Stxbp5 (syntaxin binding protein 5) - Rat Genome Database

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Gene: Stxbp5 (syntaxin binding protein 5) Rattus norvegicus
Analyze
Symbol: Stxbp5
Name: syntaxin binding protein 5
RGD ID: 708517
Description: Enables syntaxin-1 binding activity. Involved in synaptic vesicle cycle. Located in neuromuscular junction and synaptic vesicle. Is active in Schaffer collateral - CA1 synapse and presynaptic cytosol. Is extrinsic component of presynaptic membrane. Orthologous to human STXBP5 (syntaxin binding protein 5); INTERACTS WITH 2,4-dinitrotoluene; 2,6-dinitrotoluene; 4-amino-2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: lethal(2) giant larvae protein homolog 3; syntaxin binding protein 5 (tomosyn); syntaxin-binding protein 5; tomosyn; tomosyn-1
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
mRatBN7.214,182,489 - 4,335,271 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl14,185,529 - 4,335,101 (-)Ensembl
Rnor_6.013,858,917 - 4,011,684 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13,858,909 - 4,011,511 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.015,532,156 - 5,682,250 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414,428,182 - 4,579,373 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.114,428,181 - 4,579,373 (-)NCBI
Celera12,725,757 - 2,875,514 (-)NCBICelera
Cytogenetic Map1p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Additional References at PubMed
PMID:12782620   PMID:12832401   PMID:14983051   PMID:15240567   PMID:15316007   PMID:16033762   PMID:16186257   PMID:16505218   PMID:18936251   PMID:19258327   PMID:20633536   PMID:20978127  
PMID:21330375   PMID:21810271   PMID:23519441   PMID:24782308   PMID:25063806   PMID:28746398   PMID:29269412  


Genomics

Comparative Map Data
Stxbp5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.214,182,489 - 4,335,271 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl14,185,529 - 4,335,101 (-)Ensembl
Rnor_6.013,858,917 - 4,011,684 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13,858,909 - 4,011,511 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.015,532,156 - 5,682,250 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414,428,182 - 4,579,373 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.114,428,181 - 4,579,373 (-)NCBI
Celera12,725,757 - 2,875,514 (-)NCBICelera
Cytogenetic Map1p13NCBI
STXBP5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6147,204,425 - 147,390,476 (+)EnsemblGRCh38hg38GRCh38
GRCh386147,204,184 - 147,390,473 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh376147,525,553 - 147,711,612 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366147,566,565 - 147,748,588 (+)NCBINCBI36hg18NCBI36
Build 346147,566,567 - 147,748,584NCBI
Celera6148,265,949 - 148,449,151 (+)NCBI
Cytogenetic Map6q24.3NCBI
HuRef6145,089,042 - 145,275,226 (+)NCBIHuRef
CHM1_16147,788,922 - 147,975,011 (+)NCBICHM1_1
Stxbp5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39109,631,291 - 9,776,987 (-)NCBIGRCm39mm39
GRCm39 Ensembl109,631,291 - 9,776,823 (-)Ensembl
GRCm38109,755,547 - 9,901,287 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl109,755,547 - 9,901,079 (-)EnsemblGRCm38mm10GRCm38
MGSCv37109,475,345 - 9,620,838 (-)NCBIGRCm37mm9NCBIm37
MGSCv36109,445,737 - 9,590,873 (-)NCBImm8
Celera109,659,963 - 9,805,506 (-)NCBICelera
Cytogenetic Map10A1NCBI
Stxbp5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543913,580,113 - 13,743,430 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543913,580,106 - 13,743,430 (-)NCBIChiLan1.0ChiLan1.0
STXBP5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16149,719,064 - 149,905,007 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6149,719,064 - 149,902,662 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06145,006,696 - 145,192,467 (+)NCBIMhudiblu_PPA_v0panPan3
STXBP5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1138,271,238 - 38,439,088 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl138,271,154 - 38,434,042 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha139,170,639 - 39,338,349 (+)NCBI
ROS_Cfam_1.0138,443,072 - 38,612,992 (+)NCBI
UMICH_Zoey_3.1138,320,755 - 38,488,319 (+)NCBI
UNSW_CanFamBas_1.0138,190,698 - 38,358,426 (+)NCBI
UU_Cfam_GSD_1.0138,529,557 - 38,697,531 (+)NCBI
Stxbp5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946133,351,292 - 133,522,798 (+)NCBI
SpeTri2.0NW_004936489449,029 - 771,870 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
STXBP5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl118,345,363 - 18,513,252 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1118,343,826 - 18,512,750 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2120,543,226 - 20,705,846 (-)NCBISscrofa10.2Sscrofa10.2susScr3
STXBP5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11324,365,022 - 24,559,249 (-)NCBI
ChlSab1.1 Ensembl1324,367,627 - 24,559,269 (-)Ensembl
Vero_WHO_p1.0NW_023666040200,313,238 - 200,504,306 (-)NCBI
Stxbp5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462478510,692,573 - 10,874,358 (-)NCBI

Position Markers
RH144675  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.214,185,283 - 4,185,446 (+)MAPPERmRatBN7.2
Rnor_6.013,861,708 - 3,861,870NCBIRnor6.0
Rnor_5.015,534,947 - 5,535,109UniSTSRnor5.0
RGSC_v3.414,427,937 - 4,428,099UniSTSRGSC3.4
Celera12,725,512 - 2,725,674UniSTS
RH 3.4 Map177.6UniSTS
Cytogenetic Map1p13UniSTS
BF390393  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.214,279,606 - 4,279,826 (+)MAPPERmRatBN7.2
Rnor_6.013,956,028 - 3,956,247NCBIRnor6.0
Rnor_5.015,627,828 - 5,628,047UniSTSRnor5.0
RGSC_v3.414,522,518 - 4,522,736UniSTSRGSC3.4
Celera12,819,704 - 2,819,923UniSTS
RH 3.4 Map177.2UniSTS
Cytogenetic Map1p13UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354647Despr8Despair related QTL 80.0000341locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1124744506Rat
2298546Neuinf4Neuroinflammation QTL 45.1nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1128736750Rat
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1132356093Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1132356093Rat
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)1132356093Rat
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1165833076Rat
1578650Bmd6Bone mineral density QTL 612.2femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)150910843284926Rat
1578651Bmd7Bone mineral density QTL 714.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)150910843284926Rat
1578669Bss9Bone structure and strength QTL 96.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)150910843284926Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
1600360Mcs16Mammary carcinoma susceptibility QTL 162.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1224439043433040Rat
1300170Rf6Renal function QTL 63.14renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)1416280711481482Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:217
Count of miRNA genes:79
Interacting mature miRNAs:84
Transcripts:ENSRNOT00000040559, ENSRNOT00000044778, ENSRNOT00000049699
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 2 17 6 19 6 74 33 34 11
Low 1 43 40 35 35 8 11 2 7 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_030843 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_178345 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_178346 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006227623 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006227624 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008758628 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008758629 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091853 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091859 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091862 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091865 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091871 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091874 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091879 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091888 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005492935 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005492946 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005492948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC096981 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF118889 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF118890 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473994 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214558 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217480 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U92072 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000040559   ⟹   ENSRNOP00000044738
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl14,185,529 - 4,335,101 (-)Ensembl
Rnor_6.0 Ensembl13,861,953 - 4,011,511 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000044778   ⟹   ENSRNOP00000039502
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl14,187,467 - 4,335,101 (-)Ensembl
Rnor_6.0 Ensembl13,862,091 - 4,011,161 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000049699   ⟹   ENSRNOP00000049322
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl14,185,529 - 4,335,101 (-)Ensembl
Rnor_6.0 Ensembl13,858,909 - 4,011,353 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000094037   ⟹   ENSRNOP00000087436
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl14,185,529 - 4,335,101 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096129   ⟹   ENSRNOP00000095824
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl14,185,529 - 4,335,101 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100093   ⟹   ENSRNOP00000092275
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl14,185,529 - 4,335,101 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115103   ⟹   ENSRNOP00000092947
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl14,185,529 - 4,335,101 (-)Ensembl
RefSeq Acc Id: NM_030843   ⟹   NP_110470
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214,185,529 - 4,335,101 (-)NCBI
Rnor_6.013,861,953 - 4,011,511 (-)NCBI
Rnor_5.015,532,156 - 5,682,250 (-)NCBI
RGSC_v3.414,428,182 - 4,579,373 (-)RGD
Celera12,725,757 - 2,875,514 (-)RGD
Sequence:
RefSeq Acc Id: NM_178345   ⟹   NP_848035
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214,185,667 - 4,334,751 (-)NCBI
Rnor_6.013,862,091 - 4,011,161 (-)NCBI
Rnor_5.015,532,156 - 5,682,250 (-)NCBI
RGSC_v3.414,428,182 - 4,579,373 (-)RGD
Celera12,725,895 - 2,875,164 (-)NCBI
Sequence:
RefSeq Acc Id: NM_178346   ⟹   NP_848036
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214,185,667 - 4,334,751 (-)NCBI
Rnor_6.013,862,091 - 4,011,161 (-)NCBI
Rnor_5.015,532,156 - 5,682,250 (-)NCBI
RGSC_v3.414,428,182 - 4,579,373 (-)RGD
Celera12,725,895 - 2,875,164 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039091853   ⟹   XP_038947781
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214,182,489 - 4,335,267 (-)NCBI
RefSeq Acc Id: XM_039091859   ⟹   XP_038947787
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214,202,786 - 4,335,271 (-)NCBI
RefSeq Acc Id: XM_039091862   ⟹   XP_038947790
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214,206,799 - 4,335,271 (-)NCBI
RefSeq Acc Id: XM_039091865   ⟹   XP_038947793
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214,207,771 - 4,335,271 (-)NCBI
RefSeq Acc Id: XM_039091871   ⟹   XP_038947799
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214,202,786 - 4,335,270 (-)NCBI
RefSeq Acc Id: XM_039091874   ⟹   XP_038947802
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214,207,771 - 4,335,270 (-)NCBI
RefSeq Acc Id: XM_039091879   ⟹   XP_038947807
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214,202,787 - 4,335,270 (-)NCBI
RefSeq Acc Id: XM_039091888   ⟹   XP_038947816
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214,210,040 - 4,335,270 (-)NCBI
RefSeq Acc Id: XR_005492935
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214,195,715 - 4,335,271 (-)NCBI
RefSeq Acc Id: XR_005492946
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214,195,715 - 4,335,270 (-)NCBI
RefSeq Acc Id: XR_005492948
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214,195,715 - 4,335,270 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_110470   ⟸   NM_030843
- Peptide Label: isoform m
- UniProtKB: Q9WU70 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_848036   ⟸   NM_178346
- Peptide Label: isoform s
- UniProtKB: Q9WU70 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_848035   ⟸   NM_178345
- Peptide Label: isoform b
- UniProtKB: Q9WU70 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000039502   ⟸   ENSRNOT00000044778
RefSeq Acc Id: ENSRNOP00000049322   ⟸   ENSRNOT00000049699
RefSeq Acc Id: ENSRNOP00000044738   ⟸   ENSRNOT00000040559
RefSeq Acc Id: XP_038947781   ⟸   XM_039091853
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947787   ⟸   XM_039091859
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038947799   ⟸   XM_039091871
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038947807   ⟸   XM_039091879
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038947790   ⟸   XM_039091862
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038947793   ⟸   XM_039091865
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038947802   ⟸   XM_039091874
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038947816   ⟸   XM_039091888
- Peptide Label: isoform X8
RefSeq Acc Id: ENSRNOP00000087436   ⟸   ENSRNOT00000094037
RefSeq Acc Id: ENSRNOP00000092947   ⟸   ENSRNOT00000115103
RefSeq Acc Id: ENSRNOP00000092275   ⟸   ENSRNOT00000100093
RefSeq Acc Id: ENSRNOP00000095824   ⟸   ENSRNOT00000096129
Transcriptome

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

Promoters
RGD ID:13689488
Promoter ID:EPDNEW_R11
Type:single initiation site
Name:Stxbp5_1
Description:syntaxin binding protein 5
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_6.014,011,415 - 4,011,475EPDNEW

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)
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
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)
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
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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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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)
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
F344/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
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)
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
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)
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
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:708517 AgrOrtholog
Ensembl Genes ENSRNOG00000013351 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000039502 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000044738 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000049322 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000040559 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000044778 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000049699 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.130.10.10 UniProtKB/Swiss-Prot
InterPro Lethal2_giant UniProtKB/Swiss-Prot
  Lgl_C_dom UniProtKB/Swiss-Prot
  LLGL2 UniProtKB/Swiss-Prot
  V_SNARE_CC UniProtKB/Swiss-Prot
  WD40/YVTN_repeat-like_dom_sf UniProtKB/Swiss-Prot
  WD40_repeat UniProtKB/Swiss-Prot
  WD40_repeat_CS UniProtKB/Swiss-Prot
  WD40_repeat_dom UniProtKB/Swiss-Prot
  WD40_repeat_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:81022 UniProtKB/Swiss-Prot
NCBI Gene 81022 ENTREZGENE
Pfam Lgl_C UniProtKB/Swiss-Prot
  LLGL UniProtKB/Swiss-Prot
  WD40 UniProtKB/Swiss-Prot
PhenoGen Stxbp5 PhenoGen
PRINTS LETHAL2GIANT UniProtKB/Swiss-Prot
PROSITE V_SNARE UniProtKB/Swiss-Prot
  WD_REPEATS_1 UniProtKB/Swiss-Prot
  WD_REPEATS_2 UniProtKB/Swiss-Prot
  WD_REPEATS_REGION UniProtKB/Swiss-Prot
SMART WD40 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF50978 UniProtKB/Swiss-Prot
UniProt Q9WU70 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q9WU71 UniProtKB/Swiss-Prot
  Q9Z152 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-27 Stxbp5  syntaxin binding protein 5  Stxbp5  syntaxin binding protein 5 (tomosyn)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-08 Stxbp5  syntaxin binding protein 5 (tomosyn)      Symbol and Name status set to approved 1299863 APPROVED

RGD Curation Notes
Note Type Note Reference