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

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Gene: Lgi3 (leucine-rich repeat LGI family, member 3) Rattus norvegicus
Analyze
Symbol: Lgi3
Name: leucine-rich repeat LGI family, member 3
RGD ID: 1311079
Description: Predicted to be involved in regulation of exocytosis. Predicted to be located in extracellular region. Predicted to be active in synaptic vesicle. Orthologous to human LGI3 (leucine rich repeat LGI family member 3); INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; cadmium dichloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: leucine-rich repeat LGI family member 3; LOC306013
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
mRatBN7.21545,605,611 - 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_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01550,834,982 - 50,842,110 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01547,694,274 - 47,701,402 (+)NCBIRnor_WKY
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:17387609   PMID:18760330  


Genomics

Comparative Map Data
Lgi3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01550,834,982 - 50,842,110 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01547,694,274 - 47,701,402 (+)NCBIRnor_WKY
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
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38822,146,830 - 22,156,806 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 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
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391470,765,987 - 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
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
PanPan1.1818,330,815 - 18,340,403 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl818,330,815 - 18,340,403 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0821,391,765 - 21,401,770 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
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 (-)EnsemblSpeTri2.0
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
13 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:148
Count of miRNA genes:117
Interacting mature miRNAs:131
Transcripts:ENSRNOT00000015104
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
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153361105871477291Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153361105871477291Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)153405413979054139Rat
7411725Strs7Sensitivity to stroke QTL 73.8cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)154028990149308583Rat
2306968Anxrr23Anxiety related response QTL 234.83reflex trait (VT:0001961)amplitude of the acoustic startle response (CMO:0001520)154063126846187442Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)154063126898288169Rat


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 37 1 11
Low 12 13 5 4 5 8 11 35 14 37 8
Below cutoff 2 27 19 11 15 11 2 10 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000015104   ⟹   ENSRNOP00000015104
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1545,605,611 - 45,612,739 (+)Ensembl
Rnor_6.0 Ensembl1552,220,578 - 52,227,706 (+)Ensembl
RefSeq Acc Id: NM_001107277   ⟹   NP_001100747
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21545,605,611 - 45,612,739 (+)NCBI
Rnor_6.01552,220,578 - 52,227,706 (+)NCBI
Rnor_5.01555,944,095 - 55,951,223 (+)NCBI
RGSC_v3.41550,932,145 - 50,939,273 (+)RGD
Celera1545,284,005 - 45,291,134 (+)RGD
Sequence:
RefSeq Acc Id: XM_039093351   ⟹   XP_038949279
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21545,606,118 - 45,612,739 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001100747 (Get FASTA)   NCBI Sequence Viewer  
  XP_038949279 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI58672 (Get FASTA)   NCBI Sequence Viewer  
  EDM02223 (Get FASTA)   NCBI Sequence Viewer  
  EDM02224 (Get FASTA)   NCBI Sequence Viewer  
  EDM02225 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100747   ⟸   NM_001107277
- Peptide Label: precursor
- UniProtKB: D3ZN61 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000015104   ⟸   ENSRNOT00000015104
RefSeq Acc Id: XP_038949279   ⟸   XM_039093351
- Peptide Label: isoform X1
Protein Domains
LRRCT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZN61-F1-model_v2 AlphaFold D3ZN61 1-548 view protein structure

Transcriptome

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

Promoters
RGD ID:13699811
Promoter ID:EPDNEW_R10334
Type:initiation region
Name:Lgi3_2
Description:leucine-rich repeat LGI family, member 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R10335  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01552,220,515 - 52,220,575EPDNEW
RGD ID:13699812
Promoter ID:EPDNEW_R10335
Type:multiple initiation site
Name:Lgi3_1
Description:leucine-rich repeat LGI family, member 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R10334  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01552,220,712 - 52,220,772EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311079 AgrOrtholog
BioCyc Gene G2FUF-13212 BioCyc
Ensembl Genes ENSRNOG00000011323 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000015104 ENTREZGENE
  ENSRNOP00000015104.4 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000015104 ENTREZGENE
  ENSRNOT00000015104.6 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/TrEMBL
InterPro Cys-rich_flank_reg_C UniProtKB/TrEMBL
  EAR UniProtKB/TrEMBL
  EPTP UniProtKB/TrEMBL
  L_dom-like UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/TrEMBL
  Quinoprot_gluc/sorb_DH UniProtKB/TrEMBL
KEGG Report rno:306013 UniProtKB/TrEMBL
NCBI Gene 306013 ENTREZGENE
Pfam EPTP UniProtKB/TrEMBL
  LRR_8 UniProtKB/TrEMBL
PhenoGen Lgi3 PhenoGen
PROSITE EAR UniProtKB/TrEMBL
  LRR UniProtKB/TrEMBL
SMART LRR_TYP UniProtKB/TrEMBL
  LRRCT UniProtKB/TrEMBL
Superfamily-SCOP SSF50952 UniProtKB/TrEMBL
UniProt B0BN38_RAT UniProtKB/TrEMBL
  D3ZN61 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Lgi3  leucine-rich repeat LGI family, member 3   Lgi3_predicted  leucine-rich repeat LGI family, member 3 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Lgi3_predicted  leucine-rich repeat LGI family, member 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED