ENSG00000171863_ENSG00000234171:+:2:3575591:3576630

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000171863_ENSG00000234171:+:2:3575591:3576630 ENSG00000171863_ENSG00000234171 MSTRG.17912.8 + 2 3575592 3576630 309 UUCUCCCAGGAGAAAGCCAUGUUCAGUUCGAGCGCCAAGAUCGUGAAGCCCAAUGGCGAGAAGCCGGACGAGUUCGAGUCCGGCAUCUCCCAGGCUCUUCUGGAGCUGGAGAUGAACUCGGACCUCAAGGCUCAGCUCAGGGAGCUGAAUAUUACGGCAGCUAAGGAAAUUGAAGUUGGUGGUGGUCGGAAAGCUAUCAUAAUCUUUGUUCCCGUUCCUCAACUGAAAUCUUUCCAGAAAAUCCAAGUCCGGCUAGUACGCGAAUUGGAGAAAAAGUUCAGUGGGAAGCAUGUCGUCUUUAUCGCUCAGUUCUCCCAGGAGAAAGCCAUGUUCAGUUCGAGCGCCAAGAUCGUGAAGCC circ
ENSG00000171863_ENSG00000234171:+:2:3575591:3576630 ENSG00000171863_ENSG00000234171 MSTRG.17912.8 + 2 3575592 3576630 22 UUAUCGCUCAGUUCUCCCAGGA bsj
ENSG00000171863_ENSG00000234171:+:2:3575591:3576630 ENSG00000171863_ENSG00000234171 MSTRG.17912.8 + 2 3575392 3575601 210 GGUUGAGGAAAACGCCUUUUGGAGUCAGGCCCUGGAGGGGCGAGCCUUGCUCACAGGGUGGGGAUACAGCCGAUUACCCGCCCUGUGCUUUCCGAUGGCUUCUGCGGGGCGAGCGGGGCCUGGCCGGGGGGUGCGGGCGGGAGGGCGAGCCAGCGGCGCCUGCAGCCCGGGCCGCGUAACGCUGACCGCUGUGCCUUCAGUUCUCCCAGG ie_up
ENSG00000171863_ENSG00000234171:+:2:3575591:3576630 ENSG00000171863_ENSG00000234171 MSTRG.17912.8 + 2 3576621 3576830 210 UAUCGCUCAGGUAUCUGUUCUACUGUUGCAGCACGUUUCUGUUUGUGAAUUUUGCUAAAAUUGCUUGUAUUUAGACUGCAUUGGUAGUUGGAGUCAUGAAAACAAUCCUUUUAUGAAUCCAAUUGGGUAGAAAGAUAAAGUACAGGCAGAGCGCCGUGGCUUAGGCCUGUAAUCCCAGCACGGGGAGGUGGAGGCGGGUGGAUCACUGUA 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
EIF4B 4 1179 0.016181230 0.001710061 3.242202 CUCGGA,GUCGGA,UCGGAA,UCGGAC CUCGGA,CUUGGA,GUCGGA,GUUGGA,UCGGAA,UCGGAC,UUGGAA,UUGGAC
MATR3 2 739 0.009708738 0.001072411 3.178426 AAUCUU AAUCUU,AUCUUA,AUCUUG,CAUCUU
ZC3H10 3 1053 0.012944984 0.001527461 3.083186 CGAGCG,GAGCGC CAGCGA,CAGCGC,CCAGCG,CGAGCG,GAGCGA,GAGCGC,GCAGCG,GGAGCG
RBM6 2 1054 0.009708738 0.001528910 2.666780 AAUCCA,AUCCAA AAUCCA,AUCCAA,AUCCAG,CAUCCA,UAUCCA
RBFOX1 2 1077 0.009708738 0.001562242 2.635666 AGCAUG,GCAUGU AGCAUG,GCAUGA,GCAUGC,GCAUGU,UGACUG,UGCAUG
PABPC5 5 2400 0.019417476 0.003479539 2.480388 AGAAAA,AGAAAG,GAAAAU,GAAAUU AGAAAA,AGAAAG,AGAAAU,GAAAAU,GAAAGU,GAAAUU
IGF2BP1 1 831 0.006472492 0.001205738 2.424405 CCCGUU AAGCAC,ACCCGU,AGCACC,CACCCG,CCCGUU,GCACCC
HNRNPM 1 999 0.006472492 0.001449204 2.159061 AAGGAA AAGGAA,GAAGGA,GGGGGG
ZRANB2 5 3173 0.019417476 0.004599773 2.077721 GGUGGU,GUGGUG,UGGUGG AAAGGU,AGGGAA,AGGUAA,AGGUAC,AGGUAG,AGGUAU,AGGUCU,AGGUUA,AGGUUU,CGGUAA,CGGUAG,CGGUAU,CGGUCU,GAGGUU,GGGUAA,GGGUGA,GGUAAA,GGUGGU,GUAAAG,GUGGUG,UAAAGG,UGGUAA,UGGUGG
LIN28A 6 4315 0.022653722 0.006254764 1.856721 AGGAGA,GGAGAA,GGAGAU,UGGAGA AGGAGA,AGGAGU,CGGAGA,CGGAGG,CGGAGU,GGAGAA,GGAGAU,GGAGGA,GGAGGG,GGAGUA,UGGAGA,UGGAGG,UGGAGU
PABPC4 1 1251 0.006472492 0.001814403 1.834826 AAAAAG AAAAAA,AAAAAG
ACO1 1 1283 0.006472492 0.001860778 1.798415 CAGUGG CAGUGA,CAGUGC,CAGUGG,CAGUGU
SART3 3 2634 0.012944984 0.003818652 1.761258 AGAAAA,GAAAAA AAAAAA,AAAAAC,AGAAAA,GAAAAA,GAAAAC
ESRP2 2 2150 0.009708738 0.003117238 1.639016 GGGAAG,UGGGAA GGGAAA,GGGAAG,GGGAAU,GGGGAA,GGGGAG,GGGGAU,UGGGAA,UGGGGA
ZNF638 1 1773 0.006472492 0.002570888 1.332055 GUUGGU CGUUCG,CGUUCU,CGUUGG,CGUUGU,GGUUCG,GGUUCU,GGUUGG,GGUUGU,GUUCGU,GUUCUU,GUUGGU,GUUGUU,UGUUCG,UGUUCU,UGUUGG,UGUUGU
RC3H1 1 1786 0.006472492 0.002589727 1.321521 CUUCUG CCCUUC,CCUUCU,CUUCUG,UCCCUU,UCUGUG,UUCUGU
RBM5 6 6879 0.022653722 0.009970523 1.184007 AAGGAA,AGGGAG,CUCUUC,GGUGGU,UCUUCU AAAAAA,AAGGAA,AAGGAG,AAGGGG,AAGGUA,AAGGUG,AGGGAA,AGGGAG,AGGGUA,AGGGUG,AGGUAA,CAAGGA,CAAGGG,CCCCCC,CUCUUC,CUUCUC,GAAGGA,GAAGGG,GAAGGU,GAGGGA,GAGGGU,GGGGGG,GGUGGU,UCUUCU,UUCUCU
HNRNPA3 1 2140 0.006472492 0.003102746 1.060776 GCCAAG AAGGAG,AGGAGC,CAAGGA,CCAAGG,GCCAAG,GGAGCC
PABPC1 3 4443 0.012944984 0.006440262 1.007202 AGAAAA,GAAAAA AAAAAA,AAAAAC,ACAAAC,ACAAAU,ACGAAC,ACGAAU,ACUAAC,ACUAAU,AGAAAA,CAAACA,CAAACC,CAAAUA,CAAAUC,CGAACA,CGAACC,CGAAUA,CGAAUC,CUAACA,CUAACC,CUAAUA,CUAAUC,GAAAAA,GAAAAC

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
TIAL1 1 26 0.09090909 0.001768405 5.683904 UCAGUU AAAUUU,AAUUUU,AGUUUU,AUUUUG,CAGUUU,GUUUUU,UAAAUU,UAUUUU,UCAGUU,UUAAAU,UUCAGU,UUUCAG

RBP on BSJ (Exon and Intron)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
SUPV3L1 1 31 0.004761905 0.0001612253 4.884389 CCGCCC CCGCCC
IFIH1 4 146 0.011904762 0.0007406288 4.006644 GCCGCG,GGCCCU,GGCCGC,GGGCCG CCGCGG,CGCGGA,GCCGCG,GCGGAU,GGCCCU,GGCCGC,GGGCCG
ZC3H10 3 140 0.009523810 0.0007103990 3.744837 CCAGCG,CGAGCG,GAGCGC CAGCGA,CAGCGC,CCAGCG,CGAGCG,GAGCGA,GAGCGC,GCAGCG,GGAGCG
PPRC1 2 127 0.007142857 0.0006449012 3.469351 CGGCGC,GGCGCC CCGCGC,CGCGCC,CGCGCG,CGGCGC,GCGCGC,GGCGCC,GGCGCG,GGGCGC
SRP14 3 218 0.009523810 0.0011033857 3.109602 CCUGUA,CGCCUG,GCCUGU CCUGUA,CGCCUG,CUGUAG,GCCUGU
RBM6 2 191 0.007142857 0.0009673519 2.884389 AAUCCA,AUCCAA AAUCCA,AUCCAA,AUCCAG,CAUCCA,UAUCCA
PABPC3 3 310 0.009523810 0.0015669085 2.603618 AAAACA,GAAAAC AAAAAC,AAAACA,AAAACC,GAAAAC
HNRNPM 1 222 0.004761905 0.0011235389 2.083489 GGGGGG AAGGAA,GAAGGA,GGGGGG
EIF4B 1 226 0.004761905 0.0011436921 2.057840 GUUGGA CUCGGA,CUUGGA,GUCGGA,GUUGGA,UCGGAA,UCGGAC,UUGGAA,UUGGAC
LIN28A 6 900 0.016666667 0.0045395002 1.876360 GGAGGG,UGGAGG,UGGAGU AGGAGA,AGGAGU,CGGAGA,CGGAGG,CGGAGU,GGAGAA,GGAGAU,GGAGGA,GGAGGG,GGAGUA,UGGAGA,UGGAGG,UGGAGU
SAMD4A 5 790 0.014285714 0.0039852882 1.841817 CGGGCC,CUGGCC,GCGGGA,GCGGGC,GCGGGU CGGGAA,CGGGAC,CGGGCA,CGGGCC,CGGGUA,CGGGUC,CUGGAA,CUGGAC,CUGGCA,CUGGCC,CUGGUA,CUGGUC,GCGGGA,GCGGGC,GCGGGU,GCUGGA,GCUGGC,GCUGGU
AGO1 1 283 0.004761905 0.0014308746 1.734641 GGUAGU AGGUAG,GAGGUA,GGUAGU,GUAGUA,UGAGGU
SNRPB2 1 288 0.004761905 0.0014560661 1.709463 UUGCAG AUUGCA,GUAUUG,UAUUGC,UGCAGU,UUGCAG
NONO 1 364 0.004761905 0.0018389762 1.372636 GAGGAA AGAGGA,AGGAAC,GAGAGG,GAGGAA
ESRP2 3 731 0.009523810 0.0036880290 1.368689 GGGGAG,GGGGAU,UGGGGA GGGAAA,GGGAAG,GGGAAU,GGGGAA,GGGGAG,GGGGAU,UGGGAA,UGGGGA
ENOX1 3 756 0.009523810 0.0038139863 1.320239 AGUACA,AUACAG,GUACAG AAGACA,AAUACA,AGACAG,AGGACA,AGUACA,AUACAG,CAGACA,CAUACA,CGGACA,CGUACA,GGACAG,GUACAG,UAGACA,UAUACA,UGGACA,UGUACA
HNRNPH3 11 2496 0.028571429 0.0125806127 1.183371 AUUGGG,CGGGCG,CGGGGG,GAGGGG,GGAGGG,GGGAGG,GGGGAG,GGGGGG,UUGGGU AAGGGA,AAGGUG,AAUGUG,AGGGAA,AGGGGA,AUCGGG,AUGUGG,AUUGGG,CGAGGG,CGGGCG,CGGGGG,GAAGGG,GAAUGU,GAGGGG,GGAAGG,GGAAUG,GGAGGA,GGAGGG,GGGAAG,GGGAAU,GGGAGG,GGGCGU,GGGCUG,GGGGAG,GGGGCU,GGGGGC,GGGGGG,GGGUCG,GGGUGU,GGUCGA,GUCGAG,UCGAGG,UCGGGC,UGGGUG,UGUGGG,UUGGGU
RC3H1 2 631 0.007142857 0.0031841999 1.165570 CUUCUG,UUCUGU CCCUUC,CCUUCU,CUUCUG,UCCCUU,UCUGUG,UUCUGU
SRSF5 6 1578 0.016666667 0.0079554615 1.066948 AUAAAG,CGCGUA,GAGGAA,UACAGC,UGCAGC AACAGC,AAGAAG,AGAAGA,AGGAAG,AUAAAG,CAACAG,CACAGA,CACAGC,CACAUA,CACAUC,CACGGA,CACGGC,CACGUA,CACGUC,CCGCAG,CGCAGA,CGCAGC,CGCAGG,CGCAUA,CGCAUC,CGCGGA,CGCGGC,CGCGUA,CGCGUC,GAAGAA,GAGGAA,GGAAGA,UAAAGG,UACAGA,UACAGC,UACAUA,UACAUC,UACGGA,UACGGC,UACGUA,UACGUC,UGCAGA,UGCAGC,UGCAUA,UGCAUC,UGCGGA,UGCGGC,UGCGUA,UGCGUC
AGO2 2 677 0.007142857 0.0034159613 1.064210 GUGCUU,UAAAGU AAAAAA,AAAGUG,AAGUGC,AGUGCU,GUGCUU,UAAAGU
MBNL1 13 3258 0.033333333 0.0164197904 1.021530 ACGCUG,CCGCUG,CGCUGU,CUGCGG,CUUGCU,GCUUGU,GUGCUU,UCGCUC,UGCUUU,UUGCUA,UUGCUC,UUGCUU,UUUGCU ACGCUA,ACGCUC,ACGCUG,ACGCUU,AUGCCA,AUGCCC,AUGCCG,AUGCUC,AUGCUU,CCCGCU,CCGCUA,CCGCUC,CCGCUG,CCGCUU,CCUGCU,CGCUGC,CGCUGU,CGCUUC,CGCUUG,CGCUUU,CUCGCU,CUGCCA,CUGCCC,CUGCCG,CUGCCU,CUGCGG,CUGCUA,CUGCUC,CUGCUG,CUGCUU,CUUGCU,CUUGUG,GCGCUC,GCGCUG,GCGCUU,GCUGCG,GCUGCU,GCUUGC,GCUUGU,GCUUUU,GGCUUU,GUCUCG,GUGCUA,GUGCUC,GUGCUG,GUGCUU,UCCGCU,UCGCUA,UCGCUC,UCGCUG,UCGCUU,UCUCGC,UCUGCU,UGCGGC,UGCUGC,UGCUGU,UGCUUC,UGCUUU,UGUCUC,UUCGCU,UUGCCA,UUGCCC,UUGCCG,UUGCCU,UUGCUA,UUGCUC,UUGCUG,UUGCUU,UUGUGC,UUUGCU

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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