PBX2

PBX homeobox 2 | G17, HOX12, PBX2MHC

This gene encodes a ubiquitously expressed member of the TALE/PBX homeobox family. It was identified by its similarity to a homeobox gene which is involved in t(1;19) translocation in acute pre-B-cell leukemias. This protein is a transcriptional activator which binds to the TLX1 promoter. The gene is located within the major histocompatibility complex (MHC) on chromosome 6. [provided by RefSeq, Jul 2008]

Member of: DE-4 Developmental clusters: GC6 GC6 GC6 GC6

Biological processes 25 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)DNA-binding transcription factor binding (GO:0140297)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977)animal organ morphogenesis (GO:0009887)brain development (GO:0007420)chromatin (GO:0000785)chromatin binding (GO:0003682)embryonic organ development (GO:0048568)eye development (GO:0001654)neuron development (GO:0048666)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)protein binding (GO:0005515)regulation of DNA-templated transcription (GO:0006355)transcription regulator complex (GO:0005667)

Expression (TPM)

TFs regulating PBX2 0 TFs

Transcription factors with Perturb-seq knockdown data for PBX2. 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 = PBX2 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 PBX2

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of PBX2, 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
chr6:31,896,965–31,898,037	292.4 kb	Distal (>10kb) Multiome	654
chr6:31,901,114–31,902,643	287.7 kb	Distal (>10kb) Multiome	826
chr6:31,958,527–31,959,598	230.9 kb	Distal (>10kb) Multiome	953
chr6:31,971,421–31,972,872	217.7 kb	Distal (>10kb) Multiome	1059
chr6:32,048,217–32,048,679	141.6 kb	Distal (>10kb) Multiome	611
chr6:32,087,265–32,088,160	102.2 kb	Distal (>10kb) Multiome	473
chr6:32,127,621–32,128,720	61.7 kb	Distal (>10kb) Multiome	683
chr6:32,129,973–32,130,800	59.6 kb	Distal (>10kb) Multiome	717
chr6:32,144,531–32,145,041	45.2 kb	Distal (>10kb) Multiome	44
chr6:32,148,431–32,149,344	41.1 kb	Distal (>10kb) Multiome	145
chr6:32,153,307–32,155,059	35.9 kb	Distal (>10kb) Multiome	908
chr6:32,167,399–32,168,187	21.9 kb	Distal (>10kb) Multiome	411
chr6:32,175,673–32,176,347	13.8 kb	Distal (>10kb) Multiome	654
chr6:32,177,078–32,178,952	11.9 kb	Distal (>10kb) Multiome	820
chr6:32,190,108–32,191,167	410 bp	At TSS Multiome	661
chr6:32,195,084–32,196,878	5.9 kb	Proximal (<10kb) Multiome	1063
chr6:32,255,200–32,255,686	65.4 kb	Distal (>10kb) Multiome	364

Genome Browser

Genomic view of the PBX2 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.