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    Lca5 lebercilin LCA5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 300866, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Lca5provided by RGD
    Official Full Name
    lebercilin LCA5provided by RGD
    Primary source
    RGD:1308555
    See related
    EnsemblRapid:ENSRNOG00000009580 AllianceGenome:RGD:1308555
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1308555
    Summary
    Predicted to be involved in intraciliary transport. Predicted to act upstream of or within photoreceptor cell maintenance. Located in ciliary basal body and photoreceptor connecting cilium. Human ortholog(s) of this gene implicated in Leber congenital amaurosis 5. Orthologous to human LCA5 (lebercilin LCA5). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Kidney (RPKM 26.0), Testes (RPKM 15.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Lca5 in Genome Data Viewer
    Location:
    8q31
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (93187735..93255060, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (84307696..84375025, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (90926309..90984271, complement)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102554337 Neighboring gene uncharacterized LOC134480082 Neighboring gene uncharacterized LOC134480083 Neighboring gene uncharacterized LOC134479960 Neighboring gene ribosomal protein S18, pseudogene 9

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Disruption of intraflagellar protein transport in photoreceptor cilia causes Leber congenital amaurosis in humans and mice. Boldt K, et al. J Clin Invest, 2011 Jun. PMID 21606596, Free PMC Article
    2. Mutations in LCA5, encoding the ciliary protein lebercilin, cause Leber congenital amaurosis. den Hollander AI, et al. Nat Genet, 2007 Jul. PMID 17546029
    3. OFD1 is mutated in X-linked Joubert syndrome and interacts with LCA5-encoded lebercilin. Coene KL, et al. Am J Hum Genet, 2009 Oct. PMID 19800048, Free PMC Article
    4. Disruption of the retinitis pigmentosa 28 gene Fam161a in mice affects photoreceptor ciliary structure and leads to progressive retinal degeneration. Karlstetter M, et al. Hum Mol Genet, 2014 Oct 1. PMID 24833722
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. mutated OFD1 interacts with LCA5-encoded lebercilin
      Title: OFD1 is mutated in X-linked Joubert syndrome and interacts with LCA5-encoded lebercilin.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables protein-containing complex binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in intraciliary transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within intraciliary transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within intraciliary transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within photoreceptor cell maintenance ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within photoreceptor cell maintenance ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in axoneme IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in axoneme ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in ciliary basal body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in ciliary basal body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cilium ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cilium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in neuron projection ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in photoreceptor connecting cilium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in photoreceptor connecting cilium ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    lebercilin
    Names
    LCA5, lebercilin
    leber congenital amaurosis 5 protein homolog

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001393917.1 → NP_001380846.1  lebercilin

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/Swiss-Prot
      Q5U2Y9, Q5XIM2
      UniProtKB/TrEMBL
      A0A8L2RA12, A6I1R3
      Conserved Domains (2) summary
      pfam15619
      Location:111 → 296
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
      NF033930
      Location:180 → 483
      pneumo_PspA; pneumococcal surface protein A

    RNA

    1. NR_172050.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086026.1 Reference GRCr8

      Range
      93187735..93255060 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039081165.1 → XP_038937093.1  lebercilin isoform X2

      UniProtKB/TrEMBL
      A0A0G2K802, A6I1R1
      Related
      ENSRNOP00000074416.2, ENSRNOT00000086426.3
      Conserved Domains (1) summary
      pfam15619
      Location:111 → 296
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease

    2. XM_039081163.1 → XP_038937091.1  lebercilin isoform X1

      UniProtKB/Swiss-Prot
      Q5U2Y9, Q5XIM2
      UniProtKB/TrEMBL
      A0A8L2RA12, A6I1R3
      Related
      ENSRNOP00000046841.3, ENSRNOT00000044931.6
      Conserved Domains (2) summary
      pfam15619
      Location:111 → 296
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
      NF033930
      Location:180 → 483
      pneumo_PspA; pneumococcal surface protein A

    3. XM_039081164.1 → XP_038937092.1  lebercilin isoform X1

      UniProtKB/Swiss-Prot
      Q5U2Y9, Q5XIM2
      UniProtKB/TrEMBL
      A0A8L2RA12, A6I1R3
      Conserved Domains (2) summary
      pfam15619
      Location:111 → 296
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
      NF033930
      Location:180 → 483
      pneumo_PspA; pneumococcal surface protein A

    4. XM_063265191.1 → XP_063121261.1  lebercilin isoform X2

      UniProtKB/TrEMBL
      A0A0G2K802, A6I1R1

    5. XM_063265192.1 → XP_063121262.1  lebercilin isoform X2

      UniProtKB/TrEMBL
      A0A0G2K802, A6I1R1

    6. XM_063265188.1 → XP_063121258.1  lebercilin isoform X2

      UniProtKB/TrEMBL
      A0A0G2K802, A6I1R1

    7. XM_063265189.1 → XP_063121259.1  lebercilin isoform X2

      UniProtKB/TrEMBL
      A0A0G2K802, A6I1R1

    8. XM_008766251.3 → XP_008764473.1  lebercilin isoform X1

      See identical proteins and their annotated locations for XP_008764473.1

      UniProtKB/Swiss-Prot
      Q5U2Y9, Q5XIM2
      UniProtKB/TrEMBL
      A0A8L2RA12, A6I1R3
      Conserved Domains (2) summary
      pfam15619
      Location:111 → 296
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
      NF033930
      Location:180 → 483
      pneumo_PspA; pneumococcal surface protein A

    9. XM_008766255.4 → XP_008764477.1  lebercilin isoform X1

      See identical proteins and their annotated locations for XP_008764477.1

      UniProtKB/Swiss-Prot
      Q5U2Y9, Q5XIM2
      UniProtKB/TrEMBL
      A0A8L2RA12, A6I1R3
      Conserved Domains (2) summary
      pfam15619
      Location:111 → 296
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
      NF033930
      Location:180 → 483
      pneumo_PspA; pneumococcal surface protein A

    10. XM_008766256.3 → XP_008764478.1  lebercilin isoform X1

      See identical proteins and their annotated locations for XP_008764478.1

      UniProtKB/Swiss-Prot
      Q5U2Y9, Q5XIM2
      UniProtKB/TrEMBL
      A0A8L2RA12, A6I1R3
      Conserved Domains (2) summary
      pfam15619
      Location:111 → 296
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
      NF033930
      Location:180 → 483
      pneumo_PspA; pneumococcal surface protein A

    11. XM_008766252.4 → XP_008764474.1  lebercilin isoform X1

      See identical proteins and their annotated locations for XP_008764474.1

      UniProtKB/Swiss-Prot
      Q5U2Y9, Q5XIM2
      UniProtKB/TrEMBL
      A0A8L2RA12, A6I1R3
      Conserved Domains (2) summary
      pfam15619
      Location:111 → 296
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
      NF033930
      Location:180 → 483
      pneumo_PspA; pneumococcal surface protein A

    12. XM_008766249.4 → XP_008764471.1  lebercilin isoform X1

      See identical proteins and their annotated locations for XP_008764471.1

      UniProtKB/Swiss-Prot
      Q5U2Y9, Q5XIM2
      UniProtKB/TrEMBL
      A0A8L2RA12, A6I1R3
      Conserved Domains (2) summary
      pfam15619
      Location:111 → 296
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
      NF033930
      Location:180 → 483
      pneumo_PspA; pneumococcal surface protein A

    13. XM_008766258.4 → XP_008764480.1  lebercilin isoform X1

      See identical proteins and their annotated locations for XP_008764480.1

      UniProtKB/Swiss-Prot
      Q5U2Y9, Q5XIM2
      UniProtKB/TrEMBL
      A0A8L2RA12, A6I1R3
      Conserved Domains (2) summary
      pfam15619
      Location:111 → 296
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
      NF033930
      Location:180 → 483
      pneumo_PspA; pneumococcal surface protein A

    14. XM_008766257.3 → XP_008764479.1  lebercilin isoform X1

      See identical proteins and their annotated locations for XP_008764479.1

      UniProtKB/Swiss-Prot
      Q5U2Y9, Q5XIM2
      UniProtKB/TrEMBL
      A0A8L2RA12, A6I1R3
      Conserved Domains (2) summary
      pfam15619
      Location:111 → 296
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
      NF033930
      Location:180 → 483
      pneumo_PspA; pneumococcal surface protein A

    RNA

    1. XR_010053951.1 RNA Sequence

    2. XR_005487787.2 RNA Sequence

    3. XR_005487788.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5U2Y9.1 GenPept UniProtKB/Swiss-Prot:Q5U2Y9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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