ENSG00000156639:+:6:38061592:38116739

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000156639:+:6:38061592:38116739 ENSG00000156639 ENST00000287218 + 6 38061593 38116739 417 AUUUUCAAAAGAAACAGCCAGACGAUGAUUCCGCUCCAAGUACAAGUAACAGCCAAUCAGAUUUGUUUUCCGAAGAGACCACCAGUGACAACAACAAUACCUCGAUAACCACGCCAACUCUUAGUCCCAGCCAGCAGCCGCUUCCGACAGAACUGAAUGUAACUUCACCGAGUAAAGAGGAGUGUGGGCCAUGCACAGACACAGCUCAUGUCUCAUUAAUCACACCAACAAAAAGAUCCUGUGGUACAGAUUCACAGUCUGAGAAUGAGGCUUCACCAGUAAAACGGCCACGACUACUUGAGAAUACGGAACGGUCCGAGGAAACCAGUCGAUCUAAACAGAAGAGUCGACGUCGGUGCUUCCAGUGCCAAACCAAACUGGAGCUGGUGCAGCAGGAAUUGGGAUCGUGUCGCUGCGAUUUUCAAAAGAAACAGCCAGACGAUGAUUCCGCUCCAAGUACAAGUAAC circ
ENSG00000156639:+:6:38061592:38116739 ENSG00000156639 ENST00000287218 + 6 38061593 38116739 22 GUGUCGCUGCGAUUUUCAAAAG bsj
ENSG00000156639:+:6:38061592:38116739 ENSG00000156639 ENST00000287218 + 6 38061393 38061602 210 UUGGAAAACUUUUAACUCUAGUACCUUCCACUAAUCUUAAACGUUUUUGACCAGUGUUUUACUCCCAUGGUUUUUUAGUCACCCAGAUCAGUCUUUAUUAUUGGUGUUGUUGCAUUUAAUUUUUGUACCAACUUCCAUUGUUUUCUAAUCCUCAGAGACUGUGAACUCCUUAAUUAAGCUCGUUUUCUAUUUUUCUUCAGAUUUUCAAAA ie_up
ENSG00000156639:+:6:38061592:38116739 ENSG00000156639 ENST00000287218 + 6 38116730 38116939 210 UGUCGCUGCGGUAAGCAUCUCCCCCAGUGGCGUGAUGGAGACUAUAUCCUUAACACCUUGGCCCAGCUUUGGAAAUUUAAGUGGCUGAAGUCUUUCGUUCUUCUUCUGAGUACUGUAAGUUUGCUACAGUAGUGCAUGCGAUAUAGGUUUGGGGCUUGAGAAAUCAGGAGCAUAGUAUGUUUGCCUCUAAACACCCUUUAUUCUCACACA 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
ANKHD1 2 339 0.007194245 0.0004927293 3.867976 AGACGA,GACGAU AGACGA,AGACGU,GACGAA,GACGAU,GACGUA,GACGUU
CNOT4 1 314 0.004796163 0.0004564992 3.393196 GACAGA GACAGA
PABPN1 3 1222 0.009592326 0.0017723764 2.436196 AAAAGA,AGAAGA AAAAGA,AGAAGA
TUT1 1 678 0.004796163 0.0009840095 2.285137 CAAUAC AAAUAC,AAUACU,AGAUAC,CAAUAC,CGAUAC,GAUACU
YBX2 3 1480 0.009592326 0.0021462711 2.160048 AACAAC,ACAACA AACAAC,AACAUC,ACAACA,ACAACG,ACAACU,ACAUCA,ACAUCG,ACAUCU
ACO1 2 1283 0.007194245 0.0018607779 1.950937 CAGUGA,CAGUGC CAGUGA,CAGUGC,CAGUGG,CAGUGU
NONO 2 1498 0.007194245 0.0021723567 1.727582 AGAGGA,GAGGAA AGAGGA,AGGAAC,GAGAGG,GAGGAA
RBM3 3 2152 0.009592326 0.0031201361 1.620272 AAAACG,AAUACG,AGACGA AAAACG,AAAACU,AAACGA,AAACUA,AAGACG,AAGACU,AAUACG,AAUACU,AGACGA,AGACUA,AUACGA,AUACUA,GAAACG,GAAACU,GAGACG,GAGACU,GAUACG,GAUACU
RBM24 3 2357 0.009592326 0.0034172229 1.489056 AGUGUG,GAGUGU,GUGUGG AGAGUG,AGUGUG,GAGUGA,GAGUGG,GAGUGU,GUGUGA,GUGUGG,GUGUGU,UGAGUG,UGUGUG
PABPC4 1 1251 0.004796163 0.0018144033 1.402386 AAAAAG AAAAAA,AAAAAG
SSB 1 1260 0.004796163 0.0018274462 1.392052 UGUUUU CUGUUU,GCUGUU,UGCUGU,UGUUUU
RBM41 1 1318 0.004796163 0.0019115000 1.327176 UACUUG AUACAU,AUACUU,UACAUG,UACAUU,UACUUG,UACUUU,UUACAU,UUACUU
TARDBP 3 2654 0.009592326 0.0038476365 1.317908 GAAUGA,GAAUGU,UGAAUG GAAUGA,GAAUGG,GAAUGU,GUGAAU,GUGUGU,GUUGUG,GUUGUU,GUUUUG,UGAAUG,UGUGUG,UUGUGC,UUGUUC,UUUUGC
HNRNPLL 4 3534 0.011990408 0.0051229360 1.226838 ACACCA,AGACGA,CACACC,CAGACG ACAAAC,ACACAC,ACACCA,ACAUAC,ACCACA,ACCGCA,ACGACA,ACUGCA,AGACGA,CAAACA,CACACA,CACACC,CACCAC,CACCGC,CACUGC,CAGACG,CAUACA,GACGAC,GCAAAC,GCACAC,GCAUAC
CELF5 1 1415 0.004796163 0.0020520728 1.224799 GUGUGG GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU
HNRNPDL 11 8759 0.028776978 0.0126950266 1.180652 AACAGC,AAUACC,ACACCA,ACCACG,CACCAG,CCACGC,CCAGAC,UAACAG,UGUCGC AACAGC,AACCUU,AACUAA,AAUACC,AAUUUA,ACACCA,ACAGCA,ACAUUA,ACCACG,ACCAGA,ACCUUG,ACUAAC,ACUAAG,ACUAGA,ACUAGC,ACUAGG,ACUGCA,ACUUUA,AGAUAU,AGUAGC,AGUAGG,AUACCA,AUCUGA,AUGCGC,AUUAGC,AUUAGG,CACCAG,CACGCA,CACUAG,CAUUAG,CCACGC,CCAGAC,CCUUGC,CCUUUA,CGAGCA,CUAACA,CUAACU,CUAAGC,CUAAGU,CUAGAG,CUAGAU,CUAGCA,CUAGCC,CUAGCG,CUAGCU,CUAGGA,CUAGGC,CUAGUA,CUUGCC,CUUUAA,CUUUAG,GAACUA,GACUAG,GAGUAG,GAUUAG,GCACUA,GCGAGC,GCUAGU,GGACUA,GGAGUA,GGAUUA,GUAGCC,GUAGCU,UAACAG,UAAGUA,UAGGCA,UCUGAC,UGCGCA,UGUCGC,UUAGCC,UUAGGC,UUUAGG
U2AF2 1 1477 0.004796163 0.0021419234 1.162974 UUUUCC UUUUCC,UUUUUC,UUUUUU
CELF6 3 2997 0.009592326 0.0043447134 1.142620 GUGUGG,UGUGGG,UGUGGU GUGAGG,GUGAUG,GUGGGG,GUGGUG,GUGUGG,GUGUUG,UGUGAG,UGUGAU,UGUGGG,UGUGGU,UGUGUG,UGUGUU
TRA2A 8 6871 0.021582734 0.0099589296 1.115815 AAAGAA,AAGAAA,AAGAGG,AGAAGA,AGAGGA,GAAGAG,GAGGAA AAAGAA,AAGAAA,AAGAAG,AAGAGG,AGAAAG,AGAAGA,AGAGGA,AGGAAG,GAAAGA,GAAGAA,GAAGAG,GAGGAA
ENOX1 3 3195 0.009592326 0.0046316558 1.050353 AGUACA,CAGACA,GUACAG AAGACA,AAUACA,AGACAG,AGGACA,AGUACA,AUACAG,CAGACA,CAUACA,CGGACA,CGUACA,GGACAG,GUACAG,UAGACA,UAUACA,UGGACA,UGUACA
RBMX 5 4925 0.014388489 0.0071387787 1.011166 AAGUAA,ACCAAA,AGUAAC,GUAACA,UCAAAA AAGAAG,AAGGAA,AAGUAA,AAGUGU,ACCAAA,AGAAGG,AGGAAG,AGUAAC,AGUGUU,AUCAAA,AUCCCA,AUCCCC,GAAGGA,GGAAGG,GUAACA,UAACAA,UAAGAC,UCAAAA
SF1 5 4931 0.014388489 0.0071474739 1.009410 ACAGAC,ACAGUC,AGUAAC,CACAGA,CACCGA ACAGAC,ACAGUC,ACCGAC,ACGAAC,ACUAAC,ACUAAG,ACUAAU,ACUAGC,ACUGAC,ACUUAU,AGUAAC,AGUAAG,AUACUA,AUUAAC,CACAGA,CACCGA,CACUGA,CAGUCA,CGCUGA,CUAACA,GACUAA,GCUAAC,GCUGAC,GCUGCC,UAACAA,UACGAA,UACUAA,UACUAG,UACUGA,UAGUAA,UAUACU,UGCUAA,UGCUGA,UGCUGC

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
ELAVL2 1 28 0.09090909 0.001899397 5.580811 GAUUUU AAUUUA,AAUUUU,AUAUUU,AUUUAA,AUUUUG,CUUUCU,GAUUUU,GUAUUG,GUUUUU,UACUUU,UAGUUA,UAUAUA,UAUAUU,UAUGUU,UAUUGA,UAUUUU,UGUAUU,UUAAGU,UUACUU,UUAGUU,UUAUUG,UUUACU,UUUAGU,UUUCUU,UUUUAG

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 UGCAUG UGACUG,UGCAUG
MATR3 2 216 0.007142857 0.0010933091 2.707800 AAUCUU,AUCUUA AAUCUU,AUCUUA,AUCUUG,CAUCUU
RBMS1 2 217 0.007142857 0.0010983474 2.701167 AUAUAG,GAUAUA AUAUAC,AUAUAG,GAUAUA,UAUAUA
EIF4B 2 226 0.007142857 0.0011436921 2.642803 UUGGAA CUCGGA,CUUGGA,GUCGGA,GUUGGA,UCGGAA,UCGGAC,UUGGAA,UUGGAC
RBFOX1 2 287 0.007142857 0.0014510278 2.299426 GCAUGC,UGCAUG AGCAUG,GCAUGA,GCAUGC,GCAUGU,UGACUG,UGCAUG
A1CF 5 598 0.014285714 0.0030179363 2.242939 AUCAGU,GAUCAG,UAAUUA,UUAAUU AGUAUA,AUAAUU,AUCAGU,CAGUAU,GAUCAG,UAAUUA,UAAUUG,UCAGUA,UGAUCA,UUAAUU
HNRNPA0 1 200 0.004761905 0.0010126965 2.233337 AAUUUA AAUUUA,AGAUAU,AGUAGG
RBM3 4 541 0.011904762 0.0027307537 2.124168 AAAACU,AGACUA,GAGACU AAAACG,AAAACU,AAACGA,AAACUA,AAGACG,AAGACU,AAUACG,AAUACU,AGACGA,AGACUA,AUACGA,AUACUA,GAAACG,GAAACU,GAGACG,GAGACU,GAUACG,GAUACU
ACO1 2 325 0.007142857 0.0016424829 2.120623 CAGUGG,CAGUGU CAGUGA,CAGUGC,CAGUGG,CAGUGU
ERI1 1 228 0.004761905 0.0011537686 2.045185 UUCAGA UUCAGA,UUUCAG
ZNF638 4 646 0.011904762 0.0032597743 1.868695 CGUUCU,GUUCUU,GUUGUU,UGUUGU CGUUCG,CGUUCU,CGUUGG,CGUUGU,GGUUCG,GGUUCU,GGUUGG,GGUUGU,GUUCGU,GUUCUU,GUUGGU,GUUGUU,UGUUCG,UGUUCU,UGUUGG,UGUUGU
RBMS3 3 562 0.009523810 0.0028365578 1.747397 AUAUAG,CUAUAU,UAUAUC AAUAUA,AUAUAG,AUAUAU,CAUAUA,CUAUAG,CUAUAU,UAUAGA,UAUAGC,UAUAUA,UAUAUC
QKI 5 904 0.014285714 0.0045596534 1.647577 ACUAAU,CACUAA,CUAAUC,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
PABPC3 1 310 0.004761905 0.0015669085 1.603618 GAAAAC AAAAAC,AAAACA,AAAACC,GAAAAC
ZCRB1 3 666 0.009523810 0.0033605401 1.502846 AAUUAA,AUUUAA AAUUAA,ACUUAA,AUUUAA,GAAUUA,GACUUA,GAUUAA,GAUUUA,GCUUAA,GGAUUA,GGCUUA,GGUUUA,GUUUAA
SSB 2 505 0.007142857 0.0025493753 1.486358 UGUUUU CUGUUU,GCUGUU,UGCUGU,UGUUUU
RBM28 1 340 0.004761905 0.0017180572 1.470761 AGUAGU AGUAGA,AGUAGG,AGUAGU,GAGUAG,GUGUAG,UGUAGA,UGUAGG,UGUAGU
CSTF2 5 1022 0.014285714 0.0051541717 1.470761 GUGUUG,GUGUUU,UGUUUG,UGUUUU GUGUGU,GUGUUG,GUGUUU,GUUUUG,UGUGUG,UGUGUU,UGUUUG,UGUUUU
HNRNPA3 1 349 0.004761905 0.0017634019 1.433177 AGGAGC AAGGAG,AGGAGC,CAAGGA,CCAAGG,GCCAAG,GGAGCC
CELF2 4 881 0.011904762 0.0044437727 1.421682 GUAUGU,GUUGUU,UAUGUU,UGUUGU AUGUGU,GUAUGU,GUCUGU,GUGUGU,GUUGUU,UAUGUG,UAUGUU,UGUGUG,UGUUGU,UUGUGU
CELF4 3 776 0.009523810 0.0039147521 1.282618 GGUGUU,GUGUUG,GUGUUU GGUGUG,GGUGUU,GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU
PABPC5 2 596 0.007142857 0.0030078597 1.247764 AGAAAU,GAAAUU AGAAAA,AGAAAG,AGAAAU,GAAAAU,GAAAGU,GAAAUU
YTHDC1 5 1254 0.014285714 0.0063230552 1.175879 GAGUAC,GCAUGC,UAGUAC,UAGUGC,UGCUAC GAAUAC,GAAUGC,GACUAC,GACUGC,GAGUAC,GAGUGC,GCAUAC,GCAUGC,GCCUAC,GCCUGC,GCGUAC,GCGUGC,GGAUAC,GGAUGC,GGCUAC,GGCUGC,GGGUAC,GGGUGC,UAAUAC,UAAUGC,UACUAC,UACUGC,UAGUAC,UAGUGC,UCAUAC,UCAUGC,UCCUAC,UCCUGC,UCGUAC,UCGUGC,UGAUAC,UGAUGC,UGCUAC,UGCUGC,UGGUAC,UGGUGC
CELF5 2 669 0.007142857 0.0033756550 1.081334 GUGUUG,GUGUUU GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU
TIA1 22 5140 0.054761905 0.0259018541 1.080117 AUUUUC,AUUUUU,CUCCUU,CUUUUA,GUUUUA,GUUUUC,GUUUUU,UAUUUU,UUUAUU,UUUUCU,UUUUGU,UUUUUA,UUUUUC,UUUUUG,UUUUUU AUUUUC,AUUUUG,AUUUUU,CCUUUC,CUCCUU,CUUUUA,CUUUUC,CUUUUG,CUUUUU,GUUUUA,GUUUUC,GUUUUG,GUUUUU,UAUUUU,UCCUUU,UCUCCU,UUAUUU,UUCUCC,UUUAUU,UUUUAU,UUUUCG,UUUUCU,UUUUGG,UUUUGU,UUUUUA,UUUUUC,UUUUUG,UUUUUU
RALY 4 1117 0.011904762 0.0056328094 1.079612 UUUUUC,UUUUUG,UUUUUU UUUUUC,UUUUUG,UUUUUU
HNRNPCL1 5 1381 0.014285714 0.0069629182 1.036809 AUUUUU,UUUUUG,UUUUUU AUUUUU,CUUUUU,UUUUUG,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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