Lgi3 (leucine-rich repeat LGI family, member 3) - Rat Genome Database

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Gene: Lgi3 (leucine-rich repeat LGI family, member 3) Mus musculus
Analyze
Symbol: Lgi3
Name: leucine-rich repeat LGI family, member 3
RGD ID: 1322346
MGI Page MGI
Description: Involved in regulation of exocytosis. Located in juxtaparanode region of axon and synaptic vesicle. Is expressed in several structures, including autopod; gut; nervous system; respiratory system; and retina. Orthologous to human LGI3 (leucine rich repeat LGI family member 3).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: AI841179; AW049851; leubrin; leucine-rich glioma inactivated 1-like; leucine-rich glioma-inactivated protein 3; leucine-rich repeat LGI family member 3
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391470,765,982 - 70,775,764 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1470,768,125 - 70,775,764 (+)EnsemblGRCm39 Ensembl
GRCm381470,528,547 - 70,538,324 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1470,530,685 - 70,538,324 (+)EnsemblGRCm38mm10GRCm38
MGSCv371470,930,628 - 70,938,131 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361469,265,950 - 69,273,402 (+)NCBIMGSCv36mm8
Celera1468,072,371 - 68,079,876 (+)NCBICelera
Cytogenetic Map14D2NCBI
cM Map1436.32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. MGDs mouse GO annotations MGD data from the GO Consortium
2. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12023020   PMID:12477932   PMID:15226823   PMID:15489334   PMID:16141072   PMID:16141073   PMID:16341215  
PMID:16545924   PMID:16602821   PMID:18628660   PMID:18760330   PMID:19833108   PMID:20162351   PMID:20461023   PMID:21267068   PMID:21677750   PMID:21873635   PMID:22405860   PMID:23548727  
PMID:24952961   PMID:25648289   PMID:25707359   PMID:28534931   PMID:29428562   PMID:30728831   PMID:35948005   PMID:36828548   PMID:38194969   PMID:38355793  


Genomics

Comparative Map Data
Lgi3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391470,765,982 - 70,775,764 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1470,768,125 - 70,775,764 (+)EnsemblGRCm39 Ensembl
GRCm381470,528,547 - 70,538,324 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1470,530,685 - 70,538,324 (+)EnsemblGRCm38mm10GRCm38
MGSCv371470,930,628 - 70,938,131 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361469,265,950 - 69,273,402 (+)NCBIMGSCv36mm8
Celera1468,072,371 - 68,079,876 (+)NCBICelera
Cytogenetic Map14D2NCBI
cM Map1436.32NCBI
LGI3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38822,146,830 - 22,156,806 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl822,146,830 - 22,157,084 (-)EnsemblGRCh38hg38GRCh38
GRCh37822,004,343 - 22,014,319 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36822,060,288 - 22,070,289 (-)NCBINCBI36Build 36hg18NCBI36
Build 34822,060,289 - 22,070,289NCBI
Celera820,966,267 - 20,976,328 (-)NCBICelera
Cytogenetic Map8p21.3NCBI
HuRef820,546,619 - 20,556,646 (-)NCBIHuRef
CHM1_1822,206,009 - 22,216,003 (-)NCBICHM1_1
T2T-CHM13v2.0822,420,778 - 22,430,751 (-)NCBIT2T-CHM13v2.0
Lgi3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81552,015,317 - 52,022,445 (+)NCBIGRCr8
mRatBN7.21545,605,611 - 45,612,739 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1545,605,611 - 45,612,739 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1549,723,477 - 49,730,605 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01550,834,982 - 50,842,110 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01547,694,274 - 47,701,402 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01552,220,578 - 52,227,706 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1552,220,578 - 52,227,706 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01555,944,095 - 55,951,223 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41550,932,145 - 50,939,273 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11550,948,080 - 50,955,053 (+)NCBI
Celera1545,284,005 - 45,291,134 (+)NCBICelera
Cytogenetic Map15p11NCBI
Lgi3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540345,634,237 - 45,644,172 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540345,634,237 - 45,644,172 (-)NCBIChiLan1.0ChiLan1.0
LGI3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2740,648,656 - 40,658,653 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1816,373,854 - 16,383,840 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0821,391,765 - 21,401,770 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1818,330,815 - 18,340,403 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl818,330,815 - 18,340,403 (-)Ensemblpanpan1.1panPan2
LGI3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12535,097,464 - 35,105,930 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2535,097,566 - 35,105,940 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2535,687,040 - 35,695,518 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02535,308,828 - 35,317,292 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2535,308,929 - 35,316,773 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12535,254,281 - 35,262,751 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02535,108,844 - 35,117,307 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02535,264,308 - 35,272,778 (+)NCBIUU_Cfam_GSD_1.0
Lgi3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494312,596,621 - 12,603,899 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365555,966,577 - 5,973,954 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365555,966,617 - 5,973,898 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LGI3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl146,419,592 - 6,428,563 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1146,419,100 - 6,429,266 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2146,856,466 - 6,866,639 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LGI3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1820,216,373 - 20,226,744 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl820,216,372 - 20,225,599 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605222,009,472 - 22,019,709 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lgi3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475817,726,018 - 17,737,740 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475817,729,290 - 17,737,677 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lgi3
245 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:506
Count of miRNA genes:332
Interacting mature miRNAs:388
Transcripts:ENSMUST00000047331
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357589Kdnw2_mkidney weight 2 (mouse)Not determined1420887473121269804Mouse
1357527Epfpq1_mepididymal fat percentage QTL 1 (mouse)Not determined142106245071885801Mouse
27226774Tibl15_mtibia length 15, 10 week (mouse)143032195787937436Mouse
10043887Cia50_mcollagen induced arthritis QTL 50 (mouse)Not determined143743018571430320Mouse
4142419Tgq26_mtriglyceride QTL 26 (mouse)Not determined4033731974337319Mouse
1301777Bglq15_mbody growth late QTL 15 (mouse)Not determined144296241676962593Mouse
1301424Skull21_mskull morphology 21 (mouse)Not determined144296241676962593Mouse
1300805Mors3_mmodifier of obesity related sterility 3 (mouse)Not determined144303727077037418Mouse
1301091Bbaa21_mB.burgdorferi-associated arthritis 21 (mouse)Not determined144306584777066045Mouse
4141400Nilac8_mnicotine induced locomotor activity 8 (mouse)Not determined144306584777066045Mouse
1300605El5_mepilepsy 5 (mouse)Not determined144945542583455556Mouse
4142364Pbwg18_mpostnatal body weight growth 18 (mouse)Not determined145228198486282125Mouse
1301489Lbm10_mlean body mass 10 (mouse)Not determined145376129687761529Mouse
12880432Fgf23lq3_mFGF23 serum level QTL 3 (mouse)145393744087937440Mouse
10043889Cia52_mcollagen induced arthritis QTL 52 (mouse)Not determined145608238190082509Mouse
1301562Hwq1_mheart weight quantitative locus 1 (mouse)Not determined145654674590546941Mouse
1357565wrmod1_mwobbler modifier 1 (mouse)Not determined1458179640101859473Mouse
11039527Ccc2_mcolitis susceptibility in the Collaborative Cross 2 (mouse)145991861294138217Mouse
1300666Fembm2_mfemoral bone morphometry 2 (mouse)Not determined146239746096397680Mouse
14747006Mancz12_mmandible centroid size 12 (mouse)1470071977104071977Mouse

Markers in Region
AW049851  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381470,538,214 - 70,538,322UniSTSGRCm38
MGSCv371470,938,021 - 70,938,129UniSTSGRCm37
Celera1468,079,766 - 68,079,874UniSTS
Cytogenetic Map14D2UniSTS
Whitehead/MRC_RH14793.84UniSTS
AI841179  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381470,533,519 - 70,533,647UniSTSGRCm38
MGSCv371470,933,326 - 70,933,454UniSTSGRCm37
Celera1468,075,069 - 68,075,197UniSTS
Cytogenetic Map14D2UniSTS
Whitehead/MRC_RH14793.84UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000047331   ⟹   ENSMUSP00000046705
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1470,768,268 - 70,775,764 (+)Ensembl
GRCm38.p6 Ensembl1470,530,828 - 70,538,324 (+)Ensembl
RefSeq Acc Id: ENSMUST00000226376
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1470,768,125 - 70,775,467 (+)Ensembl
GRCm38.p6 Ensembl1470,530,685 - 70,538,027 (+)Ensembl
RefSeq Acc Id: ENSMUST00000226548   ⟹   ENSMUSP00000153920
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1470,768,310 - 70,771,168 (+)Ensembl
GRCm38.p6 Ensembl1470,530,870 - 70,533,728 (+)Ensembl
RefSeq Acc Id: NM_001425646   ⟹   NP_001412575
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391470,765,982 - 70,775,764 (+)NCBI
RefSeq Acc Id: NM_145219   ⟹   NP_660254
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391470,768,310 - 70,775,764 (+)NCBI
GRCm381470,530,821 - 70,538,324 (+)ENTREZGENE
MGSCv371470,930,628 - 70,938,131 (+)RGD
Celera1468,072,371 - 68,079,876 (+)RGD
cM Map14 ENTREZGENE
Sequence:
RefSeq Acc Id: NR_189573
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391470,768,310 - 70,775,764 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_660254   ⟸   NM_145219
- Peptide Label: isoform 1 precursor
- UniProtKB: Q8K406 (UniProtKB/Swiss-Prot),   Q3V1R3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000046705   ⟸   ENSMUST00000047331
RefSeq Acc Id: ENSMUSP00000153920   ⟸   ENSMUST00000226548
RefSeq Acc Id: NP_001412575   ⟸   NM_001425646
- Peptide Label: isoform 1 precursor
- UniProtKB: Q8K406 (UniProtKB/Swiss-Prot)
Protein Domains
LRRCT   LRRNT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8K406-F1-model_v2 AlphaFold Q8K406 1-548 view protein structure

Promoters
RGD ID:8682922
Promoter ID:EPDNEW_M19492
Type:initiation region
Name:Lgi3_1
Description:Mus musculus leucine-rich repeat LGI family, member 3 , 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
GRCm381470,530,870 - 70,530,930EPDNEW
RGD ID:6825120
Promoter ID:MM_KWN:17387
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Brain,   Lung
Transcripts:NM_145219,   UC007UOF.1,   UC007UOG.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361470,930,451 - 70,930,951 (+)MPROMDB
RGD ID:6849029
Promoter ID:MM_XEF:2330
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Brain,   Lung
Transcripts:NM_001039679
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361470,931,321 - 70,931,832 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2182619 AgrOrtholog
Ensembl Genes ENSMUSG00000033595 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000047331 ENTREZGENE
  ENSMUST00000047331.8 UniProtKB/Swiss-Prot
  ENSMUST00000226548.2 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
  Quinoprot_gluc/sorb_DH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:213469 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:2182619 ENTREZGENE
NCBI Gene 213469 ENTREZGENE
PANTHER LEUCINE-RICH REPEAT LGI FAMILY MEMBER 3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LEUCINE-RICH REPEAT-CONTAINING PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam EPTP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_1 UniProtKB/TrEMBL
  LRR_8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Lgi3 PhenoGen
PROSITE EAR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART LRR_TYP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRRCT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP L domain-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF50952 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A2I3BPU5_MOUSE UniProtKB/TrEMBL
  LGI3_MOUSE UniProtKB/Swiss-Prot
  Q3V1R3 ENTREZGENE, UniProtKB/TrEMBL
  Q8K406 ENTREZGENE