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    Opn1sw opsin 1, short wave sensitive [ Rattus norvegicus (Norway rat) ]

    Gene ID: 81644, updated on 18-Sep-2018

    Summary

    Official Symbol
    Opn1swprovided by RGD
    Official Full Name
    opsin 1, short wave sensitiveprovided by RGD
    Primary source
    RGD:621033
    See related
    Ensembl:ENSRNOG00000006874
    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
    Summary
    mouse homolog is a blue cone pigment gene and member of the S branch of visual pigments [RGD, Feb 2006]
    Annotation information
    Annotation category: partial on reference assembly
    Expression
    Biased expression in Spleen (RPKM 2.3), Uterus (RPKM 2.2) and 9 other tissues See more
    Orthologs

    Genomic context

    See Opn1sw in Genome Data Viewer
    Location:
    4q22
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (56653840..56656980, complement)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) 4 NC_005103.3 (56421001..56424141, complement)

    Chromosome 4 - NC_005103.4Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 71, member F1 Neighboring gene calumenin Neighboring gene transfer RNA proline (anticodon AGG) Neighboring gene coiled-coil domain containing 136

    Genomic regions, transcripts, and products

    Expression

    • 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

    Pathways from BioSystems

    General gene information

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    G protein-coupled photoreceptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    G protein-coupled receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    molecular_function ND
    No biological Data available
    more info
     
    photoreceptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    G protein-coupled receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    G protein-coupled receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    biological_process ND
    No biological Data available
    more info
     
    cellular response to light stimulus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    detection of visible light IEA
    Inferred from Electronic Annotation
    more info
     
    phototransduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    phototransduction IEA
    Inferred from Electronic Annotation
    more info
     
    protein-chromophore linkage IEA
    Inferred from Electronic Annotation
    more info
     
    visual perception IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cell body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    integral component of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    photoreceptor outer segment IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    photoreceptor outer segment IDA
    Inferred from Direct Assay
    more info
    PubMed 
    photoreceptor outer segment IEA
    Inferred from Electronic Annotation
    more info
     
    photoreceptor outer segment ISO
    Inferred from Sequence Orthology
    more info
     
    terminal bouton IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    short-wave-sensitive opsin 1
    Names
    BOP
    blue cone opsin-like pigment
    blue cone photoreceptor pigment
    blue-sensitive opsin
    opsin 1 (cone pigments), short-wave-sensitive (color blindness, tritan)
    s opsin
    short wavelength-sensitive cone opsin

    NCBI Reference Sequences (RefSeq)

    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_031015.1NP_112277.1  short-wave-sensitive opsin 1

      See identical proteins and their annotated locations for NP_112277.1

      Status: PROVISIONAL

      Source sequence(s)
      U63972
      UniProtKB/Swiss-Prot
      Q63652
      Related
      ENSRNOP00000009278.1, ENSRNOT00000009278.3
      Conserved Domains (2) summary
      pfam00001
      Location:50301
      7tm_1; 7 transmembrane receptor (rhodopsin family)
      cl21561
      Location:50319
      7tm_4; Olfactory receptor

    RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

    Reference Rnor_6.0 Primary Assembly

    Genomic

    1. NC_005103.4 Reference Rnor_6.0 Primary Assembly

      Range
      56653840..56656980 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate Rn_Celera

    Genomic

    1. AC_000072.1 Alternate Rn_Celera

      Range
      53085329..53088469 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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