LDB1
LIM domain binding 1 | CLIM2, NLI

Enables LIM domain binding activity; RNA polymerase II-specific DNA-binding transcription factor binding activity; and enzyme binding activity. Involved in negative regulation of DNA-templated transcription and positive regulation of transcription by RNA polymerase II. Located in chromatin. Part of beta-catenin-TCF complex. [provided by Alliance of Genome Resources, Jul 2025]

Member of: DE-5
Biological processes 54 terms
DNA binding (GO:0003677)DNA-binding transcription factor binding (GO:0140297)DNA-binding transcription factor binding (GO:0140297)LIM domain binding (GO:0030274)LIM domain binding (GO:0030274)LIM domain binding (GO:0030274)RNA polymerase II transcription regulator complex (GO:0090575)RNA polymerase II-specific DNA-binding transcription factor binding (GO:0061629)beta-catenin-TCF complex (GO:1990907)cell leading edge (GO:0031252)cell leading edge (GO:0031252)chromatin (GO:0000785)chromatin binding (GO:0003682)enzyme binding (GO:0019899)enzyme binding (GO:0019899)head development (GO:0060322)identical protein binding (GO:0042802)negative regulation of DNA-templated transcription (GO:0045892)negative regulation of erythrocyte differentiation (GO:0045647)negative regulation of erythrocyte differentiation (GO:0045647)negative regulation of transcription by RNA polymerase II (GO:0000122)nervous system development (GO:0007399)neuron differentiation (GO:0030182)neuron differentiation (GO:0030182)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of hemoglobin biosynthetic process (GO:0046985)positive regulation of hemoglobin biosynthetic process (GO:0046985)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription elongation by RNA polymerase II (GO:0032968)positive regulation of transcription elongation by RNA polymerase II (GO:0032968)protein binding (GO:0005515)protein homodimerization activity (GO:0042803)protein homodimerization activity (GO:0042803)protein-containing complex (GO:0032991)protein-containing complex (GO:0032991)regulation of cell migration (GO:0030334)regulation of cell migration (GO:0030334)regulation of focal adhesion assembly (GO:0051893)regulation of focal adhesion assembly (GO:0051893)regulation of kinase activity (GO:0043549)transcription by RNA polymerase II (GO:0006366)transcription coactivator activity (GO:0003713)transcription coregulator activity (GO:0003712)transcription regulator complex (GO:0005667)transcription regulator complex (GO:0005667)transcription regulator complex (GO:0005667)transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery (GO:0000972)transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery (GO:0000972)
Expression (TPM)
LDB1 — as a Regulated Gene

TFs regulating LDB1 0 TFs

Transcription factors with Perturb-seq knockdown data for LDB1. 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 = LDB1 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 LDB1

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of LDB1, 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
chr10:101,817,350–101,819,352 296.4 kb Distal (>10kb) Multiome 1004
chr10:101,828,926–101,831,154 284.1 kb Distal (>10kb) Multiome HiCAR 697
chr10:101,839,408–101,839,998 275.3 kb Distal (>10kb) Multiome 196
chr10:101,840,663–101,841,471 273.9 kb Distal (>10kb) Multiome HiCAR 499
chr10:101,843,178–101,844,328 271.2 kb Distal (>10kb) Multiome HiCAR 277
chr10:101,893,696–101,895,001 220.4 kb Distal (>10kb) Multiome 142
chr10:101,960,808–101,961,342 153.8 kb Distal (>10kb) Multiome 47
chr10:102,055,474–102,056,435 58.8 kb Distal (>10kb) Multiome 955
chr10:102,064,619–102,066,067 49.6 kb Distal (>10kb) Multiome 778
chr10:102,114,483–102,115,579 120 bp At TSS Multiome 546
chr10:102,117,456–102,117,777 2.5 kb Proximal (<10kb) 476
chr10:102,119,389–102,122,276 5.6 kb Proximal (<10kb) Multiome 934
chr10:102,132,334–102,133,845 18.0 kb Distal (>10kb) Multiome 968
chr10:102,151,480–102,152,882 37.3 kb Distal (>10kb) Multiome 1009
chr10:102,169,504–102,169,976 54.7 kb Distal (>10kb) Multiome 398
chr10:102,225,881–102,226,551 111.3 kb Distal (>10kb) Multiome 652
chr10:102,229,814–102,232,116 115.0 kb Distal (>10kb) Multiome 689
chr10:102,240,581–102,242,031 126.7 kb Distal (>10kb) Multiome 504
chr10:102,244,918–102,246,010 130.5 kb Distal (>10kb) Multiome 734
chr10:102,393,940–102,396,107 280.8 kb Distal (>10kb) Multiome 912
chr10:102,399,132–102,400,002 284.7 kb Distal (>10kb) Multiome 832
chr10:102,408,600–102,409,538 294.1 kb Distal (>10kb) Multiome 277
chr10:102,410,213–102,410,909 295.8 kb Distal (>10kb) Multiome 148
chr10:102,418,158–102,422,381 304.7 kb Distal (>10kb) Multiome 1097

Genome Browser

Genomic view of the LDB1 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.

chr10:101,807,350 – 102,432,381
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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