SAFB
scaffold attachment factor B | HET, SAFB1

This gene encodes a DNA-binding protein which has high specificity for scaffold or matrix attachment region DNA elements (S/MAR DNA). This protein is thought to be involved in attaching the base of chromatin loops to the nuclear matrix but there is conflicting evidence as to whether this protein is a component of chromatin or a nuclear matrix protein. Scaffold attachment factors are a specific subset of nuclear matrix proteins (NMP) that specifically bind to S/MAR. The encoded protein is thought to serve as a molecular base to assemble a 'transcriptosome complex' in the vicinity of actively transcribed genes. It is involved in the regulation of heat shock protein 27 transcription, can act as an estrogen receptor co-repressor and is a candidate for breast tumorigenesis. This gene is arranged head-to-head with a similar gene whose product has the same functions. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2011]

Member of: DE-5 DE-5.25 Developmental clusters: GC2
Biological processes 20 terms
Expression (TPM)
SAFB — as a Regulated Gene

TFs regulating SAFB 0 TFs

Transcription factors with Perturb-seq knockdown data for SAFB. 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 = SAFB upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

Data: Effect:
TF Mean coef Binding Outlier TF→Gene link

Elements linked to SAFB

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of SAFB, 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.

Accessibility Element Dist. to TSS Link type TFs
chr19:4,534,817–4,535,416 1087.9 kb Distal (>10kb) Multiome HiCAR 451
chr19:5,339,639–5,341,408 282.2 kb Distal (>10kb) Multiome 966
chr19:5,397,820–5,398,866 224.7 kb Distal (>10kb) Multiome 137
chr19:5,436,304–5,437,277 186.3 kb Distal (>10kb) Multiome 227
chr19:5,536,326–5,536,869 86.4 kb Distal (>10kb) Multiome 306
chr19:5,567,504–5,568,201 55.3 kb Distal (>10kb) Multiome 209
chr19:5,585,656–5,586,338 37.1 kb Distal (>10kb) Multiome 267
chr19:5,621,964–5,623,739 155 bp At TSS Multiome 857
chr19:5,679,757–5,681,464 57.7 kb Distal (>10kb) Multiome 884
chr19:5,686,329–5,687,994 63.9 kb Distal (>10kb) Multiome 693
chr19:5,689,735–5,690,874 67.2 kb Distal (>10kb) Multiome 960
chr19:5,719,717–5,721,174 97.3 kb Distal (>10kb) Multiome 985
chr19:5,790,527–5,791,509 167.8 kb Distal (>10kb) Multiome 965
chr19:5,803,750–5,806,128 182.1 kb Distal (>10kb) Multiome 858
chr19:5,826,528–5,829,726 205.0 kb Distal (>10kb) Multiome 1037
chr19:5,903,474–5,905,358 281.5 kb Distal (>10kb) Multiome 1027

Genome Browser

Genomic view of the SAFB 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.

chr19:4,524,817 – 5,915,358
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq