NOP53
NOP53 ribosome biogenesis factor | PICT-1, PICT1, GLTSCR2

Enables 5S rRNA binding activity; identical protein binding activity; and p53 binding activity. Involved in several processes, including mitotic G2 DNA damage checkpoint signaling; regulation of intracellular signal transduction; and regulation of primary metabolic process. Located in cytosol; nuclear lumen; and rDNA heterochromatin. [provided by Alliance of Genome Resources, Jul 2025]

Member of: DE-1 Developmental clusters: GC2
Biological processes 39 terms
5S rRNA binding (GO:0008097)5S rRNA binding (GO:0008097)DNA damage response (GO:0006974)DNA repair (GO:0006281)RNA binding (GO:0003723)cellular response to hypoxia (GO:0071456)cytosol (GO:0005829)fibrillar center (GO:0001650)identical protein binding (GO:0042802)mitotic G2 DNA damage checkpoint signaling (GO:0007095)negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction (GO:0051898)negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)negative regulation of protein-containing complex assembly (GO:0031333)negative regulation of signal transduction by p53 class mediator (GO:1901797)negative regulation of transcription by RNA polymerase II (GO:0000122)negative regulation of transcription of nucleolar large rRNA by RNA polymerase I (GO:1901837)nucleolus (GO:0005730)nucleolus (GO:0005730)nucleolus (GO:0005730)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)p53 binding (GO:0002039)positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)positive regulation of protein K63-linked deubiquitination (GO:1903006)protein binding (GO:0005515)protein localization to nucleolus (GO:1902570)protein localization to nucleoplasm (GO:1990173)protein stabilization (GO:0050821)rDNA heterochromatin (GO:0033553)rRNA processing (GO:0006364)regulation of RIG-I signaling pathway (GO:0039535)regulation of aerobic respiration (GO:1903715)regulation of apoptotic process (GO:0042981)regulation of cell cycle (GO:0051726)regulation of protein phosphorylation (GO:0001932)regulation of signal transduction by p53 class mediator (GO:1901796)ribosomal large subunit assembly (GO:0000027)ribosomal large subunit assembly (GO:0000027)
Expression (TPM)
NOP53 — as a Regulated Gene

TFs regulating NOP53 0 TFs

Transcription factors with Perturb-seq knockdown data for NOP53. 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 = NOP53 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 NOP53

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of NOP53, 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
chr19:47,429,865–47,430,531 315.2 kb Distal (>10kb) Multiome HiCAR 438
chr19:47,447,043–47,448,262 297.9 kb Distal (>10kb) Multiome HiCAR 510
chr19:47,471,631–47,472,340 273.5 kb Distal (>10kb) Multiome 500
chr19:47,479,940–47,480,772 265.4 kb Distal (>10kb) Multiome 147
chr19:47,483,636–47,484,543 261.4 kb Distal (>10kb) Multiome 841
chr19:47,514,152–47,515,901 230.3 kb Distal (>10kb) Multiome 895
chr19:47,600,223–47,600,983 145.0 kb Distal (>10kb) Multiome 807
chr19:47,607,980–47,609,479 136.8 kb Distal (>10kb) Multiome 832
chr19:47,647,803–47,648,987 97.1 kb Distal (>10kb) Multiome 693
chr19:47,697,956–47,698,391 47.4 kb Distal (>10kb) Multiome 453
chr19:47,729,949–47,730,505 15.4 kb Distal (>10kb) Multiome 425
chr19:47,743,369–47,743,911 1.9 kb Proximal (<10kb) Multiome 929
chr19:47,745,136–47,745,915 16 bp At TSS Multiome 784
chr19:47,765,762–47,766,380 20.5 kb Distal (>10kb) Multiome 296
chr19:47,770,120–47,770,789 24.9 kb Distal (>10kb) Multiome 127
chr19:47,778,102–47,779,241 33.0 kb Distal (>10kb) Multiome 845
chr19:47,788,509–47,789,220 43.2 kb Distal (>10kb) Multiome 365
chr19:47,790,277–47,790,794 44.9 kb Distal (>10kb) Multiome 275
chr19:47,848,678–47,850,092 104.3 kb Distal (>10kb) Multiome 398
chr19:47,863,487–47,864,048 118.1 kb Distal (>10kb) Multiome 384
chr19:47,891,593–47,892,745 146.7 kb Distal (>10kb) Multiome 522

Genome Browser

Genomic view of the NOP53 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.

chr19:47,419,865 – 47,902,745
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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