Bsn (bassoon (presynaptic cytomatrix protein)) - Rat Genome Database
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Gene: Bsn (bassoon (presynaptic cytomatrix protein)) Rattus norvegicus
Analyze
Symbol: Bsn
Name: bassoon (presynaptic cytomatrix protein)
RGD ID: 2223
Description: Exhibits dynein light chain binding activity and transcription corepressor binding activity. Involved in presynaptic active zone assembly; regulation of ubiquitin protein ligase activity; and retrograde axonal transport. Localizes to several cellular components, including axon cytoplasm; cytoplasmic vesicle; and cytoskeleton of presynaptic active zone. Colocalizes with synaptic membrane. Orthologous to human BSN (bassoon presynaptic cytomatrix protein); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 4-amino-2,6-dinitrotoluene; amphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: bassoon; neuronal double zinc finger protein; zinc finger protein 231; Znf231
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Bsnem1Ionsz  
Genetic Models: SD-Bsnem1Ionsz
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.08116,873,721 - 116,965,396 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8116,873,721 - 116,965,396 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08116,227,802 - 116,319,071 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48113,364,208 - 113,455,766 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18113,387,192 - 113,475,221 (-)NCBI
Celera8108,089,061 - 108,180,178 (-)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
epilepsy  (ISS)
heart disease  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
1. Burkhardt C, etal., FEBS Lett. 2005 Jul 4;579(17):3821-8.
2. Dick O, etal., J Comp Neurol. 2001 Oct 15;439(2):224-34.
3. Dresbach T, etal., J Biol Chem. 2006 Mar 3;281(9):6038-47. Epub 2005 Dec 21.
4. Du H, etal., Eye (Lond). 2012 Aug;26(8):1039-43. doi: 10.1038/eye.2012.80. Epub 2012 Jun 1.
5. Fejtova A, etal., J Cell Biol. 2009 Apr 20;185(2):341-55. doi: 10.1083/jcb.200807155.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. GOA data from the GO Consortium
8. Ivanova D, etal., EMBO J. 2015 Apr 15;34(8):1056-77. doi: 10.15252/embj.201488796. Epub 2015 Feb 4.
9. Ko J, etal., EMBO J. 2009 Oct 21;28(20):3244-55. doi: 10.1038/emboj.2009.249. Epub 2009 Sep 3.
10. K├Ârber C, etal., Neuron. 2015 Aug 5;87(3):521-33. doi: 10.1016/j.neuron.2015.07.001. Epub 2015 Jul 23.
11. Maas C, etal., J Neurosci. 2012 Aug 8;32(32):11095-108. doi: 10.1523/JNEUROSCI.0195-12.2012.
12. MGD data from the GO Consortium
13. NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. Ohtsuka T, etal., J Cell Biol 2002 Aug 5;158(3):577-90. Epub 2002 Aug 5.
15. RGD automated data pipeline
16. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
17. RGD automated import pipeline for gene-chemical interactions
18. Richter K, etal., J Comp Neurol. 1999 Jun 7;408(3):437-48.
19. tom Dieck S, etal., J Cell Biol 1998 Jul 27;142(2):499-509.
20. Waites CL, etal., EMBO J. 2013 Apr 3;32(7):954-69. doi: 10.1038/emboj.2013.27. Epub 2013 Feb 12.
Additional References at PubMed
PMID:8889548   PMID:10564375   PMID:10900017   PMID:12115694   PMID:12812759   PMID:14622577   PMID:14734538   PMID:15340146   PMID:15935055   PMID:17114649   PMID:19966281   PMID:20127803  
PMID:21092860   PMID:21144999   PMID:21356198   PMID:21700703   PMID:21712437   PMID:21940441   PMID:22701595   PMID:22871113   PMID:23516560   PMID:23791195   PMID:24554721   PMID:26793095  
PMID:27907191   PMID:29476059   PMID:30053369  


Genomics

Comparative Map Data
Bsn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.08116,873,721 - 116,965,396 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8116,873,721 - 116,965,396 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08116,227,802 - 116,319,071 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48113,364,208 - 113,455,766 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18113,387,192 - 113,475,221 (-)NCBI
Celera8108,089,061 - 108,180,178 (-)NCBICelera
Cytogenetic Map8q32NCBI
BSN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl349,554,477 - 49,671,549 (+)EnsemblGRCh38hg38GRCh38
GRCh38349,554,477 - 49,671,549 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37349,591,922 - 49,708,982 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36349,566,926 - 49,683,986 (+)NCBINCBI36hg18NCBI36
Build 34349,566,925 - 49,683,980NCBI
Celera349,556,534 - 49,673,679 (+)NCBI
Cytogenetic Map3p21.31NCBI
HuRef349,651,449 - 49,767,966 (+)NCBIHuRef
CHM1_1349,544,319 - 49,661,041 (+)NCBICHM1_1
Bsn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399107,973,221 - 108,067,618 (-)NCBIGRCm39mm39
GRCm389108,096,022 - 108,190,419 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9108,096,022 - 108,190,384 (-)EnsemblGRCm38mm10GRCm38
MGSCv379107,998,353 - 108,092,714 (-)NCBIGRCm37mm9NCBIm37
MGSCv369107,961,291 - 108,048,359 (-)NCBImm8
Celera9107,705,791 - 107,798,925 (-)NCBICelera
Cytogenetic Map9F1NCBI
cM Map959.07NCBI
Bsn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555321,527,477 - 1,570,670 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555321,527,336 - 1,578,394 (+)NCBIChiLan1.0ChiLan1.0
BSN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1350,729,927 - 50,841,178 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl350,790,552 - 50,841,178 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0349,483,652 - 49,603,928 (+)NCBIMhudiblu_PPA_v0panPan3
BSN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2039,605,117 - 39,642,298 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12039,601,803 - 39,696,831 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Bsn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365291,182,872 - 1,287,794 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BSN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1332,107,077 - 32,203,459 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11332,106,967 - 32,203,461 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21335,341,713 - 35,382,661 (+)NCBISscrofa10.2Sscrofa10.2susScr3
BSN
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl2211,018,966 - 11,059,701 (+)Ensembl
ChlSab1.12210,953,901 - 11,066,892 (+)NCBI
Bsn
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247303,498,118 - 3,600,488 (+)NCBI

Position Markers
D8Rat67  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.08116,926,242 - 116,926,429NCBIRnor6.0
Rnor_5.08116,279,875 - 116,280,062UniSTSRnor5.0
RGSC_v3.48113,416,613 - 113,416,800UniSTSRGSC3.4
RGSC_v3.48113,416,429 - 113,416,799RGDRGSC3.4
RGSC_v3.18113,435,884 - 113,436,254RGD
Celera8108,140,920 - 108,141,107UniSTS
Cytogenetic Map8q32UniSTS
RH 3.4 Map81118.6RGD
RH 3.4 Map81118.6UniSTS
RH 2.0 Map8874.3RGD
SHRSP x BN Map871.8999RGD
D8Wox32  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.08116,882,075 - 116,882,335NCBIRnor6.0
Rnor_5.08116,236,156 - 116,236,416UniSTSRnor5.0
RGSC_v3.48113,372,562 - 113,372,826UniSTSRGSC3.4
Celera8108,097,417 - 108,097,677UniSTS
Cytogenetic Map8q32UniSTS
BF387500  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.08116,875,287 - 116,875,443NCBIRnor6.0
Rnor_5.08116,229,368 - 116,229,524UniSTSRnor5.0
RGSC_v3.48113,365,774 - 113,365,930UniSTSRGSC3.4
Celera8108,090,629 - 108,090,785UniSTS
Cytogenetic Map8q32UniSTS
RH 3.4 Map81116.7UniSTS
BE097610  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.08116,879,061 - 116,879,252NCBIRnor6.0
Rnor_5.08116,233,142 - 116,233,333UniSTSRnor5.0
RGSC_v3.48113,369,548 - 113,369,739UniSTSRGSC3.4
Celera8108,094,403 - 108,094,594UniSTS
Cytogenetic Map8q32UniSTS
RH 3.4 Map81120.9UniSTS
D8Wox11  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.08116,873,553 - 116,873,661NCBIRnor6.0
Rnor_5.08116,227,634 - 116,227,742UniSTSRnor5.0
RGSC_v3.48113,364,040 - 113,364,148UniSTSRGSC3.4
Celera8108,088,893 - 108,089,001UniSTS
Cytogenetic Map8q32UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)89531047119211942Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810938911120496129Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)844458129118087517Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)850529480128036471Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)865717449128033050Rat
631653Bp125Blood pressure QTL 1253.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)872849686117849686Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight as a percentage of body weight (CMO:0000654)874917593121080545Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)876103982127182642Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)878805083123805083Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)878805083123805083Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)878805083123805083Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)878805083123805083Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)880697934125697934Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)883894304128894304Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)889058229132243842Rat
2313400Anxrr25Anxiety related response QTL 25aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)895963141122354314Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102051964133307652Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8104682575133307652Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)8104682575133307652Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8107769005129956433Rat
631217Activ1Activity QTL 115.9voluntary movement trait (VT:0003491)number of photobeam interruptions in an experimental apparatus (CMO:0001517)8110212979116947981Rat


Genetic Models
This gene Bsn is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:416
Count of miRNA genes:220
Interacting mature miRNAs:281
Transcripts:ENSRNOT00000042528
Prediction methods:Miranda
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 64 4
Low 8 10 16 35 2
Below cutoff 3 40 32 24 19 24 7 8 15 2 9 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000042528   ⟹   ENSRNOP00000039162
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl8116,873,721 - 116,965,396 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000082113   ⟹   ENSRNOP00000072024
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl8116,877,251 - 116,893,057 (-)Ensembl
RefSeq Acc Id: NM_019146   ⟹   NP_062019
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08116,873,721 - 116,965,396 (-)NCBI
Rnor_5.08116,227,802 - 116,319,071 (-)NCBI
RGSC_v3.48113,364,208 - 113,455,766 (-)RGD
Celera8108,089,061 - 108,180,178 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_062019 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAA76287 (Get FASTA)   NCBI Sequence Viewer  
  EDL77188 (Get FASTA)   NCBI Sequence Viewer  
  EDL77189 (Get FASTA)   NCBI Sequence Viewer  
  O88778 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_062019   ⟸   NM_019146
- UniProtKB: G3V984 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072024   ⟸   ENSRNOT00000082113
RefSeq Acc Id: ENSRNOP00000039162   ⟸   ENSRNOT00000042528
Protein Domains
zf-piccolo

Transcriptome

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

Promoters
RGD ID:13696291
Promoter ID:EPDNEW_R6816
Type:single initiation site
Name:Bsn_1
Description:bassoon
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_6.08116,965,404 - 116,965,464EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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
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/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
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 116241941 116241942 T C snv IS/Kyo (KyushuU)
8 116242551 116242552 G A snv COP/CrCrl (MCW & UW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 116888470 116888471 G A snv COP/CrCrl (MCW & UW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2223 AgrOrtholog
Ensembl Genes ENSRNOG00000030714 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000039162 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000072024 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000042528 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000082113 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Bsn UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_piccolo UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29138 UniProtKB/TrEMBL
NCBI Gene 29138 ENTREZGENE
PANTHER PTHR14113:SF1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam zf-piccolo UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Bsn PhenoGen
Superfamily-SCOP SSF57903 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.29999 ENTREZGENE
UniProt A0A0G2K1X6_RAT UniProtKB/TrEMBL
  BSN_RAT UniProtKB/Swiss-Prot
  G3V984 ENTREZGENE, UniProtKB/TrEMBL
  O88778 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-01-14 Bsn  bassoon (presynaptic cytomatrix protein)  Bsn  bassoon  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Bsn  bassoon      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localized to the axon terminals of hippocampal neurons 69780
gene_cellular_localization presynaptic cytomatrix protein 69780
gene_domains contains two double-zinc fingers, several coiled-coil domains, and a stretch of polyglutamines 69780