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Aliases for SIX6 Gene

Aliases for SIX6 Gene

  • SIX Homeobox 6 2 3 5
  • Sine Oculis Homeobox Homolog 6 3 4
  • Homeodomain Protein OPTX2 3 4
  • Optic Homeobox 2 3 4
  • OPTX2 3 4
  • Six9 3 4
  • Sine Oculis Homeobox (Drosophila) Homolog 6 2
  • Sine Oculis Homeobox Homolog 6 (Drosophila) 2
  • Sine Oculis Homeobox-Like Protein 6 3
  • Sine Oculis Homeobox Protein 6 3
  • MCOPCT2 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 Optic Disc Anomalies With Retinal And/Or Macular Dystrophy and Colobomatous Optic Disc-Macular Atrophy-Chorioretinopathy Syndrome. GO annotations related to this gene include transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific 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

Enhancers for SIX6 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around SIX6 on UCSC Golden Path with GeneCards custom track

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

Genes around SIX6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SIX6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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 Lys 49
  • 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 & Families for SIX6 Gene

Gene Families for SIX6 Gene

Suggested Antigen Peptide Sequences for SIX6 Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 homeobox DNA-binding domain.
  • Belongs to the SIX/Sine oculis homeobox family.
  • 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:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with SIX6: view
genes like me logo Genes that share phenotypes with SIX6: view

Human Phenotype Ontology for SIX6 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SIX6 Gene

MGI Knock Outs for SIX6:

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets 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 5
cytosol 2

No data available for Gene Ontology (GO) - Cellular Components for SIX6 Gene

Pathways & Interactions for SIX6 Gene

SuperPathways for SIX6 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SIX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001654 eye development IEA --
GO:0009887 organ morphogenesis TAS 10512683
genes like me logo Genes that share ontologies with SIX6: view

No data available for Pathways by source and SIGNOR curated interactions for SIX6 Gene

Drugs & Compounds for SIX6 Gene

No Compound Related Data Available

Transcripts for SIX6 Gene

mRNA/cDNA for SIX6 Gene

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

Unigene Clusters for SIX6 Gene

SIX homeobox 6:
Representative Sequences:

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 (x48.4).

Protein differential expression in normal tissues from HIPED for SIX6 Gene

This gene is overexpressed in Retina (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines 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 expression patterns with SIX6: view

Protein tissue co-expression partners for SIX6 Gene

Primer 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

(7) 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
VAR_026241 -
rs33912345 - 60,509,819(+) CGCGG(A/C/G)ACCTG reference, missense
rs713336 -- 60,508,240(+) AAGCC(G/T)ACAAG upstream-variant-2KB
rs8004739 -- 60,507,655(+) TTGCC(C/T)TGCAC upstream-variant-2KB
rs3759688 -- 60,508,861(-) CCAAA(G/T)AGGCA upstream-variant-2KB

Variation tolerance for SIX6 Gene

Residual Variation Intolerance Score: 58.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.10; 92.23% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SIX6 Gene

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

MalaCards: The human disease database

(11) MalaCards diseases for SIX6 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search SIX6 in MalaCards View complete list of genes associated with diseases


  • Optic disk anomalies with retinal and/or macular dystrophy (ODRMD) [MIM:212550]: An ocular disorder characterized by optic nerve dysplasia, optic disk anomalies, chorioretinal dystrophy and macular atrophy. Some patients have microphthalmia. {ECO:0000269 PubMed:23167593}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SIX6

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with SIX6: view

No data available for 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 67
  2. Absence of SIX6 mutations in microphthalmia, anophthalmia, and coloboma. (PMID: 15505031) Aijaz S. … Hanson I. (Invest. Ophthalmol. Vis. Sci. 2004) 3 23
  3. A homozygous SIX6 mutation is associated with optic disc anomalies and macular atrophy and reduces retinal ganglion cell differentiation. (PMID: 24702266) Yariz K.O. … Tekin M. (Clin. Genet. 2015) 3
  4. Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci. (PMID: 25429064) He M. … Qi L. (Hum. Mol. Genet. 2015) 3
  5. Association of common SIX6 polymorphisms with peripapillary retinal nerve fiber layer thickness: the Singapore Chinese Eye Study. (PMID: 25537207) Cheng C.Y. … Wong T.Y. (Invest. Ophthalmol. Vis. Sci. 2015) 3

Products for SIX6 Gene

Sources for SIX6 Gene