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    optc opticin [ Danio rerio (zebrafish) ]

    Gene ID: 445189, updated on 2-Nov-2024

    Summary

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    Official Symbol
    optcprovided by ZNC
    Official Full Name
    opticinprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-1798
    See related
    Ensembl:ENSDARG00000014358 AllianceGenome:ZFIN:ZDB-GENE-030131-1798
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    dspg3; optcl; wu:fb81a05; zgc:101047
    Summary
    Predicted to be involved in articular cartilage development and bone development. Predicted to be active in extracellular matrix. Is expressed in several structures, including axis; floor plate; immature eye; paraxial mesoderm; and somite. Orthologous to human EPYC (epiphycan) and OPTC (opticin). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    all
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    Genomic context

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    See optc in Genome Data Viewer
    Location:
    chromosome: 11
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 11 NC_007122.7 (23205886..23219348, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 11 NC_007122.6 (22952592..22966306, complement)

    Chromosome 11 - NC_007122.7Genomic Context describing neighboring genes Neighboring gene ATPase plasma membrane Ca2+ transporting 4 Neighboring gene 5S ribosomal RNA Neighboring gene uncharacterized LOC108191637 Neighboring gene colony stimulating factor 1a (macrophage)

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Molecular cloning and expression of two small leucine-rich proteoglycan (SLRP) genes, dspg3l and optcl, in zebrafish. Zhou W, et al. Gene Expr Patterns, 2006 Jun. PMID 16458084
    2. Opticin Ameliorates Hypoxia-Induced Retinal Angiogenesis by Suppression of Integrin α2-I Domain-Collagen Complex Formation and RhoA/ROCK1 Signaling. Liu X, et al. Invest Ophthalmol Vis Sci, 2022 Jan 3. PMID 35006271, Free PMC Article
    3. Transcriptome analysis of the zebrafish model of Diamond-Blackfan anemia from RPS19 deficiency via p53-dependent and -independent pathways. Jia Q, et al. PLoS One, 2013. PMID 23990987, Free PMC Article
    4. The zebrafish homologs of SET/I2PP2A oncoprotein: expression patterns and insights into their physiological roles during development. Serifi I, et al. Biochem J, 2016 Dec 15. PMID 27754889
    5. A Floor-Plate Extracellular Protein-Protein Interaction Screen Identifies Draxin as a Secreted Netrin-1 Antagonist. Gao X, et al. Cell Rep, 2015 Jul 28. PMID 26190107

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Opticin Ameliorates Hypoxia-Induced Retinal Angiogenesis by Suppression of Integrin alpha2-I Domain-Collagen Complex Formation and RhoA/ROCK1 Signaling.
      Title: Opticin Ameliorates Hypoxia-Induced Retinal Angiogenesis by Suppression of Integrin α2-I Domain-Collagen Complex Formation and RhoA/ROCK1 Signaling.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    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
    		  
    Component Evidence Code Pubs
    is_active_in extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    opticin
    Names
    dermatan sulfate proteoglycan 3

    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_001003583.2 → NP_001003583.2  opticin precursor

      See identical proteins and their annotated locations for NP_001003583.2

      Status: PROVISIONAL

      Source sequence(s)
      DQ224359
      UniProtKB/TrEMBL
      A0A8M1N1L1, Q15JE7
      Related
      ENSDARP00000018034.6, ENSDART00000003646.8
      Conserved Domains (5) summary
      smart00013
      Location:121 → 147
      LRRNT; Leucine rich repeat N-terminal domain
      cd00116
      Location:168 → 249
      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:145 → 168
      LRR_RI; leucine-rich repeat [structural motif]
      pfam12799
      Location:237 → 274
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:168 → 249
      LRR_8; Leucine rich repeat

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007122.7 Reference GRCz11 Primary Assembly

      Range
      23205886..23219348 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005172873.5 → XP_005172930.1  opticin isoform X1

      UniProtKB/TrEMBL
      A0A8M2BK46
      Conserved Domains (5) summary
      smart00013
      Location:122 → 148
      LRRNT; Leucine rich repeat N-terminal domain
      cd00116
      Location:169 → 250
      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:146 → 169
      LRR_RI; leucine-rich repeat [structural motif]
      pfam12799
      Location:238 → 275
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:169 → 250
      LRR_8; Leucine rich repeat
    Nucleotide Protein Strain
    Heading Accession and Version

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