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    Lca5 Leber congenital amaurosis 5 (human) [ Mus musculus (house mouse) ]

    Gene ID: 75782, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Lca5provided by MGI
    Official Full Name
    Leber congenital amaurosis 5 (human)provided by MGI
    Primary source
    MGI:MGI:1923032
    See related
    Ensembl:ENSMUSG00000032258 AllianceGenome:MGI:1923032
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    ORF64; 4930431B11Rik; 5730406O13Rik
    Summary
    Acts upstream of or within intraciliary transport and photoreceptor cell maintenance. Located in axoneme; ciliary basal body; and photoreceptor connecting cilium. Is expressed in several structures, including nervous system; reproductive system; sensory organ; surface ectoderm; and thymus. Used to study Leber congenital amaurosis 5. Human ortholog(s) of this gene implicated in Leber congenital amaurosis 5. Orthologous to human LCA5 (lebercilin LCA5). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in CNS E18 (RPKM 4.8), CNS E14 (RPKM 4.4) and 14 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Lca5 in Genome Data Viewer
    Location:
    9 E2; 9 45.42 cM
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (83273408..83325047, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (83391355..83442994, complement)

    Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 46122 Neighboring gene uncharacterized LOC118567674 Neighboring gene predicted gene, 40536 Neighboring gene ribosomal protein S27A, pseudogene 2 Neighboring gene STARR-positive B cell enhancer mm9_chr9:83334629-83334930 Neighboring gene predicted gene 2087 Neighboring gene STARR-seq mESC enhancer starr_24788 Neighboring gene ribosomal protein S15A, pseudogene Neighboring gene STARR-seq mESC enhancer starr_24789 Neighboring gene SH3 domain binding glutamic acid-rich protein like 2 Neighboring gene STARR-seq mESC enhancer starr_24791 Neighboring gene predicted gene, 39384

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Amelioration of Neurosensory Structure and Function in Animal and Cellular Models of a Congenital Blindness. Song JY, et al. Mol Ther, 2018 Jun 6. PMID 29673930, Free PMC Article
    2. Treatment Potential for LCA5-Associated Leber Congenital Amaurosis. Uyhazi KE, et al. Invest Ophthalmol Vis Sci, 2020 May 11. PMID 32428231, Free PMC Article
    3. 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
    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. Human chromosome 21 gene expression atlas in the mouse. Reymond A, et al. Nature, 2002 Dec 5. PMID 12466854

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Gene trapped (1) 

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within photoreceptor cell maintenance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cilium ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in neuron projection IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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
    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_027448.2 → NP_081724.1  lebercilin isoform b

      See identical proteins and their annotated locations for NP_081724.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) represents the longer transcript and encodes the longer protein (isoform b).
      Source sequence(s)
      AC146299, AK039510, BC049101
      Consensus CDS
      CCDS23374.1
      UniProtKB/Swiss-Prot
      Q80ST9, Q9CYM9, Q9D5J9
      UniProtKB/TrEMBL
      G5E886
      Related
      ENSMUSP00000034791.8, ENSMUST00000034791.15
      Conserved Domains (2) summary
      TIGR02168
      Location:114 → 478
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam15619
      Location:110 → 295
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease

    2. NM_029434.3 → NP_083710.2  lebercilin isoform a

      See identical proteins and their annotated locations for NP_083710.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) contains an alternate 3' terminal exon, compared to variant 2. It encodes isoform a, which has a shorter and distinct C-terminus, compared to isoform b.
      Source sequence(s)
      AC146299, AK015260
      Consensus CDS
      CCDS23373.1
      UniProtKB/TrEMBL
      A0A087WRS6, G5E887
      Related
      ENSMUSP00000034793.8, ENSMUST00000034793.15
      Conserved Domains (3) summary
      pfam15619
      Location:110 → 289
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
      cl14813
      Location:152 → 288
      GluZincin; Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins)
      cl19219
      Location:82 → 186
      DUF342; Protein of unknown function (DUF342)

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000075.7 Reference GRCm39 C57BL/6J

      Range
      83273408..83325047 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006511536.5 → XP_006511599.1  lebercilin isoform X1

      See identical proteins and their annotated locations for XP_006511599.1

      UniProtKB/Swiss-Prot
      Q80ST9, Q9CYM9, Q9D5J9
      UniProtKB/TrEMBL
      G5E886
      Conserved Domains (2) summary
      TIGR02168
      Location:114 → 478
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam15619
      Location:110 → 295
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease

    2. XM_006511535.5 → XP_006511598.1  lebercilin isoform X1

      See identical proteins and their annotated locations for XP_006511598.1

      UniProtKB/Swiss-Prot
      Q80ST9, Q9CYM9, Q9D5J9
      UniProtKB/TrEMBL
      G5E886
      Conserved Domains (2) summary
      TIGR02168
      Location:114 → 478
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam15619
      Location:110 → 295
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease

    3. XM_036155372.1 → XP_036011265.1  lebercilin isoform X1

      UniProtKB/Swiss-Prot
      Q80ST9, Q9CYM9, Q9D5J9
      UniProtKB/TrEMBL
      G5E886
      Conserved Domains (2) summary
      TIGR02168
      Location:114 → 478
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam15619
      Location:110 → 295
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease

    4. XM_006511534.4 → XP_006511597.1  lebercilin isoform X1

      See identical proteins and their annotated locations for XP_006511597.1

      UniProtKB/Swiss-Prot
      Q80ST9, Q9CYM9, Q9D5J9
      UniProtKB/TrEMBL
      G5E886
      Conserved Domains (2) summary
      TIGR02168
      Location:114 → 478
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam15619
      Location:110 → 295
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease

    5. XM_036155373.1 → XP_036011266.1  lebercilin isoform X1

      UniProtKB/Swiss-Prot
      Q80ST9, Q9CYM9, Q9D5J9
      UniProtKB/TrEMBL
      G5E886
      Conserved Domains (2) summary
      TIGR02168
      Location:114 → 478
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam15619
      Location:110 → 295
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease

    6. XM_006511537.4 → XP_006511600.1  lebercilin isoform X1

      See identical proteins and their annotated locations for XP_006511600.1

      UniProtKB/Swiss-Prot
      Q80ST9, Q9CYM9, Q9D5J9
      UniProtKB/TrEMBL
      G5E886
      Conserved Domains (2) summary
      TIGR02168
      Location:114 → 478
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam15619
      Location:110 → 295
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease

    7. XM_006511538.4 → XP_006511601.1  lebercilin isoform X1

      See identical proteins and their annotated locations for XP_006511601.1

      UniProtKB/Swiss-Prot
      Q80ST9, Q9CYM9, Q9D5J9
      UniProtKB/TrEMBL
      G5E886
      Conserved Domains (2) summary
      TIGR02168
      Location:114 → 478
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam15619
      Location:110 → 295
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease

    8. XM_011242833.4 → XP_011241135.1  lebercilin isoform X1

      See identical proteins and their annotated locations for XP_011241135.1

      UniProtKB/Swiss-Prot
      Q80ST9, Q9CYM9, Q9D5J9
      UniProtKB/TrEMBL
      G5E886
      Conserved Domains (2) summary
      TIGR02168
      Location:114 → 478
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam15619
      Location:110 → 295
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease

    9. XM_011242832.3 → XP_011241134.1  lebercilin isoform X1

      See identical proteins and their annotated locations for XP_011241134.1

      UniProtKB/Swiss-Prot
      Q80ST9, Q9CYM9, Q9D5J9
      UniProtKB/TrEMBL
      G5E886
      Conserved Domains (2) summary
      TIGR02168
      Location:114 → 478
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam15619
      Location:110 → 295
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease

    10. XM_030244694.2 → XP_030100554.1  lebercilin isoform X1

      UniProtKB/Swiss-Prot
      Q80ST9, Q9CYM9, Q9D5J9
      UniProtKB/TrEMBL
      G5E886
      Conserved Domains (2) summary
      TIGR02168
      Location:114 → 478
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam15619
      Location:110 → 295
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q80ST9.1 GenPept UniProtKB/Swiss-Prot:Q80ST9

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