4146,072,428 - 146,105,625 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_599203 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAD24292 (Get FASTA)   NCBI Sequence Viewer  
  Q8R553 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_599203   ⟸   NM_134376
- Peptide Label: precursor
- UniProtKB: Q8R553 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000015570   ⟸   ENSRNOT00000015570
RefSeq Acc Id: ENSRNOP00000083803   ⟸   ENSRNOT00000096523
RefSeq Acc Id: ENSRNOP00000076723   ⟸   ENSRNOT00000102207
Protein Domains
Cadherin   CLSTN_C

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8R553-F1-model_v2 AlphaFold Q8R553 1-957 view protein structure

Transcriptome

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

Promoters
RGD ID:13693379
Promoter ID:EPDNEW_R3904
Type:single initiation site
Name:Clstn3_1
Description:calsyntenin 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04157,078,109 - 157,078,169EPDNEW

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)
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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
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)
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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
FXLE16/Stm (2020)
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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
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)
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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
HXB20/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
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)
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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
LEW/Crl (2019)
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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)
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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
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)
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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)
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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)
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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)
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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
4 157057812 157057813 T C snv WKY/NCrl (2019), WAG/RijCrl (2020), PVG/Seac (2019), LEW/Crl (2019), GK/FarMcwi (2019), BUF/N (2020), CDS, WKY/N (2020)
4 157057959 157057960 A T snv GK/FarMcwi (2019), PVG/Seac (2019), BUF/N (2020), WKY/N (2020), WKY/NCrl (2019), WAG/RijCrl (2020), LEW/Crl (2019), LEW/Crl (RGD), BBDP/Wor (RGD), CDS, FHL/EurMcwi (MCW)
4 157058196 157058197 G A snv FHL/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621153 AgrOrtholog
BioCyc Gene G2FUF-43108 BioCyc
Ensembl Genes ENSRNOG00000011156 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000015570 ENTREZGENE
  ENSRNOP00000015570.1 UniProtKB/TrEMBL
  ENSRNOP00000076723.1 UniProtKB/TrEMBL
  ENSRNOP00000083803.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000015570 ENTREZGENE
  ENSRNOT00000015570.4 UniProtKB/TrEMBL
  ENSRNOT00000096523.1 UniProtKB/TrEMBL
  ENSRNOT00000102207.1 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:171393 UniProtKB/Swiss-Prot
NCBI Gene 171393 ENTREZGENE
PANTHER PTHR14139 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CLSTN_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Clstn3 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 A0A8I5Y929_RAT UniProtKB/TrEMBL
  A0A8I5ZY11_RAT UniProtKB/TrEMBL
  CSTN3_RAT UniProtKB/Swiss-Prot
  G3V7J1_RAT UniProtKB/TrEMBL
  Q8R553 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Clstn3  calsyntenin 3  Cstn3    Symbol updated 1299863 APPROVED
2002-08-07 Cstn3  calsyntenin 3      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression highest expression in GABAergic neurons 632523