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: Enables 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. Acts upstream of or within synapse organization. Located in several cellular components, including Golgi apparatus; dendrite; and filopodium tip. Is active in glutamatergic synapse and postsynaptic specialization membrane. 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
Previously 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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22108,256,236 - 109,181,530 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2108,257,824 - 109,002,464 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2114,911,902 - 115,636,061 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02113,024,456 - 113,748,622 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02107,789,905 - 108,510,927 (-)NCBIRnor_WKY
Rnor_6.02111,057,291 - 111,973,681 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2111,057,291 - 111,793,326 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02130,770,580 - 131,688,440 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42111,189,470 - 111,948,145 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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  (IEA,IMP,ISO,ISS)
calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules  (IDA,IEA,ISO,NAS)
cell adhesion  (IEA)
cell-cell adhesion involved in synapse maturation  (NAS)
cellular response to calcium ion  (IDA)
chemical synaptic transmission  (IBA)
cytoskeletal matrix organization at active zone  (IEA,IMP,ISO)
establishment of protein localization  (IEA,ISO,ISS)
excitatory synapse assembly  (IEA,ISO)
heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules  (IEA,ISO,ISS)
inhibitory postsynaptic potential  (IDA,ISO)
long-term synaptic potentiation  (IMP)
maintenance of synapse structure  (NAS)
membrane assembly  (IEA)
modulation of chemical synaptic transmission  (IBA,IMP,ISO)
negative regulation of dendritic spine morphogenesis  (IEA,ISO,ISS)
nervous system development  (ISO,ISS)
neurexin clustering involved in presynaptic membrane assembly  (IEA,ISO,ISS)
neuron cell-cell adhesion  (IBA,IDA,IEA,ISO,NAS)
neuron projection arborization  (IGI)
neuron projection development  (IGI,ISO)
neuron projection morphogenesis  (NAS)
neuronal ion channel clustering  (TAS)
NMDA glutamate receptor clustering  (IDA)
positive regulation of circadian sleep/wake cycle, wakefulness  (IEA,ISO,ISS)
positive regulation of dendritic spine development  (IDA,IEA,IMP,ISO)
positive regulation of excitatory postsynaptic potential  (IDA,IEA,IMP,ISO)
positive regulation of filopodium assembly  (IDA)
positive regulation of intracellular signal transduction  (IDA)
positive regulation of multicellular organismal process  (IEA)
positive regulation of neuromuscular synaptic transmission  (NAS)
positive regulation of neuron projection development  (NAS)
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,IEA,ISO)
positive regulation of synaptic transmission, GABAergic  (IDA,NAS)
positive regulation of synaptic transmission, glutamatergic  (IDA,IMP,NAS)
positive regulation of synaptic vesicle clustering  (IEA,ISO)
positive regulation of synaptic vesicle endocytosis  (IEA,IMP,ISO)
positive regulation of synaptic vesicle exocytosis  (IEA,IMP,ISO)
postsynaptic density protein 95 clustering  (IDA,IEA,IMP,ISO,ISS)
postsynaptic membrane assembly  (IBA,IEA,ISO,ISS)
postsynaptic specialization assembly  (IEA,ISO)
presynaptic membrane assembly  (IBA,IDA,ISO)
protein localization to synapse  (IEA,ISO,ISS)
protein targeting  (IDA)
receptor localization to synapse  (IEA,ISO,ISS)
regulation of AMPA receptor activity  (IDA)
regulation of localization  (IEA)
regulation of membrane potential  (IEA)
regulation of nervous system process  (IEA)
regulation of neuron differentiation  (IEA,ISO,ISS)
regulation of NMDA receptor activity  (IDA,IEA,IMP,ISO)
regulation of presynapse organization  (EXP,IDA,IMP)
regulation of respiratory gaseous exchange by nervous system process  (IEA,ISO)
retrograde trans-synaptic signaling by trans-synaptic protein complex  (IMP)
rhythmic process  (IEA)
synapse assembly  (IDA,ISO,ISS,NAS)
synapse maturation  (NAS)
synapse organization  (IDA,ISO)
synaptic membrane adhesion  (IEA,ISO)
synaptic vesicle clustering  (IDA,IEA,IMP,ISO,ISS)
synaptic vesicle endocytosis  (IBA)
synaptic vesicle targeting  (IEA,ISO,ISS)
synaptic vesicle transport  (IMP)
terminal button organization  (IEA,IMP,ISO)

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Structures of neuroligin-1 and the neuroligin-1/neurexin-1 beta complex reveal specific protein-protein and protein-Ca2+ interactions. Arac D, etal., Neuron. 2007 Dec 20;56(6):992-1003.
2. Neuroligin1: a cell adhesion molecule that recruits PSD-95 and NMDA receptors by distinct mechanisms during synaptogenesis. Barrow SL, etal., Neural Dev. 2009 May 18;4:17. doi: 10.1186/1749-8104-4-17.
3. A splice code for trans-synaptic cell adhesion mediated by binding of neuroligin 1 to alpha- and beta-neurexins. Boucard AA, etal., Neuron. 2005 Oct 20;48(2):229-36. doi: 10.1016/j.neuron.2005.08.026.
4. Structural basis for synaptic adhesion mediated by neuroligin-neurexin interactions. Chen X, etal., Nat Struct Mol Biol. 2008 Jan;15(1):50-6. Epub 2007 Dec 16.
5. Alternative splicing controls selective trans-synaptic interactions of the neuroligin-neurexin complex. Chih B, etal., Neuron. 2006 Jul 20;51(2):171-8. doi: 10.1016/j.neuron.2006.06.005.
6. Control of excitatory and inhibitory synapse formation by neuroligins. Chih B, etal., Science. 2005 Feb 25;307(5713):1324-8. Epub 2005 Jan 27.
7. Dissection of synapse induction by neuroligins: effect of a neuroligin mutation associated with autism. Chubykin AA, etal., J Biol Chem. 2005 Jun 10;280(23):22365-74. Epub 2005 Mar 29.
8. Activity-dependent validation of excitatory versus inhibitory synapses by neuroligin-1 versus neuroligin-2. Chubykin AA, etal., Neuron. 2007 Jun 21;54(6):919-31.
9. Expression of neurexin ligands, the neuroligins and the neurexophilins, in the developing and adult rodent olfactory bulb. Clarris HJ, etal., Int J Dev Biol 2002;46(4):649-52.
10. Characterization of the interaction of a recombinant soluble neuroligin-1 with neurexin-1beta. Comoletti D, etal., J Biol Chem. 2003 Dec 12;278(50):50497-505. Epub 2003 Sep 30.
11. Neurexin and Neuroligin-based adhesion complexes drive axonal arborisation growth independent of synaptic activity. Constance WD, etal., Elife. 2018 Mar 5;7. pii: 31659. doi: 10.7554/eLife.31659.
12. Synaptic targeting of neuroligin is independent of neurexin and SAP90/PSD95 binding. Dresbach T, etal., Mol Cell Neurosci. 2004 Nov;27(3):227-35.
13. Neuroligin-1 Knockdown Suppresses Seizure Activity by Regulating Neuronal Hyperexcitability. Fang M, etal., Mol Neurobiol. 2016 Jan;53(1):270-84. doi: 10.1007/s12035-014-8999-8. Epub 2014 Nov 27.
14. Functional excitatory synapses in HEK293 cells expressing neuroligin and glutamate receptors. Fu Z, etal., J Neurophysiol. 2003 Dec;90(6):3950-7. Epub 2003 Aug 20.
15. Retrograde modulation of presynaptic release probability through signaling mediated by PSD-95-neuroligin. Futai K, etal., Nat Neurosci. 2007 Feb;10(2):186-95. Epub 2007 Jan 21.
16. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
17. Neuroligin-1 induces neurite outgrowth through interaction with neurexin-1ß and activation of fibroblast growth factor receptor-1. Gjørlund MD, etal., FASEB J. 2012 Oct;26(10):4174-86. doi: 10.1096/fj.11-202242. Epub 2012 Jun 29.
18. Neuroligin 1: a splice site-specific ligand for beta-neurexins. Ichtchenko K, etal., Cell 1995 May 5;81(3):435-43.
19. Structures, alternative splicing, and neurexin binding of multiple neuroligins. Ichtchenko K, etal., J Biol Chem 1996 Feb 2;271(5):2676-82.
20. Binding of neuroligins to PSD-95. Irie M, etal., Science. 1997 Sep 5;277(5331):1511-5.
21. Altered synaptic properties during integration of adult-born hippocampal neurons following a seizure insult. Jackson J, etal., PLoS One. 2012;7(4):e35557. doi: 10.1371/journal.pone.0035557. Epub 2012 Apr 23.
22. Neuroligin-1 performs neurexin-dependent and neurexin-independent functions in synapse validation. Ko J, etal., EMBO J. 2009 Oct 21;28(20):3244-55. doi: 10.1038/emboj.2009.249. Epub 2009 Sep 3.
23. Structural insights into the exquisite selectivity of neurexin/neuroligin synaptic interactions. Leone P, etal., EMBO J. 2010 Jul 21;29(14):2461-71. doi: 10.1038/emboj.2010.123. Epub 2010 Jun 11.
24. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
25. Neurexin-neuroligin adhesions capture surface-diffusing AMPA receptors through PSD-95 scaffolds. Mondin M, etal., J Neurosci. 2011 Sep 21;31(38):13500-15. doi: 10.1523/JNEUROSCI.6439-10.2011.
26. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
27. Binding properties of neuroligin 1 and neurexin 1beta reveal function as heterophilic cell adhesion molecules. Nguyen T and Sudhof TC, J Biol Chem. 1997 Oct 10;272(41):26032-9.
28. Synaptic Kalirin-7 and Trio Interactomes Reveal a GEF Protein-Dependent Neuroligin-1 Mechanism of Action. Paskus JD, etal., Cell Rep. 2019 Dec 3;29(10):2944-2952.e5. doi: 10.1016/j.celrep.2019.10.115.
29. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
30. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
31. Neuroligin expressed in nonneuronal cells triggers presynaptic development in contacting axons. Scheiffele P, etal., Cell. 2000 Jun 9;101(6):657-69.
32. A subtype-specific function for the extracellular domain of neuroligin 1 in hippocampal LTP. 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.
33. Neuroligin 1 is a postsynaptic cell-adhesion molecule of excitatory synapses. Song JY, etal., Proc Natl Acad Sci U S A. 1999 Feb 2;96(3):1100-5.
34. Essential cooperation of N-cadherin and neuroligin-1 in the transsynaptic control of vesicle accumulation. 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.
35. Transcellular neuroligin-2 interactions enhance insulin secretion and are integral to pancreatic beta cell function. Suckow AT, etal., J Biol Chem. 2012 Jun 8;287(24):19816-26. doi: 10.1074/jbc.M111.280537. Epub 2012 Apr 23.
36. Abundance and Significance of Neuroligin-1 and Neurexin II in the Enteric Nervous System of Embryonic Rats. Wang D, etal., Biomed Res Int. 2017;2017:1209360. doi: 10.1155/2017/1209360. Epub 2017 Jan 18.
37. Postsynaptic Neuroligin1 regulates presynaptic maturation. 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:28875935   PMID:29592780   PMID:30049666   PMID:30790215   PMID:32915137   PMID:34353896  


Genomics

Comparative Map Data
Nlgn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22108,256,236 - 109,181,530 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2108,257,824 - 109,002,464 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2114,911,902 - 115,636,061 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02113,024,456 - 113,748,622 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02107,789,905 - 108,510,927 (-)NCBIRnor_WKY
Rnor_6.02111,057,291 - 111,973,681 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2111,057,291 - 111,793,326 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02130,770,580 - 131,688,440 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42111,189,470 - 111,948,145 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh383173,395,952 - 174,294,372 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl3173,396,284 - 174,294,372 (+)EnsemblGRCh38hg38GRCh38
GRCh373173,113,742 - 174,012,162 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363174,598,938 - 175,483,810 (+)NCBINCBI36Build 36hg18NCBI36
Build 343174,598,945 - 175,483,818NCBI
Celera3171,515,223 - 172,400,529 (+)NCBICelera
Cytogenetic Map3q26.31NCBI
HuRef3170,489,300 - 171,374,847 (+)NCBIHuRef
CHM1_13173,079,120 - 173,964,074 (+)NCBICHM1_1
T2T-CHM13v2.03176,181,719 - 177,081,314 (+)NCBIT2T-CHM13v2.0
Nlgn1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39325,475,972 - 26,387,504 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl325,480,379 - 26,386,609 (-)EnsemblGRCm39 Ensembl
GRCm38325,421,808 - 26,332,866 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl325,426,215 - 26,332,460 (-)EnsemblGRCm38mm10GRCm38
MGSCv37325,330,763 - 26,230,831 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36325,622,914 - 26,522,982 (-)NCBIMGSCv36mm8
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
NHGRI_mPanPan13171,252,234 - 172,164,121 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03170,416,885 - 171,333,094 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13178,595,014 - 179,505,810 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3178,810,253 - 179,503,756 (+)Ensemblpanpan1.1panPan2
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 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03437,484,369 - 38,313,800 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3437,659,077 - 38,308,775 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13437,576,956 - 38,230,342 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03437,390,518 - 38,201,245 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03437,647,698 - 38,463,980 (+)NCBIUU_Cfam_GSD_1.0
Nlgn1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602104,390,734 - 105,051,988 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936703758,647 - 1,414,185 (+)EnsemblSpeTri2.0
SpeTri2.0NW_004936703951,935 - 1,415,991 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NLGN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13112,035,854 - 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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11515,129,976 - 16,017,107 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606323,867,631 - 24,767,924 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nlgn1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473051,650,815 - 52,295,023 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473051,451,546 - 52,300,413 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nlgn1
5199 total Variants
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)225413423143657569Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226917817127469484Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226917817136917119Rat
2293835Kiddil5Kidney dilation QTL 53.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607157142209Rat
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607182042367Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243154682202446871Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
2293676Bmd19Bone mineral density QTL 1910.70.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)243162366111362592Rat
2293682Bmd24Bone mineral density QTL 248.90.0001femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)243162366111362592Rat
2293671Bss44Bone structure and strength QTL 4410.970.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)243162366148478373Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243171017184114403Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256043031202447032Rat
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)259134147127460910Rat
61438Cia7Collagen induced arthritis QTL 74.60.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)259324377141596857Rat
2306903Bp336Blood pressure QTL 3360.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)264366971109366971Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118275202447032Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
7411551Bw131Body weight QTL 13129.60.001body mass (VT:0001259)body weight gain (CMO:0000420)267942638112942638Rat
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)272532993157142209Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)274786664206665859Rat
631198Cm22Cardiac mass QTL 224.30.0008heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)276539322150540526Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)276539322202447032Rat
2299162Iddm32Insulin dependent diabetes mellitus QTL 322.36blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)278665616143657569Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
61392Bp6Blood pressure QTL 67arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)280270434125270434Rat
1598865Bp296Blood pressure QTL 2962.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)281018907126018907Rat
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)281689826221035911Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
1578772Stresp14Stress response QTL 1450.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)282345893130923501Rat
7207808Bmd89Bone mineral density QTL 894.1femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)288862519133862519Rat
2300165Bmd49Bone mineral density QTL 494.80.0001lumbar vertebra mineral mass (VT:0010511)bone mineral density (CMO:0001226)288862519133862519Rat
2300170Bmd45Bone mineral density QTL 4512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)288862519133862519Rat
2300185Bmd46Bone mineral density QTL 468.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)288862519133862519Rat
1598862Glom9Glomerulus QTL 93.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)292337601137337601Rat
1598863Cm65Cardiac mass QTL 652.3heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)292337601137337601Rat
631566Bp90Blood pressure QTL 900.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2102803808147803808Rat
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)2104559726149559726Rat

Markers in Region
D2Rat335  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22109,002,666 - 109,002,905 (+)MAPPERmRatBN7.2
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 (+)MAPPERmRatBN7.2
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


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
mRatBN7.2 Ensembl2108,257,824 - 108,981,046 (-)Ensembl
Rnor_6.0 Ensembl2111,059,105 - 111,065,413 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092660   ⟹   ENSRNOP00000075793
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2108,257,824 - 109,002,464 (-)Ensembl
Rnor_6.0 Ensembl2111,057,291 - 111,793,326 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107850   ⟹   ENSRNOP00000094652
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2108,257,824 - 109,002,464 (-)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_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_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_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: 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
- UniProtKB: A0A8I6GKV2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038957503   ⟸   XM_039101575
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000094652   ⟸   ENSRNOT00000107850
Protein Domains
Carboxylesterase type B

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q62765-F1-model_v2 AlphaFold Q62765 1-843 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621117 AgrOrtholog
BioCyc Gene G2FUF-53532 BioCyc
Ensembl Genes ENSRNOG00000032576 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000040172 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000040172.3 UniProtKB/Swiss-Prot
  ENSRNOP00000075793 ENTREZGENE
  ENSRNOP00000075793.2 UniProtKB/Swiss-Prot
  ENSRNOP00000094652 ENTREZGENE
  ENSRNOP00000094652.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041111 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000041111.3 UniProtKB/Swiss-Prot
  ENSRNOT00000092660 ENTREZGENE
  ENSRNOT00000092660.2 UniProtKB/Swiss-Prot
  ENSRNOT00000107850 ENTREZGENE
  ENSRNOT00000107850.1 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
KEGG Report rno:116647 UniProtKB/Swiss-Prot
NCBI Gene 116647 ENTREZGENE
PANTHER NEUROLIGIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  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, UniProtKB/TrEMBL
Superfamily-SCOP SSF53474 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0H2UHW8_RAT UniProtKB/TrEMBL
  A0A8I6GKV2 ENTREZGENE, 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