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Aliases for OPTC Gene

Aliases for OPTC Gene

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. Among its related pathways are Degradation of the extracellular matrix. Gene Ontology (GO) annotations related to this gene include extracellular matrix structural constituent. An important paralog of this gene is EPYC.

UniProtKB/Swiss-Prot for OPTC Gene

  • Binds collagen fibrils.

Gene Wiki entry for OPTC Gene

Additional gene information for OPTC Gene

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

Genomics for OPTC Gene

GeneHancer (GH) Regulatory Elements for OPTC Gene

Promoters and enhancers for OPTC Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J203494 Promoter 0.5 EPDnew 650.7 0.0 -9 0.1 OPTC PRELP GC01M203457
GH01J203624 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.3 +134.0 134036 7.2 HDGF PKNOX1 CLOCK SMAD1 ARNT SIN3A YBX1 ZNF2 ZBTB7B YY1 ATP2B4 ZC3H11A MDM4 SNRPE ZBED6 HNRNPA1P59 KDM5B PPP1R15B OPTC SOX13
GH01J203519 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 11.6 +26.7 26739 3.7 PKNOX1 SIN3A ZNF335 TCF12 ZNF366 FOS ATF7 CREM EGR2 CEBPB GC01M203457 OPTC PRELP ATP2B4 FMOD LOC100131747 BTG2 SNRPE PPFIA4 GC01P203608
GH01J203647 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 10.5 +158.9 158909 10.6 HDGF PKNOX1 SIN3A IRF4 CBX5 ZNF548 FOS JUNB REST SMARCA4 ZC3H11A MDM4 ATP2B4 SNRPE ZBED6 SNORA77 OPTC PPP1R15B LOC100131747 FMOD
GH01J203272 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 10.3 -219.8 -219765 3.6 HDGF ARNT SIN3A FEZF1 ZNF2 ZBTB7B IRF4 E2F8 ZNF207 ZNF143 CHIT1 BTG2 LINC01136 RNU6-487P FMOD LOC100131747 OPTC PRELP GC01P203263 LINC01353
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around OPTC on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the OPTC gene promoter:
  • IRF-2
  • MEF-2A
  • MEF-2
  • aMEF-2
  • GR
  • GR-alpha
  • Oct-B1
  • oct-B2
  • oct-B3
  • POU2F1

Genomic Locations for OPTC Gene

Genomic Locations for OPTC Gene
chr1:203,494,143-203,508,949
(GRCh38/hg38)
Size:
14,807 bases
Orientation:
Plus strand
chr1:203,463,271-203,478,077
(GRCh37/hg19)
Size:
14,807 bases
Orientation:
Plus strand

Genomic View for OPTC Gene

Genes around OPTC on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
OPTC Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

Post-translational modifications for OPTC Gene

Other Protein References for OPTC Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Boster Bio Antibodies for OPTC
  • Santa Cruz Biotechnology (SCBT) Antibodies for OPTC

No data available for DME Specific Peptides for OPTC Gene

Domains & Families for OPTC Gene

Gene Families for OPTC Gene

Human Protein Atlas (HPA):
  • Predicted secreted proteins

Protein 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 :
  • Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class III subfamily.
Family:
  • Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class III subfamily.
genes like me logo Genes that share domains with OPTC: view

Function for OPTC Gene

Molecular function for OPTC Gene

UniProtKB/Swiss-Prot Function:
Binds collagen fibrils.

Phenotypes From GWAS Catalog for OPTC Gene

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

Animal Models for OPTC Gene

MGI Knock Outs for OPTC:
  • Optc Optc<tm1.1Pnb>

Animal Model Products

  • Taconic Biosciences Mouse Models for OPTC

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for OPTC gene
Compartment Confidence
extracellular 5
lysosome 1

Gene Ontology (GO) - Cellular Components for OPTC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
genes like me logo Genes that share ontologies with OPTC: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for OPTC Gene

Pathways & Interactions for OPTC Gene

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

Pathways by source for OPTC Gene

Gene Ontology (GO) - Biological Process for OPTC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0022617 extracellular matrix disassembly TAS --
genes like me logo Genes that share ontologies with OPTC: view

No data available for SIGNOR curated interactions for OPTC Gene

Drugs & Compounds for OPTC Gene

(1) Drugs for OPTC Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
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:

Clone 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 from GTEx, Illumina, BioGPS, and CGAP SAGE for OPTC Gene

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

This gene is overexpressed in Testis (x7.1).

Protein differential expression in normal tissues from HIPED for OPTC Gene

This gene is overexpressed in Vitreous humor (67.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for OPTC Gene



Protein tissue co-expression partners for OPTC Gene

NURSA nuclear receptor signaling pathways regulating expression of OPTC Gene:

OPTC

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.

Evidence on tissue expression from TISSUES for OPTC Gene

  • Eye(4.8)
  • Bone marrow(4.1)
genes like me logo Genes that share expression patterns with OPTC: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 34 33
  • 97.57 (n)
OneToOne
dog
(Canis familiaris)
Mammalia OPTC 34 33
  • 81.13 (n)
OneToOne
cow
(Bos Taurus)
Mammalia OPTC 34 33
  • 80.02 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Optc 16 34 33
  • 77.18 (n)
rat
(Rattus norvegicus)
Mammalia Optc 33
  • 76.87 (n)
oppossum
(Monodelphis domestica)
Mammalia OPTC 34
  • 53 (a)
OneToOne
chicken
(Gallus gallus)
Aves OPTC 34 33
  • 64.3 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia OPTC 34
  • 52 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia optc 33
  • 56.54 (n)
zebrafish
(Danio rerio)
Actinopterygii optc 34 33
  • 57.16 (n)
OneToOne
Species where no ortholog for OPTC was found in the sources mined by GeneCards:
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for OPTC: view image

Paralogs for OPTC Gene

Paralogs for OPTC Gene

(2) SIMAP similar genes for OPTC Gene using alignment to 3 proteins:

  • OPT_HUMAN
  • Q5T2G3_HUMAN
  • Q66MN3_HUMAN
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 Variation AA Info Type
rs1000191026 -- 203,508,414(+) G/A intron_variant
rs1000428075 -- 203,505,949(+) AGAG/AG intron_variant
rs1000600219 -- 203,506,402(+) C/T intron_variant
rs1000646284 -- 203,499,957(+) T/C intron_variant
rs1000793272 -- 203,507,078(+) C/T intron_variant

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

Variant ID Type Subtype PubMed ID
esv1567874 CNV insertion 17803354
esv2762217 CNV gain 21179565
nsv1069209 CNV deletion 25765185
nsv952640 CNV deletion 24416366

Variation tolerance for OPTC Gene

Residual Variation Intolerance Score: 77.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.09; 75.38% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for OPTC Gene

Human Gene Mutation Database (HGMD)
OPTC
SNPedia medical, phenotypic, and genealogical associations of SNPs for
OPTC

SNP Genotyping and Copy Number Assay Products

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

Disorders for OPTC Gene

MalaCards: The human disease database

(6) MalaCards diseases for OPTC Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
posterior column ataxia
  • biemond ataxia
vitreous detachment
  • posterior vitreous detachment
open-angle glaucoma
  • glaucoma simplex
retinitis pigmentosa 12
  • rp12
macular degeneration, age-related, 1
  • armd1
- elite association - COSMIC cancer census association via MalaCards
Search OPTC in MalaCards View complete list of genes associated with diseases

Additional Disease Information for OPTC

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with OPTC: view

No data available for UniProtKB/Swiss-Prot and Genatlas 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 AJ … Bishop PN (The Journal of biological chemistry 2000) 2 3 4 22 58
  2. An evaluation of OPTC and EPYC as candidate genes for high myopia. (PMID: 19844586) Wang P … Zhang Q (Molecular vision 2009) 3 22 44 58
  3. Evaluation of the OPTC gene in primary open angle glaucoma: functional significance of a silent change. (PMID: 17359525) Acharya M … Ray K (BMC molecular biology 2007) 3 22 44 58
  4. Protein localization in the human eye and genetic screen of opticin. (PMID: 12019215) Friedman JS … Walter MA (Human molecular genetics 2002) 3 4 22 58
  5. 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 (Molecular vision 2000) 3 4 22 58

Products for OPTC Gene

Sources for OPTC Gene

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