ENSG00000146555:+:7:4049347:4114274

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000146555:+:7:4049347:4114274 ENSG00000146555 ENST00000404826 + 7 4049348 4114274 1221 UGCCCACCGCGCCCCCGCAGAACGUGCAGACGGAAGCCGUGAACUCCACCACCAUUCAGUUCCUGUGGAACCCUCCGCCUCAGCAGUUUAUCAAUGGCAUCAACCAGGGAUACAAGCUUCUGGCAUGGCCGGCAGAUGCCCCCGAGGCUGUCACUGUGGUCACUAUUGCCCCAGAUUUCCACGGAGUCCACCAUGGACACAUAACGAACCUGAAGAAGUUUACCGCCUACUUCACUUCCGUUCUGUGCUUCACCACCCCUGGGGACGGGCCUCCCAGCACACCUCAGCUGGUCUGGACUCAGGAAGACAAACCAGGAGCUGUGGGACAUCUGAGUUUCACAGAGAUCUUGGACACAUCUCUCAAGGUCAGCUGGCAGGAGCCCCUGGAGAAAAAUGGCAUCAUUACUGGCUAUCAGAUCUCUUGGGAAGUGUACGGCAGGAACGACUCUCGUCUCACGCACACCCUGAACAGCACGACGCACGAGUACAAGAUCCAAGGCCUCUCAUCUCUCACCACCUACACCAUCGACGUGGCCGCUGUGACUGCCGUGGGCACUGGCCUGGUGACUUCAUCCACCAUUUCUUCUGGAGUGCCCCCAGACCUUCCUGGUGCCCCAUCCAACCUGGUCAUUUCCAACAUCAGCCCUCGCUCCGCCACCCUUCAGUUCCGGCCAGGCUAUGACGGGAAAACGUCCAUCUCCAGGUGGAUUGUUGAGGGGCAGGUGGGAGCUAUCGGCGACGAGGAGGAGUGGGUCACCCUCUAUGAAGAGGAGAAUGAGCCUGAUGCCCAGAUGCUGGAGAUCCCAAACCUCACACCCUACACUCACUACAGAUUUCGAAUGAAGCAAGUGAACAUUGUUGGGCCGAGCCCCUACAGUCCGUCUUCCCGGGUCAUCCAGACCCUGCAGGCCCCACCCGACGUGGCUCCAACCAGCGUCACGGUCCGUACUGCCAGUGAGACCAGCCUGCGGCUUCGCUGGGUGCCCCUGCCGGAUUCUCAGUACAACGGGAACCCCGAGUCCGUGGGCUACAGGAUUAAGUACUGGCGCUCAGACCUCCAGUCCUCAGCAGUGGCCCAAGUCGUCAGUGACCGGCUGGAGAGAGAAUUCACCAUCGAGGAGCUGGAGGAGUGGAUGGAAUACGAGCUGCAGAUGCAGGCCUUCAACGCCGUCGGGGCUGGGCCGUGGAGCGAGGUGGUGCGGGGCCGGACGCGGGAGUCAGUGCCCACCGCGCCCCCGCAGAACGUGCAGACGGAAGCCGUGAACUCCACC circ
ENSG00000146555:+:7:4049347:4114274 ENSG00000146555 ENST00000404826 + 7 4049348 4114274 22 GCGGGAGUCAGUGCCCACCGCG bsj
ENSG00000146555:+:7:4049347:4114274 ENSG00000146555 ENST00000404826 + 7 4049148 4049357 210 AAGAGAAAAUGAAAAAUAGCCCAAUUCUCUUUCUUGGUAAUGCCACUGUAAGCUUCCCAAAACAUUCAUCACACUUCCUCGGUCUCAGUGCAAUAAUUGCCUGUGAGCAUGAUGGCAGCUAAGGGUUUCCUUUCUGUCUCUCCACCCCAUGGUCCCUCCUGCCAUUUGUUCUGCUGUCAUCAAUGACUGCCCUGCCACAGUGCCCACCGC ie_up
ENSG00000146555:+:7:4049347:4114274 ENSG00000146555 ENST00000404826 + 7 4114265 4114474 210 CGGGAGUCAGGUGAGGGGAAGGCGAUUCCCAUCCUGGAGACACCGCAUUAGAGAUGGGGCUGAGUGCCCCUGAGCCUCCAGAUCCCAGGCUAGUGGCGUCUCAUUGGCCUGUCCCACUUGUGUCUGUCUUGGAGCUUUCCUAAUCCCGGGUUUGGCCAGACUCGGCAGGAAUUUCUGUCUGAUUUCAUUAGGGCCCCAAGCCAUUCAUUG 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 0.001638002 0.0002275250 2.847840 AGGGAU AGGGAU
NXF1 2 286 0.002457002 0.0004159215 2.562516 AACCUG AACCUG
FXR1 2 411 0.002457002 0.0005970720 2.040922 ACGACG,AUGACG ACGACA,ACGACG,AUGACA,AUGACG
RBM6 6 1054 0.005733006 0.0015289102 1.906788 AUCCAA,AUCCAG,CAUCCA AAUCCA,AUCCAA,AUCCAG,CAUCCA,UAUCCA
RBM14 2 478 0.002457002 0.0006941687 1.823541 CGCGCC,CGCGGG CGCGCC,CGCGCG,CGCGGC,CGCGGG,GCGCGC,GCGCGG
IFIH1 4 904 0.004095004 0.0013115296 1.642615 GGCCGC,GGGCCG CCGCGG,CGCGGA,GCCGCG,GCGGAU,GGCCCU,GGCCGC,GGGCCG
RBFOX2 1 452 0.001638002 0.0006564894 1.319093 UGACUG UGACUG,UGCAUG
SAMD4A 16 3992 0.013923014 0.0057866714 1.266666 CGGGAA,CGGGCC,CGGGUC,CUGGAC,CUGGCA,CUGGCC,CUGGUC,GCGGGA,GCUGGA,GCUGGC,GCUGGU CGGGAA,CGGGAC,CGGGCA,CGGGCC,CGGGUA,CGGGUC,CUGGAA,CUGGAC,CUGGCA,CUGGCC,CUGGUA,CUGGUC,GCGGGA,GCGGGC,GCGGGU,GCUGGA,GCUGGC,GCUGGU
YBX1 29 7119 0.024570025 0.0103183321 1.251690 AACAUC,ACACCA,ACAUCA,ACAUCU,ACCACC,CAACCA,CACACC,CACCAC,CAUCAU,CAUCUG,CCACCA,CCAGCA,CCCUGC,CCUGCG,CUGCGG,GCCUGC,GGUCUG AACAUC,AACCAC,ACACCA,ACAUCA,ACAUCG,ACAUCU,ACCACA,ACCACC,AUCAUC,CAACCA,CACACC,CACCAC,CAGCAA,CAUCAU,CAUCGC,CAUCUG,CCACAA,CCACAC,CCACCA,CCAGCA,CCCUGC,CCUGCG,CUGCGG,GAUCUG,GCCUGC,GGUCUG,GUCUGC,UCCAGC,UGCGGU
RBMY1A1 1 489 0.001638002 0.0007101099 1.205822 ACAAGA ACAAGA,CAAGAC
YBX2 5 1480 0.004914005 0.0021462711 1.195067 AACAUC,ACAACG,ACAUCA,ACAUCU AACAAC,AACAUC,ACAACA,ACAACG,ACAACU,ACAUCA,ACAUCG,ACAUCU
ACO1 4 1283 0.004095004 0.0018607779 1.137959 CAGUGA,CAGUGC,CAGUGG CAGUGA,CAGUGC,CAGUGG,CAGUGU
PPRC1 2 780 0.002457002 0.0011318283 1.118244 CCGCGC,CGCGCC CCGCGC,CGCGCC,CGCGCG,CGGCGC,GCGCGC,GGCGCC,GGCGCG,GGGCGC
ZC3H10 3 1053 0.003276003 0.0015274610 1.100801 CCAGCG,GAGCGA,GGAGCG CAGCGA,CAGCGC,CCAGCG,CGAGCG,GAGCGA,GAGCGC,GCAGCG,GGAGCG
HNRNPLL 12 3534 0.010647011 0.0051229360 1.055406 ACAAAC,ACACCA,CACACC,CACCAC,CACCGC,CAGACG,GCACAC ACAAAC,ACACAC,ACACCA,ACAUAC,ACCACA,ACCGCA,ACGACA,ACUGCA,AGACGA,CAAACA,CACACA,CACACC,CACCAC,CACCGC,CACUGC,CAGACG,CAUACA,GACGAC,GCAAAC,GCACAC,GCAUAC

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
ACO1 1 8 0.09090909 0.0005894682 7.268867 CAGUGC CAGUGA,CAGUGC,CAGUGG
SRSF2 2 479 0.13636364 0.0314383023 2.116864 GUCAGU,UCAGUG AAAAGA,AAAGAG,AAGAGA,AAGCAG,AAGCUG,AAGGCG,AAUACC,AAUGCU,ACCACC,ACCACU,ACCAGC,ACCAGU,ACCCCC,ACCCCU,ACUCAA,AGAAGA,AGAAGC,AGAAUA,AGAAUG,AGAGAA,AGAGAU,AGAGGA,AGAGGU,AGAGUA,AGAGUG,AGAGUU,AGAUAA,AGAUCC,AGAUGC,AGCACU,AGCAGA,AGCAGU,AGCCGA,AGCCUC,AGCGGA,AGCUGU,AGGAAG,AGGAGA,AGGAGC,AGGAGG,AGGAGU,AGGCAG,AGGCGU,AGGCUG,AGGGUA,AGUAGG,AGUAGU,AGUGAC,AGUGUU,AUGAUG,AUGCUG,AUGGAG,AUUAGU,AUUCCU,AUUGAU,CAGAGA,CAGAGG,CAGAGU,CAGUAG,CAGUGG,CCACCA,CCAGAU,CCAGCC,CCAGCU,CCAGGG,CCAGGU,CCAGUC,CCAGUG,CCAGUU,CCCGCU,CCCGUG,CCGCUA,CCGGUG,CCUCCG,CCUGCG,CCUGCU,CCUGUU,CGAACG,CGAGGA,CGAGUA,CGAGUG,CGAGUU,CGCAGU,CGCUGC,CGUAAG,CGUGCG,CUACCG,CUAGAA,CUCAAG,CUCCAA,CUCCUG,CUCGUG,CUGAUG,GAAAGG,GAAGAA,GAAGCG,GAAGGC,GAAUAC,GAAUCC,GACCCC,GACGGA,GACUCA,GACUGU,GAGAAG,GAGAAU,GAGAGA,GAGAGU,GAGAUA,GAGAUG,GAGCAC,GAGCAG,GAGCUG,GAGGAA,GAGGAC,GAGGAG,GAGUGA,GAUCCC,GAUCCG,GAUGAU,GAUGCU,GAUGGA,GAUUAG,GAUUGA,GCACUG,GCAGAG,GCAGGG,GCAGGU,GCAGUA,GCAGUG,GCCACC,GCCACU,GCCCAC,GCCGAG,GCCGCC,GCCGUU,GCCUCA,GCCUCC,GCGUGU,GCUGUU,GGAACC,GGAAGG,GGAAUG,GGACCG,GGACGC,GGAGAA,GGAGAG,GGAGAU,GGAGCG,GGAGGA,GGAGUG,GGAGUU,GGAUCC,GGAUGG,GGCAGU,GGCCAC,GGCCGC,GGCCUC,GGCGUG,GGCUCC,GGCUCG,GGCUGA,GGCUGC,GGGAAU,GGGAGC,GGGCAG,GGGUAA,GGGUAC,GGGUAG,GGGUAU,GGGUGA,GGUACG,GGUAGG,GGUCAG,GGUUAC,GGUUCC,GGUUGG,GUAAGC,GUAGGC,GUCAGU,GUCGCC,GUCUAA,GUGCAG,GUUAAU,GUUCCC,GUUCCU,GUUCGA,GUUCUG,GUUGGC,GUUUCG,UAAGCU,UACGAG,UACGUG,UAGGCU,UAUGCU,UCACCG,UCAGUG,UCCAGA,UCCAGC,UCCAGG,UCCAGU,UCCUGC,UCCUGU,UCGAGU,UCGUGC,UGAGCU,UGAUCG,UGAUGG,UGCAGA,UGCAGU,UGCCGU,UGCGGU,UGCUGU,UGGAGA,UGGAGG,UGGAGU,UGGCAG,UGUUCC,UUAAUG,UUACUG,UUAGUG,UUCCAG,UUCCCG,UUCCUA,UUCCUG,UUCGAG,UUGUUG

RBP on BSJ (Exon and Intron)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
RBFOX2 1 124 0.004761905 0.0006297864 2.918604 UGACUG UGACUG,UGCAUG
RBFOX1 3 287 0.009523810 0.0014510278 2.714464 AGCAUG,GCAUGA,UGACUG AGCAUG,GCAUGA,GCAUGC,GCAUGU,UGACUG,UGCAUG
SRP14 2 218 0.007142857 0.0011033857 2.694564 GCCUGU CCUGUA,CGCCUG,CUGUAG,GCCUGU
HNRNPA1L2 1 188 0.004761905 0.0009522370 2.322146 UUAGGG AUAGGG,GUAGGG,UAGGGA,UAGGGU,UUAGGG
ACO1 2 325 0.007142857 0.0016424829 2.120623 CAGUGC CAGUGA,CAGUGC,CAGUGG,CAGUGU
EIF4B 1 226 0.004761905 0.0011436921 2.057840 CUUGGA CUCGGA,CUUGGA,GUCGGA,GUUGGA,UCGGAA,UCGGAC,UUGGAA,UUGGAC
PABPC3 1 310 0.004761905 0.0015669085 1.603618 AAAACA AAAAAC,AAAACA,AAAACC,GAAAAC
CELF1 6 1097 0.016666667 0.0055320435 1.591081 CUGUCU,UGUCUG,UUGUGU CUGUCU,GUGUGU,GUGUUG,GUUGUG,GUUUGU,UGUCUG,UGUGUG,UGUGUU,UGUUGU,UGUUUG,UUGUGU
HNRNPLL 3 748 0.009523810 0.0037736800 1.335567 ACCGCA,CACCGC ACAAAC,ACACAC,ACACCA,ACAUAC,ACCACA,ACCGCA,ACGACA,ACUGCA,AGACGA,CAAACA,CACACA,CACACC,CACCAC,CACCGC,CACUGC,CAGACG,CAUACA,GACGAC,GCAAAC,GCACAC,GCAUAC
PABPC5 2 596 0.007142857 0.0030078597 1.247764 AGAAAA,GAAAAU AGAAAA,AGAAAG,AGAAAU,GAAAAU,GAAAGU,GAAAUU
A1CF 2 598 0.007142857 0.0030179363 1.242939 AUAAUU,UAAUUG AGUAUA,AUAAUU,AUCAGU,CAGUAU,GAUCAG,UAAUUA,UAAUUG,UCAGUA,UGAUCA,UUAAUU
NOVA1 6 1428 0.016666667 0.0071997179 1.210953 AUUCAU,CAUUCA,UUCAUU AACACC,ACCACC,AGCACC,AGUCAC,AUCAAC,AUCACC,AUCAUC,AUUCAU,CAGUCA,CAUUCA,CCCCCC,GGGGGG,UCAGUC,UCAUUC,UUCAUU,UUUUUU
RC3H1 2 631 0.007142857 0.0031841999 1.165570 UUCUGU CCCUUC,CCUUCU,CUUCUG,UCCCUU,UCUGUG,UUCUGU
RBM46 4 1091 0.011904762 0.0055018138 1.113560 AAUGAA,AUCAAU,AUGAAA,AUGAUG AAUCAA,AAUCAU,AAUGAA,AAUGAU,AUCAAA,AUCAAG,AUCAAU,AUCAUA,AUCAUG,AUCAUU,AUGAAA,AUGAAG,AUGAAU,AUGAUA,AUGAUG,AUGAUU,GAUCAA,GAUCAU,GAUGAA,GAUGAU
RBM4 4 1094 0.011904762 0.0055169287 1.109602 CUCUUU,CUUCCU,UUCCUU,UUCUUG CCUCUU,CCUUCC,CCUUCU,CGCGCG,CGCGGG,CGCGGU,CUCUUU,CUUCCU,CUUCUU,GCGCGA,GCGCGC,GCGCGG,UCCUUC,UUCCUU,UUCUUG

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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