This gene belongs to the subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). The hnRNPs are RNA-binding proteins and they complex with heterogeneous nuclear RNA (hnRNA). These proteins are associated with pre-mRNAs in the nucleus and appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. While all of the hnRNPs are present in the nucleus, some seem to shuttle between the nucleus and the cytoplasm. The hnRNP proteins have distinct nucleic acid binding properties. The protein encoded by this gene has four repeats of quasi-RNA recognition motif (RRM) domains that bind RNAs. This protein binds to the intronic polypyrimidine tracts that requires pre-mRNA splicing and acts via the protein degradation ubiquitin-proteasome pathway. It may also promote the binding of U2 snRNP to pre-mRNAs. This protein is localized in the nucleoplasm and it is also detected in the perinucleolar structure. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for PTBP1. 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 = PTBP1 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 |
|---|
Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of PTBP1, 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 |
|---|---|---|---|---|
| chr19:506,451–508,366 | 290.3 kb | Distal (>10kb) Multiome | 1001 | |
| chr19:510,509–511,797 | 286.5 kb | Distal (>10kb) Multiome | 739 | |
| chr19:518,865–519,356 | 278.3 kb | Distal (>10kb) Multiome | 151 | |
| chr19:530,809–533,397 | 266.0 kb | Distal (>10kb) Multiome | 856 | |
| chr19:572,071–573,594 | 225.0 kb | Distal (>10kb) Multiome | 888 | |
| chr19:588,127–589,976 | 209.1 kb | Distal (>10kb) Multiome | 526 | |
| chr19:632,653–633,806 | 163.8 kb | Distal (>10kb) Multiome | 758 | |
| chr19:639,456–640,331 | 157.6 kb | Distal (>10kb) Multiome | 389 | |
| chr19:662,267–663,864 | 134.1 kb | Distal (>10kb) Multiome | 723 | |
| chr19:679,616–681,731 | 116.7 kb | Distal (>10kb) Multiome | 832 | |
| chr19:703,387–704,718 | 93.4 kb | Distal (>10kb) Multiome | 586 | |
| chr19:708,425–709,293 | 88.6 kb | Distal (>10kb) Multiome | 317 | |
| chr19:796,668–798,362 | 194 bp | At TSS Multiome | 956 | |
| chr19:798,668–799,351 | 1.2 kb | Proximal (<10kb) | 372 | |
| chr19:821,294–822,728 | 24.7 kb | Distal (>10kb) Multiome | 254 | |
| chr19:861,664–863,223 | 64.8 kb | Distal (>10kb) Multiome | 530 | |
| chr19:892,703–893,746 | 95.8 kb | Distal (>10kb) Multiome | 715 | |
| chr19:917,038–918,169 | 120.4 kb | Distal (>10kb) Multiome | 711 | |
| chr19:924,743–926,242 | 128.3 kb | Distal (>10kb) Multiome | 796 | |
| chr19:927,058–927,629 | 129.9 kb | Distal (>10kb) Multiome | 362 | |
| chr19:982,565–983,215 | 185.4 kb | Distal (>10kb) Multiome | 590 | |
| chr19:984,046–985,154 | 187.1 kb | Distal (>10kb) Multiome | 829 | |
| chr19:1,000,142–1,000,881 | 202.9 kb | Distal (>10kb) Multiome | 399 | |
| chr19:1,020,611–1,022,069 | 224.0 kb | Distal (>10kb) Multiome | 1017 | |
| chr19:1,026,155–1,026,856 | 229.1 kb | Distal (>10kb) Multiome | 598 | |
| chr19:1,027,770–1,028,926 | 231.1 kb | Distal (>10kb) Multiome | 584 | |
| chr19:1,039,648–1,040,400 | 242.6 kb | Distal (>10kb) Multiome | 684 | |
| chr19:1,040,481–1,041,402 | 243.8 kb | Distal (>10kb) Multiome | 556 | |
| chr19:1,044,758–1,045,598 | 247.9 kb | Distal (>10kb) Multiome | 402 | |
| chr19:1,061,840–1,062,923 | 265.1 kb | Distal (>10kb) Multiome | 204 | |
| chr19:1,063,045–1,065,722 | 267.4 kb | Distal (>10kb) Multiome | 681 | |
| chr19:1,066,682–1,067,587 | 269.8 kb | Distal (>10kb) Multiome | 489 | |
| chr19:1,071,107–1,071,721 | 273.7 kb | Distal (>10kb) Multiome | 178 | |
| chr19:1,081,317–1,083,172 | 285.0 kb | Distal (>10kb) Multiome | 484 | |
| chr19:1,094,985–1,095,654 | 298.0 kb | Distal (>10kb) Multiome | 671 |
Genomic view of the PTBP1 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.