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OPTC opticin [ Homo sapiens (human) ]

Gene ID: 26254, updated on 13-Mar-2020

Summary

Official Symbol
OPTCprovided by HGNC
Official Full Name
opticinprovided by HGNC
Primary source
HGNC:HGNC:8158
See related
Ensembl:ENSG00000188770 MIM:605127
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

Genomic context

See OPTC in Genome Data Viewer
Location:
1q32.1
Exon count:
8
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (203494153..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 bone marrow associated non-coding RNA 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 pseudogene 1 Neighboring gene small nucleolar RNA, H/ACA box 77

Genomic regions, transcripts, and products

Expression

  • 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

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
collagen fibril organization ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
extracellular matrix IDA
Inferred from Direct Assay
more info
PubMed 
extracellular region TAS
Traceable Author Statement
more info
 

NCBI Reference Sequences (RefSeq)

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
    Q9UBM4
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    203494153..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 (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
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