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Aliases for SIX6 Gene

Aliases for SIX6 Gene

  • SIX Homeobox 6 2 3
  • Sine Oculis Homeobox Homolog 6 3 4
  • Homeodomain Protein OPTX2 3 4
  • Optic Homeobox 2 3 4
  • MCOPCT2 3 6
  • OPTX2 3 4
  • Six9 3 4
  • Sine Oculis Homeobox (Drosophila) Homolog 6 2
  • Sine Oculis Homeobox Homolog 6 (Drosophila) 2
  • Homeobox Protein SIX6 3
  • ODRMD 3

External Ids for SIX6 Gene

Previous HGNC Symbols for SIX6 Gene

  • OPTX2

Previous GeneCards Identifiers for SIX6 Gene

  • GC14P058302
  • GC14P054770
  • GC14P058965
  • GC14P058966
  • GC14P060045
  • GC14P060975
  • GC14P041139

Summaries for SIX6 Gene

Entrez Gene Summary for SIX6 Gene

  • The protein encoded by this gene is a homeobox protein that is similar to the Drosophila 'sine oculis' gene product. This gene is found in a cluster of related genes on chromosome 14 and is thought to be involved in eye development. Defects in this gene are a cause of isolated microphthalmia with cataract type 2 (MCOPCT2). [provided by RefSeq, Jul 2008]

GeneCards Summary for SIX6 Gene

SIX6 (SIX Homeobox 6) is a Protein Coding gene. Diseases associated with SIX6 include microphthalmia with cataract 2 and microphthalmia cataract. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is SIX2.

UniProtKB/Swiss-Prot for SIX6 Gene

  • May be involved in eye development

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SIX6 Gene

Genomics for SIX6 Gene

Regulatory Elements for SIX6 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for SIX6 Gene

60,508,951 bp from pter
60,512,850 bp from pter
3,900 bases
Plus strand

Genomic View for SIX6 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SIX6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SIX6 Gene

Proteins for SIX6 Gene

  • Protein details for SIX6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein SIX6
    Protein Accession:
    Secondary Accessions:
    • Q6NT42
    • Q9P1X8

    Protein attributes for SIX6 Gene

    246 amino acids
    Molecular mass:
    27687 Da
    Quaternary structure:
    • Interacts with TLE4 and AES.

neXtProt entry for SIX6 Gene

Proteomics data for SIX6 Gene at MOPED

Post-translational modifications for SIX6 Gene

  • Ubiquitination at Lys49
  • Modification sites at PhosphoSitePlus

Other Protein References for SIX6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SIX6 Gene

Domains for SIX6 Gene

Gene Families for SIX6 Gene

  • SIX :Homeoboxes / SINE class

Protein Domains for SIX6 Gene

Suggested Antigen Peptide Sequences for SIX6 Gene

Graphical View of Domain Structure for InterPro Entry



  • O95475
  • Contains 1 homeobox DNA-binding domain.
  • Belongs to the SIX/Sine oculis homeobox family.
genes like me logo Genes that share domains with SIX6: view

Function for SIX6 Gene

Molecular function for SIX6 Gene

GENATLAS Biochemistry:
Drosophila sine oculis homolog SIX6 homeo box encoding gene,expressed in the developing and adult retina and in the hypohypothalamic and hypopituitary region
UniProtKB/Swiss-Prot Function:
May be involved in eye development

Gene Ontology (GO) - Molecular Function for SIX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001205 RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription IEA --
GO:0003677 DNA binding IEA --
GO:0005515 protein binding --
genes like me logo Genes that share ontologies with SIX6: view
genes like me logo Genes that share phenotypes with SIX6: view

Animal Model Products

miRNA for SIX6 Gene

miRTarBase miRNAs that target SIX6

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SIX6

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for SIX6 Gene

Localization for SIX6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SIX6 Gene

Subcellular locations from

Jensen Localization Image for SIX6 Gene COMPARTMENTS Subcellular localization image for SIX6 gene
Compartment Confidence
nucleus 3
cytosol 2

Gene Ontology (GO) - Cellular Components for SIX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with SIX6: view

Pathways for SIX6 Gene

SuperPathways for SIX6 Gene

No Data Available

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Gene Ontology (GO) - Biological Process for SIX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007601 visual perception TAS 10512683
GO:0009887 organ morphogenesis TAS 10512683
GO:0045944 positive regulation of transcription from RNA polymerase II promoter IEA --
genes like me logo Genes that share ontologies with SIX6: view

No data available for Pathways by source for SIX6 Gene

Transcripts for SIX6 Gene

mRNA/cDNA for SIX6 Gene

(41) Selected AceView cDNA sequences:
(4) Additional mRNA sequences :
(1) REFSEQ mRNAs :
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SIX6 Gene

SIX homeobox 6:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SIX6

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SIX6 Gene

No ASD Table

Relevant External Links for SIX6 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SIX6 Gene

mRNA expression in normal human tissues for SIX6 Gene

mRNA differential expression in normal tissues according to GTEx for SIX6 Gene

This gene is overexpressed in Pituitary (48.4).

Protein differential expression in normal tissues for SIX6 Gene

This gene is overexpressed in Retina (69.0).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for SIX6 Gene

SOURCE GeneReport for Unigene cluster for SIX6 Gene Hs.194756

mRNA Expression by UniProt/SwissProt for SIX6 Gene

Tissue specificity: Expressed in the developing and adult retina. Also expressed in the hypothalamic and the pituitary regions
genes like me logo Genes that share expressions with SIX6: view

Expression partners for SIX6 Gene

In Situ Assay Products

Orthologs for SIX6 Gene

This gene was present in the common ancestor of animals.

Orthologs for SIX6 Gene

Organism Taxonomy Gene Similarity Type Details
(Canis familiaris)
Mammalia SIX6 35
  • 92.95 (n)
  • 98.37 (a)
SIX6 36
  • 79 (a)
(Mus musculus)
Mammalia Six6 35
  • 90.11 (n)
  • 97.97 (a)
Six6 16
Six6 36
  • 98 (a)
(Pan troglodytes)
Mammalia SIX6 35
  • 99.73 (n)
  • 100 (a)
OPTX2 36
  • 93 (a)
(Rattus norvegicus)
Mammalia Six6 35
  • 90.51 (n)
  • 97.97 (a)
(Bos Taurus)
Mammalia SIX6 36
  • 72 (a)
(Monodelphis domestica)
Mammalia SIX6 36
  • 94 (a)
(Gallus gallus)
Aves SIX6 35
  • 84.01 (n)
  • 93.5 (a)
SIX6 36
  • 93 (a)
(Anolis carolinensis)
Reptilia SIX6 36
  • 85 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia six6 35
  • 77.32 (n)
  • 93.03 (a)
African clawed frog
(Xenopus laevis)
Amphibia six6-A 35
(Danio rerio)
Actinopterygii six6b 35
  • 75.51 (n)
  • 91.43 (a)
zgc63871 35
six6a 36
  • 91 (a)
six6b 36
  • 91 (a)
fruit fly
(Drosophila melanogaster)
Insecta Optix 37
  • 74 (a)
Six4 37
  • 56 (a)
Optix 36
  • 34 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003871 35
  • 67.56 (n)
  • 77.33 (a)
(Caenorhabditis elegans)
Secernentea ceh-32 37
  • 65 (a)
ceh-33 37
  • 52 (a)
ceh-34 37
  • 46 (a)
ceh-35 37
  • 35 (a)
ceh-32 36
  • 29 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 42 (a)
Species with no ortholog for SIX6:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 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)

Evolution for SIX6 Gene

Gene Tree for SIX6 (if available)
Gene Tree for SIX6 (if available)

Paralogs for SIX6 Gene

Paralogs for SIX6 Gene

Selected SIMAP similar genes for SIX6 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with SIX6: view

Variants for SIX6 Gene

Sequence variations from dbSNP and Humsavar for SIX6 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type MAF
rs713336 -- 60,508,240(+) AAGCC(G/T)ACAAG upstream-variant-2KB
rs1061108 -- 60,511,353(+) CGCCA(C/G)AGAAG utr-variant-3-prime
rs1956558 -- 60,509,238(+) GGTCG(C/T)CCGCT utr-variant-5-prime
rs1998189 -- 60,508,269(+) ATTTT(A/T)AAAAA upstream-variant-2KB
rs3759688 -- 60,508,861(-) CCAAA(G/T)AGGCA upstream-variant-2KB

Relevant External Links for SIX6 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for SIX6 Gene

Disorders for SIX6 Gene

(1) OMIM Diseases for SIX6 Gene (606326)


  • Microphthalmia, isolated, with cataract, 2 (MCOPCT2) [MIM:212550]: A disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues. Ocular abnormalities like opacities of the cornea and lens, scaring of the retina and choroid, and other abnormalities may also be present. {ECO:0000269 PubMed:15266624}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(1) University of Copenhagen DISEASES for SIX6 Gene

Relevant External Links for SIX6

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with SIX6: view

No data available for Novoseek inferred disease relationships and Genatlas for SIX6 Gene

Publications for SIX6 Gene

  1. Genomic cloning and characterization of the human homeobox gene SIX6 reveals a cluster of SIX genes in chromosome 14 and associates SIX6 hemizygosity with bilateral anophthalmia and pituitary anomalies. (PMID: 10512683) Gallardo M.E. … Rodriguez de Cordoba S. (Genomics 1999) 2 3 4
  2. Absence of SIX6 mutations in microphthalmia, anophthalmia, and coloboma. (PMID: 15505031) Aijaz S. … Hanson I. (Invest. Ophthalmol. Vis. Sci. 2004) 3 23 48
  3. Six9 (Optx2), a new member of the Six gene family of transcription factors, is expressed at early stages of vertebrate ocular and pituitary development. (PMID: 10381575) Lopez-Rios J. … Bovolenta P. (Mech. Dev. 1999) 3 4
  4. Analysis of the developmental SIX6 homeobox gene in patients with anophthalmia/microphthalmia. (PMID: 15266624) Gallardo M.E. … Bovolenta P. (Am. J. Med. Genet. A 2004) 3 4
  5. Mutational screening of 10 genes in Chinese patients with microphthalmia and/or coloboma. (PMID: 20057906) Zhang X. … Zhang Q. (Mol. Vis. 2009) 3 48

Products for SIX6 Gene

Sources for SIX6 Gene

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