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LCA5 Gene

protein-coding   GIFtS: 47

GC06M080252
Leber congenital amaurosis 5
(Previous name: chromosome 6 open reading frame 152 )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: C6orf152)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
C6orf152 2, 3, 5
OTTHUMP00000016774 2
OTTHUMP00000165989 2
lebercilin 2
Descriptions
Leber congenital amaurosis 5 2
Leber congenital amaurosis 5 protein 3
chromosome 6 open reading frame 152 1
External Ids
HGNC: 319231
Entrez Gene: 1676912
UniProtKB: Q86VQ03
Ensembl: ENSG000001353387
Search outside databases for aliases for LCA5 gene

Previous GC identifer: GC06U990222

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

EntrezGene summary for LCA5:
This gene encodes a protein that is thought to be involved in centrosomal or ciliary functions.
Mutations in this gene cause Leber congenital amaurosis type V. Alternative splicing results in
two transcript variants. [provided by RefSeq]

UniProtKB/Swiss-Prot: LCA5_HUMAN, Q86VQ0
Function: Might be involved in minus end-directed microtubule transport

(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)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 6q14.1   Ensembl cytogenetic band:  6q14.1   HGNC cytogenetic band: 6q14

LCA5 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 6         GeneLoc Exon Structure

GeneLoc location for GC06M080252:     (about GC identifiers)

Start:
80,251,427 bp from pter
End:
80,565,440 bp from pter
Size:
314,014 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000006.10  NT_007299.12  
(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)
About This Section

UniProtKB/Swiss-Prot: LCA5_HUMAN, Q86VQ0 (See protein sequence)
Recommended Name: Lebercilin  
Size: 697 amino acids; 80554 Da
Subcellular location: Cytoplasm, cytoskeleton. Cell projection, cilium axoneme. Cell projection,
cilium basal body. Note=In non-ciliated cells, localizes to the centrosome and its associated
microtubule array
Secondary accessions: Q9BWX7

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins (2 alternative transcripts): 
    NP_001116241.1  NP_859065.2  


    ENSEMBL proteins: 
    ENSP00000376688 ENSP00000376687 ENSP00000358861 ENSP00000376686 


    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 (Lebercilin)
    Browse Abnova for Human Recombinant Proteins
                  OriGene Purified Recombinant Human Protein: LCA5 

    3 Gene Ontology (GO) cellular component terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737 cytoplasm IEA--
    GO:0005856 cytoskeleton IEA--
    GO:0005929 cilium IEA--
    About this table

    Antibodies for LCA5: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Sigma-Aldrich Antibodies for LCA5
    Browse R&D Systems for Antibodies
    Antibodies from Abcam (Lebercilin), each with their AbpromiseSM
    Browse Abnova for Monoclonal and Polyclonal Antibodies
    Search Novus for antibodies for LCA5

    Assays for LCA5: 
    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

    ProtoNet protein and cluster: Q86VQ0

    UniProtKB/Swiss-Prot: LCA5_HUMAN, Q86VQ0
    Similarity: Belongs to the LCA5 family

    (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 (LCA5)
    Browse for Gene Knock-down Tools from Millipore
    Browse Abnova for Chimera RNAi Products
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_181714

                  Applied Biosystems Silencer® siRNAs for LCA5

                  Sigma-Aldrich siRNA for LCA5  
                         Sigma-Aldrich shRNA for LCA5  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Browse Clone Ranger at Invitrogen for clones
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                   OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_001122769
                                     Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_001122769
                                     untagged cDNA clones in CMV expression vector (see all 2): NM_001122769 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_181714

    UniProtKB/Swiss-Prot: LCA5_HUMAN, Q86VQ0
    Function: Might be involved in minus end-directed microtubule transport

    (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.)
    About This Section



    5/9 Interacting proteins for LCA5 (ENSP000003588613) via UniProtKB, MINT, and/or STRING (see all 9 )
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RDH12ENSP000002675023STRING (score=.888)
    RPGRIP1ENSP000002066603STRING (score=.869)
    CRB1ENSP000003563703STRING (score=.864)
    TULP1ENSP000002297713STRING (score=.863)
    RPE65ENSP000002623403STRING (score=.856)
    About this table

    1 Gene Ontology (GO) biological process term (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0015031 protein transport IEA--
    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)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for LCA5

    (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 (LCA5)
    Browse for Gene Knock-down Tools from Millipore
    Browse Abnova for Chimera RNAi Products
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_181714

                  Sigma-Aldrich siRNA for LCA5  
                         Sigma-Aldrich shRNA for LCA5  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_001122769  NM_181714  

    REFSEQ mRNAs for LCA5 gene (2 alternative transcripts): 

    NM_001122769.1   NM_181714.2   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_001122769  NM_181714  

                   OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_001122769
                                     Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_001122769
                                     untagged cDNA clones in CMV expression vector (see all 2): NM_001122769 

    Additional cDNA sequence: 

    AK299314.1 AL832214.1 BC050327.1 BX648161.1 

    2 DOTS entries:

    DT.40247242  DT.100751233 

    24/56 AceView cDNA sequences (see all 56 ):

    BM053085 BQ226190 BX097952 BM263977 AI742190 F01653 Z44254 AW166971 
    AI922939 CK824735 CD671730 AI287818 BQ025475 CD671729 AA348619 NM_181714 
    AI003684 BC050327 BQ777027 AA490709 BG720047 AA864885 CB963353 AW902230 

    Unigene Cluster for LCA5:

    Leber congenital amaurosis 5
    Hs.21945  [show with all ESTs]
    Unigene Representative Sequence: BC050327


    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for LCA5

    ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9
    SP1:                                                                              
    SP2:                    -     -                                                   
    SP3:                    -                                                         

    About this scheme

    ECgene alternative splicing isoforms for LCA5

    4 Ensembl transcripts including schematic representations:
    ENST00000392961  ENST00000392960  ENST00000369846  ENST00000392959  
    (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

    LCA5 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for LCA5

    1 / 2

    9 probe-sets matching LCA5 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
    83648_at2 U95-E 1 1.00 1.00 0.88 1.50 -- -- -- -- --

    71187_at2 U95-E 1 1.00 1.00 0.29 0.98 -- -- -- -- --

    51738_r_at2 U95-B 1 1.00 1.00 0.91 0.64 -- -- -- -- --

    244401_at2 U133-B 1 1.00 1.00 -- -- -- -- -- -- --

    229953_x_at2 U133-B 1 1.00 1.00 -- -- -- -- -- -- --

    242006_at2 U133-B 2 1.00 0.95 -- -- -- -- -- -- --

    244401_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    229953_x_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    242006_at2 U133Plus2 2 1.00 0.95 -- -- -- -- -- -- --
    GeneDecks  LCA5 for binary patterns associated with the probe-sets selected above  
    About GeneDecksing
    About this table    
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: ACTATTTGTC

    SOURCE GeneReport for Unigene cluster: Hs.21945
    (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 LCA5 gene from 5/7 species (see all 7 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    LCA51   -- Leber congenital amaurosis 5 88.71(n)
    83.5(a)
    481893  XM_539014.1  XP_539014.1 
    chimpanzee
    (Pan troglodytes)
    LCA51   -- Leber congenital amaurosis 5 99.38(n)
    98.85(a)
    472060  XM_001146093.1  XP_001146093.1 
    rat
    (Rattus norvegicus)
    Lca51   -- Leber congenital amaurosis 5 (human) 76.14(n)
    70.13(a)
    300866  NM_001013954.1  NP_001013976.1 
    mouse
    (Mus musculus)
    Lca51, 5 95
    Leber congenital amaurosis 5 (human)1, 5 76.86(n)1
    70.42(a)1
    757821  NM_027448.11  NP_081724.11 
     AK0152605  AK0175095  (see all 12)
    chicken
    (Gallus gallus)
    LCA51   -- Leber congenital amaurosis 5 61.55(n)
    47.86(a)
    421852  XM_419870.2  XP_419870.1 
    About this table        Species with no ortholog for LCA5

    ENSEMBL Gene Tree for LCA5
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for LCA5 gene
    LCA5L2  

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


    10/247 NCBI SNPs in LCA5 are shown (see all 247 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 118)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 6 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs26556701,2
    A,C,F,H,O80251062(+) AAGCCG/AAGTAT 1 -- ng5115Minor allele frequency- A:0.39NA EU EA WA 1396
    rs26556931,2
    A,C,F,H,O80305045(-) ATAACG/CAGTGA 1 -- ng3113Minor allele frequency- C:0.46EU EA WA NA 1160
    rs15043641,2
    A,C,F,O80251270(+) CTAGCG/ATACTG 1 -- ng513Minor allele frequency- A:0.40NA 140
    rs18758451,2
    A,C,F,H80253567(+) AAAAGC/TCTTCA 2 G/D mis120Minor allele frequency- T:0.39NA EU EA WA 1820
    rs26556941,2
    A,C,F,H80305014(-) AGAGAC/TAGATT 1 -- ng3110Minor allele frequency- T:0.47EU EA WA NA 1020
    rs22921091,2
    A,C,F80253217(+) AGACAC/TATTTT 2 -- ut31 ese33Minor allele frequency- T:0.35NA 142
    rs26556551,2
    C,F,H80285260(-) TTACTC/TATCTG 2 L/S mis116Minor allele frequency- T:0.10NA EU EA WA 1472
    rs28031951,2
    C,F,H80285392(+) GACTAC/TGACAA 2 -- ut518Minor allele frequency- T:0.09EU EA WA 838
    rs168908351,2
    C,F,H80305710(+) ACATTA/GCATGG 1 -- ng3111Minor allele frequency- G:0.12NA EU EA WA 978
    rs10571741,2
    C,F,H80252396(-) ACTAGA/CGTGGA 2 -- ut31 ese312Minor allele frequency- C:0.02MN NA EU EA WA 1166
    About this table

    HapMap Linkage Disequilibrium images for LCA5 (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 611408   disorders: 604537  

    UniProtKB/Swiss-Prot: LCA5_HUMAN, Q86VQ0

  • Defects in LCA5 are the cause of Leber congenital amaurosis type 5 (LCA5) [MIM:604537].
    LCA designates a clinically and genetically heterogeneous group of childhood retinal
    degenerations, generally inherited in an autosomal recessive manner. Affected infants have little
    or no retinal photoreceptor function as tested by electroretinography. LCA represents the most
    common genetic cause of congenital visual impairment in infants and children
  • GeneTests: LCA5

    Leber Congenital Amaurosis

    Human Gene Mutation Database: LCA5
    Human Genome Epidemiology Navigator: LCA5 (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 PubMed articles for LCA5 gene:
    (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: 167691 HGNC: 31923 AceView: C6orf152 Ensembl:ENSG00000135338 euGenes: HUgn167691
    ECgene: LCA5 H-InvDB: LCA5
    (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

      --
    (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 LCA5:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



      Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
      Invitrogen Antibodies  Invitrogen Assays
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      Invitrogen Proteins / Assays / Screening Services  Search Invitrogen catalog for LCA5-related products

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     Predesigned and custom siRNAs for LCA5 Antibodies for LCA5
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for LCA5 Browse small molecules at Sigma-Aldrich
     "Your Favorite Gene" Pathwaysfeedback


      
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     Recombinant Proteins
    (Lebercilin)
     Antibodies (Lebercilin)
     Tagged/untagged cDNA clones
     Validated SYBR primer pairs
     Purified proteins from HEK293T cells
     Western blot validated antibodies
     shRNA in GFP-retroviral vector
     Search Tocris compounds for LCA5




     Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies
     Search Novus for antibodies for LCA5

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