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Aliases for OPTC Gene

Aliases for OPTC Gene

  • Opticin 2 3
  • Oculoglycan 2 3 4
  • OPT 3 4

External Ids for OPTC Gene

Previous GeneCards Identifiers for OPTC Gene

  • GC01M201246
  • GC01M198990
  • GC01P9D0052
  • GC00P9S0052
  • GC01P200194
  • GC01P201729
  • GC01P174628

Summaries for OPTC Gene

Entrez Gene Summary for OPTC Gene

  • 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]

GeneCards Summary for OPTC Gene

OPTC (Opticin) is a Protein Coding gene. Diseases associated with OPTC include posterior column ataxia and vitreous detachment. GO annotations related to this gene include extracellular matrix structural constituent. An important paralog of this gene is OGN.

UniProtKB/Swiss-Prot for OPTC Gene

  • Binds collagen fibrils.

Gene Wiki entry for OPTC Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for OPTC Gene

Genomics for OPTC Gene

Regulatory Elements for OPTC Gene

Genomic Location for OPTC Gene

Start:
203,494,143 bp from pter
End:
203,508,949 bp from pter
Size:
14,807 bases
Orientation:
Plus strand

Genomic View for OPTC Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for OPTC Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for OPTC Gene

Proteins for OPTC Gene

  • Protein details for OPTC Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UBM4-OPT_HUMAN
    Recommended name:
    Opticin
    Protein Accession:
    Q9UBM4
    Secondary Accessions:
    • Q5T2G4

    Protein attributes for OPTC Gene

    Size:
    332 amino acids
    Molecular mass:
    37261 Da
    Quaternary structure:
    No Data Available

neXtProt entry for OPTC Gene

Proteomics data for OPTC Gene at MOPED

Post-translational modifications for OPTC Gene

Other Protein References for OPTC Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for OPTC Gene

Domains for OPTC Gene

Suggested Antigen Peptide Sequences for OPTC Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9UBM4

UniProtKB/Swiss-Prot:

OPT_HUMAN :
  • Q9UBM4
Domain:
  • Contains 1 LRRNT domain.
Family:
  • Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class III subfamily.
Similarity:
  • Contains 6 LRR (leucine-rich) repeats.
genes like me logo Genes that share domains with OPTC: view

No data available for Gene Families for OPTC Gene

Function for OPTC Gene

Molecular function for OPTC Gene

UniProtKB/Swiss-Prot Function: Binds collagen fibrils.

Gene Ontology (GO) - Molecular Function for OPTC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005201 extracellular matrix structural constituent TAS 10636917
GO:0005515 protein binding --
genes like me logo Genes that share ontologies with OPTC: view

Phenotypes for OPTC Gene

genes like me logo Genes that share phenotypes with OPTC: view

Animal Models for OPTC Gene

MGI Knock Outs for OPTC:

Animal Model Products

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for OPTC

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for OPTC Gene

Localization for OPTC Gene

Subcellular locations from UniProtKB/Swiss-Prot for OPTC Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for OPTC Gene COMPARTMENTS Subcellular localization image for OPTC gene
Compartment Confidence
extracellular 4
lysosome 1

Gene Ontology (GO) - Cellular Components for OPTC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0031012 extracellular matrix --
genes like me logo Genes that share ontologies with OPTC: view

Pathways for OPTC Gene

SuperPathways for OPTC Gene

No Data Available

Gene Ontology (GO) - Biological Process for OPTC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016525 negative regulation of angiogenesis IEA --
genes like me logo Genes that share ontologies with OPTC: view

No data available for Pathways by source for OPTC Gene

Compounds for OPTC Gene

(1) Novoseek inferred chemical compound relationships for OPTC Gene

Compound -log(P) Hits PubMed IDs
cysteine 16.4 1
genes like me logo Genes that share compounds with OPTC: view

Transcripts for OPTC Gene

mRNA/cDNA for OPTC Gene

Unigene Clusters for OPTC Gene

Opticin:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for OPTC

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for OPTC

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for OPTC Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7 ^ 8
SP1:
SP2: -

Relevant External Links for OPTC Gene

GeneLoc Exon Structure for
OPTC
ECgene alternative splicing isoforms for
OPTC

Expression for OPTC Gene

mRNA expression in normal human tissues for OPTC Gene

mRNA differential expression in normal tissues according to GTEx for OPTC Gene

This gene is overexpressed in Testis (7.1).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for OPTC Gene

SOURCE GeneReport for Unigene cluster for OPTC Gene Hs.632468

mRNA Expression by UniProt/SwissProt for OPTC Gene

Q9UBM4-OPT_HUMAN
Tissue specificity: Retina, iris, ligament, skin and fetal liver.
genes like me logo Genes that share expressions with OPTC: view

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for OPTC Gene

Orthologs for OPTC Gene

This gene was present in the common ancestor of chordates.

Orthologs for OPTC Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia OPTC 35
  • 97.57 (n)
  • 97.14 (a)
OPTC 36
  • 96 (a)
OneToOne
cow
(Bos Taurus)
Mammalia OPTC 35
  • 80.02 (n)
  • 74.92 (a)
OPTC 36
  • 74 (a)
OneToOne
dog
(Canis familiaris)
Mammalia OPTC 35
  • 81.13 (n)
  • 78.46 (a)
OPTC 36
  • 74 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Optc 35
  • 77.18 (n)
  • 73.57 (a)
Optc 16
Optc 36
  • 60 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia OPTC 36
  • 53 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Optc 35
  • 76.87 (n)
  • 70.54 (a)
chicken
(Gallus gallus)
Aves OPTC 35
  • 64.3 (n)
  • 56.45 (a)
OPTC 36
  • 51 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia OPTC 36
  • 52 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia optc 35
  • 56.54 (n)
  • 51.31 (a)
zebrafish
(Danio rerio)
Actinopterygii optc 35
  • 57.16 (n)
  • 50 (a)
optc 36
  • 41 (a)
OneToOne
Species with no ortholog for OPTC:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for OPTC Gene

ENSEMBL:
Gene Tree for OPTC (if available)
TreeFam:
Gene Tree for OPTC (if available)

Paralogs for OPTC Gene

Paralogs for OPTC Gene

Selected SIMAP similar genes for OPTC Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with OPTC: view

Variants for OPTC Gene

Sequence variations from dbSNP and Humsavar for OPTC Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs747672 -- 203,498,105(+) CTCAT(G/T)ACCCG intron-variant
rs747673 -- 203,498,295(+) TGGCA(C/G)AGCCA intron-variant
rs747814 -- 203,498,712(-) GAACC(A/G)AGGCA reference, synonymous-codon
rs751621 -- 203,493,150(+) GAAAA(C/T)TTGAA upstream-variant-2KB
rs754754 -- 203,503,916(+) AATGT(C/T)TTTCA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for OPTC Gene

Variant ID Type Subtype PubMed ID
esv1567874 CNV Insertion 17803354

Relevant External Links for OPTC Gene

HapMap Linkage Disequilibrium report
OPTC
Human Gene Mutation Database (HGMD)
OPTC

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for OPTC Gene

Disorders for OPTC Gene

MalaCards: The human disease database

MalaCards: The human disease database. (3) Diseases for OPTC Gene including...

Search for OPTC Gene in MalaCards »

(1) University of Copenhagen DISEASES for OPTC Gene

(2) Novoseek inferred disease relationships for OPTC Gene

Disease -log(P) Hits PubMed IDs
collagen fibril 80.7 2
glaucoma open-angle 48.8 2

Relevant External Links for OPTC

Genetic Association Database (GAD)
OPTC
Human Genome Epidemiology (HuGE) Navigator
OPTC
genes like me logo Genes that share disorders with OPTC: view

No data available for UniProtKB/Swiss-Prot for OPTC Gene

Publications for OPTC Gene

  1. Identification in vitreous and molecular cloning of opticin, a novel member of the family of leucine-rich repeat proteins of the extracellular matrix. (PMID: 10636917) Reardon A.J. … Bishop P.N. (J. Biol. Chem. 2000) 2 3 4 23
  2. Cloning, modeling, and chromosomal localization for a small leucine- rich repeat proteoglycan (SLRP) family member expressed in human eye. (PMID: 10837509) Hobby P. … Wistow G.J. (Mol. Vis. 2000) 3 4 23
  3. Protein localization in the human eye and genetic screen of opticin. (PMID: 12019215) Friedman J.S. … Walter M.A. (Hum. Mol. Genet. 2002) 3 4 23
  4. Evaluation of the OPTC gene in primary open angle glaucoma: functional significance of a silent change. (PMID: 17359525) Acharya M. … Ray K. (BMC Mol. Biol. 2007) 3 23 48
  5. An evaluation of OPTC and EPYC as candidate genes for high myopia. (PMID: 19844586) Wang P. … Zhang Q. (Mol. Vis. 2009) 3 23 48

Products for OPTC Gene

Sources for OPTC Gene

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