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lca5 lebercilin LCA5 [ Danio rerio (zebrafish) ]

Gene ID: 100151323, updated on 27-Mar-2024

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. Predicted to be active in axoneme. 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, Apr 2022]
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:
9
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 23 NC_007134.7 (31380606..31400875, 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 intraciliary transport IBA
Inferred from Biological aspect of Ancestor
more info
  
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 
Component Evidence Code Pubs
is_active_in axoneme IBA
Inferred from Biological aspect of Ancestor
more info
  

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: Danio rerio Annotation Release 106 details...Open this link in a new tab

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
    31380606..31400875 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_021470016.1 → XP_021325691.1  lebercilin isoform X6

    UniProtKB/TrEMBL
    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_021470013.1 → XP_021325688.1  lebercilin isoform X3

    UniProtKB/TrEMBL
    A0A8M9PFL3
    Conserved Domains (2) summary
    pfam15619
    Location:161 → 340
    Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
    cl26511
    Location:143 → 562
    Neuromodulin_N; Gap junction protein N-terminal region

  3. XM_021470011.1 → XP_021325686.1  lebercilin isoform X1

    UniProtKB/TrEMBL
    A0A8M9PTM7
    Conserved Domains (2) summary
    pfam15619
    Location:161 → 340
    Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
    cl26511
    Location:143 → 566
    Neuromodulin_N; Gap junction protein N-terminal region

  4. XM_021470014.1 → XP_021325689.1  lebercilin isoform X4

    UniProtKB/TrEMBL
    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_021470012.1 → XP_021325687.1  lebercilin isoform X2

    UniProtKB/TrEMBL
    A0A8M9P5L0
    Conserved Domains (2) summary
    pfam15619
    Location:161 → 340
    Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
    cl26511
    Location:143 → 565
    Neuromodulin_N; Gap junction protein N-terminal region

  6. XM_021470010.1 → XP_021325685.1  lebercilin isoform X1

    UniProtKB/TrEMBL
    A0A8M9PTM7
    Conserved Domains (2) summary
    pfam15619
    Location:161 → 340
    Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
    cl26511
    Location:143 → 566
    Neuromodulin_N; Gap junction protein N-terminal region

  7. XM_021470015.1 → XP_021325690.1  lebercilin isoform X5

    UniProtKB/TrEMBL
    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

Reference GRCz11 ALT_DRER_TU_1

Genomic

  1. NW_018395159.1 Reference GRCz11 ALT_DRER_TU_1

    Range
    215983..236189 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017353736.2 → XP_017209225.2  lebercilin isoform X6

    UniProtKB/TrEMBL
    A0A8M6YW27
    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_017353735.2 → XP_017209224.2  lebercilin isoform X3

    UniProtKB/TrEMBL
    A0A8M6Z3Y4
    Conserved Domains (2) summary
    pfam15619
    Location:161 → 340
    Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
    cl26511
    Location:143 → 562
    Neuromodulin_N; Gap junction protein N-terminal region

  3. XM_017353734.2 → XP_017209223.2  lebercilin isoform X1

    UniProtKB/TrEMBL
    A0A8M6YVF9
    Conserved Domains (2) summary
    pfam15619
    Location:161 → 340
    Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
    cl26511
    Location:143 → 566
    Neuromodulin_N; Gap junction protein N-terminal region

  4. XM_021473730.1 → XP_021329405.1  lebercilin isoform X2

    UniProtKB/TrEMBL
    A0A8M9Q832
    Conserved Domains (2) summary
    pfam15619
    Location:161 → 340
    Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
    cl26511
    Location:143 → 565
    Neuromodulin_N; Gap junction protein N-terminal region

  5. XM_009297009.3 → XP_009295284.2  lebercilin isoform X5

    UniProtKB/TrEMBL
    A0A8M3AVL5
    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

  6. XM_009297008.3 → XP_009295283.2  lebercilin isoform X4

    UniProtKB/TrEMBL
    A0A8M3AYN7
    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_009297006.3 → XP_009295281.2  lebercilin isoform X1

    UniProtKB/TrEMBL
    A0A8M6YVF9
    Conserved Domains (2) summary
    pfam15619
    Location:161 → 340
    Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
    cl26511
    Location:143 → 566
    Neuromodulin_N; Gap junction protein N-terminal region
Nucleotide Protein Strain
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