SIX3

SIX homeobox 3 | HPE2

This gene encodes a member of the sine oculis homeobox transcription factor family. The encoded protein plays a role in eye development. Mutations in this gene have been associated with holoprosencephaly type 2. [provided by RefSeq, Oct 2009]

Member of: DE-4 Developmental clusters: GC6

Biological processes 67 terms

DNA binding (GO:0003677)DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228)DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)apoptotic process involved in development (GO:1902742)apoptotic process involved in development (GO:1902742)brain development (GO:0007420)brain development (GO:0007420)cell proliferation in forebrain (GO:0021846)cell proliferation in forebrain (GO:0021846)chromatin (GO:0000785)epithelial cell maturation (GO:0002070)epithelial cell maturation (GO:0002070)eye development (GO:0001654)eye development (GO:0001654)forebrain dorsal/ventral pattern formation (GO:0021798)gene expression (GO:0010467)histone deacetylase binding (GO:0042826)lens development in camera-type eye (GO:0002088)lens development in camera-type eye (GO:0002088)lens fiber cell apoptotic process (GO:1990086)lens fiber cell apoptotic process (GO:1990086)lens fiber cell differentiation (GO:0070306)lens fiber cell differentiation (GO:0070306)negative regulation of DNA-templated transcription (GO:0045892)negative regulation of neuron differentiation (GO:0045665)negative regulation of neuron differentiation (GO:0045665)neuroblast differentiation (GO:0014016)neuroblast differentiation (GO:0014016)neuroblast migration (GO:0097402)neuroblast migration (GO:0097402)nucleus (GO:0005634)nucleus (GO:0005634)optic vesicle morphogenesis (GO:0003404)optic vesicle morphogenesis (GO:0003404)pituitary gland development (GO:0021983)pituitary gland development (GO:0021983)positive regulation of transcription by RNA polymerase II (GO:0045944)protein binding (GO:0005515)proximal/distal axis specification (GO:0009946)proximal/distal axis specification (GO:0009946)regulation of cell cycle phase transition (GO:1901987)regulation of cell cycle phase transition (GO:1901987)regulation of cell population proliferation (GO:0042127)regulation of cell population proliferation (GO:0042127)regulation of neural precursor cell proliferation (GO:2000177)regulation of neural precursor cell proliferation (GO:2000177)regulation of neural retina development (GO:0061074)regulation of neural retina development (GO:0061074)regulation of neuroblast proliferation (GO:1902692)regulation of neuroblast proliferation (GO:1902692)regulation of transcription by RNA polymerase II (GO:0006357)sequence-specific DNA binding (GO:0043565)sequence-specific double-stranded DNA binding (GO:1990837)telencephalon development (GO:0021537)telencephalon regionalization (GO:0021978)telencephalon regionalization (GO:0021978)transcription corepressor binding (GO:0001222)transcription corepressor binding (GO:0001222)transcription regulator complex (GO:0005667)visual perception (GO:0007601)visual perception (GO:0007601)

Expression (TPM)

TFs regulating SIX3 0 TFs

Transcription factors with Perturb-seq knockdown data for SIX3. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = SIX3 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

TF	Mean coef	Binding	Outlier	TF→Gene link

Rows:

Elements linked to SIX3

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of SIX3, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Element	Dist. to TSS	Link type	TFs
chr2:44,674,098–44,675,273	266.9 kb	Distal (>10kb) Multiome HiCAR	276
chr2:44,768,426–44,769,321	172.8 kb	Distal (>10kb) Multiome HiCAR	118
chr2:44,778,216–44,779,112	163.1 kb	Distal (>10kb) Multiome HiCAR	285
chr2:44,789,787–44,791,030	151.2 kb	Distal (>10kb) Multiome HiCAR	179
chr2:44,801,102–44,802,191	140.2 kb	Distal (>10kb) Multiome	262
chr2:44,802,563–44,803,392	138.7 kb	Distal (>10kb) Multiome	292
chr2:44,804,663–44,806,066	136.3 kb	Distal (>10kb) Multiome	247
chr2:44,881,511–44,882,032	59.9 kb	Distal (>10kb) Multiome	68
chr2:44,925,120–44,926,259	16.0 kb	Distal (>10kb) Multiome	76
chr2:44,928,632–44,930,007	12.3 kb	Distal (>10kb) Multiome	186
chr2:44,932,798–44,933,373	8.3 kb	Proximal (<10kb)	62
chr2:44,934,122–44,936,090	5.8 kb	Proximal (<10kb) Multiome	246
chr2:44,937,044–44,939,675	4.0 kb	Proximal (<10kb) Multiome	512
chr2:44,939,777–44,940,009	1.7 kb	Proximal (<10kb)	43
chr2:44,940,953–44,942,676	6 bp	At TSS Multiome	260
chr2:44,943,778–44,944,903	2.1 kb	Proximal (<10kb)	119
chr2:44,945,722–44,946,385	4.4 kb	Proximal (<10kb) Multiome	150
chr2:44,949,379–44,950,322	8.2 kb	Proximal (<10kb) Multiome	186
chr2:44,951,821–44,953,211	10.7 kb	Distal (>10kb) Multiome	430
chr2:44,955,189–44,956,345	14.1 kb	Distal (>10kb) Multiome	554
chr2:45,000,269–45,001,482	59.0 kb	Distal (>10kb) Multiome	111
chr2:45,008,227–45,010,649	67.9 kb	Distal (>10kb) Multiome	554
chr2:45,013,210–45,014,745	72.5 kb	Distal (>10kb) Multiome	393
chr2:45,068,171–45,068,872	126.8 kb	Distal (>10kb) Multiome	85
chr2:45,168,959–45,170,811	228.3 kb	Distal (>10kb) Multiome	356

Genome Browser

Genomic view of the SIX3 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.