ENSG00000099203:-:19:10834933:10836430

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000099203:-:19:10834933:10836430 ENSG00000099203 MSTRG.16429.1 - 19 10834934 10836430 704 CGGCCGAGAAGAGAGCCGAAGCCUUUGAGAAAAAUAUUCCCAGACGGUUGAGUGUUUCUGGGCACAUCAGGCAUUCAUUCGGGCCGCCUGCCCUCUAGUGGGGGGGUCCUUCACUCCUGGCACCUCUGGUUACGGACAACAUACAGAAGCCACUGCCAAUGAGCUCCGCCGAGUAGCACCGGGGCAGGGCUAGCGCUUAAAGGAGCCGCGACCCCUUUGCAGACCAGAGGGUGACCCGGAUGAUGGCGGCCGGCGCGGCCCUAGCCCUGGCCUUGUGGCUACUAAUGCCACCAGUGGAGGUGGGAGGGGCGGGGCCCCCGCCAAUCCAGGACGGUGAGUUCACGUUCCUGUUGCCGGCGGGGAGGAAGCAGUGUUUCUACCAGUCCGCGCCGGCCAACGCAAGCCUCGAGACCGAAUACCAGGUGAUCGGAGGUGCUGGACUGGACGUGGACUUCACGCUGGAGAGCCCUCAGGGCGUGCUGUUGGUCAGCGAGUCCCGCAAGGCUGAUGGGGUACACACGGUGGAGCCAACGGAGGCCGGGGACUACAAGCUGUGCUUUGACAACUCCUUCAGCACCAUCUCCGAGAAGCUGGUGUUCUUUGAACUGAUCUUUGACAGCCUCCAGGAUGACGAGGAGGUCGAAGGAUGGGCAGAGGCUGUGGAGCCCGAGGAGAUGCUGGAUGUUAAAAUGGAGGACAUCAAGCGGCCGAGAAGAGAGCCGAAGCCUUUGAGAAAAAUAUUCCCAGACGGUUG circ
ENSG00000099203:-:19:10834933:10836430 ENSG00000099203 MSTRG.16429.1 - 19 10834934 10836430 22 AGGACAUCAAGCGGCCGAGAAG bsj
ENSG00000099203:-:19:10834933:10836430 ENSG00000099203 MSTRG.16429.1 - 19 10836421 10836630 210 CAGGGCCACGCCUAGACGCUAUUUUUGGGUCCACUCCACCACGUCGGUCCCGCCAAAGGUUGUCACGCGCGGCGCACUCUGGGAAAACCACGUGGAGGUGACUAAAAAGGACCCUGCCGCCUGUAACUUUAGUUGUCUUAGCUACUGCCUACAAAAGAUGCGCCAUCAUGGCACUUAUUUUUGUAAUUUUCCUCCACCAGCGGCCGAGAA ie_up
ENSG00000099203:-:19:10834933:10836430 ENSG00000099203 MSTRG.16429.1 - 19 10834734 10834943 210 GGACAUCAAGGUGUGUCCAGGCUGCGCUGGGGCCACUCCUUCCAGAUCUCUAGGAUUCACCUGGGGUGCCCCCCUUGGGCUGACCCAGCCUCCCCUCCGUAGUUGUGCCCUCCAACUGAAUUAUAGUAAGAGUAGCAGCUCUUAAAAUAAGUAGUUCAUUUCAGGCCGGGCACGGUGGCUCACGCCUGUAAUCCCAGCACUUUGGGAGGC 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
RBM14 3 478 0.005681818 0.0006941687 3.032994 CGCGCC,CGCGGC,GCGCGG CGCGCC,CGCGCG,CGCGGC,CGCGGG,GCGCGC,GCGCGG
RBM25 1 268 0.002840909 0.0003898359 2.865414 UCGGGC AUCGGG,CGGGCA,UCGGGC
PPRC1 4 780 0.007102273 0.0011318283 2.649626 CCGCGC,CGCGCC,CGGCGC,GGCGCG CCGCGC,CGCGCC,CGCGCG,CGGCGC,GCGCGC,GGCGCC,GGCGCG,GGGCGC
IFIH1 4 904 0.007102273 0.0013115296 2.437030 GCCGCG,GGCCCU,GGCCGC,GGGCCG CCGCGG,CGCGGA,GCCGCG,GCGGAU,GGCCCU,GGCCGC,GGGCCG
FXR1 1 411 0.002840909 0.0005970720 2.250376 AUGACG ACGACA,ACGACG,AUGACA,AUGACG
HNRNPM 3 999 0.005681818 0.0014492040 1.971092 GAAGGA,GGGGGG AAGGAA,GAAGGA,GGGGGG
G3BP2 5 1644 0.008522727 0.0023839405 1.837967 AGGAUG,GGAUGA,GGAUGG AGGAUA,AGGAUG,AGGAUU,GGAUAA,GGAUAG,GGAUGA,GGAUGG,GGAUUA,GGAUUG
IGF2BP1 2 831 0.004261364 0.0012057377 1.821399 AGCACC AAGCAC,ACCCGU,AGCACC,CACCCG,CCCGUU,GCACCC
YBX2 4 1480 0.007102273 0.0021462711 1.726448 ACAACA,ACAACU,ACAUCA AACAAC,AACAUC,ACAACA,ACAACG,ACAACU,ACAUCA,ACAUCG,ACAUCU
RBM8A 1 611 0.002840909 0.0008869128 1.679488 CGCGCC ACGCGC,AUGCGC,CGCGCC,CGCGCG,CGCGCU,GCGCGC,GUGCGC,UGCGCC,UGCGCG,UGCGCU
RBM6 2 1054 0.004261364 0.0015289102 1.478812 AAUCCA,AUCCAG AAUCCA,AUCCAA,AUCCAG,CAUCCA,UAUCCA
ZNF638 4 1773 0.007102273 0.0025708878 1.466014 GUUCUU,GUUGGU,UGUUCU,UGUUGG CGUUCG,CGUUCU,CGUUGG,CGUUGU,GGUUCG,GGUUCU,GGUUGG,GGUUGU,GUUCGU,GUUCUU,GUUGGU,GUUGUU,UGUUCG,UGUUCU,UGUUGG,UGUUGU
HNRNPA3 5 2140 0.008522727 0.0031027457 1.457770 AAGGAG,AGGAGC,GGAGCC AAGGAG,AGGAGC,CAAGGA,CCAAGG,GCCAAG,GGAGCC
LIN28A 10 4315 0.015625000 0.0062547643 1.320829 AGGAGA,CGGAGG,GGAGAU,GGAGGA,GGAGGG,UGGAGA,UGGAGG AGGAGA,AGGAGU,CGGAGA,CGGAGG,CGGAGU,GGAGAA,GGAGAU,GGAGGA,GGAGGG,GGAGUA,UGGAGA,UGGAGG,UGGAGU
SAMD4A 9 3992 0.014204545 0.0057866714 1.295547 CGGGCC,CUGGAC,CUGGCA,CUGGCC,GCUGGA,GCUGGU CGGGAA,CGGGAC,CGGGCA,CGGGCC,CGGGUA,CGGGUC,CUGGAA,CUGGAC,CUGGCA,CUGGCC,CUGGUA,CUGGUC,GCGGGA,GCGGGC,GCGGGU,GCUGGA,GCUGGC,GCUGGU
RBM28 1 822 0.002840909 0.0011926949 1.252128 GAGUAG AGUAGA,AGUAGG,AGUAGU,GAGUAG,GUGUAG,UGUAGA,UGUAGG,UGUAGU
SSB 2 1260 0.004261364 0.0018274462 1.221486 GCUGUU,UGCUGU CUGUUU,GCUGUU,UGCUGU,UGUUUU
SRP14 1 847 0.002840909 0.0012289250 1.208956 CGCCUG CCUGUA,CGCCUG,CUGUAG,GCCUGU
ACO1 2 1283 0.004261364 0.0018607779 1.195409 CAGUGG,CAGUGU CAGUGA,CAGUGC,CAGUGG,CAGUGU
FXR2 7 3434 0.011363636 0.0049780156 1.190782 AGACGG,GACGAG,GGACAA,GGACGG,UGACAA,UGACAG,UGACGA AGACAA,AGACAG,AGACGA,AGACGG,GACAAA,GACAAG,GACAGA,GACAGG,GACGAA,GACGAG,GACGGA,GACGGG,GGACAA,GGACAG,GGACGA,GGACGG,UGACAA,UGACAG,UGACGA,UGACGG
NOVA1 8 3872 0.012784091 0.0056127669 1.187566 AGCACC,AUUCAU,CAUUCA,GGGGGG,UCAUUC,UUCAUU AACACC,ACCACC,AGCACC,AGUCAC,AUCAAC,AUCACC,AUCAUC,AUUCAU,CAGUCA,CAUUCA,CCCCCC,GGGGGG,UCAGUC,UCAUUC,UUCAUU,UUUUUU
CELF4 3 1782 0.005681818 0.0025839306 1.136785 GGUGUU,GUGUUU GGUGUG,GGUGUU,GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU
CELF5 2 1415 0.004261364 0.0020520728 1.054233 GUGUUU GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
FMR1 2 117 0.13636364 0.007728583 4.141111 AAGCGG,AGCGGC AAAAAA,AAGGAA,AAGGAU,AAGGGA,ACUGGG,ACUGGU,AGCAGC,AGCGAA,AGGAAG,AGGAAU,AGGAGG,AGGAGU,AGGAUG,AGGAUU,AGGCAC,AGGGAG,AGUGGC,AUGGAG,CAGCUG,CUAUGG,CUGAGG,CUGGGC,CUGGUG,GAAGGA,GAAGGG,GACAAG,GACAGG,GAGGAU,GCAGCU,GCAUAG,GCGAAG,GCUAAG,GCUGAG,GCUGGG,GGACAA,GGACAG,GGCAUA,GGCUGA,GGCUGG,GGGCAU,GGGCUA,GGGCUG,GUGCGA,GUGGCU,UAAGGA,UAGUGG,UAUGGA,UGACAA,UGACAG,UGAGGA,UGCGGC,UGGAGU,UGGCUG
SRSF2 1 479 0.09090909 0.031438302 1.531901 AAGCGG 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 3 53 0.009523810 0.0002720677 5.129501 CGCGCG,CGCGGC,GCGCGG CGCGCC,CGCGCG,CGCGGC,CGCGGG,GCGCGC,GCGCGG
RBM8A 5 84 0.014285714 0.0004282547 5.059960 ACGCGC,AUGCGC,CGCGCG,UGCGCC,UGCGCU ACGCGC,AUGCGC,CGCGCC,CGCGCG,CGCGCU,GCGCGC,GUGCGC,UGCGCC,UGCGCG,UGCGCU
RBM25 1 53 0.004761905 0.0002720677 4.129501 CGGGCA AUCGGG,CGGGCA,UCGGGC
SRP14 6 218 0.016666667 0.0011033857 3.916956 CCUGUA,CGCCUG,GCCUGU CCUGUA,CGCCUG,CUGUAG,GCCUGU
PPRC1 2 127 0.007142857 0.0006449012 3.469351 CGCGCG,CGGCGC CCGCGC,CGCGCC,CGCGCG,CGGCGC,GCGCGC,GGCGCC,GGCGCG,GGGCGC
ZC3H10 1 140 0.004761905 0.0007103990 2.744837 CCAGCG CAGCGA,CAGCGC,CCAGCG,CGAGCG,GAGCGA,GAGCGC,GCAGCG,GGAGCG
PABPN1 1 178 0.004761905 0.0009018541 2.400573 AAAAGA AAAAGA,AGAAGA
PABPC3 2 310 0.007142857 0.0015669085 2.188580 AAAACC,GAAAAC AAAAAC,AAAACA,AAAACC,GAAAAC
RBM28 2 340 0.007142857 0.0017180572 2.055723 AGUAGU,GAGUAG AGUAGA,AGUAGG,AGUAGU,GAGUAG,GUGUAG,UGUAGA,UGUAGG,UGUAGU
ERI1 1 228 0.004761905 0.0011537686 2.045185 UUUCAG UUCAGA,UUUCAG
SNRNP70 1 253 0.004761905 0.0012797259 1.895704 AUCAAG AAUCAA,AUCAAG,AUUCAA,GAUCAA,GUUCAA,UUCAAG
YBX2 1 263 0.004761905 0.0013301088 1.839994 ACAUCA AACAAC,AACAUC,ACAACA,ACAACG,ACAACU,ACAUCA,ACAUCG,ACAUCU
YBX1 8 1321 0.021428571 0.0066606207 1.685807 AACCAC,ACAUCA,CACCAC,CAUCAU,CCACCA,CCAGCA,CCCUGC 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
MSI1 4 961 0.011904762 0.0048468360 1.296424 AGUAAG,UAGUAA,UAGUUG AGGAAG,AGGAGG,AGGUAG,AGGUGG,AGUAAG,AGUAGG,AGUUAG,AGUUGG,UAGGAA,UAGGAG,UAGGUA,UAGGUG,UAGUAA,UAGUAG,UAGUUA,UAGUUG
SF1 5 1294 0.014285714 0.0065245869 1.130615 ACUUAU,AGUAAG,GACUAA,GCUGAC,UAGUAA 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
RBM4 4 1094 0.011904762 0.0055169287 1.109602 CCUUCC,CGCGCG,GCGCGG,UCCUUC CCUCUU,CCUUCC,CCUUCU,CGCGCG,CGCGGG,CGCGGU,CUCUUU,CUUCCU,CUUCUU,GCGCGA,GCGCGC,GCGCGG,UCCUUC,UUCCUU,UUCUUG
HNRNPDL 11 2689 0.028571429 0.0135530028 1.075961 ACCACG,ACUUUA,AGUAGC,AUGCGC,CACCAG,CCACGC,CUAGGA,CUUUAG,GAGUAG,UAAGUA 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
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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