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    Nyx nyctalopin [ Rattus norvegicus (Norway rat) ]

    Gene ID: 302516, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Nyxprovided by RGD
    Official Full Name
    nyctalopinprovided by RGD
    Primary source
    RGD:1561300
    See related
    EnsemblRapid:ENSRNOG00000009646 AllianceGenome:RGD:1561300
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1561300
    Summary
    Predicted to act upstream of or within visual perception. Predicted to be active in extracellular matrix and extracellular space. Human ortholog(s) of this gene implicated in congenital stationary night blindness 1A and night blindness. Orthologous to human NYX (nyctalopin). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Brain (RPKM 20.1), Adrenal (RPKM 6.0) and 3 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Nyx in Genome Data Viewer
    Location:
    Xq12
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) X NC_086039.1 (11953680..11974716, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) X NC_051356.1 (9280864..9301900, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) X NC_005120.4 (10197547..10218583, complement)

    Chromosome X - NC_086039.1Genomic Context describing neighboring genes Neighboring gene calcium/calmodulin dependent serine protein kinase Neighboring gene uncharacterized LOC120099226 Neighboring gene transfer RNA aspartic acid (anticodon GUC) 13 Neighboring gene uncharacterized LOC120099244 Neighboring gene Glyceraldehyde-3-phosphate dehydrogenase, pseudogene 81

    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. A naturally-occurring mutation in Cacna1f in a rat model of congenital stationary night blindness. Gu Y, et al. Mol Vis, 2008 Jan 9. PMID 18246026, Free PMC Article
    2. Mutations in NYX, encoding the leucine-rich proteoglycan nyctalopin, cause X-linked complete congenital stationary night blindness. Bech-Hansen NT, et al. Nat Genet, 2000 Nov. PMID 11062471
    3. Contribution of Kir4.1 to the mouse electroretinogram. Wu J, et al. Mol Vis, 2004 Sep 1. PMID 15359216, Free PMC Article
    4. Identification of the gene and the mutation responsible for the mouse nob phenotype. Gregg RG, et al. Invest Ophthalmol Vis Sci, 2003 Jan. PMID 12506099
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    acts_upstream_of_or_within visual perception ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    nyctalopin

    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_001100967.1 → NP_001094437.1  nyctalopin precursor

      See identical proteins and their annotated locations for NP_001094437.1

      Status: PROVISIONAL

      Source sequence(s)
      DQ393414
      UniProtKB/TrEMBL
      A1XIQ3, A6JZY0, F7EKE5
      Related
      ENSRNOP00000013382.5, ENSRNOT00000013382.7
      Conserved Domains (5) summary
      smart00013
      Location:25 → 56
      LRRNT; Leucine rich repeat N-terminal domain
      smart00082
      Location:331 → 366
      LRRCT; Leucine rich repeat C-terminal domain
      cd00116
      Location:68 → 312
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      sd00033
      Location:63 → 82
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:249 → 309
      LRR_8; Leucine rich repeat

    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_086039.1 Reference GRCr8

      Range
      11953680..11974716 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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