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    OPTC opticin [ Homo sapiens (human) ]

    Gene ID: 26254, updated on 2-Nov-2024

    Summary

    Official Symbol
    OPTCprovided by HGNC
    Official Full Name
    opticinprovided by HGNC
    Primary source
    HGNC:HGNC:8158
    See related
    Ensembl:ENSG00000188770 MIM:605127; AllianceGenome:HGNC:8158
    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
    OPT
    Summary
    Opticin belongs to class III of the small leucine-rich repeat protein (SLRP) family. Members of this family are typically associated with the extracellular matrix. Opticin is present in significant quantities in the vitreous of the eye and also localizes to the cornea, iris, ciliary body, optic nerve, choroid, retina, and fetal liver. Opticin may noncovalently bind collagen fibrils and regulate fibril morphology, spacing, and organization. The opticin gene is mapped to a region of chromosome 1 that is associated with the inherited eye diseases age-related macular degeneration (AMD) and posterior column ataxia with retinosa pigmentosa (AXPC1). [provided by RefSeq, Jul 2008]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See OPTC in Genome Data Viewer
    Location:
    1q32.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (203494153..203508949)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (202757006..202772142)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (203463281..203478077)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904487 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2351 Neighboring gene MPRA-validated peak660 silencer Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:203460588-203461386 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:203462774-203463002 Neighboring gene uncharacterized LOC105371688 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:203473836-203474011 Neighboring gene proline and arginine rich end leucine rich repeat protein Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:203480878-203481618 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:203481606-203482805 Neighboring gene uncharacterized LOC124904488 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203486279-203487110 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203487943-203488774 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203488775-203489607 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203491273-203492103 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203525277-203526201 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203526215-203526792 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203541106-203541988 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1721 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203569376-203569876 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203569877-203570377 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:203594954-203595828 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:203595829-203596701 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1722 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1723 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203598915-203599601 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1724 Neighboring gene ATPase plasma membrane Ca2+ transporting 4 Neighboring gene NSA2 pseudogene 1

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid.
    EBI GWAS Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of opticin (OPTC) by siRNA enhances the early stages of HIV-1 replication in HeLa-CD4 cells infected with viral pseudotypes HIV89.6R and HIV8.2N PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables extracellular matrix structural constituent TAS
    Traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in angiogenesis IEA
    Inferred from Electronic Annotation
    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of angiogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    is_active_in extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_022886.1 RefSeqGene

      Range
      5011..19807
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_014359.4NP_055174.1  opticin precursor

      See identical proteins and their annotated locations for NP_055174.1

      Status: REVIEWED

      Source sequence(s)
      AJ133790, BF724878
      Consensus CDS
      CCDS1439.1
      UniProtKB/Swiss-Prot
      Q5T2G4, Q9UBM4
      UniProtKB/TrEMBL
      Q5T2G3
      Related
      ENSP00000356191.2, ENST00000367222.7
      Conserved Domains (3) summary
      sd00033
      Location:155178
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:153213
      LRR_8; Leucine rich repeat
      cl26018
      Location:115327
      NEL; C-terminal novel E3 ligase, LRR-interacting

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      203494153..203508949
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      202757006..202772142
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)