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LGI1 Gene

protein-coding   GIFtS: 62

GC10P095507
leucine-rich, glioma inactivated 1
(Previous names: epilepsy, partial )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: EPT)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
EPITEMPIN 1, 2
EPT 2, 3, 5
ETL1 1, 2, 5
Epitempin-1 3
IB1099 1, 2
OTTHUMP00000020121 2
Descriptions
epilepsy, partial 1
leucine-rich, glioma inactivated 1 2
External Ids
HGNC: 65721
Entrez Gene: 92112
UniProtKB: O959703
Ensembl: ENSG000001082317
Search outside databases for aliases for LGI1 gene

Previous GC identifers: GC10P094410 GC10P094751 GC10P095648 GC10P095182

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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EntrezGene summary for LGI1:
This gene is rearranged as a result of translocations in glioblastoma cell lines. The protein
contains a hydrophobic segment representing a putative transmembrane domain with the amino
terminus located outside the cell. It also contains leucine-rich repeats with conserved
cysteine-rich flanking sequences. This gene is predominantly expressed in neural tissues and its
expression is reduced in low grade brain tumors and significantly reduced or absent in malignant
gliomas. Mutations in this gene result in autosomal dominant lateral temporal epilepsy. [provided
by RefSeq]

Gene Wiki entry for LGI1
(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
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Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the LGI1 gene  

Entrez Gene cytogenetic band: 10q24   Ensembl cytogenetic band:  10q23.33   HGNC cytogenetic band: 10q24

LGI1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10P095507:     (about GC identifiers)

Start:
95,507,632 bp from pter
End:
95,547,906 bp from pter
Size:
40,275 bases
Orientation:
plus strand
RefSeq DNA sequence:
NC_000010.9  NT_030059.12  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: LGI1_HUMAN, O95970 (See protein sequence)
Recommended Name: Leucine-rich glioma-inactivated protein 1 precursor  
Size: 557 amino acids; 63818 Da
Subcellular location: Secreted (Potential)
Secondary accessions: Q5W001 Q5W002 Q8NI23 Q96LF5
Alternative splicing: 2 isoforms:  O95970-1   O95970-2   

REFSEQ proteins: NP_005088.1  

ENSEMBL proteins: 
ENSP00000360472 ENSP00000360467 


Human Recombinant Proteins 
Browse Drug Discovery Central at Invitrogen for human recombinant proteins
Browse Purified and Recombinant Proteins at Millipore
Browse Human Recombinant Proteins at Sigma-Aldrich  
Browse R&D Systems for human recombinant proteins
Browse recombinant and purified proteins available from Enzo Life Sciences
Recombinant Proteins from Abcam (Lgi1)
Human Recombinant Proteins from Abnova (LGI1)
                Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

1 Gene Ontology (GO) cellular component term (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0005576 extracellular region IEA--
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Antibodies for LGI1: 
Browse Antibodies Central at Invitrogen
Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
Sigma-Aldrich Antibodies for LGI1
Browse R&D Systems for Antibodies
Antibodies from Abcam (Lgi1), each with their AbpromiseSM
Monoclonal and Polyclonal Antibodies from Abnova (LGI1)
Novus Biologicals Antibody for LGI1

Assays for LGI1: 
Browse Invitrogen for biochemical assays
Browse Kits and Assays available from Millipore
Browse R&D Systems for biochemical assays
Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

5/6 InterPro domains/families (see all 6 ):
 IPR000483 LRR_C
 IPR000372 Leu-rich_rpt_Cys-rich-reg_N
 IPR003591 Leu-rich_rpt_typical-subtyp
 IPR009039 EAR
 IPR001611 Leu-rich_rpt


   GeneDecks  LGI1 for the domains selected above  
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Graphical View of Domain Structure for InterPro Entry O95970

ProtoNet protein and cluster: O95970

2 Blocks protein families:
IPB000372 Cysteine-rich flanking region
IPB000483 Cysteine-rich flanking region


UniProtKB/Swiss-Prot: LGI1_HUMAN, O95970
Similarity: Contains 7 EAR repeats
Similarity: Contains 3 LRR (leucine-rich) repeats

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (LGI1)
Browse for Gene Knock-down Tools from Millipore
Browse Abnova for Chimera RNAi Products
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_005097

              Applied Biosystems Silencer® siRNAs for LGI1

              Sigma-Aldrich siRNA and siRNA Panels for LGI1  
                     Sigma-Aldrich shRNA for LGI1  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Clones:Invitrogen Clones for LGI1
Browse Clones for the Expression of Recombinant Proteins Available from Millipore
              OriGene GFP tagged cDNA clone in CMV expression vector: NM_005097
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_005097
                                 untagged cDNA clone in CMV expression vector: NM_005097 

Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
              OriGene genome-wide validated SYBR primer pairs: NM_005097

Genatlas biochemistry entry for LGI1:
leucine-rich,glioma inactivated 1,rearranged in glioblastoma cell line t(10;19)(q24;q13),potential
adhesion protein,expressed in the brain

1 Gene Ontology (GO) molecular function term (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0005515 protein binding IEA--
About this table

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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 Gene Network CentralTM Interacting Genes and Proteins Network for  LGI1 


4 Interacting proteins for LGI1 (ENSP000003604723) via UniProtKB, MINT, and/or STRING
InteractantInteraction Details
GeneCardExternal ID(s)
ENSG00000008277ENSP000002657273STRING (score=.991)
ADAM11ENSP000002005573STRING (score=.901)
ANP32AENSP000002679183STRING (score=.792)
DLG4ENSP000002938133STRING (score=.786)
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2 Gene Ontology (GO) biological process terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0007399 nervous system development TAS9879993
GO:0008283 cell proliferation TAS9879993
About this table
(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
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Browse drugs & compounds from Enzo Life Sciences
Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for LGI1
2 Novoseek chemical compound relationships for LGI1 gene
Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
potassium 24.18 3 18440780 (1)
sodium 14.30 1 17981785 (1)
About this table


(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (LGI1)
Browse for Gene Knock-down Tools from Millipore
Browse Abnova for Chimera RNAi Products
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_005097

              Sigma-Aldrich siRNA and siRNA Panels for LGI1  
                     Sigma-Aldrich shRNA for LGI1  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Applied Biosystems Silencer® siRNAs: 

NM_005097  

REFSEQ mRNAs for LGI1 gene: 

NM_005097.2   

Applied Biosystems TaqMan ® Gene Expression Assays: 

NM_005097  

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_005097
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_005097
                                 untagged cDNA clone in CMV expression vector: NM_005097 

Additional cDNA sequence: 

AB209408.1 AF055636.1 AF473548.1 AK289706.1 AK303956.1 AK309416.1 AY358885.1 BC022500.1 
CR621199.1 CR621328.1 

6 DOTS entries:

DT.40131478  DT.91666709  DT.311317  DT.40302079  DT.91666707  DT.100670435 

24/51 AceView cDNA sequences (see all 51 ):

AY358885 AI240096 CR621199 CR621328 AA296979 AI918747 NM_005097 BC022500 
BQ718988 BP373601 AI802297 H46267 BF475263 BI752989 BX508343 AI989349 
AI039940 BP350084 BI603719 BG699594 H05383 BI550706 AA992473 AA992136 

highest scoring ESTs for LGI1:

AA992136 AA992473 AF055636 AI039940 AI621238 AI989349 AW590515 AY358885 BC022500 CD298918 

Unigene Cluster for LGI1:

Leucine-rich, glioma inactivated 1
Hs.533670  [show with all ESTs]
Unigene Representative Sequence: AB209408


GeneLoc Exon Structure

4 Alternative Splicing Database (ASD) splice patterns (SP) for LGI1

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8
SP1:                    -                       -           -               
SP2:                    -                       -                           
SP3:                                                                        
SP4:                                                        -               

About this scheme

ECgene alternative splicing isoforms for LGI1

2 Ensembl transcripts including schematic representations:
ENST00000371418  ENST00000371413  
(Experimental results according to 1GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
About This Section

LGI1 expression in normal and diseased human tissues

 Applied Biosystems TaqMan ® Gene Expression Assays for LGI1

1 / 2 / 3

4 probe-sets matching LGI1 gene


Affymetrix
probe-set
Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
38888_at2, 3 U95-A 1 1.00 1.00 0.99 0.81 AF055636 0.80 1.00 0.91 1
81337_at2, 3 U95-D 1 1.00 1.00 0.97 1.22 AI357583 0.60 1.00 0.82 1

206349_at2, 3 U133-A 1 1.00 1.00 -- -- NM_005097 0.60 1.00 0.82 1

206349_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
GeneDecks  LGI1 for binary patterns associated with the probe-sets selected above  
About GeneDecksing
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Data from (Publications) and GNF BioGPS
    About these images
About these images

CGAP SAGE TAG: TGTACAGAAA

SOURCE GeneReport for Unigene cluster: Hs.533670

Expression variation in blood from EXPOLDB for LGI1

UniProtKB/Swiss-Prot: LGI1_HUMAN, O95970
Tissue specificity: Predominantly expressed in neural tissues, especially in brain. Expression is
reduced in low-grade brain tumors and significantly reduced or absent in malignant gliomas

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section


Orthologs for LGI1 gene from 5/9 species (see all 9 )
Organism Gene Locus Description Human
Similarity
NCBI accessions
dog
(Canis familiaris)
LGI11   -- leucine-rich, glioma inactivated 1 96.23(n)
99.28(a)
477777  XM_534971.2  XP_534971.2 
chimpanzee
(Pan troglodytes)
LGI11   -- leucine-rich, glioma inactivated 1 99.88(n)
99.82(a)
450619  XM_001149068.1  XP_001149068.1 
cow
(Bos taurus)
LGI11   -- leucine-rich, glioma inactivated 1 95(n)
98.87(a)
617080  NM_001046591.2  NP_001040056.2 
rat
(Rattus norvegicus)
Lgi11   -- leucine-rich, glioma inactivated 1 91.98(n)
96.95(a)
252892  NM_145769.2  NP_665712.1 
mouse
(Mus musculus)
Lgi11, 5 195
leucine-rich repeat LGI family, member 11, 5 91.92(n)1
96.95(a)1
568391  NM_020278.21  NP_064674.11 
 AF2468185  AK0454435  (see all 9)
About this table        Species with no ortholog for LGI1

ENSEMBL Gene Tree for LGI1
(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section

Paralogs for LGI1 gene
LGI32  LGI42  LGI22  

(According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section


10/277 NCBI SNPs in LGI1 are shown (see all 277 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 156)
ABGenomic DataTranscription DataAllele Frequencies
SNP IDValidChr 10 posSequenceRecsAA
Chg
TypeMoreRecsAllele
freq
PopTotal
sample
More
------------
rs37585321,2
C,F,H95507161(-) TGGGTC/TCCCCA 1 -- ng514Minor allele frequency- T:0.16EU EA WA 414
rs107861361,2
A,F,H95506048(+) atgccA/Gttccc 1 -- ng514Minor allele frequency- G:0.39EU EA WA 406
rs94206271,2
C,F,H95506180(+) TAGAAC/TTGCAA 1 -- ng514Minor allele frequency- T:0.04EU EA WA 410
--
rs70699401,2
A,C95506074(+) CTCACC/GAACCC 1 -- ng510--------
--
rs38344141,2
C,F95507073(-) CTCTCTT/-CTCCC 1 -- ng51 trp32Minor allele frequency- -:0.15MN EA 1252
--
rs70699341,2
A,C95506066(+) GGAGTC/GTTCTC 1 -- ng510--------
rs175026621,2
F,H95547765(+) GTAACT/CGTTCT 1 -- ut317Minor allele frequency- C:0.00NA EU EA WA 562
rs11118201,2
C,F,H95542643(+) GATTTC/TGATTG 1 F/F syn111Minor allele frequency- T:0.02EA NA EU WA 686
rs15385981,2
A,C,F,H,O95538743(+) ACTACC/TTGGTG 1 -- int110Minor allele frequency- T:0.22NA EA EU WA 610
rs11088771,2
A,C,F,H,O95542915(+) CTTATT/CATTTC 1 -- int18Minor allele frequency- C:0.27NA EU EA WA 566
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HapMap Linkage Disequilibrium images for LGI1 (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
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OMIM: 604619   disorders: 600512  137800  

UniProtKB/Swiss-Prot: LGI1_HUMAN, O95970

  • Defects in LGI1 are the cause of lateral temporal lobe epilepsy autosomal dominant (ADLTE)
    [MIM:600512]; also known as autosomal dominant partial epilepsy with auditory features (ADPEAF).
    ADLTE is a form of epilepsy characterized by partial seizures, usually preceded by auditory signs
  • 10/14 Novoseek disease relationships for LGI1 gene (see all 14 )

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    adpeaf 99.09 52 15079010 (6), 18440780 (4), 15857855 (3), 17681454 (3) (see all 19)
    epilepsy lateral temporal 98.44 12 18625862 (3), 19191227 (2), 17296837 (2), 15009222 (2) (see all 8)
    epilepsies partial 81.23 23 15079011 (3), 18711109 (2), 12771268 (2), 15816978 (1) (see all 15)
    epilepsy temporal lobe 74.60 13 12023020 (2), 15660777 (1), 15021241 (1), 18355961 (1) (see all 11)
    seizures febrile 74.04 3 14598228 (2), 17981785 (1)
    epilepsy generalized 66.52 2 15079011 (1), 17981785 (1)
    epilepsy 65.05 16 15660777 (2), 15827762 (2), 15816978 (1), 15857855 (1) (see all 14)
    epilepsy, idiopathic generalized 64.65 1 15079011 (1)
    glioma 61.06 26 12821932 (5), 15047712 (4), 14598228 (2), 15827762 (2) (see all 13)
    malignant glioma 55.24 8 11907806 (1), 15827762 (1), 12821932 (1), 10920229 (1)
    About this table

    GeneTests: LGI1
    Autosomal Dominant Partial Epilepsy with Auditory Features

    Human Gene Mutation Database: LGI1
    Human Genome Epidemiology Navigator: LGI1 (1 document)

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    10/64 PubMed articles for LGI1 gene (see all 64 ):
    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section

     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)
    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
    About This Section

    Entrez Gene: 9211 HGNC: 6572 AceView: LGI1 Ensembl:ENSG00000108231 euGenes: HUgn9211
    ECgene: LGI1 H-InvDB: LGI1
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

    NameDescription
    ATLAS Chromosomes in Cancer entry for LGI1 Genetics and Cytogenetics in Oncology and Haematology
    GeneReviewshttp://www.genetests.org/query?gene=LGI1
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for LGI1:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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     Predesigned and custom siRNAs for LGI1 Antibodies for LGI1
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for LGI1 Browse small molecules at Sigma-Aldrich
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