Lgi1 (leucine-rich repeat LGI family, member 1) - Rat Genome Database

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Gene: Lgi1 (leucine-rich repeat LGI family, member 1) Mus musculus
Analyze
Symbol: Lgi1
Name: leucine-rich repeat LGI family, member 1
RGD ID: 733104
MGI Page MGI
Description: Involved in neurotransmitter receptor localization to postsynaptic specialization membrane. Located in extracellular space. Is active in glutamatergic synapse and synaptic cleft. Is expressed in several structures, including central nervous system; diaphragm; sensory organ; and skeletal musculature. Used to study familial temporal lobe epilepsy 1. Human ortholog(s) of this gene implicated in familial temporal lobe epilepsy 1. Orthologous to human LGI1 (leucine rich glioma inactivated 1).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: BB130740; leucine-rich glioma-inactivated protein 1; leucine-rich, glioma inactivated 1
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Gm3888  
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391938,253,135 - 38,297,387 (+)NCBIGRCm39mm39
GRCm39 Ensembl1938,252,984 - 38,300,662 (+)Ensembl
GRCm381938,264,687 - 38,308,939 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1938,264,536 - 38,312,214 (+)EnsemblGRCm38mm10GRCm38
MGSCv371938,339,272 - 38,383,429 (+)NCBIGRCm37mm9NCBIm37
MGSCv361938,329,926 - 38,374,083 (+)NCBImm8
Celera1939,059,488 - 39,103,642 (+)NCBICelera
Cytogenetic Map19C3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12477932   PMID:15489334   PMID:15857855   PMID:16141072   PMID:16141073   PMID:16341215   PMID:16602821  
PMID:16787412   PMID:18563303   PMID:18974846   PMID:19701204   PMID:19833108   PMID:20130004   PMID:20133599   PMID:20659958   PMID:20857514   PMID:21267068   PMID:21569517   PMID:21873635  
PMID:21966449   PMID:22262888   PMID:22612501   PMID:22794259   PMID:23375831   PMID:24227725   PMID:24427155   PMID:25234641   PMID:25346110   PMID:25471260   PMID:25485908   PMID:25707359  
PMID:26025364   PMID:26178195   PMID:26878798   PMID:27507650   PMID:28671696   PMID:28673977   PMID:29491011   PMID:30225353   PMID:30489685   PMID:30562941   PMID:31276752   PMID:32325033  
PMID:33104247   PMID:33397806   PMID:35167164  


Genomics

Comparative Map Data
Lgi1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391938,253,135 - 38,297,387 (+)NCBIGRCm39mm39
GRCm39 Ensembl1938,252,984 - 38,300,662 (+)Ensembl
GRCm381938,264,687 - 38,308,939 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1938,264,536 - 38,312,214 (+)EnsemblGRCm38mm10GRCm38
MGSCv371938,339,272 - 38,383,429 (+)NCBIGRCm37mm9NCBIm37
MGSCv361938,329,926 - 38,374,083 (+)NCBImm8
Celera1939,059,488 - 39,103,642 (+)NCBICelera
Cytogenetic Map19C3NCBI
LGI1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381093,757,936 - 93,798,159 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1093,757,840 - 93,806,272 (+)EnsemblGRCh38hg38GRCh38
GRCh371095,517,693 - 95,557,916 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361095,507,668 - 95,547,906 (+)NCBINCBI36hg18NCBI36
Build 341095,507,667 - 95,547,906NCBI
Celera1089,258,689 - 89,298,048 (+)NCBI
Cytogenetic Map10q23.33NCBI
HuRef1089,145,309 - 89,184,670 (+)NCBIHuRef
CHM1_11095,800,134 - 95,839,500 (+)NCBICHM1_1
Lgi1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21236,043,376 - 236,084,270 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1236,042,954 - 236,084,616 (+)Ensembl
Rnor_6.01256,955,944 - 256,996,835 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1256,955,652 - 256,999,253 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01264,436,441 - 264,477,332 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41242,593,236 - 242,634,141 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11242,809,453 - 242,810,274 (+)NCBI
Celera1233,136,652 - 233,177,516 (+)NCBICelera
Cytogenetic Map1q53NCBI
Lgi1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955507267,892 - 305,026 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955507268,032 - 304,949 (+)NCBIChiLan1.0ChiLan1.0
LGI1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11094,016,703 - 94,056,820 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1094,016,703 - 94,056,820 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01090,506,131 - 90,546,582 (+)NCBIMhudiblu_PPA_v0panPan3
LGI1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1287,966,485 - 8,005,995 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl287,966,593 - 8,012,313 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha288,142,279 - 8,181,152 (+)NCBI
ROS_Cfam_1.0288,226,366 - 8,265,262 (+)NCBI
ROS_Cfam_1.0 Ensembl288,225,835 - 8,272,347 (+)Ensembl
UMICH_Zoey_3.1287,945,864 - 7,984,726 (+)NCBI
UNSW_CanFamBas_1.0287,975,424 - 8,014,295 (+)NCBI
UU_Cfam_GSD_1.0288,145,234 - 8,184,124 (+)NCBI
Lgi1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721339,607,174 - 39,643,265 (-)NCBI
SpeTri2.0NW_0049366011,242,022 - 1,275,842 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LGI1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl14105,219,544 - 105,256,648 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.114105,219,901 - 105,251,423 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214114,951,215 - 114,982,754 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LGI1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1986,993,964 - 87,033,725 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl986,994,307 - 87,035,807 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604847,769,144 - 47,809,266 (+)NCBIVero_WHO_p1.0
Lgi1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247375,024,691 - 5,060,248 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
BB130740  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381938,308,816 - 38,308,911UniSTSGRCm38
MGSCv371938,383,306 - 38,383,401UniSTSGRCm37
Celera1939,103,519 - 39,103,614UniSTS
Cytogenetic Map19C3UniSTS
Whitehead/MRC_RH19360.62UniSTS
Lgi1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map19C3UniSTS
cM Map1932.9UniSTS


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1301639Stnn_mstriatal neuron number (mouse)Not determined193395195261420004Mouse
1301741Lith2_mlithogenic gene 2 (mouse)Not determined193299215861420004Mouse
1301451Ath16_matherosclerosis 16 (mouse)Not determined192542691759427005Mouse
1301479Sluc1_msusceptibility to lung cancer 1 (mouse)Not determined193601694446761521Mouse
1301942Pas13_mpulmonary adenoma susceptibility 13 (mouse)Not determined193014123161420004Mouse
1302004Lfp2_mlong free running period 2 (mouse)Not determined191829516252295381Mouse
1302170Tanidd1_mtally ho associated non-insulin dependednt diabetes mellitus 1 (mouse)Not determined193675259761420004Mouse
1302019Pgia23_mproteoglycan induced arthritis 23 (mouse)Not determined19978745343787602Mouse
1302063Eae19_mexperimental allergic encephalomyelitis 19 (mouse)Not determined191829516252295381Mouse
4141019Tgq29_mtriglyceride QTL 29 (mouse)Not determined3459678661420004Mouse
1300856Nobq2_mNew Zealand obese QTL 2 (mouse)Not determined193089788061420004Mouse
1302123Tlsr8_mthymic lymphoma suppressor region 8 (mouse)Not determined192513600242388916Mouse
1300683Fembm7_mfemoral bone morphometry 7 (mouse)Not determined193014122461420004Mouse
1301410Cd8mts6_mCD8 memory T cell subset 6 (mouse)Not determined193014123161420004Mouse
1301336Alcp23_malcohol preference locus 23 (mouse)Not determined191591260749912719Mouse
1301228Iba4_minduction of brown adipocytes 4 (mouse)Not determined19930571543305821Mouse
4141138Femwf11_mfemur work to failure 11 (mouse)Not determined2814034861420004Mouse
1301633Alcp24_malcohol preference locus 24 (mouse)Not determined191591260749912719Mouse
1558876W3q14_mweight 3 weeks QTL 14 (mouse)Not determined192231332653911504Mouse
4141650Chldq9_mcholesterol and HDL QTL 9 (mouse)Not determined193788298261420004Mouse
4141659Pbwg20_mpostnatal body weight growth 20 (mouse)Not determined192137870555378928Mouse
4142343Moen2_mmodifier of engrailed QTL 2 (mouse)Not determined192023431454234461Mouse
10412251Mnp_mmodifier of Niemann Pick type C1 (mouse)Not determined192023431454234461Mouse
13506250Renmq1_mrenal mercury accumulation QTL 1 (mouse)192738559461385705Mouse
14928311Manh85_mmandible shape 85 (mouse)191191478945914789Mouse
12790634Ebm1_mEpidermolysis Bullosa modifier 1 (mouse)192498843958988439Mouse
13504736Ifvrq6_minfluenza virus resistance QTL 6 (mouse)193690291044913949Mouse
11039522Tbbr4_mTrypanosoma brucei brucei response 4 (mouse)19531332639313470Mouse
10413881Moe2_mmodifier of epilepsy 2 (mouse)191492301648923138Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:903
Count of miRNA genes:532
Interacting mature miRNAs:661
Transcripts:ENSMUST00000087252, ENSMUST00000130039, ENSMUST00000134832
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


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000087252   ⟹   ENSMUSP00000084507
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1938,253,015 - 38,297,386 (+)Ensembl
GRCm38.p6 Ensembl1938,264,567 - 38,308,938 (+)Ensembl
RefSeq Acc Id: ENSMUST00000130039
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1938,253,858 - 38,289,717 (+)Ensembl
GRCm38.p6 Ensembl1938,265,410 - 38,301,269 (+)Ensembl
RefSeq Acc Id: ENSMUST00000134832
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1938,253,261 - 38,257,494 (+)Ensembl
GRCm38.p6 Ensembl1938,264,813 - 38,269,046 (+)Ensembl
RefSeq Acc Id: ENSMUST00000196090   ⟹   ENSMUSP00000143538
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1938,253,119 - 38,294,950 (+)Ensembl
GRCm38.p6 Ensembl1938,264,671 - 38,306,502 (+)Ensembl
RefSeq Acc Id: ENSMUST00000197123   ⟹   ENSMUSP00000142953
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1938,253,108 - 38,286,431 (+)Ensembl
GRCm38.p6 Ensembl1938,264,660 - 38,297,983 (+)Ensembl
RefSeq Acc Id: ENSMUST00000198045   ⟹   ENSMUSP00000143292
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1938,253,094 - 38,295,256 (+)Ensembl
GRCm38.p6 Ensembl1938,264,646 - 38,306,808 (+)Ensembl
RefSeq Acc Id: ENSMUST00000198518   ⟹   ENSMUSP00000143128
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1938,252,984 - 38,300,662 (+)Ensembl
GRCm38.p6 Ensembl1938,264,536 - 38,312,214 (+)Ensembl
RefSeq Acc Id: ENSMUST00000199665
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1938,253,210 - 38,254,362 (+)Ensembl
GRCm38.p6 Ensembl1938,264,762 - 38,265,914 (+)Ensembl
RefSeq Acc Id: ENSMUST00000199812   ⟹   ENSMUSP00000143502
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1938,253,025 - 38,295,257 (+)Ensembl
GRCm38.p6 Ensembl1938,264,577 - 38,306,809 (+)Ensembl
RefSeq Acc Id: NM_020278   ⟹   NP_064674
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391938,253,135 - 38,297,387 (+)NCBI
GRCm381938,264,687 - 38,308,939 (+)NCBI
MGSCv371938,339,272 - 38,383,429 (+)RGD
Celera1939,059,488 - 39,103,642 (+)RGD
cM Map19 ENTREZGENE
Sequence:
RefSeq Acc Id: NR_157558
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391938,253,135 - 38,297,387 (+)NCBI
GRCm381938,264,687 - 38,308,939 (+)NCBI
Sequence:
RefSeq Acc Id: NR_157559
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391938,253,831 - 38,297,387 (+)NCBI
GRCm381938,265,383 - 38,308,939 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_064674 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH66090 (Get FASTA)   NCBI Sequence Viewer  
  BAC32370 (Get FASTA)   NCBI Sequence Viewer  
  EDL41805 (Get FASTA)   NCBI Sequence Viewer  
  Q9JIA1 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_064674   ⟸   NM_020278
- Peptide Label: precursor
- UniProtKB: Q9JIA1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000143128   ⟸   ENSMUST00000198518
RefSeq Acc Id: ENSMUSP00000143292   ⟸   ENSMUST00000198045
RefSeq Acc Id: ENSMUSP00000142953   ⟸   ENSMUST00000197123
RefSeq Acc Id: ENSMUSP00000143502   ⟸   ENSMUST00000199812
RefSeq Acc Id: ENSMUSP00000084507   ⟸   ENSMUST00000087252
RefSeq Acc Id: ENSMUSP00000143538   ⟸   ENSMUST00000196090
Protein Domains
LRRCT   LRRNT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9JIA1-F1-model_v2 AlphaFold Q9JIA1 1-557 view protein structure

Promoters
RGD ID:13679408
Promoter ID:EPDNEW_M23853
Type:initiation region
Name:Lgi1_1
Description:Mus musculus leucine-rich repeat LGI family, member 1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381938,264,687 - 38,264,747EPDNEW
RGD ID:6830160
Promoter ID:MM_KWN:26981
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Brain
Transcripts:NM_020278,   OTTMUST00000039288,   OTTMUST00000039289,   UC008HJK.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361938,338,366 - 38,338,866 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1861691 AgrOrtholog
Ensembl Genes ENSMUSG00000067242 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000084507 UniProtKB/TrEMBL
  ENSMUSP00000142953 UniProtKB/TrEMBL
  ENSMUSP00000143128 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000143292 UniProtKB/TrEMBL
  ENSMUSP00000143502 UniProtKB/TrEMBL
  ENSMUSP00000143538 UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000087252 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUST00000196090 UniProtKB/TrEMBL
  ENSMUST00000197123 UniProtKB/TrEMBL
  ENSMUST00000198045 UniProtKB/TrEMBL
  ENSMUST00000198518 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000199812 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Cys-rich_flank_reg_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EAR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EPTP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:56839 UniProtKB/Swiss-Prot
MGD MGI:1861691 ENTREZGENE
NCBI Gene 56839 ENTREZGENE
Pfam EPTP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Lgi1 PhenoGen
PROSITE EAR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART LRR_TYP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRRCT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JEY8_MOUSE UniProtKB/TrEMBL
  A0A0G2JFT0_MOUSE UniProtKB/TrEMBL
  A0A0G2JGB7_MOUSE UniProtKB/TrEMBL
  A0A0G2JGE8_MOUSE UniProtKB/TrEMBL
  LGI1_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE