ENSG00000140470:-:15:100254135:100281401

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000140470:-:15:100254135:100281401 ENSG00000140470 ENST00000268070 - 15 100254136 100281401 459 AAAAGAAGAAGCCGACGUGGGGCAGGCCUUCGCGGGACUGGCGGGAGCGGAGGAACGCUAUCCGGCUCACCAGCGAGCACACGGUGGAGACCCUGGUGGUGGCCGACGCCGACAUGGUGCAGUACCACGGGGCCGAGGCCGCCCAGAGGUUCAUCCUGACCGUCAUGAACAUGGUAUACAAUAUGUUUCAGCACCAGAGCCUGGGGAUUAAAAUUAACAUUCAAGUGACCAAGCUUGUCCUGCUACGACAACGUCCCGCUAAGUUGUCCAUUGGGCACCAUGGUGAGCGGUCCCUGGAGAGCUUCUGUCACUGGCAGAACGAGGAGUAUGGAGGAGCGCGAUACCUCGGCAAUAACCAGGUUCCCGGCGGGAAGGACGACCCGCCCCUGGUGGAUGCUGCCGUGUUUGUGACCAGGACAGAUUUCUGUGUACACAAGGAUGAACCGUGUGACACUGUUGAAAAGAAGAAGCCGACGUGGGGCAGGCCUUCGCGGGACUGGCGGGAGCGG circ
ENSG00000140470:-:15:100254135:100281401 ENSG00000140470 ENST00000268070 - 15 100254136 100281401 22 UGACACUGUUGAAAAGAAGAAG bsj
ENSG00000140470:-:15:100254135:100281401 ENSG00000140470 ENST00000268070 - 15 100281392 100281601 210 CCCUUCUUUUGGGCCAGCACCCCCCUACGUGAGUGAACUCGGGGCACCCACAUGACGGUGGAGAUUGCUGGGUGCUGGGCCCCUCUAGGCCUGUCGAGACUGACCACUCUCUCGGGCAGGCUUGACAGAAGGCCUGUUCACUGCAUGGUUUUGGAAGUCAGUAAGCCAAGGACCGCACAAAUGUUUCCAUCAUUUUCUAGAAAAGAAGAA ie_up
ENSG00000140470:-:15:100254135:100281401 ENSG00000140470 ENST00000268070 - 15 100253936 100254145 210 GACACUGUUGGUAAGUUUAGAGUUGAAAUAAUAAUCUAAGGGGCUGAUACACCCUGGGAGAAUCUGGAGACUUCCUGGUCACAGUGGAGGAGCUGUCCUCAAACAAGCACUGCACAUUCUGUUGCCUUCCUUCCUGUAAGUUGGUCUUUGACUUUCCUUUUUUUAUUUUCCUGAAAUGAUUUGAAGUUAUUGAUGGCAGAAGGCAUCUAG 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
SUPV3L1 2 199 0.006535948 0.0002898408 4.495064 CCGCCC CCGCCC
CNOT4 1 314 0.004357298 0.0004564992 3.254750 GACAGA GACAGA
ZC3H10 5 1053 0.013071895 0.0015274610 3.097261 CAGCGA,CCAGCG,GAGCGC,GGAGCG CAGCGA,CAGCGC,CCAGCG,CGAGCG,GAGCGA,GAGCGC,GCAGCG,GGAGCG
FXR1 1 411 0.004357298 0.0005970720 2.867457 ACGACA ACGACA,ACGACG,AUGACA,AUGACG
SRSF11 2 688 0.006535948 0.0009985015 2.710560 AAGAAG AAGAAG
RBM14 1 478 0.004357298 0.0006941687 2.650076 CGCGGG CGCGCC,CGCGCG,CGCGGC,CGCGGG,GCGCGC,GCGCGG
IFIH1 2 904 0.006535948 0.0013115296 2.317146 GGCCGC,GGGCCG CCGCGG,CGCGGA,GCCGCG,GCGGAU,GGCCCU,GGCCGC,GGGCCG
ERI1 1 632 0.004357298 0.0009173461 2.247896 UUUCAG UUCAGA,UUUCAG
TUT1 1 678 0.004357298 0.0009840095 2.146690 CGAUAC AAAUAC,AAUACU,AGAUAC,CAAUAC,CGAUAC,GAUACU
RC3H1 4 1786 0.010893246 0.0025897275 2.072562 CUUCUG,UCUGUG,UUCUGU CCCUUC,CCUUCU,CUUCUG,UCCCUU,UCUGUG,UUCUGU
ZCRB1 3 1605 0.008714597 0.0023274215 1.904701 AAUUAA,GAUUAA,GGAUUA AAUUAA,ACUUAA,AUUUAA,GAAUUA,GACUUA,GAUUAA,GAUUUA,GCUUAA,GGAUUA,GGCUUA,GGUUUA,GUUUAA
PABPN1 2 1222 0.006535948 0.0017723764 1.882711 AAAAGA,AGAAGA AAAAGA,AGAAGA
G3BP2 3 1644 0.008714597 0.0023839405 1.870086 AGGAUG,GGAUGA,GGAUUA AGGAUA,AGGAUG,AGGAUU,GGAUAA,GGAUAG,GGAUGA,GGAUGG,GGAUUA,GGAUUG
SNRNP70 2 1237 0.006535948 0.0017941145 1.865124 AUUCAA,UUCAAG AAUCAA,AUCAAG,AUUCAA,GAUCAA,GUUCAA,UUCAAG
IGF2BP1 1 831 0.004357298 0.0012057377 1.853518 AGCACC AAGCAC,ACCCGU,AGCACC,CACCCG,CCCGUU,GCACCC
ZRANB2 6 3173 0.015250545 0.0045997733 1.729226 GAGGUU,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 8 4315 0.019607843 0.0062547643 1.648403 AGGAGU,CGGAGG,GGAGGA,GGAGUA,UGGAGA,UGGAGG AGGAGA,AGGAGU,CGGAGA,CGGAGG,CGGAGU,GGAGAA,GGAGAU,GGAGGA,GGAGGG,GGAGUA,UGGAGA,UGGAGG,UGGAGU
SNRPB2 1 991 0.004357298 0.0014376103 1.599761 UGCAGU AUUGCA,GUAUUG,UAUUGC,UGCAGU,UUGCAG
NONO 2 1498 0.006535948 0.0021723567 1.589135 AGGAAC,GAGGAA AGAGGA,AGGAAC,GAGAGG,GAGGAA
HNRNPM 1 999 0.004357298 0.0014492040 1.588173 GAAGGA AAGGAA,GAAGGA,GGGGGG
ESRP2 3 2150 0.008714597 0.0031172377 1.483166 GGGAAG,GGGGAU,UGGGGA GGGAAA,GGGAAG,GGGAAU,GGGGAA,GGGGAG,GGGGAU,UGGGAA,UGGGGA
SAMD4A 6 3992 0.015250545 0.0057866714 1.398055 CGGGAA,CGGGAC,CUGGCA,GCGGGA CGGGAA,CGGGAC,CGGGCA,CGGGCC,CGGGUA,CGGGUC,CUGGAA,CUGGAC,CUGGCA,CUGGCC,CUGGUA,CUGGUC,GCGGGA,GCGGGC,GCGGGU,GCUGGA,GCUGGC,GCUGGU
FUS 5 3648 0.013071895 0.0052881452 1.305635 CGGUGG,UGGUGA,UGGUGG AAAAAA,CGGUGA,CGGUGG,GGGGGG,GGGUGA,GGGUGC,GGGUGG,GGGUGU,UGGUGA,UGGUGG,UGGUGU,UUUUUU
SRSF9 32 20254 0.071895425 0.0293536261 1.292361 AGGAAC,AGGACA,AGGAGC,AUGAAC,GAAGCC,GAAGGA,GGAACG,GGAAGG,GGACAG,GGAGAG,GGAGCG,GGAGGA,GGAUGC,GGGAGC,GGUGCA,GGUGGA,GGUGGC,UGAAAA,UGAACA,UGACCA,UGACCG,UGAGCG,UGGAGG,UGGUGC,UGGUGG AGGAAA,AGGAAC,AGGACA,AGGACC,AGGAGA,AGGAGC,AUGAAA,AUGAAC,AUGACA,AUGACC,AUGAGA,AUGAGC,CUGGAU,GAAGCA,GAAGCC,GAAGGA,GAAGGC,GAUGCA,GAUGCC,GAUGGA,GAUGGC,GGAAAA,GGAAAG,GGAACA,GGAACG,GGAAGC,GGAAGG,GGACAA,GGACAG,GGACCA,GGACCG,GGAGAA,GGAGAG,GGAGCA,GGAGCC,GGAGCG,GGAGGA,GGAGGC,GGAUGC,GGAUGG,GGGAGC,GGGAGG,GGGUGC,GGGUGG,GGUGCA,GGUGCC,GGUGGA,GGUGGC,UGAAAA,UGAAAG,UGAACA,UGAACG,UGAAGC,UGAAGG,UGACAA,UGACAG,UGACCA,UGACCG,UGAGAA,UGAGAG,UGAGCA,UGAGCG,UGAUGC,UGAUGG,UGGAGC,UGGAGG,UGGAUU,UGGUGC,UGGUGG
SRSF4 5 3740 0.013071895 0.0054214720 1.269712 AAGAAG,AGAAGA,GAAGAA,GAGGAA AAGAAG,AGAAGA,AGGAAG,GAAGAA,GAGGAA,GGAAGA
ENOX1 4 3195 0.010893246 0.0046316558 1.233834 AGGACA,GGACAG,UAUACA,UGUACA AAGACA,AAUACA,AGACAG,AGGACA,AGUACA,AUACAG,CAGACA,CAUACA,CGGACA,CGUACA,GGACAG,GUACAG,UAGACA,UAUACA,UGGACA,UGUACA
CSTF2 2 1967 0.006535948 0.0028520334 1.196406 GUGUUU,UGUUUG GUGUGU,GUGUUG,GUGUUU,GUUUUG,UGUGUG,UGUGUU,UGUUUG,UGUUUU
CELF5 1 1415 0.004357298 0.0020520728 1.086352 GUGUUU GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU
HNRNPA3 2 2140 0.006535948 0.0031027457 1.074851 AGGAGC,CAAGGA AAGGAG,AGGAGC,CAAGGA,CCAAGG,GCCAAG,GGAGCC
YBX2 1 1480 0.004357298 0.0021462711 1.021602 ACAACG AACAAC,AACAUC,ACAACA,ACAACG,ACAACU,ACAUCA,ACAUCG,ACAUCU

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
SRSF9 1 134 0.09090909 0.008842023 3.361976 UGAAAA AGGAAA,AGGAAC,AGGACA,AGGACC,AGGAGA,AGGAGC,AUGAAC,AUGACA,AUGAGA,AUGAGC,CUGGAU,GAAGCA,GAAGCC,GAAGGA,GAAGGC,GAUGCA,GAUGCC,GAUGGA,GAUGGC,GGAAAA,GGAAAG,GGAACA,GGAACG,GGAAGC,GGAAGG,GGACAA,GGACAG,GGACCA,GGACCG,GGAGAA,GGAGAG,GGAGCA,GGAGCG,GGAGGA,GGAGGC,GGAUGG,GGGAGC,GGGUGG,GGUGCA,GGUGCC,GGUGGA,GGUGGC,UGAAAA,UGAACA,UGAACG,UGAAGC,UGAAGG,UGACAA,UGACAG,UGAGAA,UGAGAG,UGAGCA,UGAUGG,UGGAGC,UGGAGG,UGGUGC

RBP on BSJ (Exon and Intron)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
RBM25 2 53 0.007142857 0.0002720677 4.714464 CGGGCA,UCGGGC AUCGGG,CGGGCA,UCGGGC
CNOT4 1 65 0.004761905 0.0003325272 3.839994 GACAGA GACAGA
IGF2BP1 4 173 0.011904762 0.0008766626 3.763373 AAGCAC,AGCACC,GCACCC AAGCAC,ACCCGU,AGCACC,CACCCG,CCCGUU,GCACCC
FXR1 1 69 0.004761905 0.0003526804 3.755106 AUGACG ACGACA,ACGACG,AUGACA,AUGACG
SRSF11 1 82 0.004761905 0.0004181782 3.509349 AAGAAG AAGAAG
SRP14 3 218 0.009523810 0.0011033857 3.109602 CCUGUA,GCCUGU CCUGUA,CGCCUG,CUGUAG,GCCUGU
PABPN1 2 178 0.007142857 0.0009018541 2.985535 AAAAGA,AGAAGA AAAAGA,AGAAGA
RBFOX2 1 124 0.004761905 0.0006297864 2.918604 UGCAUG UGACUG,UGCAUG
HNRNPA3 4 349 0.011904762 0.0017634019 2.755106 AGGAGC,CAAGGA,CCAAGG,GCCAAG AAGGAG,AGGAGC,CAAGGA,CCAAGG,GCCAAG,GGAGCC
PTBP2 1 146 0.004761905 0.0007406288 2.684716 CUCUCU CUCUCU
RBM4 10 1094 0.026190476 0.0055169287 2.247105 CCUUCC,CCUUCU,CUUCCU,CUUCUU,UCCUUC,UUCCUU CCUCUU,CCUUCC,CCUUCU,CGCGCG,CGCGGG,CGCGGU,CUCUUU,CUUCCU,CUUCUU,GCGCGA,GCGCGC,GCGCGG,UCCUUC,UUCCUU,UUCUUG
HNRNPLL 6 748 0.016666667 0.0037736800 2.142922 ACCGCA,ACUGCA,CAAACA,CACUGC ACAAAC,ACACAC,ACACCA,ACAUAC,ACCACA,ACCGCA,ACGACA,ACUGCA,AGACGA,CAAACA,CACACA,CACACC,CACCAC,CACCGC,CACUGC,CAGACG,CAUACA,GACGAC,GCAAAC,GCACAC,GCAUAC
EIF4B 1 226 0.004761905 0.0011436921 2.057840 UUGGAA CUCGGA,CUUGGA,GUCGGA,GUUGGA,UCGGAA,UCGGAC,UUGGAA,UUGGAC
LIN28A 6 900 0.016666667 0.0045395002 1.876360 GGAGAA,GGAGAU,GGAGGA,UGGAGA,UGGAGG AGGAGA,AGGAGU,CGGAGA,CGGAGG,CGGAGU,GGAGAA,GGAGAU,GGAGGA,GGAGGG,GGAGUA,UGGAGA,UGGAGG,UGGAGU
SRSF4 3 558 0.009523810 0.0028164047 1.757684 AAGAAG,AGAAGA,GAAGAA AAGAAG,AGAAGA,AGGAAG,GAAGAA,GAGGAA,GGAAGA
RBFOX1 1 287 0.004761905 0.0014510278 1.714464 UGCAUG AGCAUG,GCAUGA,GCAUGC,GCAUGU,UGACUG,UGCAUG
RC3H1 3 631 0.009523810 0.0031841999 1.580608 CCCUUC,CCUUCU,UUCUGU CCCUUC,CCUUCU,CUUCUG,UCCCUU,UCUGUG,UUCUGU
ZNF638 3 646 0.009523810 0.0032597743 1.546767 GUUGGU,UGUUGG CGUUCG,CGUUCU,CGUUGG,CGUUGU,GGUUCG,GGUUCU,GGUUGG,GGUUGU,GUUCGU,GUUCUU,GUUGGU,GUUGUU,UGUUCG,UGUUCU,UGUUGG,UGUUGU
ACO1 1 325 0.004761905 0.0016424829 1.535660 CAGUGG CAGUGA,CAGUGC,CAGUGG,CAGUGU
RBM3 2 541 0.007142857 0.0027307537 1.387202 GAGACU AAAACG,AAAACU,AAACGA,AAACUA,AAGACG,AAGACU,AAUACG,AAUACU,AGACGA,AGACUA,AUACGA,AUACUA,GAAACG,GAAACU,GAGACG,GAGACU,GAUACG,GAUACU
FXR2 3 730 0.009523810 0.0036829907 1.370661 GACAGA,UGACAG,UGACGG AGACAA,AGACAG,AGACGA,AGACGG,GACAAA,GACAAG,GACAGA,GACAGG,GACGAA,GACGAG,GACGGA,GACGGG,GGACAA,GGACAG,GGACGA,GGACGG,UGACAA,UGACAG,UGACGA,UGACGG
TRA2B 6 1447 0.016666667 0.0072954454 1.191898 AAAGAA,AAGAAG,AGAAGA,AGAAGG,GAAGAA AAAGAA,AAGAAC,AAGAAG,AAGAAU,AAGGAA,AAUAAG,AGAAGA,AGAAGG,AGGAAA,AGGAAG,AUAAGA,GAAAGA,GAAGAA,GAAGGA,GAAUUA,GGAAGG,UAAGAA
SNRPA 8 1947 0.021428571 0.0098145909 1.126536 GGAGAU,GUUUCC,UGCACA,UUCCUG,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
SRSF7 12 2893 0.030952381 0.0145808142 1.085979 AAGAAG,AAGGAC,AAUGAU,AGAAGA,AUUGAU,CGAGAC,GAAGAA,GAAGGC,GAGACU,UCGAGA AAAGGA,AAGAAG,AAGGAC,AAGGCG,AAUGAU,ACGAAU,ACGACG,ACGAGA,ACGAUA,ACGAUU,ACUACG,ACUAGA,AGAAGA,AGACGA,AGACUA,AGAGAA,AGAGAC,AGAGAG,AGAGAU,AGAGGA,AGAUCA,AGAUCU,AGGAAG,AGGACA,AGGCGA,AUAGAA,AUAGAC,AUUGAC,AUUGAU,CAGAGA,CCGAGA,CGAAUG,CGACGA,CGAGAC,CGAGAG,CGAGAU,CGAUAG,CGAUUG,CUACGA,CUAGAG,CUCUUC,CUGAGA,CUUCAC,GAAGAA,GAAGGC,GAAUGA,GACAAA,GACGAC,GACGAG,GACGAU,GACUAC,GAGACU,GAGAGA,GAGAUC,GAGGAA,GAUAGA,GAUUGA,GGAAGG,GGACAA,GGACGA,UACGAU,UAGAGA,UCAACA,UCGAGA,UCGAUU,UCUCCG,UCUUCA,UGAGAG,UGGACA
TRA2A 4 1133 0.011904762 0.0057134220 1.059112 AAAGAA,AAGAAG,AGAAGA,GAAGAA AAAGAA,AAGAAA,AAGAAG,AAGAGG,AGAAAG,AGAAGA,AGAGGA,AGGAAG,GAAAGA,GAAGAA,GAAGAG,GAGGAA
CPEB4 2 691 0.007142857 0.0034864974 1.034723 UUUUUU UUUUUU
DDX19B 2 691 0.007142857 0.0034864974 1.034723 UUUUUU UUUUUU
EIF4A3 2 691 0.007142857 0.0034864974 1.034723 UUUUUU UUUUUU

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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