ENSG00000136813:-:9:111386376:111391824

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000136813:-:9:111386376:111391824 ENSG00000136813 ENST00000259335 - 9 111386377 111391824 435 AGUUAAACAUGAAGUUUCUGGAGAGACAGUGGUAUUUCAAGGGGGAGCUCUUGGCAAAACACCAGAUGGUCAGGGCCUUUCUACUUACAAGGAACUUUGUUCUCUGGCAAGUGAUCUUAGCCAGCCAGAUCUGGUGUAUAAAUUUAUGAAUUUAGCCAACCAUCAUGCAAUGUGGAACUCUAGGAAGGGUGCUGCUUUUGGUUUUAAUGUAAUUGCUACCAGAGCUGGAGAGCAGCUGGCUCCUUUUCUGCCUCAGCUAGUUCCUCGACUUUAUCGUUACCAGUUUGAUCCCAACCUUGGCAUUCGACAGGCCAUGACAAGUAUUUGGAAUGCGUUGGUCACUGACAAAUCCAUGGUGGAUAAAUAUUUGAAAGAAAUUCUUCAAGAUUUGGUUAAGAACCUUACAAGCAAUAUGUGGCGAGUUCGAGAAUCCAGAGUUAAACAUGAAGUUUCUGGAGAGACAGUGGUAUUUCAAGGGGGAGCUC circ
ENSG00000136813:-:9:111386376:111391824 ENSG00000136813 ENST00000259335 - 9 111386377 111391824 22 CGAGAAUCCAGAGUUAAACAUG bsj
ENSG00000136813:-:9:111386376:111391824 ENSG00000136813 ENST00000259335 - 9 111391815 111392024 210 UAGUGAUCCACCCACCUCGGCCUCCCAAAGUGCUGGGAUUAUAGGUGUGAGCCACCGCGCCCGGCCGGAAAGGACUUUUAUAUCUUGUACACAGUAAAUGCUUGAUAGGAAGUUUUAUCACUUUGUAAAUGAAUCGUAUUGGCUAGUUGAAUGUUGGUAUGAAAAGCUUGAAGCUUAUUGAAAUUAUUGUUUUGGUUUAGAGUUAAACAU ie_up
ENSG00000136813:-:9:111386376:111391824 ENSG00000136813 ENST00000259335 - 9 111386177 111386386 210 GAGAAUCCAGGUACCGUUUUUAGGAAUAUAAGUUUAGUCAAAUAAAACUGAAUUUUUUUCCCUUCAAAAUUUCUAGGUUUUAUACUUUGUGCAAAAGGAAUAAAUUAAAACUACUAAAAAGCUGGCCGGGCGUGGUGGCUCACACCUGUGAUCCCAGCACAUGGGGAGGCUGAGGUGGGUGGAUCACCUGAGGUGAGGAGUUCAAGACCA 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 2 453 0.006896552 0.0006579386 3.389850 AAUUUA AAUUUA,AGAUAU,AGUAGG
FXR1 1 411 0.004597701 0.0005970720 2.944936 AUGACA ACGACA,ACGACG,AUGACA,AUGACG
RBM6 3 1054 0.009195402 0.0015289102 2.588409 AAUCCA,AUCCAG AAUCCA,AUCCAA,AUCCAG,CAUCCA,UAUCCA
MATR3 1 739 0.004597701 0.0010724109 2.100055 AUCUUA AAUCUU,AUCUUA,AUCUUG,CAUCUU
SNRNP70 2 1237 0.006896552 0.0017941145 1.942603 UUCAAG AAUCAA,AUCAAG,AUUCAA,GAUCAA,GUUCAA,UUCAAG
NELFE 6 3028 0.016091954 0.0043896388 1.874165 CUCUGG,CUGGCU,UCUCUG,UCUGGC,UCUGGU,UGGUUA CUCUCU,CUCUGG,CUGGCU,CUGGUU,GCUAAC,GGCUAA,GGUCUC,GGUUAG,GUCUCU,UCUCUC,UCUCUG,UCUGGC,UCUGGU,UGGCUA,UGGUUA
ZNF638 3 1773 0.009195402 0.0025708878 1.838646 CGUUGG,GUUGGU,UGUUCU CGUUCG,CGUUCU,CGUUGG,CGUUGU,GGUUCG,GGUUCU,GGUUGG,GGUUGU,GUUCGU,GUUCUU,GUUGGU,GUUGUU,UGUUCG,UGUUCU,UGUUGG,UGUUGU
FXR2 6 3434 0.016091954 0.0049780156 1.692697 AGACAG,GACAAA,GACAAG,GACAGG,UGACAA AGACAA,AGACAG,AGACGA,AGACGG,GACAAA,GACAAG,GACAGA,GACAGG,GACGAA,GACGAG,GACGGA,GACGGG,GGACAA,GGACAG,GGACGA,GGACGG,UGACAA,UGACAG,UGACGA,UGACGG
HNRNPM 1 999 0.004597701 0.0014492040 1.665652 AAGGAA AAGGAA,GAAGGA,GGGGGG
HNRNPDL 14 8759 0.034482759 0.0126950266 1.441612 AACCUU,AAUUUA,ACACCA,ACCAGA,ACCUUG,ACUUUA,CACCAG,CUAGGA,GCUAGU,UUAGCC 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
EIF4B 1 1179 0.004597701 0.0017100607 1.426865 UUGGAA CUCGGA,CUUGGA,GUCGGA,GUUGGA,UCGGAA,UCGGAC,UUGGAA,UUGGAC
PABPC3 1 1234 0.004597701 0.0017897669 1.361141 AAAACA AAAAAC,AAAACA,AAAACC,GAAAAC
PUM2 2 1890 0.006896552 0.0027404447 1.331465 UAAAUA,UGUAUA GUAAAU,GUACAU,GUAGAU,GUAUAU,UAAAUA,UACAUA,UACAUC,UAGAUA,UAUAUA,UGUAAA,UGUACA,UGUAGA,UGUAUA
ZFP36L2 1 1277 0.004597701 0.0018520827 1.311764 AUUUAU AUUUAU,UAUUUA,UUAUUU,UUUAUU
ACO1 1 1283 0.004597701 0.0018607779 1.305007 CAGUGG CAGUGA,CAGUGC,CAGUGG,CAGUGU
ELAVL1 7 5554 0.018390805 0.0080503280 1.191865 AUUUAU,UGGUUU,UUGGUU,UUUGGU,UUUGUU AUUUAU,CCCCCC,UAGUUU,UAUUUA,UAUUUU,UGAUUU,UGGUUU,UGUUUU,UUAGUU,UUAUUU,UUGAUU,UUGGUU,UUGUUU,UUUAGU,UUUAUU,UUUGGU,UUUGUU,UUUUUG,UUUUUU
HNRNPD 3 2837 0.009195402 0.0041128408 1.160777 AAUUUA,AUUUAU AAAAAA,AAUUUA,AGAUAU,AGUAGG,AUUUAU,UAUUUA,UUAGAG,UUAGGA,UUAGGG,UUAUUU,UUUAUU
PUM1 7 5823 0.018390805 0.0084401638 1.123642 AAUAUU,UAAAUA,UAAUGU,UGUAAU,UGUAUA,UUAAUG,UUUAAU AAUAUU,AAUGUU,AAUUGU,ACAUAA,AGAAUU,AGAUAA,AUUGUA,CAGAAU,CCAGAA,CUUGUA,GAAUUG,GUAAAU,GUAAUA,GUACAU,GUAGAU,GUAUAU,GUCCAG,UAAAUA,UAAUAU,UAAUGU,UACAUA,UACAUC,UAGAUA,UAUAUA,UGUAAA,UGUAAU,UGUACA,UGUAGA,UGUAUA,UGUCCA,UUAAUG,UUGUAC,UUGUAG,UUUAAU
NONO 1 1498 0.004597701 0.0021723567 1.081652 AGGAAC AGAGGA,AGGAAC,GAGAGG,GAGGAA

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
SRSF2 3 479 0.1818182 0.0314383 2.531901 AGAGUU,CAGAGU,UCCAGA 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
RBM14 1 53 0.004761905 0.0002720677 4.129501 CGCGCC CGCGCC,CGCGCG,CGCGGC,CGCGGG,GCGCGC,GCGCGG
RBM8A 1 84 0.004761905 0.0004282547 3.474998 CGCGCC ACGCGC,AUGCGC,CGCGCC,CGCGCG,CGCGCU,GCGCGC,GUGCGC,UGCGCC,UGCGCG,UGCGCU
PPRC1 2 127 0.007142857 0.0006449012 3.469351 CCGCGC,CGCGCC CCGCGC,CGCGCC,CGCGCG,CGGCGC,GCGCGC,GGCGCC,GGCGCG,GGGCGC
RBMY1A1 1 95 0.004761905 0.0004836759 3.299426 CAAGAC ACAAGA,CAAGAC
RBM42 1 103 0.004761905 0.0005239823 3.183949 AACUAC AACUAA,AACUAC,ACUAAG,ACUACG
RBM6 2 191 0.007142857 0.0009673519 2.884389 AAUCCA,AUCCAG AAUCCA,AUCCAA,AUCCAG,CAUCCA,UAUCCA
SNRNP70 2 253 0.007142857 0.0012797259 2.480666 GUUCAA,UUCAAG AAUCAA,AUCAAG,AUUCAA,GAUCAA,GUUCAA,UUCAAG
AGO1 2 283 0.007142857 0.0014308746 2.319604 UGAGGU AGGUAG,GAGGUA,GGUAGU,GUAGUA,UGAGGU
MATR3 1 216 0.004761905 0.0010933091 2.122837 AUCUUG AAUCUU,AUCUUA,AUCUUG,CAUCUU
HNRNPM 1 222 0.004761905 0.0011235389 2.083489 AAGGAA AAGGAA,GAAGGA,GGGGGG
RBM3 3 541 0.009523810 0.0027307537 1.802240 AAAACU,AAACUA AAAACG,AAAACU,AAACGA,AAACUA,AAGACG,AAGACU,AAUACG,AAUACU,AGACGA,AGACUA,AUACGA,AUACUA,GAAACG,GAAACU,GAGACG,GAGACU,GAUACG,GAUACU
MSI1 6 961 0.016666667 0.0048468360 1.781850 AGGAAG,AGGUGG,UAGGAA,UAGGUG,UAGUUG AGGAAG,AGGAGG,AGGUAG,AGGUGG,AGUAAG,AGUAGG,AGUUAG,AGUUGG,UAGGAA,UAGGAG,UAGGUA,UAGGUG,UAGUAA,UAGUAG,UAGUUA,UAGUUG
SNRPB2 1 288 0.004761905 0.0014560661 1.709463 GUAUUG AUUGCA,GUAUUG,UAUUGC,UGCAGU,UUGCAG
KHDRBS3 10 1646 0.026190476 0.0082980653 1.658195 AAAUAA,AAUAAA,AUAAAA,AUUAAA,UAAAAC,UUAAAC,UUUUUU AAAUAA,AAUAAA,AGAUAA,AUAAAA,AUAAAC,AUAAAG,AUUAAA,GAUAAA,UAAAAC,UAAAUA,UUAAAC,UUUUUU
PUM2 4 764 0.011904762 0.0038542926 1.627001 GUAAAU,UGUAAA,UGUACA GUAAAU,GUACAU,GUAGAU,GUAUAU,UAAAUA,UACAUA,UACAUC,UAGAUA,UAUAUA,UGUAAA,UGUACA,UGUAGA,UGUAUA
ZCRB1 3 666 0.009523810 0.0033605401 1.502846 AAUUAA,GGAUUA,GGUUUA AAUUAA,ACUUAA,AUUUAA,GAAUUA,GACUUA,GAUUAA,GAUUUA,GCUUAA,GGAUUA,GGCUUA,GGUUUA,GUUUAA
RBM41 2 502 0.007142857 0.0025342604 1.494937 AUACUU,UACUUU AUACAU,AUACUU,UACAUG,UACAUU,UACUUG,UACUUU,UUACAU,UUACUU
AGO2 3 677 0.009523810 0.0034159613 1.479247 AAAGUG,AAGUGC,AGUGCU AAAAAA,AAAGUG,AAGUGC,AGUGCU,GUGCUU,UAAAGU
KHDRBS2 5 1051 0.014285714 0.0053002821 1.430432 AAUAAA,AUAAAA,UUUUUU AAUAAA,AUAAAA,AUAAAC,GAUAAA,UUUUUU
RBMS3 2 562 0.007142857 0.0028365578 1.332360 AAUAUA,UAUAUC AAUAUA,AUAUAG,AUAUAU,CAUAUA,CUAUAG,CUAUAU,UAUAGA,UAUAGC,UAUAUA,UAUAUC
KHDRBS1 9 1945 0.023809524 0.0098045143 1.280021 AUAAAA,CAAAAU,CUAAAA,UAAAAA,UAAAAC,UUAAAA,UUUUUU AUAAAA,AUUUAA,AUUUAC,CAAAAU,CUAAAA,CUAAAU,GAAAAC,UAAAAA,UAAAAC,UAAAAG,UUAAAA,UUAAAU,UUUUAC,UUUUUU
TARDBP 4 1034 0.011904762 0.0052146312 1.190902 GAAUGU,GUUUUG,UGAAUG,UUGUGC GAAUGA,GAAUGG,GAAUGU,GUGAAU,GUGUGU,GUUGUG,GUUGUU,GUUUUG,UGAAUG,UGUGUG,UUGUGC,UUGUUC,UUUUGC
RC3H1 2 631 0.007142857 0.0031841999 1.165570 CCCUUC,UCCCUU CCCUUC,CCUUCU,CUUCUG,UCCCUU,UCUGUG,UUCUGU
U2AF2 4 1071 0.011904762 0.0054010480 1.140228 UUUUCC,UUUUUC,UUUUUU UUUUCC,UUUUUC,UUUUUU
ZNF638 2 646 0.007142857 0.0032597743 1.131729 GUUGGU,UGUUGG CGUUCG,CGUUCU,CGUUGG,CGUUGU,GGUUCG,GGUUCU,GGUUGG,GGUUGU,GUUCGU,GUUCUU,GUUGGU,GUUGUU,UGUUCG,UGUUCU,UGUUGG,UGUUGU
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
PABPC4 1 462 0.004761905 0.0023327287 1.029520 AAAAAG AAAAAA,AAAAAG

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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