ENSG00000185104:-:1:50535368:50596216

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000185104:-:1:50535368:50596216 ENSG00000185104 ENST00000396153 - 1 50535369 50596216 750 AUGUGUCUUGCUGAAUCAGGGCUCUCUUAUCCCUGCCAUCGACUUACAGUGGGAAGAAGAUCUUCACCUGCACAGACCCGGGAACAGUCGGAAGAACAAAUCACCGAUGUUCAUAUGGUUAGUGAUAGCGAUGGAGAUGACUUUGAAGAUGCUACAGAAUUUGGGGUGGAUGAUGGAGAAGUAUUUGGCAUGGCGUCAUCUGCCUUGAGAAAAUCUCCAAUGAUGCCAGAAAACGCAGAAAAUGAAGGAGAUGCCUUAUUACAAUUUACAGCAGAGUUUUCUUCAAGAUAUGGUGAUUGCCAUCCUGUAUUUUUUAUUGGCUCAUUAGAAGCUGCUUUUCAAGAGGCCUUCUAUGUGAAAGCCCGAGAUAGAAAGCUUCUUGCUAUCUACCUCCACCAUGAUGAAAGUGUGUUAACCAACGUGUUCUGCUCACAAAUGCUUUGUGCUGAAUCCAUUGUUUCUUAUCUGAGUCAAAAUUUUAUAACCUGGGCUUGGGAUCUGACAAAGGACUCCAACAGAGCAAGAUUUCUCACUAUGUGCAAUAGACACUUUGGCAGUGUUGUGGCACAAACCAUUCGGACUCAAAAAACGGAUCAGUUUCCGCUUUUCCUGAUUAUUAUGGGAAAGCGAUCAUCUAAUGAAGUGUUGAAUGUGAUACAAGGGAACACAACAGUAGAUGAGUUAAUGAUGAGACUCAUGGCUGCAAUGGAGAUCUUCACAGCCCAACAACAGGAAGAUAUAAAGGACGAGAUGUGUCUUGCUGAAUCAGGGCUCUCUUAUCCCUGCCAUCGACUUACAGU circ
ENSG00000185104:-:1:50535368:50596216 ENSG00000185104 ENST00000396153 - 1 50535369 50596216 22 UAAAGGACGAGAUGUGUCUUGC bsj
ENSG00000185104:-:1:50535368:50596216 ENSG00000185104 ENST00000396153 - 1 50596207 50596416 210 AAUUAGCCUUAGCUACCAUAACAUCCCAUGUGUGGAAAAAUUUCAAAUUUUCAAAGCCUUCCUGGUAAUGUAAUACCCAGGAUACUAGAGUUAGCUUUCUAAUCUAGCUUCAGCAAUAAUAGAAAAUACCUGAAAAGUCAAAUCCUUUUGUGAAACAUGGCCGUAUUUUGUUUACAAAUGAUGGAUUCUACUUUUUGCAGAUGUGUCUUG ie_up
ENSG00000185104:-:1:50535368:50596216 ENSG00000185104 ENST00000396153 - 1 50535169 50535378 210 AAAGGACGAGGUAAGGUUAUGCAGAUCUUUAAUAGGAUUUUGAUGAGAUUUUAAUAGGAUUUUAAUUUGUCAAAUGAUGAUACAUGCCUAUGAUAUGAUCGAUAAAUAAGGAUGAUGAAGAUGCAUUUCCAAAUUUACCAAGGGUUUUUAUGCUAUGGAGUUUACCUUUCAGUCCAUUCUUUUUAUGACCCCAAGACCCAAUAAUUUGUU 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
HNRNPA0 3 453 0.005333333 0.0006579386 3.019013 AAUUUA,AGAUAU AAUUUA,AGAUAU,AGUAGG
PTBP2 1 267 0.002666667 0.0003883867 2.779472 CUCUCU CUCUCU
NXF1 1 286 0.002666667 0.0004159215 2.680654 AACCUG AACCUG
RBMS1 1 497 0.002666667 0.0007217036 1.885559 GAUAUA AUAUAC,AUAUAG,GAUAUA,UAUAUA
CELF5 4 1415 0.006666667 0.0020520728 1.699884 GUGUGU,GUGUUG,UGUGUU GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU
EIF4B 3 1179 0.005333333 0.0017100607 1.640990 GUCGGA,UCGGAA,UCGGAC CUCGGA,CUUGGA,GUCGGA,GUUGGA,UCGGAA,UCGGAC,UUGGAA,UUGGAC
PABPC5 7 2400 0.010666667 0.0034795387 1.616141 AGAAAA,AGAAAG,GAAAAU,GAAAGU AGAAAA,AGAAAG,AGAAAU,GAAAAU,GAAAGU,GAAAUU
RBM46 14 4554 0.020000000 0.0066011240 1.599216 AAUGAA,AAUGAU,AUGAAA,AUGAAG,AUGAUG,GAUCAU,GAUGAA,GAUGAU AAUCAA,AAUCAU,AAUGAA,AAUGAU,AUCAAA,AUCAAG,AUCAAU,AUCAUA,AUCAUG,AUCAUU,AUGAAA,AUGAAG,AUGAAU,AUGAUA,AUGAUG,AUGAUU,GAUCAA,GAUCAU,GAUGAA,GAUGAU
CELF2 5 1886 0.008000000 0.0027346479 1.548645 AUGUGU,GUGUGU,UAUGUG,UGUUGU AUGUGU,GUAUGU,GUCUGU,GUGUGU,GUUGUU,UAUGUG,UAUGUU,UGUGUG,UGUUGU,UUGUGU
CELF1 6 2391 0.009333333 0.0034664959 1.428914 GUGUGU,GUGUUG,GUUGUG,UGUGUU,UGUUGU CUGUCU,GUGUGU,GUGUUG,GUUGUG,GUUUGU,UGUCUG,UGUGUG,UGUGUU,UGUUGU,UGUUUG,UUGUGU
SRSF11 1 688 0.002666667 0.0009985015 1.417201 AAGAAG AAGAAG
CELF4 4 1782 0.006666667 0.0025839306 1.367398 GUGUGU,GUGUUG,UGUGUU GGUGUG,GGUGUU,GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU
YBX2 3 1480 0.005333333 0.0021462711 1.313205 AACAAC,ACAACA AACAAC,AACAUC,ACAACA,ACAACG,ACAACU,ACAUCA,ACAUCG,ACAUCU
PABPC1 11 4443 0.016000000 0.0064402624 1.312881 AAAAAA,AAAAAC,ACAAAC,ACAAAU,AGAAAA,CAAACC,CAAAUC,GAAAAC AAAAAA,AAAAAC,ACAAAC,ACAAAU,ACGAAC,ACGAAU,ACUAAC,ACUAAU,AGAAAA,CAAACA,CAAACC,CAAAUA,CAAAUC,CGAACA,CGAACC,CGAAUA,CGAAUC,CUAACA,CUAACC,CUAAUA,CUAAUC,GAAAAA,GAAAAC
SART3 6 2634 0.009333333 0.0038186524 1.289329 AAAAAA,AAAAAC,AGAAAA,GAAAAC AAAAAA,AAAAAC,AGAAAA,GAAAAA,GAAAAC
CSTF2 4 1967 0.006666667 0.0028520334 1.224975 GUGUGU,GUGUUG,UGUGUU GUGUGU,GUGUUG,GUGUUU,GUUUUG,UGUGUG,UGUGUU,UGUUUG,UGUUUU
QKI 6 2805 0.009333333 0.0040664663 1.198617 ACUCAU,AUCUAA,AUCUAC,UAACCU,UCAUAU,UCUAAU AAUCAU,ACACAC,ACACUA,ACUAAC,ACUAAU,ACUCAU,ACUUAU,AUCAUA,AUCUAA,AUCUAC,AUUAAC,CACACU,CACUAA,CUAACA,CUAACC,CUAACG,CUAAUC,CUACUC,CUCAUA,UAACCU,UAAUCA,UACUCA,UCAUAU,UCUAAU,UCUACU
IGHMBP2 1 813 0.002666667 0.0011796520 1.176676 AAAAAA AAAAAA
CPEB4 1 821 0.002666667 0.0011912456 1.162567 UUUUUU UUUUUU
DDX19B 1 821 0.002666667 0.0011912456 1.162567 UUUUUU UUUUUU
EIF4A3 1 821 0.002666667 0.0011912456 1.162567 UUUUUU UUUUUU
RBM28 1 822 0.002666667 0.0011926949 1.160813 AGUAGA AGUAGA,AGUAGG,AGUAGU,GAGUAG,GUGUAG,UGUAGA,UGUAGG,UGUAGU
PABPC3 2 1234 0.004000000 0.0017897669 1.160228 AAAAAC,GAAAAC AAAAAC,AAAACA,AAAACC,GAAAAC
SNRNP70 2 1237 0.004000000 0.0017941145 1.156728 UUCAAG AAUCAA,AUCAAG,AUUCAA,GAUCAA,GUUCAA,UUCAAG
SRSF4 8 3740 0.012000000 0.0054214720 1.146278 AAGAAG,AGAAGA,AGGAAG,GAAGAA,GGAAGA AAGAAG,AGAAGA,AGGAAG,GAAGAA,GAGGAA,GGAAGA
SRP14 1 847 0.002666667 0.0012289250 1.117641 CCUGUA CCUGUA,CGCCUG,CUGUAG,GCCUGU
ACO1 2 1283 0.004000000 0.0018607779 1.104094 CAGUGG,CAGUGU CAGUGA,CAGUGC,CAGUGG,CAGUGU
ESRP2 4 2150 0.006666667 0.0031172377 1.096697 GGGAAA,GGGAAG,UGGGAA GGGAAA,GGGAAG,GGGAAU,GGGGAA,GGGGAG,GGGGAU,UGGGAA,UGGGGA
TARDBP 5 2654 0.008000000 0.0038476365 1.056027 GAAUGU,GUGUGU,GUUGUG,UGAAUG,UUGUGC GAAUGA,GAAUGG,GAAUGU,GUGAAU,GUGUGU,GUUGUG,GUUGUU,GUUUUG,UGAAUG,UGUGUG,UUGUGC,UUGUUC,UUUUGC

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
SRSF7 2 128 0.1363636 0.008449044 4.012527 ACGAGA,CGAGAU AAGGAC,AAGGCG,AAUGAU,ACGAAU,ACUACG,AGAAGA,AGAGAA,AGAGAC,AGAGAG,AGAGAU,AGAGGA,AGAUCA,AGAUCU,AGGAAG,AGGACA,AUAGAC,AUUGAC,AUUGAU,CAGAGA,CGAAUG,CUCUUC,CUGAGA,GAAGAA,GAAGGC,GAAUGA,GACAAA,GACGAC,GAGACU,GAGAGA,GAGAUC,GAGGAA,GAUAGA,GAUUGA,GGAAGG,GGACAA,GGACGA,UAGAGA,UCUUCA,UGAGAG,UGGACA
SRSF2 3 479 0.1818182 0.031438302 2.531901 ACGAGA,CGAGAU,GAGAUG 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
RBMY1A1 1 95 0.004761905 0.0004836759 3.299426 CAAGAC ACAAGA,CAAGAC
TUT1 2 230 0.007142857 0.0011638452 2.617602 AAAUAC,GAUACU AAAUAC,AAUACU,AGAUAC,CAAUAC,CGAUAC,GAUACU
G3BP2 5 490 0.014285714 0.0024738009 2.529772 AGGAUA,AGGAUG,AGGAUU,GGAUGA AGGAUA,AGGAUG,AGGAUU,GGAUAA,GGAUAG,GGAUGA,GGAUGG,GGAUUA,GGAUUG
RBM46 11 1091 0.028571429 0.0055018138 2.376594 AAUGAU,AUGAAG,AUGAUA,AUGAUG,GAUGAA,GAUGAU AAUCAA,AAUCAU,AAUGAA,AAUGAU,AUCAAA,AUCAAG,AUCAAU,AUCAUA,AUCAUG,AUCAUU,AUGAAA,AUGAAG,AUGAAU,AUGAUA,AUGAUG,AUGAUU,GAUCAA,GAUCAU,GAUGAA,GAUGAU
HNRNPA0 1 200 0.004761905 0.0010126965 2.233337 AAUUUA AAUUUA,AGAUAU,AGUAGG
ERI1 1 228 0.004761905 0.0011537686 2.045185 UUUCAG UUCAGA,UUUCAG
RBM41 3 502 0.009523810 0.0025342604 1.909974 AUACAU,UACAUG,UACUUU AUACAU,AUACUU,UACAUG,UACAUU,UACUUG,UACUUU,UUACAU,UUACUU
YBX2 1 263 0.004761905 0.0013301088 1.839994 AACAUC AACAAC,AACAUC,ACAACA,ACAACG,ACAACU,ACAUCA,ACAUCG,ACAUCU
AGO1 1 283 0.004761905 0.0014308746 1.734641 GAGGUA AGGUAG,GAGGUA,GGUAGU,GUAGUA,UGAGGU
SNRPB2 1 288 0.004761905 0.0014560661 1.709463 UUGCAG AUUGCA,GUAUUG,UAUUGC,UGCAGU,UUGCAG
HNRNPA3 1 349 0.004761905 0.0017634019 1.433177 CCAAGG AAGGAG,AGGAGC,CAAGGA,CCAAGG,GCCAAG,GGAGCC
RBM3 2 541 0.007142857 0.0027307537 1.387202 AUACUA,GAUACU AAAACG,AAAACU,AAACGA,AAACUA,AAGACG,AAGACU,AAUACG,AAUACU,AGACGA,AGACUA,AUACGA,AUACUA,GAAACG,GAAACU,GAGACG,GAGACU,GAUACG,GAUACU
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,UUAAUU AGUAUA,AUAAUU,AUCAGU,CAGUAU,GAUCAG,UAAUUA,UAAUUG,UCAGUA,UGAUCA,UUAAUU
PABPC1 5 1321 0.014285714 0.0066606207 1.100845 ACAAAU,AGAAAA,CAAAUC,CUAAUC,GAAAAA AAAAAA,AAAAAC,ACAAAC,ACAAAU,ACGAAC,ACGAAU,ACUAAC,ACUAAU,AGAAAA,CAAACA,CAAACC,CAAAUA,CAAAUC,CGAACA,CGAACC,CGAAUA,CGAAUC,CUAACA,CUAACC,CUAAUA,CUAAUC,GAAAAA,GAAAAC
CELF2 3 881 0.009523810 0.0044437727 1.099754 AUGUGU,UGUGUG AUGUGU,GUAUGU,GUCUGU,GUGUGU,GUUGUU,UAUGUG,UAUGUU,UGUGUG,UGUUGU,UUGUGU
CELF5 2 669 0.007142857 0.0033756550 1.081334 GUGUGG,UGUGUG GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU
TIAL1 24 5597 0.059523810 0.0282043531 1.077549 AAAUUU,AAUUUU,AUUUUA,AUUUUC,AUUUUG,CUUUUG,CUUUUU,GUUUUU,UAUUUU,UUCAGU,UUUCAG,UUUUAA,UUUUAU,UUUUCA,UUUUUA,UUUUUG AAAUUU,AAUUUU,AGUUUU,AUUUUA,AUUUUC,AUUUUG,AUUUUU,CAGUUU,CUUUUA,CUUUUC,CUUUUG,CUUUUU,GUUUUC,GUUUUU,UAAAUU,UAUUUU,UCAGUU,UUAAAU,UUAUUU,UUCAGU,UUUAAA,UUUAUU,UUUCAG,UUUUAA,UUUUAU,UUUUCA,UUUUUA,UUUUUC,UUUUUG,UUUUUU
QKI 3 904 0.009523810 0.0045596534 1.062615 CUAAUC,UCUAAU,UCUACU AAUCAU,ACACAC,ACACUA,ACUAAC,ACUAAU,ACUCAU,ACUUAU,AUCAUA,AUCUAA,AUCUAC,AUUAAC,CACACU,CACUAA,CUAACA,CUAACC,CUAACG,CUAAUC,CUACUC,CUCAUA,UAACCU,UAAUCA,UACUCA,UCAUAU,UCUAAU,UCUACU

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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