Free for academic non-profit institutions. Other users need a Commercial license

Aliases for SIX4 Gene

Aliases for SIX4 Gene

  • SIX Homeobox 4 2 3
  • Sine Oculis Homeobox Homolog 4 3 4
  • Sine Oculis Homeobox (Drosophila) Homolog 4 2
  • Sine Oculis Homeobox Homolog 4 (Drosophila) 2
  • Homeobox Protein SIX4 3
  • AREC3 3

External Ids for SIX4 Gene

Previous GeneCards Identifiers for SIX4 Gene

  • GC14M058506
  • GC14M054973
  • GC14M059170
  • GC14M060249
  • GC14M061176
  • GC14M041338

Summaries for SIX4 Gene

Entrez Gene Summary for SIX4 Gene

  • This gene encodes a member of the homeobox family, subfamily SIX. The drosophila homolog is a nuclear homeoprotein required for eye development. Studies in mouse show that this gene product functions as a transcription factor, and may have a role in the differentiation or maturation of neuronal cells. [provided by RefSeq, May 2010]

GeneCards Summary for SIX4 Gene

SIX4 (SIX Homeobox 4) is a Protein Coding gene. Among its related pathways are Transcriptional misregulation in cancer. 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 SIX6.

UniProtKB/Swiss-Prot for SIX4 Gene

  • Transcriptional regulator which can act as both a transcriptional repressor and activator by binding a DNA sequence on these target genes and is involved in processes like cell differentiation, cell migration and cell survival. Transactivates gene expression by binding a 5-[CAT]A[CT][CT][CTG]GA[GAT]-3 motif present in the Trex site and a 5-TCA[AG][AG]TTNC-3 motif present in the MEF3 site of the muscle-specific genes enhancer. Acts cooperatively with EYA proteins to transactivate their target genes through interaction and nuclear translocation of EYA protein. Acts synergistically with SIX1 to regulate target genes involved in formation of various organs, including muscle, kidney, gonad, ganglia, olfactory epithelium and cranial skeleton. Plays a role in several important steps of muscle development. Controls the genesis of hypaxial myogenic progenitors in the dermomyotome by transactivating PAX3 and the delamination and migration of the hypaxial precursors from the ventral lip to the limb buds through the transactivation of PAX3, MET and LBX1. Controls myoblast determination by transactivating MYF5, MYOD1 and MYF6. Controls somitic differentiation in myocyte through MYOG transactivation. Plays a role in synaptogenesis and sarcomere organization by participating in myofiber specialization during embryogenesis by activating fast muscle program in the primary myotome resulting in an up-regulation of fast muscle genes, including ATP2A1, MYL1 and TNNT3. Simultaneously, is also able to activate inhibitors of slow muscle genes, such as SOX6, HRASLS, and HDAC4, thereby restricting the activation of the slow muscle genes. During muscle regeneration, negatively regulates differentiation of muscle satellite cells through down-regulation of MYOG expression. During kidney development regulates the early stages of metanephros development and ureteric bud formation through regulation of GDNF, SALL1, PAX8 and PAX2 expression. Plays a role in gonad development by regulating both testis determination and size determination. In gonadal sex determination, transactivates ZFPM2 by binding a MEF3 consensus sequence, resulting in SRY up-regulation. In gonadal size determination, transactivates NR5A1 by binding a MEF3 consensus sequence resulting in gonadal precursor cell formation regulation. During olfactory development mediates the specification and patterning of olfactory placode through fibroblast growth factor and BMP4 signaling pathways and also regulates epithelial cell proliferation during placode formation. Promotes survival of sensory neurons during early trigeminal gangliogenesis. In the developing dorsal root ganglia, up-regulates SLC12A2 transcription. Regulates early thymus/parathyroid organogenesis through regulation of GCM2 and FOXN1 expression. Forms gustatory papillae during development of the tongue. Also plays a role during embryonic cranial skeleton morphogenesis.

Gene Wiki entry for SIX4 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SIX4 Gene

Genomics for SIX4 Gene

Regulatory Elements for SIX4 Gene

Epigenetics Products

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

Genomic Location for SIX4 Gene

Start:
60,709,528 bp from pter
End:
60,724,348 bp from pter
Size:
14,821 bases
Orientation:
Minus strand

Genomic View for SIX4 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SIX4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SIX4 Gene

Proteins for SIX4 Gene

  • Protein details for SIX4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UIU6-SIX4_HUMAN
    Recommended name:
    Homeobox protein SIX4
    Protein Accession:
    Q9UIU6
    Secondary Accessions:
    • Q4QQH5
    • Q4V764

    Protein attributes for SIX4 Gene

    Size:
    781 amino acids
    Molecular mass:
    82933 Da
    Quaternary structure:
    • Interacts with EYA3; acts cooperatively with EYA3 to transactivate target genes through interaction and nuclear translocation of EYA3 protein.
    SequenceCaution:
    • Sequence=BAA86223.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=EAW80786.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for SIX4 Gene

Proteomics data for SIX4 Gene at MOPED

Post-translational modifications for SIX4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SIX4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SIX4 Gene

Domains for SIX4 Gene

Gene Families for SIX4 Gene

HGNC:
  • SIX :Homeoboxes / SINE class

Protein Domains for SIX4 Gene

Suggested Antigen Peptide Sequences for SIX4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9UIU6

UniProtKB/Swiss-Prot:

SIX4_HUMAN :
  • Q9UIU6
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 SIX4: view

Function for SIX4 Gene

Molecular function for SIX4 Gene

GENATLAS Biochemistry: Drosophila sine oculis homolog SIX4 homeo box encoding gene,expressed in mouse in the nucleus of neuronal cells in developing brain,spinal cord and various ganglia,not deleted in a adult tissues,also expressed in developing mouse retina,putatively involved in differentiation or maturation of neuronal cells and retinal development
UniProtKB/Swiss-Prot Function: Transcriptional regulator which can act as both a transcriptional repressor and activator by binding a DNA sequence on these target genes and is involved in processes like cell differentiation, cell migration and cell survival. Transactivates gene expression by binding a 5-[CAT]A[CT][CT][CTG]GA[GAT]-3 motif present in the Trex site and a 5-TCA[AG][AG]TTNC-3 motif present in the MEF3 site of the muscle-specific genes enhancer. Acts cooperatively with EYA proteins to transactivate their target genes through interaction and nuclear translocation of EYA protein. Acts synergistically with SIX1 to regulate target genes involved in formation of various organs, including muscle, kidney, gonad, ganglia, olfactory epithelium and cranial skeleton. Plays a role in several important steps of muscle development. Controls the genesis of hypaxial myogenic progenitors in the dermomyotome by transactivating PAX3 and the delamination and migration of the hypaxial precursors from the ventral lip to the limb buds through the transactivation of PAX3, MET and LBX1. Controls myoblast determination by transactivating MYF5, MYOD1 and MYF6. Controls somitic differentiation in myocyte through MYOG transactivation. Plays a role in synaptogenesis and sarcomere organization by participating in myofiber specialization during embryogenesis by activating fast muscle program in the primary myotome resulting in an up-regulation of fast muscle genes, including ATP2A1, MYL1 and TNNT3. Simultaneously, is also able to activate inhibitors of slow muscle genes, such as SOX6, HRASLS, and HDAC4, thereby restricting the activation of the slow muscle genes. During muscle regeneration, negatively regulates differentiation of muscle satellite cells through down-regulation of MYOG expression. During kidney development regulates the early stages of metanephros development and ureteric bud formation through regulation of GDNF, SALL1, PAX8 and PAX2 expression. Plays a role in gonad development by regulating both testis determination and size determination. In gonadal sex determination, transactivates ZFPM2 by binding a MEF3 consensus sequence, resulting in SRY up-regulation. In gonadal size determination, transactivates NR5A1 by binding a MEF3 consensus sequence resulting in gonadal precursor cell formation regulation. During olfactory development mediates the specification and patterning of olfactory placode through fibroblast growth factor and BMP4 signaling pathways and also regulates epithelial cell proliferation during placode formation. Promotes survival of sensory neurons during early trigeminal gangliogenesis. In the developing dorsal root ganglia, up-regulates SLC12A2 transcription. Regulates early thymus/parathyroid organogenesis through regulation of GCM2 and FOXN1 expression. Forms gustatory papillae during development of the tongue. Also plays a role during embryonic cranial skeleton morphogenesis.

Gene Ontology (GO) - Molecular Function for SIX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding --
GO:0003700 sequence-specific DNA binding transcription factor activity IEA --
GO:0005515 protein binding --
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with SIX4: view
genes like me logo Genes that share phenotypes with SIX4: view

Animal Model Products

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SIX4

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for SIX4 Gene

Localization for SIX4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SIX4 Gene

Nucleus. Cytoplasm.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SIX4 Gene COMPARTMENTS Subcellular localization image for SIX4 gene
Compartment Confidence
nucleus 3
cytosol 2

Gene Ontology (GO) - Cellular Components for SIX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS --
GO:0005737 cytoplasm ISS --
genes like me logo Genes that share ontologies with SIX4: view

Pathways for SIX4 Gene

genes like me logo Genes that share pathways with SIX4: view

Pathways by source for SIX4 Gene

1 KEGG pathway for SIX4 Gene

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Gene Ontology (GO) - Biological Process for SIX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated --
GO:0007519 skeletal muscle tissue development ISS --
GO:0008582 regulation of synaptic growth at neuromuscular junction IEA --
GO:0008584 male gonad development ISS --
genes like me logo Genes that share ontologies with SIX4: view

Transcripts for SIX4 Gene

mRNA/cDNA for SIX4 Gene

(6) Additional mRNA sequences :
(6) Selected AceView cDNA sequences:
(2) REFSEQ mRNAs :
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SIX4 Gene

SIX homeobox 4:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SIX4

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for SIX4

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SIX4 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5
SP1: - -
SP2:

Relevant External Links for SIX4 Gene

GeneLoc Exon Structure for
SIX4
ECgene alternative splicing isoforms for
SIX4

Expression for SIX4 Gene

mRNA expression in normal human tissues for SIX4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SIX4 Gene

This gene is overexpressed in Muscle - Skeletal (15.7).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for SIX4 Gene

SOURCE GeneReport for Unigene cluster for SIX4 Gene Hs.97849

genes like me logo Genes that share expressions with SIX4: view

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt for SIX4 Gene

Orthologs for SIX4 Gene

This gene was present in the common ancestor of animals.

Orthologs for SIX4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SIX4 35
  • 99.35 (n)
  • 99.31 (a)
SIX4 36
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SIX4 35
  • 93.28 (n)
  • 94.32 (a)
SIX4 36
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Six4 35
  • 90.09 (n)
  • 91.21 (a)
Six4 16
Six4 36
  • 91 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SIX4 36
  • 83 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SIX4 36
  • 70 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Six4 35
  • 90.46 (n)
  • 91.6 (a)
chicken
(Gallus gallus)
Aves SIX4 35
  • 78.8 (n)
  • 80.23 (a)
SIX4 36
  • 79 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SIX4 36
  • 64 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.7384 35
tropical clawed frog
(Silurana tropicalis)
Amphibia six4 35
  • 69.93 (n)
  • 65.29 (a)
Str.18391 35
zebrafish
(Danio rerio)
Actinopterygii -- 35
six4a 35
  • 60.56 (n)
  • 60.71 (a)
six4a 36
  • 47 (a)
OneToMany
six4b 36
  • 46 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Six4 36
  • 36 (a)
OneToMany
Six4 37
  • 65 (a)
worm
(Caenorhabditis elegans)
Secernentea unc-39 36
  • 28 (a)
ManyToMany
ceh-33 37
  • 53 (a)
ceh-35 37
  • 38 (a)
ceh-34 37
  • 50 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.8582 35
Species with no ortholog for SIX4:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • cow (Bos Taurus)
  • 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)
  • 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 SIX4 Gene

ENSEMBL:
Gene Tree for SIX4 (if available)
TreeFam:
Gene Tree for SIX4 (if available)

Paralogs for SIX4 Gene

Paralogs for SIX4 Gene

Selected SIMAP similar genes for SIX4 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with SIX4: view

Variants for SIX4 Gene

Sequence variations from dbSNP and Humsavar for SIX4 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type MAF
rs717174 -- 60,725,317(-) TGGAT(C/T)ATCCC upstream-variant-2KB
rs2180830 -- 60,709,767(-) TGTAT(A/G)TCATG utr-variant-3-prime
rs2351272 -- 60,719,027(+) CATAG(A/T)GGATC intron-variant
rs3049887 -- 60,725,567(+) GCTAA(-/T)TTTTT upstream-variant-2KB
rs3742636 - 60,713,939(-) CCTGC(A/C)TCCAC reference, missense

Structural Variations from Database of Genomic Variants (DGV) for SIX4 Gene

Variant ID Type Subtype PubMed ID
nsv902001 CNV Loss 21882294

Relevant External Links for SIX4 Gene

HapMap Linkage Disequilibrium report
SIX4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SIX4 Gene

Disorders for SIX4 Gene

(1) University of Copenhagen DISEASES for SIX4 Gene

genes like me logo Genes that share disorders with SIX4: view

No data available for UniProtKB/Swiss-Prot for SIX4 Gene

Publications for SIX4 Gene

  1. Structure and chromosome mapping of the human SIX4 and murine Six4 genes. (PMID: 10640827) Ozaki H. … Kawakami K. (Cytogenet. Cell Genet. 1999) 2 3 4
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4
  3. 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. System-wide changes to SUMO modifications in response to heat shock. (PMID: 19471022) Golebiowski F. … Hay R.T. (Sci Signal 2009) 3
  5. Comparative proteomic analysis identifies a role for SUMO in protein quality control. (PMID: 21693764) Tatham M.H. … Hay R.T. (Sci Signal 2011) 3

Products for SIX4 Gene

Sources for SIX4 Gene

Back to Top

Content