Nlgn3 (neuroligin 3) - Rat Genome Database

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Gene: Nlgn3 (neuroligin 3) Rattus norvegicus
Analyze
Symbol: Nlgn3
Name: neuroligin 3
RGD ID: 621119
Description: Enables cell adhesion molecule binding activity; neurexin family protein binding activity; and signaling receptor activity. Involved in several processes, including inhibitory postsynaptic potential; neuron cell-cell adhesion; and synapse assembly. Located in several cellular components, including GABA-ergic synapse; glutamatergic synapse; and neuronal cell body. Is integral component of postsynaptic membrane. Is integral component of postsynaptic specialization membrane. Colocalizes with dendrite; excitatory synapse; and inhibitory synapse. Used to study autism spectrum disorder. Biomarker of sciatic neuropathy. Human ortholog(s) of this gene implicated in Asperger syndrome and autistic disorder. Orthologous to human NLGN3 (neuroligin 3); INTERACTS WITH 17alpha-ethynylestradiol; 2,2',4,4'-Tetrabromodiphenyl ether; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: gliotactin homolog; neuroligin-3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Nlgn3em1Sage  
Genetic Models: SD-Nlgn3em1Sage
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X66,427,926 - 66,457,378 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblX66,429,458 - 66,451,876 (+)Ensembl
Rnor_6.0X71,199,390 - 71,227,460 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX71,199,491 - 71,222,732 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X72,051,846 - 72,075,119 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X89,376,193 - 89,398,665 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X89,449,625 - 89,471,949 (+)NCBI
CeleraX66,785,377 - 66,807,774 (+)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adult behavior  (IEA,ISO)
axon extension  (IMP)
cell adhesion  (IEA)
chemical synaptic transmission  (IBA)
circadian sleep/wake cycle  (IMP)
excitatory postsynaptic potential  (ISO,ISS)
inhibitory postsynaptic potential  (IDA,ISO)
learning  (IEA,ISO)
long-term synaptic potentiation  (ISO)
modulation of chemical synaptic transmission  (IBA,IEA,ISO,ISS)
negative regulation of dendritic spine morphogenesis  (ISO)
negative regulation of excitatory postsynaptic potential  (ISO)
neuron cell-cell adhesion  (IBA,IDA)
oligodendrocyte differentiation  (ISO)
positive regulation of AMPA receptor activity  (ISO,ISS)
positive regulation of dendritic spine development  (IMP)
positive regulation of excitatory postsynaptic potential  (ISO,ISS)
positive regulation of inhibitory postsynaptic potential  (IDA)
positive regulation of protein localization to synapse  (IMP)
positive regulation of synapse assembly  (IDA,ISO)
positive regulation of synaptic transmission, glutamatergic  (ISO,ISS)
positive regulation of synaptic vesicle clustering  (ISO)
postsynaptic membrane assembly  (IBA,ISO,ISS)
postsynaptic specialization assembly  (IDA)
prepulse inhibition  (IMP)
presynaptic membrane assembly  (IBA,IDA)
receptor-mediated endocytosis  (IDA)
regulation of AMPA receptor activity  (ISO,ISS)
regulation of dendritic spine morphogenesis  (ISO,ISS)
regulation of long-term synaptic potentiation  (ISO,ISS)
regulation of NMDA receptor activity  (ISO,ISS)
regulation of respiratory gaseous exchange by nervous system process  (ISO,ISS)
regulation of synaptic transmission, glutamatergic  (ISO,ISS)
regulation of terminal button organization  (ISO,ISS)
rhythmic synaptic transmission  (IMP)
social behavior  (IEA,ISO,ISS)
synapse assembly  (IDA)
synapse organization  (IDA,IEA,ISO)
synaptic vesicle endocytosis  (IBA)
visual learning  (ISO)
vocalization behavior  (IEA,ISO)

Molecular Function

References

References - curated
1. Budreck EC and Scheiffele P, Eur J Neurosci. 2007 Oct;26(7):1738-48.
2. Chih B, etal., Science. 2005 Feb 25;307(5713):1324-8. Epub 2005 Jan 27.
3. Chubykin AA, etal., J Biol Chem. 2005 Jun 10;280(23):22365-74. Epub 2005 Mar 29.
4. Comoletti D, etal., J Neurosci. 2004 May 19;24(20):4889-93.
5. Etherton M, etal., Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13764-9. doi: 10.1073/pnas.1111093108. Epub 2011 Aug 1.
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. Gutierrez RC, etal., Neuroscience. 2009 Aug 4;162(1):208-21. doi: 10.1016/j.neuroscience.2009.04.062. Epub 2009 May 3.
9. Hamilton SM, etal., Behav Neurosci. 2014 Apr;128(2):103-9. doi: 10.1037/a0035988.
10. Ichtchenko K, etal., J Biol Chem 1996 Feb 2;271(5):2676-82.
11. Levinson JN, etal., Neuroscience. 2010 Feb 3;165(3):782-93. doi: 10.1016/j.neuroscience.2009.11.016. Epub 2009 Nov 13.
12. MGD data from the GO Consortium
13. NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. OMIM Disease Annotation Pipeline
15. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
16. RGD automated import pipeline for gene-chemical interactions
17. Suckow AT, etal., J Biol Chem. 2012 Jun 8;287(24):19816-26. doi: 10.1074/jbc.M111.280537. Epub 2012 Apr 23.
18. Thomas AM, etal., Sleep. 2017 Oct 1;40(10). pii: 4100612. doi: 10.1093/sleep/zsx138.
19. Zelano J, etal., J Comp Neurol. 2007 Jul 10;503(2):308-18.
Additional References at PubMed
PMID:11329178   PMID:12669065   PMID:15150161   PMID:15620359   PMID:16982420   PMID:17292328   PMID:17823315   PMID:18755801   PMID:19139271   PMID:19816407   PMID:20615874   PMID:21532576  
PMID:21642956   PMID:21788371   PMID:22671294   PMID:25565602   PMID:26621873   PMID:27805570   PMID:30790215  


Genomics

Comparative Map Data
Nlgn3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X66,427,926 - 66,457,378 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblX66,429,458 - 66,451,876 (+)Ensembl
Rnor_6.0X71,199,390 - 71,227,460 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX71,199,491 - 71,222,732 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X72,051,846 - 72,075,119 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X89,376,193 - 89,398,665 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X89,449,625 - 89,471,949 (+)NCBI
CeleraX66,785,377 - 66,807,774 (+)NCBICelera
Cytogenetic MapXq22NCBI
NLGN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX71,144,831 - 71,171,201 (+)EnsemblGRCh38hg38GRCh38
GRCh38X71,144,389 - 71,175,307 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X70,364,691 - 70,391,051 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X70,281,436 - 70,307,776 (+)NCBINCBI36hg18NCBI36
Build 34X70,147,731 - 70,174,070NCBI
CeleraX70,718,556 - 70,744,930 (+)NCBI
Cytogenetic MapXq13.1NCBI
HuRefX64,183,444 - 64,209,758 (+)NCBIHuRef
CHM1_1X70,257,401 - 70,284,066 (+)NCBICHM1_1
Nlgn3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X100,342,785 - 100,364,956 (+)NCBIGRCm39mm39
GRCm39 EnsemblX100,342,774 - 100,369,569 (+)Ensembl
GRCm38X101,299,179 - 101,321,350 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX101,299,168 - 101,325,963 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X98,494,520 - 98,516,689 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X97,501,929 - 97,524,067 (+)NCBImm8
CeleraX88,215,228 - 88,237,795 (+)NCBICelera
Cytogenetic MapXDNCBI
Nlgn3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495547510,712,170 - 10,735,857 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495547510,712,170 - 10,735,857 (+)NCBIChiLan1.0ChiLan1.0
NLGN3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X70,469,764 - 70,496,526 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX70,469,764 - 70,496,526 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X60,413,098 - 60,439,359 (+)NCBIMhudiblu_PPA_v0panPan3
NLGN3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X55,510,729 - 55,532,396 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX55,513,626 - 55,531,371 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX46,337,800 - 46,359,510 (+)NCBI
ROS_Cfam_1.0X56,479,897 - 56,501,589 (+)NCBI
UMICH_Zoey_3.1X54,447,828 - 54,469,515 (+)NCBI
UNSW_CanFamBas_1.0X55,779,249 - 55,800,946 (+)NCBI
UU_Cfam_GSD_1.0X55,706,411 - 55,728,100 (+)NCBI
Nlgn3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X46,672,077 - 46,696,110 (-)NCBI
SpeTri2.0NW_004936762435,729 - 458,261 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NLGN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX57,176,103 - 57,201,486 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X57,174,506 - 57,204,770 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X64,705,492 - 64,727,915 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NLGN3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X60,941,371 - 60,967,942 (+)NCBI
ChlSab1.1 EnsemblX60,941,654 - 60,967,936 (+)Ensembl
Vero_WHO_p1.0NW_0236660652,802,397 - 2,828,656 (+)NCBI
Nlgn3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249031,437,663 - 1,465,955 (+)NCBI

Position Markers
RH79662  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X66,427,531 - 66,427,714 (+)MAPPERmRatBN7.2
Rnor_6.0X71,197,572 - 71,197,754NCBIRnor6.0
Rnor_5.0X72,050,050 - 72,050,232UniSTSRnor5.0
RGSC_v3.4X89,374,249 - 89,374,431UniSTSRGSC3.4
CeleraX66,783,433 - 66,783,615UniSTS
Cytogenetic MapXq31UniSTS
MARC_10371-10372:999098922:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X66,449,655 - 66,449,979 (+)MAPPERmRatBN7.2
Rnor_6.0X71,219,732 - 71,220,055NCBIRnor6.0
Rnor_5.0X72,071,783 - 72,072,106UniSTSRnor5.0
RGSC_v3.4X89,396,446 - 89,396,769UniSTSRGSC3.4
CeleraX66,805,555 - 66,805,878UniSTS
Cytogenetic MapXq31UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat


Genetic Models
This gene Nlgn3 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:422
Count of miRNA genes:106
Interacting mature miRNAs:122
Transcripts:ENSRNOT00000005077, ENSRNOT00000005102, ENSRNOT00000042648, ENSRNOT00000050672
Prediction methods:Microtar, Miranda, Pita, 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 74 2 6
Low 3 43 29 13 19 13 7 8 29 31 11 7
Below cutoff 28 28 28 1 3 4 4 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000005077   ⟹   ENSRNOP00000005077
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX66,429,476 - 66,451,876 (+)Ensembl
Rnor_6.0 EnsemblX71,199,516 - 71,222,006 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000005102   ⟹   ENSRNOP00000005102
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX66,429,458 - 66,451,876 (+)Ensembl
Rnor_6.0 EnsemblX71,199,532 - 71,222,732 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076168   ⟹   ENSRNOP00000068393
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX66,429,458 - 66,451,876 (+)Ensembl
Rnor_6.0 EnsemblX71,199,491 - 71,220,041 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000108642   ⟹   ENSRNOP00000080050
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX66,429,476 - 66,451,876 (+)Ensembl
RefSeq Acc Id: NM_134336   ⟹   NP_599163
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X66,429,476 - 66,451,876 (+)NCBI
Rnor_6.0X71,199,516 - 71,221,951 (+)NCBI
Rnor_5.0X72,051,846 - 72,075,119 (+)NCBI
RGSC_v3.4X89,376,193 - 89,398,665 (+)RGD
CeleraX66,785,377 - 66,807,774 (+)RGD
Sequence:
RefSeq Acc Id: XM_006257054   ⟹   XP_006257116
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X66,427,926 - 66,452,659 (+)NCBI
Rnor_6.0X71,199,390 - 71,222,734 (+)NCBI
Rnor_5.0X72,051,846 - 72,075,119 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006257055   ⟹   XP_006257117
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X66,427,926 - 66,452,659 (+)NCBI
Rnor_6.0X71,199,390 - 71,222,734 (+)NCBI
Rnor_5.0X72,051,846 - 72,075,119 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008773251   ⟹   XP_008771473
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X66,427,926 - 66,457,378 (+)NCBI
Rnor_6.0X71,199,390 - 71,227,460 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099439   ⟹   XP_038955367
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X66,427,926 - 66,457,378 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_599163   ⟸   NM_134336
- Peptide Label: precursor
- UniProtKB: Q62889 (UniProtKB/Swiss-Prot),   F1LPZ8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257116   ⟸   XM_006257054
- Peptide Label: isoform X2
- UniProtKB: D3ZDC0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257117   ⟸   XM_006257055
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008771473   ⟸   XM_008773251
- Peptide Label: isoform X1
- UniProtKB: F1LPZ8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000005077   ⟸   ENSRNOT00000005077
RefSeq Acc Id: ENSRNOP00000005102   ⟸   ENSRNOT00000005102
RefSeq Acc Id: ENSRNOP00000068393   ⟸   ENSRNOT00000076168
RefSeq Acc Id: XP_038955367   ⟸   XM_039099439
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000080050   ⟸   ENSRNOT00000108642
Protein Domains
COesterase

Transcriptome

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

Promoters
RGD ID:13701879
Promoter ID:EPDNEW_R12399
Type:single initiation site
Name:Nlgn3_1
Description:neuroligin 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X71,199,501 - 71,199,561EPDNEW

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)
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-Lx/CubMcwi (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
BN/NHsdMcwi (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
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)
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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)
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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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/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
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)
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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
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)
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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
FHH/EurMcwi (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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
FXLE16/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (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)
GK/FarMcwi (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
GK/Ox (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
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)
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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
HXB20/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/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
HXB4/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/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
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)
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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: 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)
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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
LEXF11/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/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
LEXF1C/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
LEXF2B/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
LEXF3/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (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: 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)
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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: 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)
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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
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
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)
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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
PVG/Seac (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
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)
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)
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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)
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)
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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
SHRSP/A3NCrl (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: 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)
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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
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)
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)
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621119 AgrOrtholog
Ensembl Genes ENSRNOG00000003812 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000005077 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000005102 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068393 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000005077 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000005102 UniProtKB/TrEMBL
  ENSRNOT00000076168 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.1820 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro AB_hydrolase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CarbesteraseB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Carboxylesterase_B_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nlgn UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NLGN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:171297 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 171297 ENTREZGENE
PANTHER PTHR43903:SF4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam COesterase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nlgn3 PhenoGen
PRINTS NEUROLIGIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CARBOXYLESTERASE_B_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53474 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A096MK63_RAT UniProtKB/TrEMBL
  D3ZDC0 ENTREZGENE, UniProtKB/TrEMBL
  F1LPZ8 ENTREZGENE, UniProtKB/TrEMBL
  NLGN3_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-26 Nlgn3  neuroligin 3      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Nlgn3  neuroligin 3      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains contains a large esterase homology domain, a single transmembrane region, and a short cytoplasmic domain 729051
gene_function binds beta-neurexins 729051