SATB2

SATB homeobox 2 | FLJ21474, KIAA1034

This gene encodes a DNA binding protein that specifically binds nuclear matrix attachment regions. The encoded protein is involved in transcription regulation and chromatin remodeling. Defects in this gene are associated with isolated cleft palate and cognitive disability. Alternate splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Feb 2010]

Member of: DE-2 DE-2.22

Biological processes 28 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 (GO:0003700)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 transcription regulatory region sequence-specific DNA binding (GO:0000977)RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977)chromatin (GO:0000785)chromatin binding (GO:0003682)chromatin remodeling (GO:0006338)chromatin remodeling (GO:0006338)histone deacetylase binding (GO:0042826)histone deacetylase complex (GO:0000118)nuclear lumen (GO:0031981)nuclear matrix (GO:0016363)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of transcription by RNA polymerase II (GO:0045944)protein binding (GO:0005515)regulation of transcription by RNA polymerase II (GO:0006357)regulation of transcription by RNA polymerase II (GO:0006357)sequence-specific DNA binding (GO:0043565)transcription regulator complex (GO:0005667)

Expression (TPM)

TFs regulating SATB2 0 TFs

Transcription factors with Perturb-seq knockdown data for SATB2. 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 = SATB2 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 SATB2

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of SATB2, 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
chr2:197,704,733–197,706,212	1752.3 kb	Distal (>10kb) Multiome HiCAR	870
chr2:198,875,206–198,876,212	581.8 kb	Distal (>10kb) Multiome HiCAR	94
chr2:199,411,536–199,412,384	45.8 kb	Distal (>10kb) Multiome	102
chr2:199,447,059–199,447,484	10.0 kb	Proximal (<10kb)	34
chr2:199,455,411–199,456,654	1.7 kb	Proximal (<10kb) Multiome	863
chr2:199,456,911–199,460,483	2.0 kb	Proximal (<10kb) Multiome	1064
chr2:199,461,810–199,465,006	5.9 kb	Proximal (<10kb) Multiome	700
chr2:199,466,045–199,466,262	8.6 kb	Proximal (<10kb)	26
chr2:199,466,565–199,466,722	9.1 kb	Proximal (<10kb)	20
chr2:199,466,957–199,467,868	9.5 kb	Proximal (<10kb)	138
chr2:199,468,395–199,470,562	9.7 kb	Proximal (<10kb)	280
chr2:199,470,681–199,471,964	14.0 kb	Distal (>10kb) Multiome	611

Genome Browser

Genomic view of the SATB2 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.