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LRRC1 Gene

protein-coding   GIFtS: 53
GCID: GC06P053706

Leucine Rich Repeat Containing 1

(Previous name: leucine-rich repeat-containing 1)
  Search for LRRC1
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Leucine Rich Repeat Containing 11 2     LAP And No PDZ Protein2 3
LANO2 3 5     dJ523E19.12
Leucine-Rich Repeat-Containing 11 2     LAP (Leucine-Rich Repeats And PDZ) And No PDZ Protein2
LANO Adapter Protein2 3     Leucine-Rich Repeat-Containing Protein 12

External Ids:    HGNC: 143071   Entrez Gene: 552272   Ensembl: ENSG000001372697   OMIM: 6081955   UniProtKB: Q9BTT63   

Export aliases for LRRC1 gene to outside databases

Previous GC identifers: GC00U990863 GC06P053660 GC06P053767 GC06P053492


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for LRRC1 Gene:
LRRC1 (leucine rich repeat containing 1) is a protein-coding gene. An important paralog of this gene is LRRC8E.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000006.11  NC_018917.2  NT_007592.16  
Regulatory elements:
   Regulatory transcription factor binding sites in the LRRC1 gene promoter:
         Max1   RP58   AML1a   Egr-1   HNF-1A   E47   AREB6   HNF-1   Hlf   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): LRRC1 promoter sequence
   Search Chromatin IP Primers for LRRC1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat LRRC1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 6p12.1   Ensembl cytogenetic band:  6p12.1   HGNC cytogenetic band: 6p12.2

LRRC1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LRRC1 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P053706:  view genomic region     (about GC identifiers)

Start:
53,659,295 bp from pter      End:
53,788,919 bp from pter
Size:
129,625 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: LRRC1_HUMAN, Q9BTT6 (See protein sequence)
Recommended Name: Leucine-rich repeat-containing protein 1  
Size: 524 amino acids; 59242 Da
Subunit: Interacts with DLG1 and DLG4. May form a complex with DLG1 and ERBB2IP, where interaction between LRRC1
and ERBB2IP is indirect
Sequence caution: Sequence=BAA91801.1; Type=Frameshift; Positions=262;
Secondary accessions: Q5TGN3 Q9HAC0 Q9NVF1
Alternative splicing: 2 isoforms:  Q9BTT6-1   Q9BTT6-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for LRRC1: NX_Q9BTT6

Explore proteomics data for LRRC1 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys60, Lys63, Lys381
  • Modification sites at PhosphoSitePlus

  • See LRRC1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_060684.4  
    ENSEMBL proteins: 
     ENSP00000435217   ENSP00000359925   ENSP00000359919  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR001611 Leu-rich_rpt
     IPR025875 Leu-rich_rpt_4

    Graphical View of Domain Structure for InterPro Entry Q9BTT6

    ProtoNet protein and cluster: Q9BTT6

    UniProtKB/Swiss-Prot: LRRC1_HUMAN, Q9BTT6
    Similarity: Contains 17 LRR (leucine-rich) repeats


    Find genes that share domains with LRRC1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
         
    Find genes that share ontologies with LRRC1           About GenesLikeMe


    Phenotypes:
         3 GenomeRNAi human phenotypes for LRRC1:
     Decreased melanin production  G0/1 arrest  Increased G1 DNA content 

    Animal Models:
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    miRNA
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    miRTarBase miRNAs that target LRRC1:
    hsa-mir-22-3p (MIRT030660), hsa-mir-124-3p (MIRT002712)

    Block miRNA regulation of human, mouse, rat LRRC1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate LRRC1 (see all 23):
    hsa-miR-142-3p hsa-miR-3910 hsa-miR-3200-5p hsa-miR-300 hsa-miR-199b-3p hsa-miR-199a-3p hsa-miR-3129-5p hsa-miR-124
    SwitchGear 3'UTR luciferase reporter plasmidLRRC1 3' UTR sequence
    Inhib. RNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    LRRC1_HUMAN, Q9BTT6: Cytoplasm. Membrane; Peripheral membrane protein. Note=Localized at the basolateral side of
    epithelial cells
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol2
    nucleus2
    plasma membrane2
    extracellular1
    mitochondrion1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IEA--
    GO:0016020membrane IEA--

    Find genes that share ontologies with LRRC1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for LRRC1
    Interactions:

        Search GeneGlobe Interaction Network for LRRC1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 22)

    Selected Interacting proteins for LRRC1 (Q9BTT62, 3 ENSP000003599254) via UniProtKB, MINT, STRING, and/or I2D (see all 577)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    KIAA1377Q9P2H02, 3MINT-65337 I2D: score=5 
    CRMP1Q141942, 3MINT-65336 I2D: score=4 
    ERBB2IPQ96RT13, ENSP000003703304I2D: score=3 STRING: ENSP00000370330
    SLX4Q8IY923, ENSP000002940084I2D: score=2 STRING: ENSP00000294008
    DLG1Q129593, ENSP000003457314I2D: score=3 STRING: ENSP00000345731
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for LRRC1



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for LRRC1 gene (2 alternative transcripts): 
    NM_025168.1  NM_018214.4  

    Unigene Cluster for LRRC1:

    Leucine rich repeat containing 1
    Hs.606493  [show with all ESTs]
    Unigene Representative Sequence: NM_018214
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000487251 ENST00000370888(uc003pcd.1) ENST00000370882 ENST00000490222

    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate LRRC1 (see all 23):
    hsa-miR-142-3p hsa-miR-3910 hsa-miR-3200-5p hsa-miR-300 hsa-miR-199b-3p hsa-miR-199a-3p hsa-miR-3129-5p hsa-miR-124
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    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat LRRC1
      QuantiFast Probe-based Assays in human, mouse, rat LRRC1

    Additional mRNA sequence: 

    AF332199.1 AF359380.1 AJ420513.1 AK001637.1 AK292248.1 BC003193.1 

    6 DOTS entries:

    DT.409860  DT.95165918  DT.70103763  DT.95206216  DT.121393288  DT.75142061 

    Selected AceView cDNA sequences (see all 109):

    CA777835 AA237081 D62624 BF063416 AK021896 BC003193 CA777562 NM_025168 
    BF338148 BE219599 AL703396 BG750806 BE140861 BM926879 BI764145 BQ573829 
    BI818867 CB241846 AJ420513 D62890 AI569940 BE279901 AF332199 BI765219 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for LRRC1    About this scheme

    ExUns: 1 ^ 2a · 2b · 2c · 2d ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15 ^ 16a · 16b
    SP1:                                                  -                                         -     -                                 
    SP2:                                                  -                                                                                 
    SP3:                                                                                                                                    
    SP4:                                                                                                                                    
    SP5:                                                                                                                                    


    ECgene alternative splicing isoforms for LRRC1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    LRRC1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TCCAATCAGT
    LRRC1 Expression
    About this image


    LRRC1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 4) fully expand
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Ovary (Reproductive System)
             Oviduct
     
     Bone (Muscoskeletal System)
             Chondrocyte-like cells
     
     Cartilage (Muscoskeletal System)
             Chondrocyte-like cells
    LRRC1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    LRRC1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.606493

    UniProtKB/Swiss-Prot: LRRC1_HUMAN, Q9BTT6
    Tissue specificity: Expressed strongly in testis and placenta, followed by heart, lung, kidney, thyroid, trachea,
    colon, prostate and pancreas

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for LRRC1 gene from Selected species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Lrrc11 , 5 leucine rich repeat containing 11, 5 88.68(n)1
    93.13(a)1
      9 (43.36 cM)5
    2143451  NM_001146048.11  NP_001139520.11 
     774308235 
    chicken
    (Gallus gallus)
    Aves LRRC11 leucine rich repeat containing 1 81.99(n)
    87.87(a)
      421891  XM_419907.4  XP_419907.3 
    lizard
    (Anolis carolinensis)
    Reptilia LRRC16
    leucine rich repeat containing 1
    86(a)
    1 ↔ 1
    GL343342.1(36339-134867)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.152002 Xenopus laevis transcribed sequence with moderate similarity more 76.68(n)    CA791258.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.109552 Transcribed sequence with moderate similarity to protein more 78.19(n)    57069206 
    fruit fly
    (Drosophila melanogaster)
    Insecta scrib6
    scribbled
    11(a)
    1 → many
    3R(22362072-22429773)
    worm
    (Caenorhabditis elegans)
    Secernentea let-4136
    Protein LET-413, isoform b
    30(a)
    1 → many
    V(7972924-7977774) WBGene00002632


    ENSEMBL Gene Tree for LRRC1 (if available)
    TreeFam Gene Tree for LRRC1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for LRRC1 gene
    LRRC8E2  LRRC72  ERBB2IP2  RSU12  LRRC8A2  MFHAS12  LRRIQ42  SCRIB2  
    SHOC22  LRRD12  LRRC8D2  LRRC8B2  LRRC8C2  LRRC402  
    10 SIMAP similar genes for LRRC1 using alignment to 2 protein entries:     LRRC1_HUMAN (see all proteins):
    SCRIB    ERBB2IP    LRRC7    LRRC8C    LRCH3    LRRD1
    RSU1    LRRC8E    PHLPP1    LRRC28

    Find genes that share paralogs with LRRC1           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for LRRC1 (see all 2641)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1822349791,2
    C--53657935(+) GGACAC/GGTCTT 1 -- us2k10--------
    rs2010841921,2
    C--53658026(+) GCCTT-/TTTTTAAT 1 -- us2k10--------
    rs113635701,2
    C--53658031(+) TTTAA-/TTTTTT 1 -- us2k1 tfbs3 trp30--------
    rs773331311,2
    C,F--53658049(+) AAGCAG/TTTGGA 1 -- us2k11Minor allele frequency- T:0.09EA 120
    rs1389225411,2
    C--53658206(+) TCTGTA/GAGAAC 1 -- us2k10--------
    rs38138501,2
    C,F,A,H--53658211(-) CCTGCG/ATTCTC 1 -- us2k123Minor allele frequency- A:0.19NS EA NA CSA WA 2584
    rs1494316351,2
    --53658232(+) GGACAA/CACAAA 1 -- us2k10--------
    rs1447711981,2
    --53658266(+) ACGGAG/TTTTCG 1 -- us2k10--------
    rs1853336531,2
    --53658300(+) GGTGAC/TAATGC 1 -- us2k10--------
    rs1397242461,2
    --53658499(+) ACTTTA/GCCTTG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for LRRC1 (53659295 - 53788919 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for LRRC1:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2667284CNV Deletion23128226
    nsv5306CNV Insertion18451855
    esv5680CNV Gain19470904
    nsv830664CNV Gain17160897

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 608195    OMIM disorders: --

    1 disease from the University of Copenhagen DISEASES database for LRRC1:
    Idiopathic generalized epilepsy

    Find genes that share disorders with LRRC1           About GenesLikeMe

    Genetic Association Database (GAD): LRRC1

    Export disorders for LRRC1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for LRRC1 gene, integrated from 10 sources (see all 20):
    (articles sorted by number of sources associating them with LRRC1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. Identification and mutational analysis of candidate genes for juvenile myoclonic epilepsy on 6p11-p12: LRRC1, GCLC, KIAA0057 and CLIC5. (PubMed id 12200217)1, 2 Suzuki T.... Yamakawa K. (Epilepsy Res. 2002)
    4. Lano, a novel LAP protein directly connected to MAGUK proteins in epithelial cells. (PubMed id 11440998)1, 2 Saito H.... Borg J.-P. (J. Biol. Chem. 2001)
    5. Aberrant upregulation of LRRC1 contributes to human hepatocellular carcinoma. (PubMed id 23645086)1 Li Y....Han Z.G. (Mol. Biol. Rep. 2013)
    6. The protein interaction landscape of the human CMGC kinase group. (PubMed id 23602568)1 Varjosalo M....Gstaiger M. (Cell Rep 2013)
    7. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (Cell 2012)
    8. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (Nat. Cell Biol. 2012)
    9. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
    10. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
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      Query String
    PubMed
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 55227 HGNC: 14307 AceView: LRRC1 Ensembl:ENSG00000137269 euGenes: HUgn55227
    ECgene: LRRC1 H-InvDB: LRRC1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for LRRC1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for LRRC1 gene:
    Search GeneIP for patents involving LRRC1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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