Conserved long-range base pairings are associated with pre-mRNA processing of human genes

1. SupplementaryDataFile1.bed<br> The full list of PCCRs, GRCh37 Human Genome assembly. The list is provided in BED12+ format, where columns 1-12 correspond to the track hub, and columns 13-28 contain extra information. 13: PCCR id<br> 14: CCR1<br> 15: CCR2<br> 16: structure in dot-bracket notation<br> 17: icSHAPE_delta_reactivity score<br> 18: ENSEMBL gene id<br> 19: NCBI gene name<br> 20: Presence of A-to-I editing sites (TRUE/FALSE)<br> 21: Presence of forked eCLIP peaks in both CCRs<br> 22: phastCons.score1<br> 23: phastCons.score2<br> 24: phastCons.score3<br> 25: Evidence from RIC-seq data<br> 26: Raw E-value (the product of R-scape E-values of all base pairs in the structure)<br> 27: E-value (adjusted with Benjamini-Hochberg correction)<br> 28: Free energy 2. SupplementaryDataFile2.bed<br> The full list of PCCRs, GRCh38 Human Genome assembly. The columns are as in SupplementaryDataFile1.bed. 3. SupplementaryDataFile3.tsv<br> RNA bridges, GRCh37 Human Genome assembly. The columns are as follows<br> 1: PCCR coordinates<br> 2: eClip peak coordinates<br> 3: exon coordinates<br> 4: RBP name<br> 5: NCBI gene name<br> 6: Change of the exon inclusion rate in RBP KD (delta PSI)<br> 7: PCCR id<br> 8: PCCR energy<br> 9: PCCR spread<br> 10: Difference of icSHAPE reactivity of CCR<br> 11: E-value<br> 12: number of PCCRs in the cluster 4. SupplementaryDataFile4.tsv<br> Exon loop-outs, GRCh37 Human Genome assembly. The columns are as in SupplementaryDataFile3.tsv. 5. SupplementaryDataFile5.bed<br> A stringent set of intramolecular RIC-seq RNA contacts (provided by a courtesy of Prof. Xue, PMID:32499643). The contact are between part A and part B. The columns are as follows 1: chrA, chromosome of part A<br> 2: startA, start of part A<br> 3: endA, end of part A<br> 4: chrB, chromosome of part B<br> 5: startB, start of part B<br> 6: endB, end of part B<br> 7: Cluster ID<br> 8: Number Of Chimeric Reads