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OPTC opticin [ Homo sapiens (human) ]

Gene ID: 26254, updated on 12-Mar-2017
Official Symbol
OPTCprovided by HGNC
Official Full Name
opticinprovided by HGNC
Primary source
HGNC:HGNC:8158
See related
Ensembl:ENSG00000188770 MIM:605127; Vega:OTTHUMG00000036100
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]
Orthologs
Location:
1q32.1
Exon count:
8
Annotation release Status Assembly Chr Location
108 current GRCh38.p7 (GCF_000001405.33) 1 NC_000001.11 (203494143..203508949)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (203463271..203478077)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985249 Neighboring gene uncharacterized LOC105371688 Neighboring gene proline and arginine rich end leucine rich repeat protein Neighboring gene ATPase plasma membrane Ca2+ transporting 4 Neighboring gene NSA2 ribosome biogenesis homolog (S. cerevisiae) pseudogene Neighboring gene small nucleolar RNA, H/ACA box 77

  • Project title: 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

NHGRI GWAS Catalog

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

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

  • Degradation of the extracellular matrix, organism-specific biosystem (from REACTOME)
    Degradation of the extracellular matrix, organism-specific biosystemMatrix metalloproteinases (MMPs), previously referred to as matrixins because of their role in degradation of the extracellular matrix (ECM), are zinc and calcium dependent proteases belonging to the...
  • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
    Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
extracellular matrix structural constituent TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
extracellular matrix disassembly TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
extracellular region TAS
Traceable Author Statement
more info
 
proteinaceous extracellular matrix IEA
Inferred from Electronic Annotation
more info
 

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
    5001..19807
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_014359.3NP_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
    Q9UBM4
    Related
    ENSP00000356191, OTTHUMP00000034332, ENST00000367222, OTTHUMT00000087964
    Conserved Domains (4) summary
    cd00116
    Location:170281
    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:155178
    LRR_RI; leucine-rich repeat [structural motif]
    pfam12799
    Location:157194
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:153213
    LRR_8; Leucine rich repeat

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

Reference GRCh38.p7 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p7 Primary Assembly

    Range
    203494143..203508949
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011509406.2XP_011507708.1  opticin isoform X1

    See identical proteins and their annotated locations for XP_011507708.1

    UniProtKB/Swiss-Prot
    Q9UBM4
    Conserved Domains (4) summary
    cd00116
    Location:170281
    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:155178
    LRR_RI; leucine-rich repeat [structural motif]
    pfam12799
    Location:157194
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:153213
    LRR_8; Leucine rich repeat

Alternate CHM1_1.1

Genomic

  1. NC_018912.2 Alternate CHM1_1.1

    Range
    204886108..204900814
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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