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Lca5 lebercilin LCA5 [ Rattus norvegicus (Norway rat) ]

Gene ID: 300866, updated on 13-Apr-2024

Summary

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Official Symbol
Lca5provided by RGD
Official Full Name
lebercilin LCA5provided by RGD
Primary source
RGD:1308555
See related
Ensembl: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, Apr 2022]
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, ENSRNOT00000086426.2
    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, ENSRNOT00000044931.5
    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
    Related
    ENSRNOP00000075180.2
    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

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