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    lca5 lebercilin LCA5 [ Danio rerio (zebrafish) ]

    Gene ID: 100151323, updated on 4-Jan-2025

    Summary

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    Official Symbol
    lca5provided by ZNC
    Official Full Name
    lebercilin LCA5provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-090313-268
    See related
    Ensembl:ENSDARG00000076153 AllianceGenome:ZFIN:ZDB-GENE-090313-268
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    si:dkey-241o6.2
    Summary
    Involved in photoreceptor cell maintenance and photoreceptor cell outer segment organization. Used to study Leber congenital amaurosis. Human ortholog(s) of this gene implicated in Leber congenital amaurosis 5. Orthologous to human LCA5 (lebercilin LCA5). [provided by Alliance of Genome Resources, Jan 2025]
    Orthologs
    human mouse all
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    Genomic context

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    See lca5 in Genome Data Viewer
    Location:
    chromosome: 23
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 23 NC_007134.7 (31380607..31400832, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 23 NC_007134.6 (31453994..31474293, complement)

    Chromosome 23 - NC_007134.7Genomic Context describing neighboring genes Neighboring gene pleckstrin homology domain interacting protein Neighboring gene high mobility group nucleosomal binding domain 3 Neighboring gene si:dkeyp-79f12.7 Neighboring gene SH3 domain binding glutamate-rich protein like 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Knocking out lca5 in zebrafish causes cone-rod dystrophy due to impaired outer segment protein trafficking. Qu Z, et al. Biochim Biophys Acta Mol Basis Dis, 2019 Oct 1. PMID 31348989
    2. Transcriptomic analyses reveal novel genes with sexually dimorphic expression in the zebrafish gonad and brain. Sreenivasan R, et al. PLoS One, 2008 Mar 12. PMID 18335061, Free PMC Article
    3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article
    4. Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. Pasquier J, et al. BMC Genomics, 2016 May 18. PMID 27189481, Free PMC Article

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Knocking out lca5 in zebrafish causes cone-rod dystrophy due to impaired outer segment protein trafficking.
      Title: Knocking out lca5 in zebrafish causes cone-rod dystrophy due to impaired outer segment protein trafficking.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    Gene Ontology Provided by ZFIN

    Process Evidence Code Pubs
    involved_in photoreceptor cell maintenance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in photoreceptor cell outer segment organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    Lebercilin; lebercilin
    Names
    Leber congenital amaurosis 5

    NCBI Reference Sequences (RefSeq)

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    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007134.7 Reference GRCz11 Primary Assembly

      Range
      31380607..31400832 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021470016.2 → XP_021325691.1  lebercilin isoform X4

      UniProtKB/TrEMBL
      A0A8M9PFL3, A0A8M9PTN2
      Related
      ENSDARP00000099722.4, ENSDART00000112619.4
      Conserved Domains (2) summary
      pfam15619
      Location:161 → 340
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
      cl26511
      Location:143 → 549
      Neuromodulin_N; Gap junction protein N-terminal region

    2. XM_021470015.2 → XP_021325690.1  lebercilin isoform X2

      UniProtKB/TrEMBL
      A0A8M9P5L0, A0A8M9PWZ1, E9QG33
      Related
      ENSDARP00000115551.2, ENSDART00000132736.4
      Conserved Domains (2) summary
      pfam15619
      Location:161 → 340
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
      cl26511
      Location:143 → 550
      Neuromodulin_N; Gap junction protein N-terminal region

    3. XM_068216924.1 → XP_068073025.1  lebercilin isoform X3

      UniProtKB/TrEMBL
      A0A8M9PFL3

    4. XM_021470014.2 → XP_021325689.1  lebercilin isoform X1

      UniProtKB/TrEMBL
      A0A8M9P5L0, A0A8M9PLA8
      Conserved Domains (2) summary
      pfam15619
      Location:161 → 340
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
      cl26511
      Location:143 → 551
      Neuromodulin_N; Gap junction protein N-terminal region

    5. XM_068216923.1 → XP_068073024.1  lebercilin isoform X1

      UniProtKB/TrEMBL
      A0A8M9P5L0, A0A8M9PLA8

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018395159.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      215983..260004 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068219068.1 → XP_068075169.1  lebercilin isoform X1

      UniProtKB/TrEMBL
      A0A8M3AYN7, A0A8M9Q832

    2. XM_068219069.1 → XP_068075170.1  lebercilin isoform X2

      UniProtKB/TrEMBL
      A0A8M3AVL5, A0A8M9Q832

    3. XM_017353736.3 → XP_017209225.2  lebercilin isoform X4

      UniProtKB/TrEMBL
      A0A8M6YW27, A0A8M6Z3Y4
      Conserved Domains (2) summary
      pfam15619
      Location:161 → 340
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
      cl26511
      Location:143 → 549
      Neuromodulin_N; Gap junction protein N-terminal region

    4. XM_009297009.4 → XP_009295284.2  lebercilin isoform X2

      UniProtKB/TrEMBL
      A0A8M3AVL5, A0A8M9Q832
      Conserved Domains (2) summary
      pfam15619
      Location:161 → 340
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
      cl26511
      Location:143 → 550
      Neuromodulin_N; Gap junction protein N-terminal region

    5. XM_068219070.1 → XP_068075171.1  lebercilin isoform X3

      UniProtKB/TrEMBL
      A0A8M6Z3Y4

    6. XM_009297008.4 → XP_009295283.2  lebercilin isoform X1

      UniProtKB/TrEMBL
      A0A8M3AYN7, A0A8M9Q832
      Conserved Domains (2) summary
      pfam15619
      Location:161 → 340
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
      cl26511
      Location:143 → 551
      Neuromodulin_N; Gap junction protein N-terminal region

    7. XM_068219067.1 → XP_068075168.1  lebercilin isoform X1

      UniProtKB/TrEMBL
      A0A8M3AYN7, A0A8M9Q832
    Nucleotide Protein Strain
    Heading Accession and Version

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