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Aliases for SIX1 Gene

Aliases for SIX1 Gene

  • SIX Homeobox 1 2 3 5
  • Sine Oculis Homeobox Homolog 1 3 4
  • Sine Oculis Homeobox (Drosophila) Homolog 1 2
  • Sine Oculis Homeobox Homolog 1 (Drosophila) 2
  • Deafness, Autosomal Dominant 23 2
  • Homeobox Protein SIX1 3
  • DFNA23 3
  • TIP39 3
  • BOS3 3

External Ids for SIX1 Gene

Previous HGNC Symbols for SIX1 Gene

  • DFNA23

Previous GeneCards Identifiers for SIX1 Gene

  • GC14M058438
  • GC14M054906
  • GC14M059102
  • GC14M060182
  • GC14M061111
  • GC14M041274
  • GC14M061113

Summaries for SIX1 Gene

Entrez Gene Summary for SIX1 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 limb development. Defects in this gene are a cause of autosomal dominant deafness type 23 (DFNA23) and branchiootic syndrome type 3 (BOS3). [provided by RefSeq, Jul 2008]

GeneCards Summary for SIX1 Gene

SIX1 (SIX Homeobox 1) is a Protein Coding gene. Diseases associated with SIX1 include Brachiootic Syndrome 3 and Deafness, Autosomal Dominant 23. Among its related pathways are Transcriptional misregulation in cancer and Wnt / Hedgehog / Notch. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and chromatin binding. An important paralog of this gene is SIX2.

UniProtKB/Swiss-Prot for SIX1 Gene

  • Transcription factor that is involved in the regulation of cell proliferation, apoptosis and embryonic development. Plays an important role in the development of several organs, including kidney, muscle and inner ear. Depending on context, functions as transcriptional repressor or activator. Lacks an activation domain, and requires interaction with EYA family members for transcription activation. Mediates nuclear translocation of EYA1 and EYA2. Binds the 5-TCA[AG][AG]TTNC-3 motif present in the MEF3 element in the MYOG promoter. Regulates the expression of numerous genes, including MYC, CCND1 and EZR. Acts as activator of the IGFBP5 promoter, probably coactivated by EYA2. Repression of precursor cell proliferation in myoblasts is switched to activation through recruitment of EYA3 to the SIX1-DACH1 complex. During myogenesis, seems to act together with EYA2 and DACH2 (By similarity). Regulates the expression of CCNA1.

Gene Wiki entry for SIX1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SIX1 Gene

Genomics for SIX1 Gene

Regulatory Elements for SIX1 Gene

Enhancers for SIX1 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
GH14F061024 1 Ensembl ENCODE 15.2 -367.7 -367673 2.1 SOX13 CTCF SAP130 JUN EBF1 RAD21 TEAD3 GATA3 ZNF143 SMC3 SIX1 TRMT5 SLC38A6 RNU6-398P PRKCH LOC101927756
GH14F060636 1.2 Ensembl ENCODE 11.2 +20.3 20291 2.6 CBX3 PKNOX1 ATF1 NFRKB ARID4B SIN3A RARA ETV6 FOS CREM C14orf39 TRMT5 SIX1 SIX4 TMEM30B SALRNA1 RPS15AP4
GH14F061100 1.8 FANTOM5 Ensembl ENCODE 5.1 -444.6 -444644 4.6 PKNOX1 MLX ARID4B SIN3A FEZF1 DMAP1 YY1 FOS SP5 NFYC SLC38A6 TRMT5 C14orf39 SIX1 PPM1A LOC105378182 LOC101927756
GH14F060989 1.6 FANTOM5 Ensembl ENCODE 4.5 -331.5 -331465 1.0 HDGF HDAC1 PKNOX1 ARNT TBL1XR1 RAD21 CHAMP1 GATA2 CREM ZNF654 SIX4 SIX1 SLC38A6 TRMT5 LOC101927756
GH14F061238 0.6 ENCODE 10.5 -580.9 -580899 1.5 SMARCA4 ETV1 HLF GTF2A2 PRDM1 GABPA PRKCH TMEM30B SIX1 SIX4 SLC38A6 TRMT5 C14orf39
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SIX1 on UCSC Golden Path with GeneCards custom track

Promoters for SIX1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001457825 959 1801 ARID4B SIN3A DMAP1 ZNF48 ZNF2 RAD21 RARA ZNF263 SP5 ZNF843

Genomic Location for SIX1 Gene

Chromosome:
14
Start:
60,643,415 bp from pter
End:
60,658,259 bp from pter
Size:
14,845 bases
Orientation:
Minus strand

Genomic View for SIX1 Gene

Genes around SIX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SIX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SIX1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SIX1 Gene

Proteins for SIX1 Gene

  • Protein details for SIX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q15475-SIX1_HUMAN
    Recommended name:
    Homeobox protein SIX1
    Protein Accession:
    Q15475
    Secondary Accessions:
    • Q53Y16
    • Q96H64

    Protein attributes for SIX1 Gene

    Size:
    284 amino acids
    Molecular mass:
    32210 Da
    Quaternary structure:
    • Interacts with DACH1 and EYA3 (By similarity). Interacts with EYA1 and EYA2. Interacts with CDC20. Interacts with TBX18 (PubMed:26235987).

    Three dimensional structures from OCA and Proteopedia for SIX1 Gene

neXtProt entry for SIX1 Gene

Post-translational modifications for SIX1 Gene

  • Phosphorylated during interphase; becomes hyperphosphorylated during mitosis. Hyperphosphorylation impairs binding to promoter elements.
  • Ubiquitinated by the anaphase promoting complex (APC), leading to its proteasomal degradation.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SIX1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SIX1 Gene

Domains & Families for SIX1 Gene

Suggested Antigen Peptide Sequences for SIX1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q15475

UniProtKB/Swiss-Prot:

SIX1_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 SIX1: view

Function for SIX1 Gene

Molecular function for SIX1 Gene

GENATLAS Biochemistry:
Drosophila sine oculis homolog SIX1 homeo box encoding gene,expressed during development in limb tendons,also expressed in skeletal and smooth muscle
UniProtKB/Swiss-Prot Function:
Transcription factor that is involved in the regulation of cell proliferation, apoptosis and embryonic development. Plays an important role in the development of several organs, including kidney, muscle and inner ear. Depending on context, functions as transcriptional repressor or activator. Lacks an activation domain, and requires interaction with EYA family members for transcription activation. Mediates nuclear translocation of EYA1 and EYA2. Binds the 5-TCA[AG][AG]TTNC-3 motif present in the MEF3 element in the MYOG promoter. Regulates the expression of numerous genes, including MYC, CCND1 and EZR. Acts as activator of the IGFBP5 promoter, probably coactivated by EYA2. Repression of precursor cell proliferation in myoblasts is switched to activation through recruitment of EYA3 to the SIX1-DACH1 complex. During myogenesis, seems to act together with EYA2 and DACH2 (By similarity). Regulates the expression of CCNA1.

Gene Ontology (GO) - Molecular Function for SIX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding IMP 15141091
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding IMP 15141091
GO:0001223 transcription coactivator binding IEA --
GO:0003677 DNA binding IDA 19497856
GO:0003682 chromatin binding IEA --
genes like me logo Genes that share ontologies with SIX1: view
genes like me logo Genes that share phenotypes with SIX1: view

Human Phenotype Ontology for SIX1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SIX1 Gene

MGI Knock Outs for SIX1:

Animal Model Products

miRNA for SIX1 Gene

miRTarBase miRNAs that target SIX1
Targeted motifs for SIX1 Gene
HOMER Transcription Factor Regulatory Elements motif SIX1
  • Consensus sequence: GKVTCADRTTWC Submotif: canonical Cell Type: Myoblast GEO ID: GSE20150

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SIX1

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) and Transcription Factor Targets for SIX1 Gene

Localization for SIX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SIX1 Gene

Nucleus. Cytoplasm.

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 SIX1 gene
Compartment Confidence
nucleus 5
extracellular 1
cytoskeleton 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for SIX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 16670092
GO:0005667 transcription factor complex IEA,ISS --
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with SIX1: view

Pathways & Interactions for SIX1 Gene

genes like me logo Genes that share pathways with SIX1: view

Pathways by source for SIX1 Gene

1 Cell Signaling Technology pathway for SIX1 Gene
1 KEGG pathway for SIX1 Gene

SIGNOR curated interactions for SIX1 Gene

Activates:

Gene Ontology (GO) - Biological Process for SIX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IEA --
GO:0001657 ureteric bud development IEA,ISS --
GO:0001658 branching involved in ureteric bud morphogenesis IEA,ISS --
GO:0001759 organ induction IEA,ISS --
GO:0001822 kidney development IEA,ISS --
genes like me logo Genes that share ontologies with SIX1: view

Transcripts for SIX1 Gene

Unigene Clusters for SIX1 Gene

SIX homeobox 1:
Representative Sequences:

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SIX1

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SIX1 Gene

No ASD Table

Relevant External Links for SIX1 Gene

GeneLoc Exon Structure for
SIX1
ECgene alternative splicing isoforms for
SIX1

Expression for SIX1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SIX1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SIX1 Gene

This gene is overexpressed in Muscle - Skeletal (x20.7) and Pituitary (x8.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SIX1 Gene



NURSA nuclear receptor signaling pathways regulating expression of SIX1 Gene:

SIX1

SOURCE GeneReport for Unigene cluster for SIX1 Gene:

Hs.633506

mRNA Expression by UniProt/SwissProt for SIX1 Gene:

Q15475-SIX1_HUMAN
Tissue specificity: Specifically expressed in skeletal muscle.
genes like me logo Genes that share expression patterns with SIX1: view

No data available for Protein differential expression in normal tissues and Protein tissue co-expression partners for SIX1 Gene

Orthologs for SIX1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SIX1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SIX1 34 35
  • 100 (n)
dog
(Canis familiaris)
Mammalia SIX1 34 35
  • 94.48 (n)
oppossum
(Monodelphis domestica)
Mammalia SIX1 35
  • 94 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Six1 34 16 35
  • 93.31 (n)
cow
(Bos Taurus)
Mammalia SIX1 34 35
  • 93.19 (n)
-- 35
  • 5 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Six1 34
  • 93.19 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SIX1 35
  • 91 (a)
OneToOne
chicken
(Gallus gallus)
Aves SIX1 34 35
  • 85.22 (n)
lizard
(Anolis carolinensis)
Reptilia SIX1 35
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia six1 34
  • 78.4 (n)
Str.9229 34
African clawed frog
(Xenopus laevis)
Amphibia Six1 34
zebrafish
(Danio rerio)
Actinopterygii six1b 34 35
  • 77.46 (n)
Dr.27681 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.722 34
fruit fly
(Drosophila melanogaster)
Insecta so 36 34 35
  • 76.32 (n)
Six4 36
  • 62 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011695 34
  • 74.29 (n)
worm
(Caenorhabditis elegans)
Secernentea ceh-33 36 35
  • 61 (a)
ceh-32 36
  • 56 (a)
ceh-34 36
  • 53 (a)
ceh-35 36
  • 38 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 24 (a)
ManyToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.7135 34
Species where no ortholog for SIX1 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)
  • 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 SIX1 Gene

ENSEMBL:
Gene Tree for SIX1 (if available)
TreeFam:
Gene Tree for SIX1 (if available)

Paralogs for SIX1 Gene

Paralogs for SIX1 Gene

(6) SIMAP similar genes for SIX1 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with SIX1: view

Variants for SIX1 Gene

Sequence variations from dbSNP and Humsavar for SIX1 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type
rs104894478 Branchiootic syndrome 3 (BOS3) [MIM:608389], Pathogenic 60,648,804(-) CAGCT(A/G)CTGCT reference, missense
rs121909770 Branchiootic syndrome 3 (BOS3) [MIM:608389], Pathogenic 60,648,826(-) CCATC(A/T)GGGAC reference, missense
rs397515560 Branchiootic syndrome 3 (BOS3) [MIM:608389], Pathogenic 60,648,873(-) CGCCG(G/T)GGGCA reference, missense
rs397515561 Branchiootic syndrome 3 (BOS3) [MIM:608389], Pathogenic 60,648,856(-) GGGTG(C/T)GCCGA reference, missense
rs397515562 Branchiootic syndrome 3 (BOS3) [MIM:608389], Pathogenic 60,649,140(-) GTGCG(A/T)GTGCG reference, missense

Structural Variations from Database of Genomic Variants (DGV) for SIX1 Gene

Variant ID Type Subtype PubMed ID
nsv1295 CNV deletion 18451855
nsv564880 CNV gain 21841781
nsv564881 CNV gain 21841781
nsv819505 CNV gain 19587683
nsv952846 CNV deletion 24416366

Variation tolerance for SIX1 Gene

Residual Variation Intolerance Score: 30% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.26; 5.90% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SIX1 Gene

Human Gene Mutation Database (HGMD)
SIX1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SIX1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SIX1 Gene

Disorders for SIX1 Gene

MalaCards: The human disease database

(17) MalaCards diseases for SIX1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
brachiootic syndrome 3
  • branchiootic syndrome 3
deafness, autosomal dominant 23
  • autosomal dominant nonsyndromic deafness 23
branchiootorenal syndrome 1, with or without cataracts
  • anterior segment anomalies with or without cataract
six1-related branchiootorenal spectrum disorders
  • bos3
branchiootorenal/branchiootic syndrome
  • branchiootic syndrome 1
- elite association - COSMIC cancer census association via MalaCards
Search SIX1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SIX1_HUMAN
  • Branchiootic syndrome 3 (BOS3) [MIM:608389]: A syndrome characterized by usually bilateral branchial cleft fistulas or cysts, sensorineural and/or conductive hearing loss, pre-auricular pits, and structural defects of the outer, middle or inner ear. Otic defects include malformed and hypoplastic pinnae, a narrowed external ear canal, bulbous internal auditory canal, stapes fixation, malformed and hypoplastic cochlea. Branchial and otic anomalies overlap with those seen in individuals with the branchiootorenal syndrome. However renal anomalies are absent in branchiootic syndrome patients. {ECO:0000269 PubMed:15141091, ECO:0000269 PubMed:17637804, ECO:0000269 PubMed:18330911, ECO:0000269 PubMed:21280147}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Deafness, autosomal dominant, 23 (DFNA23) [MIM:605192]: A form of non-syndromic deafness characterized by prelingual, bilateral, symmetric hearing loss with a conductive component present in some but not all patients. {ECO:0000269 PubMed:15141091}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Note=Defects in SIX1 could be a cause of branchiootorenal syndrome (BOR). BOR is an autosomal dominant disorder manifested by various combinations of preauricular pits, branchial fistulae or cysts, lacrimal duct stenosis, hearing loss, structural defects of the outer, middle, or inner ear, and renal dysplasia. Associated defects include asthenic habitus, long narrow facies, constricted palate, deep overbite, and myopia. Hearing loss may be due to mondini type cochlear defect and stapes fixation. Penetrance of BOR syndrome is high, although expressivity can be extremely variable. {ECO:0000305 PubMed:15141091, ECO:0000305 PubMed:19497856}.

Relevant External Links for SIX1

Human Genome Epidemiology (HuGE) Navigator
SIX1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SIX1
genes like me logo Genes that share disorders with SIX1: view

No data available for Genatlas for SIX1 Gene

Publications for SIX1 Gene

  1. SIX1 mutations cause branchio-oto-renal syndrome by disruption of EYA1-SIX1-DNA complexes. (PMID: 15141091) Ruf R.G. … Hildebrandt F. (Proc. Natl. Acad. Sci. U.S.A. 2004) 2 3 4 22 64
  2. Biochemical and functional characterization of six SIX1 Branchio-oto- renal syndrome mutations. (PMID: 19497856) Patrick A.N. … Ford H.L. (J. Biol. Chem. 2009) 3 4 22 64
  3. SIX1 mutation screening in 247 branchio-oto-renal syndrome families: a recurrent missense mutation associated with BOR. (PMID: 18330911) Kochhar A. … Smith R.J. (Hum. Mutat. 2008) 3 4 22 64
  4. Cell cycle regulation of the human Six1 homeoprotein is mediated by APC(Cdh1). (PMID: 17130831) Christensen K.L. … Ford H.L. (Oncogene 2007) 3 4 22 64
  5. Branchio-oto-renal syndrome: detection of EYA1 and SIX1 mutations in five out of six Danish families by combining linkage, MLPA and sequencing analyses. (PMID: 17637804) Sanggaard K.M. … Tranebjaerg L. (Eur. J. Hum. Genet. 2007) 3 4 22 64

Products for SIX1 Gene

Sources for SIX1 Gene

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