Syn3 (synapsin III) - Rat Genome Database

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Gene: Syn3 (synapsin III) Rattus norvegicus
Analyze
Symbol: Syn3
Name: synapsin III
RGD ID: 3799
Description: Enables ATP binding activity. Predicted to be involved in neurotransmitter secretion and synaptic vesicle clustering. Located in synaptic vesicle. Is extrinsic component of synaptic vesicle membrane. Orthologous to human SYN3 (synapsin III); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC100910134; synapsin 3; synapsin-3; synapsin-3-like
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
mRatBN7.2716,216,055 - 17,808,790 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl717,376,372 - 17,808,790 (+)Ensembl
Rnor_6.0723,403,896 - 23,808,602 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl723,403,891 - 23,808,602 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0723,553,831 - 23,958,150 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4719,544,439 - 19,940,847 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1719,552,680 - 19,953,765 (+)NCBI
Celera714,630,545 - 15,035,838 (+)NCBICelera
Cytogenetic Map7q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function
ATP binding  (IDA,IEA)
protein binding  (IPI)

References

Additional References at PubMed
PMID:10358015   PMID:12040043   PMID:15071120   PMID:17114649   PMID:25843720  


Genomics

Comparative Map Data
Syn3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2716,216,055 - 17,808,790 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl717,376,372 - 17,808,790 (+)Ensembl
Rnor_6.0723,403,896 - 23,808,602 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl723,403,891 - 23,808,602 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0723,553,831 - 23,958,150 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4719,544,439 - 19,940,847 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1719,552,680 - 19,953,765 (+)NCBI
Celera714,630,545 - 15,035,838 (+)NCBICelera
Cytogenetic Map7q13NCBI
SYN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2232,507,820 - 33,058,381 (-)EnsemblGRCh38hg38GRCh38
GRCh382232,507,820 - 33,058,381 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372232,903,807 - 33,454,367 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362231,238,540 - 31,732,683 (-)NCBINCBI36hg18NCBI36
Build 342231,233,093 - 31,727,237NCBI
Celera2216,710,711 - 17,256,522 (-)NCBI
Cytogenetic Map22q12.3NCBI
HuRef2215,865,721 - 16,411,951 (-)NCBIHuRef
CHM1_12232,867,892 - 33,413,788 (-)NCBICHM1_1
Syn3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391085,884,610 - 86,336,730 (-)NCBIGRCm39mm39
GRCm39 Ensembl1085,890,989 - 86,334,760 (-)Ensembl
GRCm381086,048,746 - 86,498,926 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1086,055,125 - 86,498,896 (-)EnsemblGRCm38mm10GRCm38
MGSCv371085,511,491 - 85,961,641 (-)NCBIGRCm37mm9NCBIm37
MGSCv361085,485,308 - 85,928,638 (-)NCBImm8
Celera1088,022,524 - 88,480,347 (-)NCBICelera
Cytogenetic Map10C1NCBI
Syn3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540541,455,465 - 41,762,920 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540541,450,081 - 41,762,894 (-)NCBIChiLan1.0ChiLan1.0
SYN3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12231,373,466 - 31,920,997 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2231,373,604 - 31,866,798 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02213,517,932 - 14,069,661 (-)NCBIMhudiblu_PPA_v0panPan3
SYN3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11030,475,134 - 30,927,758 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1030,482,870 - 30,923,257 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1030,458,198 - 30,910,923 (+)NCBI
ROS_Cfam_1.01031,316,595 - 31,770,135 (+)NCBI
UMICH_Zoey_3.11031,058,009 - 31,509,813 (+)NCBI
UNSW_CanFamBas_1.01031,347,117 - 31,799,406 (+)NCBI
UU_Cfam_GSD_1.01031,531,822 - 31,985,721 (+)NCBI
Syn3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494513,825,984 - 14,243,677 (+)NCBI
SpeTri2.0NW_0049364926,836,441 - 7,253,867 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl512,017,784 - 12,578,953 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1512,017,741 - 12,501,995 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2512,196,607 - 12,291,334 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SYN3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11915,330,179 - 15,821,965 (-)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666045110,129,396 - 110,678,492 (+)NCBIVero_WHO_p1.0
Syn3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247501,663,309 - 1,976,738 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D7Mgh9  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0723,645,249 - 23,645,397NCBIRnor6.0
Rnor_5.0723,795,488 - 23,795,636UniSTSRnor5.0
RGSC_v3.4719,778,187 - 19,778,336RGDRGSC3.4
RGSC_v3.4719,778,188 - 19,778,336UniSTSRGSC3.4
RGSC_v3.1719,788,447 - 19,788,596RGD
Celera714,861,467 - 14,861,602UniSTS
RH 2.0 Map779.3RGD
Cytogenetic Map7q13UniSTS
D7Rat40  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2717,777,285 - 17,777,527 (+)MAPPERmRatBN7.2
Rnor_6.0723,783,311 - 23,783,552NCBIRnor6.0
Rnor_5.0723,933,259 - 23,933,500UniSTSRnor5.0
RGSC_v3.4719,915,731 - 19,916,213RGDRGSC3.4
RGSC_v3.4719,915,925 - 19,916,166UniSTSRGSC3.4
RGSC_v3.1719,928,649 - 19,929,131RGD
Celera715,011,032 - 15,011,271UniSTS
RH 2.0 Map778.0RGD
SHRSP x BN Map76.87RGD
Cytogenetic Map7q13UniSTS
D7Rat216  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2717,678,338 - 17,678,552 (+)MAPPERmRatBN7.2
Rnor_6.0723,700,654 - 23,700,867NCBIRnor6.0
Rnor_5.0723,850,893 - 23,851,106UniSTSRnor5.0
RGSC_v3.4719,833,592 - 19,833,806RGDRGSC3.4
RGSC_v3.4719,833,593 - 19,833,806UniSTSRGSC3.4
RGSC_v3.1719,847,222 - 19,847,649RGD
Celera714,916,655 - 14,916,868UniSTS
SHRSP x BN Map76.87RGD
SHRSP x BN Map76.87UniSTS
Cytogenetic Map7q13UniSTS
RH128273  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2717,523,310 - 17,523,527 (+)MAPPERmRatBN7.2
Rnor_6.0723,545,609 - 23,545,825NCBIRnor6.0
Rnor_5.0723,695,848 - 23,696,064UniSTSRnor5.0
RGSC_v3.4719,678,548 - 19,678,764UniSTSRGSC3.4
Celera714,762,644 - 14,762,860UniSTS
Cytogenetic Map7q13UniSTS
RH129267  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2717,523,345 - 17,523,536 (+)MAPPERmRatBN7.2
Rnor_6.0723,545,644 - 23,545,834NCBIRnor6.0
Rnor_5.0723,695,883 - 23,696,073UniSTSRnor5.0
RGSC_v3.4719,678,583 - 19,678,773UniSTSRGSC3.4
Celera714,762,679 - 14,762,869UniSTS
Cytogenetic Map7q13UniSTS
RH94615  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2717,524,335 - 17,524,409 (+)MAPPERmRatBN7.2
Rnor_6.0723,546,634 - 23,546,707NCBIRnor6.0
Rnor_5.0723,696,873 - 23,696,946UniSTSRnor5.0
RGSC_v3.4719,679,573 - 19,679,646UniSTSRGSC3.4
Celera714,763,669 - 14,763,742UniSTS
Cytogenetic Map7q13UniSTS
RH143027  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2717,679,415 - 17,679,605 (+)MAPPERmRatBN7.2
Rnor_6.0723,701,731 - 23,701,920NCBIRnor6.0
Rnor_5.0723,851,970 - 23,852,159UniSTSRnor5.0
RGSC_v3.4719,834,670 - 19,834,859UniSTSRGSC3.4
Celera714,917,732 - 14,917,921UniSTS
Cytogenetic Map7q13UniSTS
RH144261  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2717,551,976 - 17,552,083 (+)MAPPERmRatBN7.2
Rnor_6.0723,574,271 - 23,574,377NCBIRnor6.0
Rnor_5.0723,724,510 - 23,724,616UniSTSRnor5.0
RGSC_v3.4719,707,210 - 19,707,316UniSTSRGSC3.4
Celera714,791,244 - 14,791,350UniSTS
Cytogenetic Map7q13UniSTS
BI278238  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2717,523,117 - 17,523,220 (+)MAPPERmRatBN7.2
Rnor_6.0723,545,416 - 23,545,518NCBIRnor6.0
Rnor_5.0723,695,655 - 23,695,757UniSTSRnor5.0
RGSC_v3.4719,678,355 - 19,678,457UniSTSRGSC3.4
Celera714,762,451 - 14,762,553UniSTS
Cytogenetic Map7q13UniSTS
BF400160  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2717,802,723 - 17,802,823 (+)MAPPERmRatBN7.2
Rnor_6.0723,808,746 - 23,808,845NCBIRnor6.0
Rnor_5.0723,958,294 - 23,958,393UniSTSRnor5.0
RGSC_v3.4719,940,991 - 19,941,090UniSTSRGSC3.4
Celera715,035,982 - 15,036,081UniSTS
Cytogenetic Map7q13UniSTS
RH135110  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2717,522,418 - 17,522,611 (+)MAPPERmRatBN7.2
Rnor_6.0723,544,717 - 23,544,909NCBIRnor6.0
Rnor_5.0723,694,956 - 23,695,148UniSTSRnor5.0
RGSC_v3.4719,677,656 - 19,677,848UniSTSRGSC3.4
Celera714,761,752 - 14,761,944UniSTS
Cytogenetic Map7q13UniSTS
RH141014  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2717,521,115 - 17,521,310 (+)MAPPERmRatBN7.2
Rnor_6.0723,543,414 - 23,543,608NCBIRnor6.0
Rnor_5.0723,693,653 - 23,693,847UniSTSRnor5.0
RGSC_v3.4719,676,353 - 19,676,547UniSTSRGSC3.4
Celera714,760,452 - 14,760,643UniSTS
Cytogenetic Map7q13UniSTS
Timp3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2717,523,945 - 17,524,436 (+)MAPPERmRatBN7.2
Rnor_6.0723,546,244 - 23,546,734NCBIRnor6.0
Rnor_5.0723,696,483 - 23,696,973UniSTSRnor5.0
RGSC_v3.4719,679,183 - 19,679,673UniSTSRGSC3.4
Celera714,763,279 - 14,763,769UniSTS
Cytogenetic Map7q13UniSTS
G45201  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2717,562,016 - 17,562,389 (+)MAPPERmRatBN7.2
mRatBN7.2717,562,046 - 17,562,389 (+)MAPPERmRatBN7.2
Rnor_6.0723,584,341 - 23,584,683NCBIRnor6.0
Rnor_6.0723,584,311 - 23,584,683NCBIRnor6.0
Rnor_5.0723,734,580 - 23,734,922UniSTSRnor5.0
Rnor_5.0723,734,550 - 23,734,922UniSTSRnor5.0
RGSC_v3.4719,717,250 - 19,717,622UniSTSRGSC3.4
RGSC_v3.4719,717,280 - 19,717,622UniSTSRGSC3.4
Celera714,801,206 - 14,801,548UniSTS
Celera714,801,176 - 14,801,548UniSTS
Cytogenetic Map7q13UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:322
Count of miRNA genes:199
Interacting mature miRNAs:233
Transcripts:ENSRNOT00000037918
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 57
Low 3 35 32 16 18 16 2 3 17 35 41 11 2
Below cutoff 8 25 25 1 25 6 8 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000037918   ⟹   ENSRNOP00000036740
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl717,376,372 - 17,808,790 (+)Ensembl
Rnor_6.0 Ensembl723,403,891 - 23,808,602 (+)Ensembl
RefSeq Acc Id: NM_017109   ⟹   NP_058805
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2717,376,364 - 17,808,790 (+)NCBI
Rnor_6.0723,403,896 - 23,808,602 (+)NCBI
Rnor_5.0723,553,831 - 23,958,150 (+)NCBI
RGSC_v3.4719,544,439 - 19,940,847 (+)RGD
Celera714,630,545 - 15,035,838 (+)RGD
Sequence:
RefSeq Acc Id: XM_039078556   ⟹   XP_038934484
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2716,216,058 - 17,808,790 (+)NCBI
RefSeq Acc Id: XM_039078557   ⟹   XP_038934485
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2716,955,344 - 17,802,580 (+)NCBI
RefSeq Acc Id: XM_039078558   ⟹   XP_038934486
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2716,216,078 - 17,807,632 (+)NCBI
RefSeq Acc Id: XM_039078559   ⟹   XP_038934487
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2716,216,055 - 17,802,580 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_058805   ⟸   NM_017109
- UniProtKB: O70441 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000036740   ⟸   ENSRNOT00000037918
RefSeq Acc Id: XP_038934487   ⟸   XM_039078559
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934484   ⟸   XM_039078556
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934486   ⟸   XM_039078558
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934485   ⟸   XM_039078557
- Peptide Label: isoform X1
Protein Domains
Synapsin   Synapsin_C

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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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/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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
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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Sequenced By: MCW
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
Sequenced By: MCW
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)
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Sequenced By: MCW
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/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 (2020)
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Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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/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)
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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
F344/Stm (2019)
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Sequenced By: MCW
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
Sequenced By: MCW
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
FHH/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)
FHH/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
FHL/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)
FHL/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
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
GH/OmrMcwi (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)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
GK/Ox (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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
LE/Stm (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
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
LEW/Crl (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
LEW/NCrlBR (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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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/MavRrrc (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
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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/MavRrrc (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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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/MavRrrc (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
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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/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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
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
MHS/Gib (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
MNS/Gib (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
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
MR/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
MWF/Hsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
SHRSP/Gcrc (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
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WAG/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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/Gcrc (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
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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/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
WKY/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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/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
WKY/NHsd (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
WN/N (2020)
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Sequenced By: MCW
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
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:3799 AgrOrtholog
Ensembl Genes ENSRNOG00000026866 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000036740 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000037918 UniProtKB/TrEMBL
Gene3D-CATH 3.30.1490.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro ATP_grasp_subdomain_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PreATP-grasp_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYN2/3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Synapsin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Synapsin_ATP-bd_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Synapsin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Synapsin_P_site UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Synapsin_pre-ATP-grasp_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29130 UniProtKB/Swiss-Prot
NCBI Gene 29130 ENTREZGENE
PANTHER PTHR10841:SF20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Synapsin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Synapsin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Synapsin_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Syn3 PhenoGen
PRINTS SYNAPSIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE SYNAPSIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYNAPSIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF52440 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A096MIT7_RAT UniProtKB/TrEMBL
  O70441 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Syn3  synapsin III  LOC100910134  synapsin-3-like  Data Merged 737654 PROVISIONAL
2012-07-05 LOC100910134  synapsin-3-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2004-09-10 Syn3  synapsin III    synapsin 3  Name updated 1299863 APPROVED
2002-06-10 Syn3  synapsin 3      Name updated 70585 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_function binds ATP with high affinity and ADP with a lower affinity 70029
gene_regulation ATP binding is inhibited by Ca2+ 70029