U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Optc opticin [ Rattus norvegicus (Norway rat) ]

Gene ID: 304802, updated on 10-Oct-2024

Summary

Go to the top of the page Help
Official Symbol
Optcprovided by RGD
Official Full Name
opticinprovided by RGD
Primary source
RGD:1304916
See related
EnsemblRapid:ENSRNOG00000003059 AllianceGenome:RGD:1304916
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to be involved in collagen fibril organization. Predicted to act upstream of or within negative regulation of angiogenesis. Predicted to be active in extracellular matrix. Orthologous to human OPTC (opticin). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Thymus (RPKM 8.0), Lung (RPKM 6.9) and 9 other tissues See more
Orthologs
human mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See Optc in Genome Data Viewer
Location:
13q13
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 13 NC_086031.1 (47906145..47920334, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 13 NC_051348.1 (45353954..45368254, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (50735509..50748908, complement)

Chromosome 13 - NC_086031.1Genomic Context describing neighboring genes Neighboring gene ATPase plasma membrane Ca2+ transporting 4 Neighboring gene uncharacterized LOC134481499 Neighboring gene uncharacterized LOC134481498 Neighboring gene uncharacterized LOC102557118 Neighboring gene proline and arginine rich end leucine rich repeat protein Neighboring gene uncharacterized LOC134481559 Neighboring gene uncharacterized LOC134481558

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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

Go to the top of the pageHelp

Related articles in PubMed

  1. In vivo effect of opticin deficiency in cartilage in a surgically induced mouse model of osteoarthritis. Farrán A, et al. Sci Rep, 2018 Jan 11. PMID 29323130, Free PMC Article
  2. The vitreous glycoprotein opticin inhibits preretinal neovascularization. Le Goff MM, et al. Invest Ophthalmol Vis Sci, 2012 Jan 25. PMID 22159013, Free PMC Article
  3. Identification of opticin, a member of the small leucine-rich repeat proteoglycan family, in human articular tissues: a novel target for MMP-13 in osteoarthritis. Monfort J, et al. Osteoarthritis Cartilage, 2008 Jul. PMID 18164633
  4. Female-specific hypertension loci on rat chromosome 13. Hoffman MJ, et al. Hypertension, 2013 Sep. PMID 23817491, Free PMC Article
  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

Go to the top of the page Help

Markers

Homology

Gene Ontology Provided by RGD

Process Evidence Code Pubs
acts_upstream_of angiogenesis ISO
Inferred from Sequence Orthology
more info
  
involved_in articular cartilage development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in bone development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in collagen fibril organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in collagen fibril organization ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within negative regulation of angiogenesis ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
is_active_in extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular matrix ISO
Inferred from Sequence Orthology
more info
  

General protein information

Go to the top of the page Help
Preferred Names
opticin

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_001395559.1 → NP_001382488.1  opticin precursor

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000013
    UniProtKB/TrEMBL
    A0A096MJH6
    Conserved Domains (3) summary
    PRK15370
    Location:212 → 342
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    PRK15387
    Location:156 → 260
    PRK15387; type III secretion system effector E3 ubiquitin transferase SspH2
    sd00033
    Location:169 → 192
    LRR_RI; leucine-rich repeat [structural motif]

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_086031.1 Reference GRCr8

    Range
    47906145..47920334 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039090712.2 → XP_038946640.1  opticin isoform X1

    UniProtKB/TrEMBL
    A6IC95
    Conserved Domains (3) summary
    PRK15370
    Location:270 → 366
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    sd00033
    Location:226 → 250
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:228 → 285
    LRR_8; Leucine rich repeat

  2. XM_063272294.1 → XP_063128364.1  opticin isoform X2

    UniProtKB/TrEMBL
    A0A096MK02
    Related
    ENSRNOP00000068329.1, ENSRNOT00000076673.4

  3. XM_039090714.2 → XP_038946642.1  opticin isoform X3

    Conserved Domains (2) summary
    PRK15370
    Location:34 → 187
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    sd00033
    Location:49 → 71
    LRR_RI; leucine-rich repeat [structural motif]

  4. XM_063272297.1 → XP_063128367.1  opticin isoform X5

  5. XM_063272295.1 → XP_063128365.1  opticin isoform X4

RNA

  1. XR_010056916.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001107176.1: Suppressed sequence

    Description
    NM_001107176.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools