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

Gene ID: 75782, updated on 21-Apr-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, Apr 2022]
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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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. Treatment Potential for LCA5-Associated Leber Congenital Amaurosis. Uyhazi KE, et al. Invest Ophthalmol Vis Sci, 2020 May 11. PMID 32428231, Free PMC Article
  2. 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
  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)
  • Gene trapped (1) 
  • Endonuclease-mediated (2) 

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 
acts_upstream_of_or_within 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 cell projection IEA
Inferred from Electronic Annotation
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 IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cilium ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoskeleton IEA
Inferred from Electronic Annotation
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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