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OPN1LW opsin 1, long wave sensitive [ Homo sapiens (human) ]

Gene ID: 5956, updated on 2-Nov-2024

Summary

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Official Symbol
OPN1LWprovided by HGNC
Official Full Name
opsin 1, long wave sensitiveprovided by HGNC
Primary source
HGNC:HGNC:9936
See related
Ensembl:ENSG00000102076 MIM:300822; AllianceGenome:HGNC:9936
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CBP; RCP; ROP; CBBM; COD5
Summary
This gene encodes for a light absorbing visual pigment of the opsin gene family. The encoded protein is called red cone photopigment or long-wavelength sensitive opsin. Opsins are G-protein coupled receptors with seven transmembrane domains, an N-terminal extracellular domain, and a C-terminal cytoplasmic domain. This gene and the medium-wavelength opsin gene are tandemly arrayed on the X chromosome and frequent unequal recombination and gene conversion may occur between these sequences. X chromosomes may have fusions of the medium- and long-wavelength opsin genes or may have more than one copy of these genes. Defects in this gene are the cause of partial, protanopic colorblindness. [provided by RefSeq, Jul 2008]
Expression
Low expression observed in reference dataset See more
Orthologs
all
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Genomic context

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See OPN1LW in Genome Data Viewer
Location:
Xq28
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (154144243..154159032)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152417896..152432685)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153409717..153424507)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153285318-153286287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30052 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153297889-153298431 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153298432-153298975 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153298976-153299518 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chrX:153301355-153301920 Neighboring gene microRNA 718 Neighboring gene methyl-CpG binding protein 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153306499-153306999 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30053 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21083 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:153362776-153363014 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21085 Neighboring gene Sharpr-MPRA regulatory region 3572 Neighboring gene opsin locus control region Neighboring gene TEX28 pseudogene 2 Neighboring gene opsin 1, medium wave sensitive Neighboring gene TEX28 pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Unique Haplotypes in OPN1LW as a Common Cause of High Myopia With or Without Protanopia: A Potential Window Into Myopic Mechanism. Wang Y, et al. Invest Ophthalmol Vis Sci, 2023 Apr 3. PMID 37097228, Free PMC Article
  2. Unique haplotype in exon 3 of cone opsin mRNA affects splicing of its precursor, leading to congenital color vision defect. Ueyama H, et al. Biochem Biophys Res Commun, 2012 Jul 20. PMID 22732407
  3. Thyroid hormone controls cone opsin expression in the retina of adult rodents. Glaschke A, et al. J Neurosci, 2011 Mar 30. PMID 21451022, Free PMC Article
  4. Unique Variants in OPN1LW Cause Both Syndromic and Nonsyndromic X-Linked High Myopia Mapped to MYP1. Li J, et al. Invest Ophthalmol Vis Sci, 2015 Jun. PMID 26114493
  5. The influence of L-opsin gene polymorphisms and neural ageing on spatio-chromatic contrast sensitivity in 20-71 year olds. Dees EW, et al. Vision Res, 2015 Nov. PMID 26368273

See all (65) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Unique Haplotypes in OPN1LW as a Common Cause of High Myopia With or Without Protanopia: A Potential Window Into Myopic Mechanism.
    Title: Unique Haplotypes in OPN1LW as a Common Cause of High Myopia With or Without Protanopia: A Potential Window Into Myopic Mechanism.
  2. The landscape of submicroscopic structural variants at the OPN1LW/OPN1MW gene cluster on Xq28 underlying blue cone monochromacy.
    Title: The landscape of submicroscopic structural variants at the OPN1LW/OPN1MW gene cluster on Xq28 underlying blue cone monochromacy.
  3. Novel OPN1LW/OPN1MW Exon 3 Haplotype-Associated Splicing Defect in Patients with X-Linked Cone Dysfunction.
    Title: Novel OPN1LW/OPN1MW Exon 3 Haplotype-Associated Splicing Defect in Patients with X-Linked Cone Dysfunction.
  4. Insight from OPN1LW Gene Haplotypes into the Cause and Prevention of Myopia.
    Title: Insight from OPN1LW Gene Haplotypes into the Cause and Prevention of Myopia.
  5. Intermixing the OPN1LW and OPN1MW Genes Disrupts the Exonic Splicing Code Causing an Array of Vision Disorders.
    Title: Intermixing the OPN1LW and OPN1MW Genes Disrupts the Exonic Splicing Code Causing an Array of Vision Disorders.
  6. Visual and ocular findings in a family with X-linked cone dysfunction and protanopia.
    Title: Visual and ocular findings in a family with X-linked cone dysfunction and protanopia.
  7. These results suggest that O-glycosylation is a fundamental feature of red and green cone opsins, which may be relevant to their function or to cone cell development, and that differences in this post-translational modification also could contribute to the different morphologies of rod and cone photoreceptors.
    Title: Human red and green cone opsins are O-glycosylated at an N-terminal Ser/Thr-rich domain conserved in vertebrates.
  8. Differential stability of variant OPN1LW gene transcripts in myopic Australian islander patients has been reported.
    Title: Differential stability of variant OPN1LW gene transcripts in myopic patients.
  9. Molecular genetic analysis of the OPN1LW/OPN1MW gene cluster revealed a novel deletion of about 73 kb in the patient encompassing the LCR.
    Title: A 73,128 bp de novo deletion encompassing the OPN1LW/OPN1MW gene cluster in sporadic Blue Cone Monochromacy: a case report.
  10. OPN1LW and OPN1MW restore M-cone function in a mouse model of human blue cone monochromacy.
    Title: Human L- and M-opsins restore M-cone function in a mouse model for human blue cone monochromacy.
Submit: New GeneRIF Correction See all GeneRIFs (35)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Cone monochromatism
MedGen: C0339537 OMIM: 303700 GeneReviews: Not available
not available
Protan defect
MedGen: C0155015 OMIM: 303900 GeneReviews: Not available
not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables G protein-coupled photoreceptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables photoreceptor activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in G protein-coupled receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cellular response to light stimulus IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in detection of visible light IEA
Inferred from Electronic Annotation
more info
  
involved_in phototransduction IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of cytokinesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in signal transduction TAS
Traceable Author Statement
more info
 PubMed 
involved_in visual perception IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in photoreceptor disc membrane TAS
Traceable Author Statement
more info
  
is_active_in photoreceptor outer segment IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
long-wave-sensitive opsin 1
Names
cone dystrophy 5 (X-linked)
opsin 1 (cone pigments), long-wave-sensitive
red cone opsin
red cone photoreceptor pigment
red-sensitive opsin

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.

Genomic

  1. NG_009105.2 RefSeqGene

    Range
    4993..19782
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_020061.6 → NP_064445.2  long-wave-sensitive opsin 1

    Status: REVIEWED

    Source sequence(s)
    BM688032, BQ639996, BU726889, DN693335, EL949562
    Consensus CDS
    CCDS14742.1
    UniProtKB/Swiss-Prot
    P04000
    UniProtKB/TrEMBL
    Q68CR4
    Related
    ENSP00000358967.4, ENST00000369951.9
    Conserved Domains (2) summary
    pfam00001
    Location:71 → 322
    7tm_1; 7 transmembrane receptor (rhodopsin family)
    cl21561
    Location:68 → 264
    7tm_4; Olfactory receptor

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    154144243..154159032
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    152417896..152432685
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P04000.2 GenPept UniProtKB/Swiss-Prot:P04000

Gene LinkOut

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