Nlgn1 (neuroligin 1) - Rat Genome Database

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Gene: Nlgn1 (neuroligin 1) Rattus norvegicus
Analyze
Symbol: Nlgn1
Name: neuroligin 1
RGD ID: 621117
Description: Exhibits several functions, including cell adhesion molecule binding activity; identical protein binding activity; and neurexin family protein binding activity. Involved in several processes, including modulation of chemical synaptic transmission; positive regulation of cellular component organization; and synapse organization. Localizes to several cellular components, including dendrite; filopodium tip; and integral component of postsynaptic specialization membrane. Colocalizes with NMDA selective glutamate receptor complex and postsynaptic density. Biomarker of status epilepticus. Orthologous to human NLGN1 (neuroligin 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; androgen antagonist; atrazine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: neuroligin I; neuroligin-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22108,256,236 - 109,181,530 (-)NCBI
Rnor_6.0 Ensembl2111,057,291 - 111,793,326 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02111,057,291 - 111,973,681 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02130,770,580 - 131,688,440 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42111,189,470 - 111,948,145 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12111,133,661 - 111,893,471 (-)NCBI
Celera2103,515,760 - 104,229,754 (-)NCBICelera
Cytogenetic Map2q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
AMPA glutamate receptor clustering  (IMP,ISO,ISS)
calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules  (IDA,ISO)
cell adhesion  (IEA)
cellular response to calcium ion  (IDA)
chemical synaptic transmission  (IBA)
cytoskeletal matrix organization at active zone  (IMP,ISO)
establishment of protein localization  (ISO,ISS)
excitatory synapse assembly  (ISO)
heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules  (ISO,ISS)
inhibitory postsynaptic potential  (IDA,ISO)
long-term synaptic potentiation  (IMP)
modulation of chemical synaptic transmission  (IBA,IEA,IMP,ISO)
negative regulation of dendritic spine morphogenesis  (ISO,ISS)
nervous system development  (ISO,ISS)
neurexin clustering involved in presynaptic membrane assembly  (ISO,ISS)
neuron cell-cell adhesion  (IBA,IDA,ISO)
neuron projection arborization  (IGI)
neuron projection development  (IGI,ISO)
neuronal ion channel clustering  (TAS)
NMDA glutamate receptor clustering  (IDA)
positive regulation of circadian sleep/wake cycle, wakefulness  (ISO,ISS)
positive regulation of dendritic spine development  (IDA,IMP,ISO)
positive regulation of excitatory postsynaptic potential  (IDA,IMP,ISO)
positive regulation of filopodium assembly  (IDA)
positive regulation of intracellular signal transduction  (IDA)
positive regulation of presynaptic active zone assembly  (IDA)
positive regulation of protein localization to synapse  (IMP)
positive regulation of ruffle assembly  (IDA)
positive regulation of synapse assembly  (IDA,ISO)
positive regulation of synaptic transmission, GABAergic  (IDA)
positive regulation of synaptic transmission, glutamatergic  (IDA,IMP)
positive regulation of synaptic vesicle clustering  (ISO)
positive regulation of synaptic vesicle endocytosis  (IMP,ISO)
positive regulation of synaptic vesicle exocytosis  (IMP,ISO)
postsynaptic density protein 95 clustering  (IDA,IMP,ISO,ISS)
postsynaptic membrane assembly  (IBA,ISO,ISS)
postsynaptic specialization assembly  (ISO)
presynaptic membrane assembly  (IBA,IDA,ISO)
protein localization to synapse  (ISO,ISS)
protein targeting  (IDA)
receptor localization to synapse  (ISO,ISS)
regulation of AMPA receptor activity  (IDA)
regulation of neuron differentiation  (ISO,ISS)
regulation of NMDA receptor activity  (IDA,IMP,ISO)
regulation of presynapse organization  (EXP,IDA,IMP)
regulation of respiratory gaseous exchange by nervous system process  (ISO)
retrograde trans-synaptic signaling by trans-synaptic protein complex  (IMP)
rhythmic process  (IEA)
synapse assembly  (IDA,ISO,ISS)
synapse organization  (IEA,ISO)
synaptic membrane adhesion  (ISO)
synaptic vesicle clustering  (IDA,IMP,ISO,ISS)
synaptic vesicle endocytosis  (IBA)
synaptic vesicle targeting  (ISO,ISS)
synaptic vesicle transport  (IMP)
terminal button organization  (IMP,ISO)

Molecular Function

References

References - curated
1. Arac D, etal., Neuron. 2007 Dec 20;56(6):992-1003.
2. Barrow SL, etal., Neural Dev. 2009 May 18;4:17. doi: 10.1186/1749-8104-4-17.
3. Chih B, etal., Science. 2005 Feb 25;307(5713):1324-8. Epub 2005 Jan 27.
4. Chubykin AA, etal., J Biol Chem. 2005 Jun 10;280(23):22365-74. Epub 2005 Mar 29.
5. Chubykin AA, etal., Neuron. 2007 Jun 21;54(6):919-31.
6. Clarris HJ, etal., Int J Dev Biol 2002;46(4):649-52.
7. Comoletti D, etal., J Biol Chem. 2003 Dec 12;278(50):50497-505. Epub 2003 Sep 30.
8. Dresbach T, etal., Mol Cell Neurosci. 2004 Nov;27(3):227-35.
9. Fang M, etal., Mol Neurobiol. 2016 Jan;53(1):270-84. doi: 10.1007/s12035-014-8999-8. Epub 2014 Nov 27.
10. Fu Z, etal., J Neurophysiol. 2003 Dec;90(6):3950-7. Epub 2003 Aug 20.
11. Futai K, etal., Nat Neurosci. 2007 Feb;10(2):186-95. Epub 2007 Jan 21.
12. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
13. Gjørlund MD, etal., FASEB J. 2012 Oct;26(10):4174-86. doi: 10.1096/fj.11-202242. Epub 2012 Jun 29.
14. Ichtchenko K, etal., Cell 1995 May 5;81(3):435-43.
15. Ichtchenko K, etal., J Biol Chem 1996 Feb 2;271(5):2676-82.
16. Irie M, etal., Science. 1997 Sep 5;277(5331):1511-5.
17. Jackson J, etal., PLoS One. 2012;7(4):e35557. doi: 10.1371/journal.pone.0035557. Epub 2012 Apr 23.
18. Ko J, etal., EMBO J. 2009 Oct 21;28(20):3244-55. doi: 10.1038/emboj.2009.249. Epub 2009 Sep 3.
19. Leone P, etal., EMBO J. 2010 Jul 21;29(14):2461-71. doi: 10.1038/emboj.2010.123. Epub 2010 Jun 11.
20. MGD data from the GO Consortium
21. Mondin M, etal., J Neurosci. 2011 Sep 21;31(38):13500-15. doi: 10.1523/JNEUROSCI.6439-10.2011.
22. NCBI rat LocusLink and RefSeq merged data July 26, 2002
23. Nguyen T and Sudhof TC, J Biol Chem. 1997 Oct 10;272(41):26032-9.
24. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
25. RGD automated import pipeline for gene-chemical interactions
26. Scheiffele P, etal., Cell. 2000 Jun 9;101(6):657-69.
27. Shipman SL and Nicoll RA, Neuron. 2012 Oct 18;76(2):309-16. doi: 10.1016/j.neuron.2012.07.024. Epub 2012 Oct 17.
28. Song JY, etal., Proc Natl Acad Sci U S A. 1999 Feb 2;96(3):1100-5.
29. Stan A, etal., Proc Natl Acad Sci U S A. 2010 Jun 15;107(24):11116-21. doi: 10.1073/pnas.0914233107. Epub 2010 Jun 1.
30. Suckow AT, etal., J Biol Chem. 2012 Jun 8;287(24):19816-26. doi: 10.1074/jbc.M111.280537. Epub 2012 Apr 23.
31. Wittenmayer N, etal., Proc Natl Acad Sci U S A. 2009 Aug 11;106(32):13564-9. doi: 10.1073/pnas.0905819106. Epub 2009 Jul 23.
Additional References at PubMed
PMID:9694864   PMID:11329178   PMID:12202822   PMID:12796785   PMID:14769026   PMID:15458844   PMID:15620359   PMID:16298368   PMID:16982420   PMID:17474715   PMID:18334216   PMID:18579781  
PMID:18755801   PMID:19098102   PMID:19105974   PMID:20176955   PMID:20573900   PMID:20739565   PMID:20869594   PMID:21056983   PMID:21356198   PMID:21532576   PMID:21788371   PMID:21911064  
PMID:22671294   PMID:22840401   PMID:22960622   PMID:23143522   PMID:23269831   PMID:23426688   PMID:23716671   PMID:23791195   PMID:24613359   PMID:24860089   PMID:25157101   PMID:26325471  
PMID:26440732   PMID:26771491   PMID:27423632   PMID:28194405   PMID:28875935   PMID:29592780   PMID:30049666   PMID:30790215   PMID:32915137  


Genomics

Comparative Map Data
Nlgn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22108,256,236 - 109,181,530 (-)NCBI
Rnor_6.0 Ensembl2111,057,291 - 111,793,326 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02111,057,291 - 111,973,681 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02130,770,580 - 131,688,440 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42111,189,470 - 111,948,145 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12111,133,661 - 111,893,471 (-)NCBI
Celera2103,515,760 - 104,229,754 (-)NCBICelera
Cytogenetic Map2q24NCBI
NLGN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3173,396,284 - 174,286,644 (+)EnsemblGRCh38hg38GRCh38
GRCh383173,395,929 - 174,294,372 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh373173,113,742 - 174,012,162 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363174,598,938 - 175,483,810 (+)NCBINCBI36hg18NCBI36
Build 343174,598,945 - 175,483,818NCBI
Celera3171,515,223 - 172,400,529 (+)NCBI
Cytogenetic Map3q26.31NCBI
HuRef3170,489,300 - 171,374,847 (+)NCBIHuRef
CHM1_13173,079,120 - 173,964,074 (+)NCBICHM1_1
Nlgn1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39325,475,972 - 26,387,504 (-)NCBIGRCm39mm39
GRCm39 Ensembl325,480,379 - 26,386,609 (-)Ensembl
GRCm38325,421,808 - 26,332,866 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl325,426,215 - 26,332,460 (-)EnsemblGRCm38mm10GRCm38
MGSCv37325,330,763 - 26,230,831 (-)NCBIGRCm37mm9NCBIm37
MGSCv36325,622,914 - 26,522,982 (-)NCBImm8
Celera325,414,194 - 26,317,921 (-)NCBICelera
Cytogenetic Map3A3NCBI
Nlgn1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554203,549,021 - 4,167,493 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554203,360,745 - 4,171,587 (+)NCBIChiLan1.0ChiLan1.0
NLGN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13178,595,014 - 179,505,810 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3178,810,253 - 179,503,756 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03170,416,885 - 171,333,094 (+)NCBIMhudiblu_PPA_v0panPan3
NLGN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13437,397,772 - 38,203,634 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3437,572,629 - 38,203,177 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3446,409,660 - 47,225,945 (+)NCBI
ROS_Cfam_1.03437,484,369 - 38,313,800 (+)NCBI
UMICH_Zoey_3.13437,576,956 - 38,230,342 (+)NCBI
UNSW_CanFamBas_1.03437,390,518 - 38,201,245 (+)NCBI
UU_Cfam_GSD_1.03437,647,698 - 38,463,980 (+)NCBI
Nlgn1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602104,390,734 - 105,051,988 (+)NCBI
SpeTri2.0NW_004936703951,935 - 1,415,991 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NLGN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13112,036,053 - 112,725,618 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113111,851,007 - 112,727,202 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213120,802,484 - 121,025,494 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NLGN1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11515,129,976 - 16,017,107 (-)NCBI
Vero_WHO_p1.0NW_02366606323,867,631 - 24,767,924 (-)NCBI
Nlgn1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473051,451,546 - 52,300,413 (+)NCBI

Position Markers
D2Rat335  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22109,002,666 - 109,002,905 (+)MAPPER
Rnor_6.02111,793,698 - 111,793,936NCBIRnor6.0
Rnor_5.02131,507,359 - 131,507,597UniSTSRnor5.0
RGSC_v3.42111,948,880 - 111,949,118RGDRGSC3.4
RGSC_v3.42111,948,881 - 111,949,119UniSTSRGSC3.4
RGSC_v3.12111,893,842 - 111,894,080RGD
Celera2104,230,490 - 104,230,717UniSTS
SHRSP x BN Map238.8198RGD
SHRSP x BN Map238.8198UniSTS
Cytogenetic Map2q24UniSTS
BF394648  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22108,497,744 - 108,497,968 (+)MAPPER
Rnor_6.02111,293,266 - 111,293,489NCBIRnor6.0
Rnor_5.02131,006,639 - 131,006,862UniSTSRnor5.0
RGSC_v3.42111,433,889 - 111,434,112UniSTSRGSC3.4
Celera2103,744,650 - 103,744,873UniSTS
RH 3.4 Map2725.8UniSTS
Cytogenetic Map2q24UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)216679272245624402Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)223837491149614623Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)223837491169852800Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)223837491169852800Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491169852800Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491169852800Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)223837491169852800Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)223837491169852800Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491218957222Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491218957222Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)223837719169852670Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)223837719169852670Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226186097135654963Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226186097142053534Rat
12879841Cm87Cardiac mass QTL 870.026heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)227161361148295267Rat
12879842Cm88Cardiac mass QTL 880.042heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)227161361148295267Rat
12879843Am3Aortic mass QTL 30.016aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)227161361148295267Rat
12879844Kidm62Kidney mass QTL 620.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)227161361148295267Rat
2306903Bp336Blood pressure QTL 3360.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)236245223112175725Rat
2293835Kiddil5Kidney dilation QTL 53.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242776916169852800Rat
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242776916195645082Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242776916217498710Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242776916217498710Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243133606217498545Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243133606217498545Rat
2293676Bmd19Bone mineral density QTL 1910.70.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)243141290114164944Rat
2293682Bmd24Bone mineral density QTL 248.90.0001femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)243141290114164944Rat
2293671Bss44Bone structure and strength QTL 4410.970.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)243141290154583160Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243149788198704485Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246537589217498710Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256244671217498710Rat
1558648Smcn1Smooth muscle cell number QTL 10.039blood vessel smooth muscle cell quantity (VT:0010525)aorta smooth muscle cell count per unit vessel length (CMO:0001646)260131410135646395Rat
61438Cia7Collagen induced arthritis QTL 74.60.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)260325352147522851Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266828049217498710Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266828236243550655Rat
1358900Bw48Body weight QTL 484.88body mass (VT:0001259)body weight (CMO:0000012)268865414169852800Rat
1581578Cm49Cardiac mass QTL 494.90.01heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)268866454149614466Rat
7411551Bw131Body weight QTL 13129.60.001body mass (VT:0001259)body weight gain (CMO:0000420)270132175115132175Rat
2317041Aia14Adjuvant induced arthritis QTL 143.29joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)271495404116495404Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)275687495221880419Rat
631198Cm22Cardiac mass QTL 224.30.0008heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)278321410158159410Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)278321410217498710Rat
2299162Iddm32Insulin dependent diabetes mellitus QTL 322.36blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)280631950149614623Rat
61392Bp6Blood pressure QTL 67arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)282574487127574487Rat
1598865Bp296Blood pressure QTL 2962.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)283656855128656855Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)283754907237610852Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)283819608239166203Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)283819608243901375Rat
1578772Stresp14Stress response QTL 1450.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)284424139132130578Rat
2300165Bmd49Bone mineral density QTL 494.80.0001lumbar vertebra mineral mass (VT:0010511)bone mineral density (CMO:0001226)291664872136664872Rat
2300170Bmd45Bone mineral density QTL 4512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)291664872136664872Rat
2300185Bmd46Bone mineral density QTL 468.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)291664872136664872Rat
7207808Bmd89Bone mineral density QTL 894.1femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)291664872136664872Rat
1558653Prcr1Prostate cancer resistance QTL 15prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)293995316169852800Rat
1598862Glom9Glomerulus QTL 93.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)295946719140946719Rat
1598863Cm65Cardiac mass QTL 652.3heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)295946719140946719Rat
2317886Alcrsp23Alcohol response QTL 232.40.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)296844330141844330Rat
9589093Slep10Serum leptin concentration QTL 103.840.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)2102356980147356980Rat
631566Bp90Blood pressure QTL 900.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2108880910153880910Rat
8662836Vetf8Vascular elastic tissue fragility QTL 80.66thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2110965721155965721Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:38
Count of miRNA genes:16
Interacting mature miRNAs:19
Transcripts:ENSRNOT00000041111, ENSRNOT00000043276
Prediction methods: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 64
Low 12 4 8 4 10 30 2
Below cutoff 3 16 13 5 1 5 4 4 23 7 7 4

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_053868 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760890 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590583 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590584 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590585 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590586 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590587 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590588 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590589 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590590 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101567 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101568 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101569 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101570 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101571 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101572 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101573 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101574 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101575 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101576 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101577 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101578 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473961 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000067 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U22952 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000041111   ⟹   ENSRNOP00000040172
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2111,059,105 - 111,065,413 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092660   ⟹   ENSRNOP00000075793
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2111,057,291 - 111,793,326 (-)Ensembl
RefSeq Acc Id: NM_053868   ⟹   NP_446320
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22108,257,824 - 109,001,931 (-)NCBI
Rnor_6.02111,058,792 - 111,792,962 (-)NCBI
Rnor_5.02130,770,580 - 131,688,440 (-)NCBI
RGSC_v3.42111,189,470 - 111,948,145 (-)RGD
Celera2103,515,760 - 104,229,754 (-)RGD
Sequence:
RefSeq Acc Id: XM_008760890   ⟹   XP_008759112
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02111,057,291 - 111,544,655 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017590583   ⟹   XP_017446072
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22108,256,236 - 109,002,510 (-)NCBI
Rnor_6.02111,057,291 - 111,793,762 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017590584   ⟹   XP_017446073
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02111,057,291 - 111,973,195 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017590585   ⟹   XP_017446074
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02111,057,291 - 111,970,819 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017590586   ⟹   XP_017446075
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02111,057,291 - 111,973,681 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017590587   ⟹   XP_017446076
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02111,057,291 - 111,793,762 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017590588   ⟹   XP_017446077
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02111,057,291 - 111,774,007 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017590589   ⟹   XP_017446078
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02111,057,291 - 111,970,819 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017590590   ⟹   XP_017446079
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22108,256,236 - 109,002,512 (-)NCBI
Rnor_6.02111,057,291 - 111,793,762 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039101567   ⟹   XP_038957495
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22108,256,236 - 109,002,513 (-)NCBI
RefSeq Acc Id: XM_039101568   ⟹   XP_038957496
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22108,256,236 - 109,180,818 (-)NCBI
RefSeq Acc Id: XM_039101569   ⟹   XP_038957497
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22108,256,236 - 109,181,530 (-)NCBI
RefSeq Acc Id: XM_039101570   ⟹   XP_038957498
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22108,256,236 - 109,180,818 (-)NCBI
RefSeq Acc Id: XM_039101571   ⟹   XP_038957499
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22108,256,236 - 109,180,818 (-)NCBI
RefSeq Acc Id: XM_039101572   ⟹   XP_038957500
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22108,256,236 - 109,181,530 (-)NCBI
RefSeq Acc Id: XM_039101573   ⟹   XP_038957501
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22108,256,236 - 109,181,530 (-)NCBI
RefSeq Acc Id: XM_039101574   ⟹   XP_038957502
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22108,256,236 - 109,002,513 (-)NCBI
RefSeq Acc Id: XM_039101575   ⟹   XP_038957503
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22108,256,236 - 108,982,692 (-)NCBI
RefSeq Acc Id: XM_039101576   ⟹   XP_038957504
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22108,256,236 - 109,002,517 (-)NCBI
RefSeq Acc Id: XM_039101577   ⟹   XP_038957505
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22108,256,236 - 109,002,512 (-)NCBI
RefSeq Acc Id: XM_039101578   ⟹   XP_038957506
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22108,256,236 - 109,002,515 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_446320   ⟸   NM_053868
- Peptide Label: precursor
- UniProtKB: Q62765 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008759112   ⟸   XM_008760890
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017446075   ⟸   XM_017590586
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017446073   ⟸   XM_017590584
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017446078   ⟸   XM_017590589
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017446074   ⟸   XM_017590585
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017446076   ⟸   XM_017590587
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017446079   ⟸   XM_017590590
- Peptide Label: isoform X6
- UniProtKB: Q62765 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017446072   ⟸   XM_017590583
- Peptide Label: isoform X5
- UniProtKB: Q62765 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017446077   ⟸   XM_017590588
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000040172   ⟸   ENSRNOT00000041111
RefSeq Acc Id: ENSRNOP00000075793   ⟸   ENSRNOT00000092660
RefSeq Acc Id: XP_038957500   ⟸   XM_039101572
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038957501   ⟸   XM_039101573
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038957497   ⟸   XM_039101569
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038957498   ⟸   XM_039101570
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038957499   ⟸   XM_039101571
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038957496   ⟸   XM_039101568
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038957504   ⟸   XM_039101576
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038957506   ⟸   XM_039101578
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038957502   ⟸   XM_039101574
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038957495   ⟸   XM_039101567
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038957505   ⟸   XM_039101577
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038957503   ⟸   XM_039101575
- Peptide Label: isoform X1
Protein Domains
COesterase

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (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)
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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)
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)
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 (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
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
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
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
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
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 (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
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)
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
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 (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 (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)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621117 AgrOrtholog
Ensembl Genes ENSRNOG00000032576 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000040172 UniProtKB/TrEMBL
  ENSRNOP00000075793 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000041111 UniProtKB/TrEMBL
  ENSRNOT00000092660 ENTREZGENE, UniProtKB/Swiss-Prot
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
  Nlgn UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NLGN1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:116647 UniProtKB/Swiss-Prot
NCBI Gene 116647 ENTREZGENE
PANTHER PTHR43903:SF2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam COesterase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nlgn1 PhenoGen
PRINTS NEUROLIGIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CARBOXYLESTERASE_B_2 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF53474 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0H2UHW8_RAT UniProtKB/TrEMBL
  NLGN1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-26 Nlgn1  neuroligin 1      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Nlgn1  neuroligin 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed by second order mitral cells during early postnatal development in the olfactory bulb 727397