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 space and juxtaparanode region of axon. Predicted to be active in synaptic vesicle. Orthologous to human LGI3 (leucine rich repeat LGI family member 3); INTERACTS WITH 4,4'-sulfonyldiphenol; 6-propyl-2-thiouracil; amitrole.
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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81552,015,317 - 52,022,445 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1552,015,230 - 52,022,443 (+)EnsemblGRCr8
mRatBN7.21545,605,611 - 45,612,739 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1545,605,611 - 45,612,739 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1549,723,477 - 49,730,605 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01550,834,982 - 50,842,110 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01547,694,274 - 47,701,402 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01552,220,578 - 52,227,706 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1552,220,578 - 52,227,706 (+)Ensemblrn6Rnor6.0
Rnor_5.01555,944,095 - 55,951,223 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41550,932,145 - 50,939,273 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1545,284,005 - 45,291,134 (+)NCBICelera
RGSC_v3.11550,948,080 - 50,955,053 (+)NCBI
Cytogenetic Map15p11NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
regulation of exocytosis  (IBA,IEA,ISO)

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
GRCr81552,015,317 - 52,022,445 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1552,015,230 - 52,022,443 (+)EnsemblGRCr8
mRatBN7.21545,605,611 - 45,612,739 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1545,605,611 - 45,612,739 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1549,723,477 - 49,730,605 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01550,834,982 - 50,842,110 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01547,694,274 - 47,701,402 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01552,220,578 - 52,227,706 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1552,220,578 - 52,227,706 (+)Ensemblrn6Rnor6.0
Rnor_5.01555,944,095 - 55,951,223 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41550,932,145 - 50,939,273 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1545,284,005 - 45,291,134 (+)NCBICelera
RGSC_v3.11550,948,080 - 50,955,053 (+)NCBI
Cytogenetic Map15p11NCBI
LGI3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38822,146,830 - 22,156,806 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl822,146,824 - 22,157,084 (-)Ensemblhg38GRCh38
GRCh37822,004,343 - 22,014,319 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36822,060,288 - 22,070,289 (-)NCBIBuild 36Build 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
GRCm391470,765,982 - 70,775,764 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1470,768,125 - 70,775,764 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381470,528,547 - 70,538,324 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1470,530,685 - 70,538,324 (+)Ensemblmm10GRCm38
MGSCv371470,930,628 - 70,938,131 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361469,265,950 - 69,273,402 (+)NCBIMGSCv36mm8
Celera1468,072,371 - 68,079,876 (+)NCBICelera
Cytogenetic Map14D2NCBI
cM Map1436.32NCBI
Lgi3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540345,634,237 - 45,644,172 (-)Ensembl
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 (-)EnsemblpanPan2panpan1.1
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2535,687,040 - 35,695,518 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02535,308,828 - 35,317,292 (+)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 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 (-)EnsemblsusScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475817,729,290 - 17,737,677 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Lgi3
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11253,815,062 - 53,822,187 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Lgi3
49 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1544806773104695021Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15231575953331089Rat
152025253Hrtrt24Heart rate QTL 243.82heart pumping trait (VT:2000009)153185580392671517Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)154367724488677244Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152852773273527732Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)154367724488677244Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1525285835104695021Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)152233635152597086Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1525285835104695021Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151915576287086765Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)154046315285463152Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151492659471614418Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)152233635167336351Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)154367724488677244Rat
2306968Anxrr23Anxiety related response QTL 234.83reflex trait (VT:0001961)amplitude of the acoustic startle response (CMO:0001520)154480677352597086Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)154367724488677244Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1525285835104695021Rat
7411725Strs7Sensitivity to stroke QTL 73.8cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)154446544756583797Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)154367724488677244Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
13 11 61 161 63 62 31 33 31 6 209 125 9 141 32 85 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000015104   ⟹   ENSRNOP00000015104
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1552,015,230 - 52,022,443 (+)Ensembl
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
GRCr81552,015,317 - 52,022,445 (+)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81552,015,824 - 52,022,445 (+)NCBI
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  
Ensembl Protein ENSRNOP00000015104
  ENSRNOP00000015104.4
RefSeq Acc Id: NP_001100747   ⟸   NM_001107277
- Peptide Label: precursor
- UniProtKB: D3ZN61 (UniProtKB/TrEMBL),   A6HTL0 (UniProtKB/TrEMBL),   A6HTL1 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000015104   ⟸   ENSRNOT00000015104
RefSeq Acc Id: XP_038949279   ⟸   XM_039093351
- Peptide Label: isoform X1
- UniProtKB: A6HTL1 (UniProtKB/TrEMBL)
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 Transcript ENSRNOT00000015104 ENTREZGENE
  ENSRNOT00000015104.7 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
  LGI_related UniProtKB/TrEMBL
  Quinoprot_gluc/sorb_DH UniProtKB/TrEMBL
KEGG Report rno:306013 UniProtKB/TrEMBL
NCBI Gene 306013 ENTREZGENE
PANTHER LEUCINE-RICH REPEAT LGI FAMILY MEMBER 3 UniProtKB/TrEMBL
  LEUCINE-RICH REPEAT-CONTAINING PROTEIN UniProtKB/TrEMBL
Pfam EPTP UniProtKB/TrEMBL
  LRR_8 UniProtKB/TrEMBL
PhenoGen Lgi3 PhenoGen
PROSITE EAR UniProtKB/TrEMBL
  LRR UniProtKB/TrEMBL
RatGTEx ENSRNOG00000011323 RatGTEx
SMART LRR_TYP UniProtKB/TrEMBL
  LRRCT UniProtKB/TrEMBL
Superfamily-SCOP L domain-like UniProtKB/TrEMBL
  SSF50952 UniProtKB/TrEMBL
UniProt A6HTL0 ENTREZGENE, UniProtKB/TrEMBL
  A6HTL1 ENTREZGENE, UniProtKB/TrEMBL
  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