ENSG00000128683:+:2:170836792:170854022

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000128683:+:2:170836792:170854022 ENSG00000128683 ENST00000493875 + 2 170836793 170854022 978 GUCAUCCUCGAUUUUUCAACCAGCUCUCCACUGGAUUGGAUAUUAUUGGCCUAGCUGGAGAAUGGCUGACAUCAACGGCCAAUACCAACAUGUUUACAUAUGAAAUUGCACCAGUGUUUGUCCUCAUGGAACAAAUAACACUUAAGAAGAUGAGAGAGAUAGUUGGAUGGUCAAGUAAAGAUGGUGAUGGGAUAUUUUCUCCUGGGGGCGCCAUAUCCAACAUGUACAGCAUCAUGGCUGCUCGCUACAAGUACUUCCCGGAAGUUAAGACAAAGGGCAUGGCGGCUGUGCCUAAACUGGUCCUCUUCACCUCAGAACAGAGUCACUAUUCCAUAAAGAAAGCUGGGGCUGCACUUGGCUUUGGAACUGACAAUGUGAUUUUGAUAAAGUGCAAUGAAAGGGGGAAAAUAAUUCCAGCUGAUUUUGAGGCAAAAAUUCUUGAAGCCAAACAGAAGGGAUAUGUUCCCUUUUAUGUCAAUGCAACUGCUGGCACGACUGUUUAUGGAGCUUUUGAUCCGAUACAAGAGAUUGCAGAUAUAUGUGAGAAAUAUAACCUUUGGUUGCAUGUCGAUGGAUUUAACUUCUCACAAUUGGCCAAUAGGAUCAUCUGCCUUGCUACUGAACUAAUGACUAACAAAGGCUGUGUCACGUGGCAUCCCAACUAUUCAGUAAACAUGCAUCAUGGCUGCCUGGGGAGGUGGGCUGCUCAUGUCCAGGAAGCACCGCCAUAAACUCAACGGCAUAGAAAGGGCCAACUCAGUCACCUGGAACCCUCACAAGAUGAUGGGCGUGCUGUUGCAGUGCUCUGCCAUUCUCGUCAAGGAAAAGGGUAUACUCCAAGGAUGCAACCAGAUGUGUGCAGGAUACCUCUUCCAGCCAGACAAGCAGUAUGAUGUCUCCUACGACACCGGGGACAAGGCAAUUCAGUGUGGCCGCCACGUGGAUAUCUUCAAGUUCUGGCUGAUGUGGAAAGCAAAGGUCAUCCUCGAUUUUUCAACCAGCUCUCCACUGGAUUGGAUAUUAUUGGC circ
ENSG00000128683:+:2:170836792:170854022 ENSG00000128683 ENST00000493875 + 2 170836793 170854022 22 GGAAAGCAAAGGUCAUCCUCGA bsj
ENSG00000128683:+:2:170836792:170854022 ENSG00000128683 ENST00000493875 + 2 170836593 170836802 210 UUUGAGGGACAUUAUGAAUGUUAAUGUUGGUAUAGGGUGGGUCAACCUGCCCUUCCUUUUUCAAUAUCCUUGAGCAGCCUUAUUCGACAUAUCACUGGGAUGGAAGCCCCAUCAGUGUGACCCAGUGGGGCAGGCCGUUUGCCUUCAAGAUAGGUUGAGAAAUCUGCAUUUGCCUUGAUGCUUUUCUGUUUCCUAUCUAGGUCAUCCUCG ie_up
ENSG00000128683:+:2:170836792:170854022 ENSG00000128683 ENST00000493875 + 2 170854013 170854222 210 GAAAGCAAAGGUAUGAAGGGAAUAGUUCAGGAAAUAGAGCAGAAAUGUAAUUUGCACAGACUGGCUGGCAAAAGAGGGGCAAAGAUAUAUCACAGAUAAUUCACUAUAUGGGGAAUCAAUAUCUAGAUAAUUGAAUUAACUGUGUUUUCUUUGUGAAUGAAAUUACUUUAUUCCUUAUGUCAAAUUCUCUCUCCUUUUGUUCAGUCUCCU ie_down
  • Note:
    • id: unique identifier.
    • gene: represents the gene from which the circRNA arises.
    • transcript: transcript whose exon coordinates overlap with the detected back-spliced junction coordinate and used in the downstream analysis.
    • strand: is the strand from which the gene is transcribed.
    • chrom: is the chromosome from which the circRNA is derived.
    • startGR: is the 5’ coordinate of the genomic range from which the sequence are extracted.
    • endGR: is the 3’ coordinate of the genomic range from which the sequence are extracted.
    • length: length of the extracted sequences.
    • seq: sequence used in the downstream analysis.
    • type: type of sequences retrieved. If type = “circ” the sequences derive from the internal circRNA sequences. If type = “bsj” the sequences derive from the back spliced junctions (BSJ). If type = “ie_up” the Intron or Exon sequences derive from the up-stream of BSJ up to 210 bp. If type = “ie_down” the Intron or Exon sequences derive from the down-stream of BSJ up to 210 bp.

2. RNA Binding Proteins Analysis

RBP on full sequence

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
ESRP1 1 156 0.002044990 0.0002275250 3.167997 AGGGAU AGGGAU
RBMY1A1 2 489 0.003067485 0.0007101099 2.110942 ACAAGA ACAAGA,CAAGAC
SNRPB2 5 991 0.006134969 0.0014376103 2.093383 AUUGCA,UGCAGU,UUGCAG AUUGCA,GUAUUG,UAUUGC,UGCAGU,UUGCAG
RBM42 1 407 0.002044990 0.0005912752 1.790192 AACUAA AACUAA,AACUAC,ACUAAG,ACUACG
FXR1 1 411 0.002044990 0.0005970720 1.776117 ACGACA ACGACA,ACGACG,AUGACA,AUGACG
AKAP1 1 426 0.002044990 0.0006188101 1.724525 AUAUAU AUAUAU,UAUAUA
TUT1 2 678 0.003067485 0.0009840095 1.640312 CAAUAC,CGAUAC AAAUAC,AAUACU,AGAUAC,CAAUAC,CGAUAC,GAUACU
RBFOX2 1 452 0.002044990 0.0006564894 1.639250 UGCAUG UGACUG,UGCAUG
HNRNPA0 1 453 0.002044990 0.0006579386 1.636069 AGAUAU AAUUUA,AGAUAU,AGUAGG
RBMS1 1 497 0.002044990 0.0007217036 1.502615 GAUAUA AUAUAC,AUAUAG,GAUAUA,UAUAUA
HNRNPAB 6 1782 0.007157464 0.0025839306 1.469881 AAGACA,ACAAAG,AGACAA,GACAAA AAAGAC,AAGACA,ACAAAG,AGACAA,AUAGCA,CAAAGA,GACAAA
PPRC1 2 780 0.003067485 0.0011318283 1.438401 GGCGCC,GGGCGC CCGCGC,CGCGCC,CGCGCG,CGGCGC,GCGCGC,GGCGCC,GGCGCG,GGGCGC
IGF2BP1 2 831 0.003067485 0.0012057377 1.347140 AAGCAC,AGCACC AAGCAC,ACCCGU,AGCACC,CACCCG,CCCGUU,GCACCC
SSB 3 1260 0.004089980 0.0018274462 1.162265 CUGUUU,GCUGUU,UGCUGU CUGUUU,GCUGUU,UGCUGU,UGUUUU
ACO1 3 1283 0.004089980 0.0018607779 1.136188 CAGUGC,CAGUGU CAGUGA,CAGUGC,CAGUGG,CAGUGU
G3BP2 4 1644 0.005112474 0.0023839405 1.100673 AGGAUA,AGGAUG,GGAUGG,GGAUUG AGGAUA,AGGAUG,AGGAUU,GGAUAA,GGAUAG,GGAUGA,GGAUGG,GGAUUA,GGAUUG
SRSF11 1 688 0.002044990 0.0009985015 1.034257 AAGAAG AAGAAG
RBM6 2 1054 0.003067485 0.0015289102 1.004552 AUCCAA,UAUCCA AAUCCA,AUCCAA,AUCCAG,CAUCCA,UAUCCA

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
ZRANB2 1 45 0.09090909 0.003012837 4.91523 AAAGGU AAAGGU,AGGGAA,AGGUAA,AGGUAC,AGGUAG,AGGUAU,AGGUCU,AGGUUA,AGGUUU,GAGGUU,GGGUAA,GGGUGA,GGUAAA,GGUGGU,GUAAAG,UAAAGG,UGGUAA

RBP on BSJ (Exon and Intron)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
NXF1 1 43 0.004761905 0.0002216848 4.424957 AACCUG AACCUG
HNRNPA1L2 2 188 0.007142857 0.0009522370 2.907109 AUAGGG,UAGGGU AUAGGG,GUAGGG,UAGGGA,UAGGGU,UUAGGG
PTBP2 1 146 0.004761905 0.0007406288 2.684716 CUCUCU CUCUCU
SNRNP70 2 253 0.007142857 0.0012797259 2.480666 AAUCAA,UUCAAG AAUCAA,AUCAAG,AUUCAA,GAUCAA,GUUCAA,UUCAAG
PABPN1 1 178 0.004761905 0.0009018541 2.400573 AAAAGA AAAAGA,AGAAGA
HNRNPA0 1 200 0.004761905 0.0010126965 2.233337 AGAUAU AAUUUA,AGAUAU,AGUAGG
ACO1 2 325 0.007142857 0.0016424829 2.120623 CAGUGG,CAGUGU CAGUGA,CAGUGC,CAGUGG,CAGUGU
RBMS1 1 217 0.004761905 0.0010983474 2.116204 GAUAUA AUAUAC,AUAUAG,GAUAUA,UAUAUA
AKAP1 1 221 0.004761905 0.0011185006 2.089973 AUAUAU AUAUAU,UAUAUA
A1CF 4 598 0.011904762 0.0030179363 1.979904 AUAAUU,AUCAGU,UAAUUG AGUAUA,AUAAUU,AUCAGU,CAGUAU,GAUCAG,UAAUUA,UAAUUG,UCAGUA,UGAUCA,UUAAUU
RBMS3 3 562 0.009523810 0.0028365578 1.747397 AUAUAU,CUAUAU,UAUAUC AAUAUA,AUAUAG,AUAUAU,CAUAUA,CUAUAG,CUAUAU,UAUAGA,UAUAGC,UAUAUA,UAUAUC
ESRP2 4 731 0.011904762 0.0036880290 1.690617 GGGAAU,GGGGAA,UGGGGA GGGAAA,GGGAAG,GGGAAU,GGGGAA,GGGGAG,GGGGAU,UGGGAA,UGGGGA
TARDBP 6 1034 0.016666667 0.0052146312 1.676328 GAAUGA,GAAUGU,GUGAAU,UGAAUG,UUGUUC GAAUGA,GAAUGG,GAAUGU,GUGAAU,GUGUGU,GUUGUG,GUUGUU,GUUUUG,UGAAUG,UGUGUG,UUGUGC,UUGUUC,UUUUGC
PABPC5 3 596 0.009523810 0.0030078597 1.662801 AGAAAU,GAAAUU AGAAAA,AGAAAG,AGAAAU,GAAAAU,GAAAGU,GAAAUU
RBM46 6 1091 0.016666667 0.0055018138 1.598986 AAUCAA,AAUGAA,AUCAAU,AUGAAA,AUGAAG,AUGAAU AAUCAA,AAUCAU,AAUGAA,AAUGAU,AUCAAA,AUCAAG,AUCAAU,AUCAUA,AUCAUG,AUCAUU,AUGAAA,AUGAAG,AUGAAU,AUGAUA,AUGAUG,AUGAUU,GAUCAA,GAUCAU,GAUGAA,GAUGAU
RBM41 2 502 0.007142857 0.0025342604 1.494937 UACUUU,UUACUU AUACAU,AUACUU,UACAUG,UACAUU,UACUUG,UACUUU,UUACAU,UUACUU
SSB 2 505 0.007142857 0.0025493753 1.486358 CUGUUU,UGUUUU CUGUUU,GCUGUU,UGCUGU,UGUUUU
HNRNPAB 1 351 0.004761905 0.0017734784 1.424957 CAAAGA AAAGAC,AAGACA,ACAAAG,AGACAA,AUAGCA,CAAAGA,GACAAA
SNRPA 9 1947 0.023809524 0.0098145909 1.278539 ACCUGC,AUUCCU,GAGCAG,GGUAUG,GUUUCC,UGCACA,UUGCAC,UUUCCU ACCUGC,AGCAGU,AGGAGA,AGUAGG,AGUAGU,AUACCU,AUGCAC,AUGCUG,AUUCCU,AUUGCA,CAGUAG,CCUGCU,CUGCUA,GAGCAG,GAUACC,GAUUCC,GCAGUA,GGAGAU,GGGUAU,GGUAUG,GUAGGC,GUAGGG,GUAGUC,GUAGUG,GUAUGC,GUUACC,GUUUCC,UACCUG,UAUGCU,UCCUGC,UGCACA,UGCACC,UGCACG,UUACCU,UUCCUG,UUGCAC,UUUCCU
RC3H1 2 631 0.007142857 0.0031841999 1.165570 CCCUUC,UUCUGU CCCUUC,CCUUCU,CUUCUG,UCCCUU,UCUGUG,UUCUGU
NELFE 4 1059 0.011904762 0.0053405885 1.156468 CUCUCU,CUGGCU,UCUCUC CUCUCU,CUCUGG,CUGGCU,CUGGUU,GCUAAC,GGCUAA,GGUCUC,GGUUAG,GUCUCU,UCUCUC,UCUCUG,UCUGGC,UCUGGU,UGGCUA,UGGUUA
ZNF638 2 646 0.007142857 0.0032597743 1.131729 GUUGGU,UGUUGG CGUUCG,CGUUCU,CGUUGG,CGUUGU,GGUUCG,GGUUCU,GGUUGG,GGUUGU,GUUCGU,GUUCUU,GUUGGU,GUUGUU,UGUUCG,UGUUCU,UGUUGG,UGUUGU
RBM4 4 1094 0.011904762 0.0055169287 1.109602 CCUUCC,CUUCCU,UUCCUU CCUCUU,CCUUCC,CCUUCU,CGCGCG,CGCGGG,CGCGGU,CUCUUU,CUUCCU,CUUCUU,GCGCGA,GCGCGC,GCGCGG,UCCUUC,UUCCUU,UUCUUG
ZCRB1 2 666 0.007142857 0.0033605401 1.087808 AAUUAA,GAAUUA AAUUAA,ACUUAA,AUUUAA,GAAUUA,GACUUA,GAUUAA,GAUUUA,GCUUAA,GGAUUA,GGCUUA,GGUUUA,GUUUAA
CELF5 2 669 0.007142857 0.0033756550 1.081334 GUGUUU,UGUGUU GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU

Help

  • Note:
    • foreground: number of motifs found in the foreground target sequences (e.g. predicted circRNAs).
    • background: number of motifs found in the background target sequences (e.g. randomly generated circRNAs).
    • foregroundNorm: number of motifs found in the foreground target sequences (+1) divided by the number (or length) of sequences analyzed.
    • backgroundNorm: number of motifs found in background target sequences (+1) divided by the number (or length) of sequences analyzed.
    • log2FC: log2 fold change calculated in this way (foregroundNorm)/(backgroundNorm).
    • motifF: motifs of the corresponding RBP found in the foreground sequences.
    • motifB: motifs of the corresponding RBP found in the background sequences.

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