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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
  • Homeobox Protein SIX6 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 Six6-Related Eye Disorders. 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 SIX3.

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 Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH14F060640 1.9 VISTA Ensembl ENCODE 9.9 +141.2 141233 19.2 PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 ZNF263 SP3 C14orf39 TRMT5 PCNX4 SIX4 TMEM30B MNAT1 SIX6 RNU6-398P PPM1A SLC38A6
GH14F060485 0.9 ENCODE 11.4 -23.0 -22995 1.5 CBX3 CREB3L1 KLF13 EGR2 ZNF202 SP3 CEBPB REST ZNF518A SP1 C14orf39 TRMT5 SIX6 SALL4P7 GNRHR2P1
GH14F060311 0.8 FANTOM5 10.2 -197.3 -197328 0.3 ATF1 MAX ZEB2 BRCA1 ATF2 OSR2 GATA3 JUND ATF3 ZNF366 SIX6 PPM1A LOC101927729 GC14P060353
GH14F060310 0.5 FANTOM5 10.2 -198.8 -198775 0.2 RFX1 MYNN KLF9 PPM1A SIX6 LOC101927729 GC14P060353
GH14F060315 0.4 ENCODE 10.2 -193.4 -193362 1.0 GATA3 RFX1 PPM1A LOC101927702 SIX6 LOC101927729 GC14P060353
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SIX6 on UCSC Golden Path with GeneCards custom track

Genomic Location for SIX6 Gene

Chromosome:
14
Start:
60,508,951 bp from pter
End:
60,512,850 bp from pter
Size:
3,900 bases
Orientation:
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:
    O95475-SIX6_HUMAN
    Recommended name:
    Homeobox protein SIX6
    Protein Accession:
    O95475
    Secondary Accessions:
    • Q6NT42
    • Q9P1X8

    Protein attributes for SIX6 Gene

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

neXtProt entry for SIX6 Gene

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

O95475

UniProtKB/Swiss-Prot:

SIX6_HUMAN :
  • Contains 1 homeobox DNA-binding domain.
  • Belongs to the SIX/Sine oculis homeobox family.
Domain:
  • Contains 1 homeobox DNA-binding domain.
Family:
  • 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 transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific binding IEA --
GO:0003677 DNA 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

Inhibitory RNA Products

Clone Products

Flow Cytometry 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

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 SIX6 gene
Compartment Confidence
nucleus 5
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 & Interactions 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:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription from RNA polymerase II promoter IEA --
GO:0006366 transcription from RNA polymerase II promoter IEA --
GO:0007275 multicellular organism development IEA --
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

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:

Inhibitory RNA Products

Clone 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
SIX6
ECgene alternative splicing isoforms for
SIX6

Expression for SIX6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE 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



Protein tissue co-expression partners for SIX6 Gene

NURSA nuclear receptor signaling pathways regulating expression of SIX6 Gene:

SIX6

SOURCE GeneReport for Unigene cluster for SIX6 Gene:

Hs.194756

mRNA Expression by UniProt/SwissProt for SIX6 Gene:

O95475-SIX6_HUMAN
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

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
chimpanzee
(Pan troglodytes)
Mammalia SIX6 34
  • 99.73 (n)
OPTX2 35
  • 93 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SIX6 35
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SIX6 34 35
  • 92.95 (n)
rat
(Rattus norvegicus)
Mammalia Six6 34
  • 90.51 (n)
mouse
(Mus musculus)
Mammalia Six6 34 16 35
  • 90.11 (n)
cow
(Bos Taurus)
Mammalia SIX6 35
  • 72 (a)
OneToOne
chicken
(Gallus gallus)
Aves SIX6 34 35
  • 84.01 (n)
lizard
(Anolis carolinensis)
Reptilia SIX6 35
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia six6 34
  • 77.32 (n)
African clawed frog
(Xenopus laevis)
Amphibia six6-A 34
zebrafish
(Danio rerio)
Actinopterygii six6a 35
  • 91 (a)
OneToMany
six6b 34 35
  • 75.51 (n)
zgc63871 34
fruit fly
(Drosophila melanogaster)
Insecta Optix 36 35
  • 74 (a)
Six4 36
  • 56 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003871 34
  • 67.56 (n)
worm
(Caenorhabditis elegans)
Secernentea ceh-32 36 35
  • 65 (a)
ceh-33 36
  • 52 (a)
ceh-34 36
  • 46 (a)
ceh-35 36
  • 35 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 42 (a)
OneToMany
Species where no ortholog for SIX6 was found in the sources mined by GeneCards:
  • 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

ENSEMBL:
Gene Tree for SIX6 (if available)
TreeFam:
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
rs786204851 Pathogenic 60,509,508(+) GTCGC(C/T)GCCCG reference, missense
rs786205142 Pathogenic 60,509,930(+) TCAAA(-/AACCG)CCGAC reference, frameshift-variant
rs104894480 Uncertain significance 60,509,891(+) AGGCA(A/G)CCGGA reference, missense
rs33912345 Benign 60,509,819(+) CGCGG(A/C)ACCTG reference, missense
rs10151958 -- 60,510,557(+) TCGAT(C/T)AGCCA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SIX6 Gene

Variant ID Type Subtype PubMed ID
nsv564880 CNV gain 21841781
nsv564881 CNV gain 21841781

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)
SIX6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SIX6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SIX6 Gene

Disorders for SIX6 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
optic disc anomalies with retinal and/or macular dystrophy
  • colobomatous optic disc-macular atrophy-chorioretinopathy syndrome
six6-related eye disorders
sox2-related eye disorders
microphthalmia
  • microphthalmos
branchiootic syndrome
  • branchiootic syndrome 1
- elite association - COSMIC cancer census association via MalaCards
Search SIX6 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SIX6_HUMAN
  • 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)
SIX6
Human Genome Epidemiology (HuGE) Navigator
SIX6
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SIX6
genes like me logo Genes that share disorders with SIX6: view

No data available for Genatlas for SIX6 Gene

Publications for SIX6 Gene

  1. Absence of SIX6 mutations in microphthalmia, anophthalmia, and coloboma. (PMID: 15505031) Aijaz S. … Hanson I. (Invest. Ophthalmol. Vis. Sci. 2004) 3 22 46 64
  2. 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 64
  3. Mutational screening of 10 genes in Chinese patients with microphthalmia and/or coloboma. (PMID: 20057906) Zhang X. … Zhang Q. (Mol. Vis. 2009) 3 46 64
  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 64
  5. 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 64

Products for SIX6 Gene

Sources for SIX6 Gene

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