ENSG00000157985:+:2:236049058:236049281

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000157985:+:2:236049058:236049281 ENSG00000157985 ENST00000409538 + 2 236049059 236049281 223 AUCCCAACUGGGCCAGUUUGAACUUGGGAGCCCUCAUGUGCAUCGAAUGCUCAGGGAUCCACCGGAAUCUUGGCACCCACCUUUCCCGAGUCCGAUCUCUGGACCUGGAUGACUGGCCAGUCGAGCUCAUCAAGGUGAUGUCAUCCAUCGGGAACGAGCUAGCCAACAGCGUCUGGGAAGAGAGCAGCCAGGGGCGGACGAAACCAUCGGUAGACUCCACAAGAUCCCAACUGGGCCAGUUUGAACUUGGGAGCCCUCAUGUGCAUCGAAUGC circ
ENSG00000157985:+:2:236049058:236049281 ENSG00000157985 ENST00000409538 + 2 236049059 236049281 22 GACUCCACAAGAUCCCAACUGG bsj
ENSG00000157985:+:2:236049058:236049281 ENSG00000157985 ENST00000409538 + 2 236048859 236049068 210 UUCUGAAGCUACUACCAACGGCCAGUCAUUUGGGACACCUGAAACAGGACUGAGCACUGGCUAGGGAGCAUUUUUUCUCGCCAUGGAUGUGGUUCUGUCGUUGUGAAGUUUGACUGAUUCGUCGCCUUGUGUUUCUAAGAACGGUUGGAAUGAUGCAUGAUGGUCUGAUUGCGUUUAGCGUUCUGUUCCUCUUCCCGUAGAUCCCAACUG ie_up
ENSG00000157985:+:2:236049058:236049281 ENSG00000157985 ENST00000409538 + 2 236049272 236049481 210 ACUCCACAAGGUAGGAACUUUGGAAGAUGCCUGGCUCCCGACACGUUUGCCAACAGUUAGGCAACUGGAAGUGAUCAUAAUGACAGCCACGGUUGGGAAGGCCCUGAUAACCUGUAGGAAUUCGGGAAUUCCGAUUCAUCCGGCAUAGGAAUGUCUGUGUUUAAAGUUGGUCUUGAGCAGACGUGGAUAAUUCACACUCCUUAAUUUUUU 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
ESRP1 1 156 0.00896861 0.0002275250 5.300787 AGGGAU AGGGAU
RBM25 1 268 0.00896861 0.0003898359 4.523946 AUCGGG AUCGGG,CGGGCA,UCGGGC
ANKHD1 1 339 0.00896861 0.0004927293 4.186017 GACGAA AGACGA,AGACGU,GACGAA,GACGAU,GACGUA,GACGUU
RBFOX2 1 452 0.00896861 0.0006564894 3.772041 UGACUG UGACUG,UGCAUG
RBMY1A1 1 489 0.00896861 0.0007101099 3.658770 ACAAGA ACAAGA,CAAGAC
MATR3 2 739 0.01345291 0.0010724109 3.648989 AAUCUU,AUCUUG AAUCUU,AUCUUA,AUCUUG,CAUCUU
IGF2BP1 1 831 0.00896861 0.0012057377 2.894968 GCACCC AAGCAC,ACCCGU,AGCACC,CACCCG,CCCGUU,GCACCC
RBM6 1 1054 0.00896861 0.0015289102 2.552381 CAUCCA AAUCCA,AUCCAA,AUCCAG,CAUCCA,UAUCCA
RBFOX1 1 1077 0.00896861 0.0015622419 2.521267 UGACUG AGCAUG,GCAUGA,GCAUGC,GCAUGU,UGACUG,UGCAUG
SNRNP70 1 1237 0.00896861 0.0017941145 2.321612 AUCAAG AAUCAA,AUCAAG,AUUCAA,GAUCAA,GUUCAA,UUCAAG
ESRP2 2 2150 0.01345291 0.0031172377 2.109579 GGGAAG,UGGGAA GGGAAA,GGGAAG,GGGAAU,GGGGAA,GGGGAG,GGGGAU,UGGGAA,UGGGGA
G3BP2 1 1644 0.00896861 0.0023839405 1.911536 GGAUGA AGGAUA,AGGAUG,AGGAUU,GGAUAA,GGAUAG,GGAUGA,GGAUGG,GGAUUA,GGAUUG
SAMD4A 3 3992 0.01793722 0.0057866714 1.632151 CGGGAA,CUGGAC,CUGGCC CGGGAA,CGGGAC,CGGGCA,CGGGCC,CGGGUA,CGGGUC,CUGGAA,CUGGAC,CUGGCA,CUGGCC,CUGGUA,CUGGUC,GCGGGA,GCGGGC,GCGGGU,GCUGGA,GCUGGC,GCUGGU
NELFE 2 3028 0.01345291 0.0043896388 1.615745 CUCUGG,UCUCUG CUCUCU,CUCUGG,CUGGCU,CUGGUU,GCUAAC,GGCUAA,GGUCUC,GGUUAG,GUCUCU,UCUCUC,UCUCUG,UCUGGC,UCUGGU,UGGCUA,UGGUUA
HNRNPA3 1 2140 0.00896861 0.0031027457 1.531339 GGAGCC AAGGAG,AGGAGC,CAAGGA,CCAAGG,GCCAAG,GGAGCC
FXR2 2 3434 0.01345291 0.0049780156 1.434276 GACGAA,GGACGA AGACAA,AGACAG,AGACGA,AGACGG,GACAAA,GACAAG,GACAGA,GACAGG,GACGAA,GACGAG,GACGGA,GACGGG,GGACAA,GGACAG,GGACGA,GGACGG,UGACAA,UGACAG,UGACGA,UGACGG
CELF6 1 2997 0.00896861 0.0043447134 1.045623 GUGAUG GUGAGG,GUGAUG,GUGGGG,GUGGUG,GUGUGG,GUGUUG,UGUGAG,UGUGAU,UGUGGG,UGUGGU,UGUGUG,UGUGUU
HNRNPH3 4 7688 0.02242152 0.0111429292 1.008756 AAGGUG,AUCGGG,GGGAAG,GUCGAG AAGGGA,AAGGUG,AAUGUG,AGGGAA,AGGGGA,AUCGGG,AUGUGG,AUUGGG,CGAGGG,CGGGCG,CGGGGG,GAAGGG,GAAUGU,GAGGGG,GGAAGG,GGAAUG,GGAGGA,GGAGGG,GGGAAG,GGGAAU,GGGAGG,GGGCGU,GGGCUG,GGGGAG,GGGGCU,GGGGGC,GGGGGG,GGGUCG,GGGUGU,GGUCGA,GUCGAG,UCGAGG,UCGGGC,UGGGUG,UGUGGG,UUGGGU

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
RBMY1A1 1 7 0.09090909 0.0005239717 7.438792 ACAAGA ACAAGA,CAAGAC
SRSF2 2 479 0.13636364 0.0314383023 2.116864 AGAUCC,GAUCCC 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
NXF1 1 43 0.004761905 0.0002216848 4.424957 AACCUG AACCUG
ANKHD1 1 56 0.004761905 0.0002871826 4.051499 AGACGU AGACGA,AGACGU,GACGAA,GACGAU,GACGUA,GACGUU
FXR1 1 69 0.004761905 0.0003526804 3.755106 AUGACA ACGACA,ACGACG,AUGACA,AUGACG
RBFOX2 2 124 0.007142857 0.0006297864 3.503567 UGACUG,UGCAUG UGACUG,UGCAUG
EIF4B 3 226 0.009523810 0.0011436921 3.057840 GUUGGA,UUGGAA CUCGGA,CUUGGA,GUCGGA,GUUGGA,UCGGAA,UCGGAC,UUGGAA,UUGGAC
RBFOX1 3 287 0.009523810 0.0014510278 2.714464 GCAUGA,UGACUG,UGCAUG AGCAUG,GCAUGA,GCAUGC,GCAUGU,UGACUG,UGCAUG
SRP14 2 218 0.007142857 0.0011033857 2.694564 CCUGUA,CUGUAG CCUGUA,CGCCUG,CUGUAG,GCCUGU
IFIH1 1 146 0.004761905 0.0007406288 2.684716 GGCCCU CCGCGG,CGCGGA,GCCGCG,GCGGAU,GGCCCU,GGCCGC,GGGCCG
ZNF638 6 646 0.016666667 0.0032597743 2.354122 CGUUCU,CGUUGU,GGUUCU,GGUUGG,GUUGGU CGUUCG,CGUUCU,CGUUGG,CGUUGU,GGUUCG,GGUUCU,GGUUGG,GGUUGU,GUUCGU,GUUCUU,GUUGGU,GUUGUU,UGUUCG,UGUUCU,UGUUGG,UGUUGU
HNRNPA1L2 1 188 0.004761905 0.0009522370 2.322146 UAGGGA AUAGGG,GUAGGG,UAGGGA,UAGGGU,UUAGGG
CELF5 4 669 0.011904762 0.0033756550 1.818299 GUGUUU,UGUGUU GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU
MSI1 6 961 0.016666667 0.0048468360 1.781850 AGGUAG,AGUUAG,AGUUGG,UAGGAA AGGAAG,AGGAGG,AGGUAG,AGGUGG,AGUAAG,AGUAGG,AGUUAG,AGUUGG,UAGGAA,UAGGAG,UAGGUA,UAGGUG,UAGUAA,UAGUAG,UAGUUA,UAGUUG
AGO1 1 283 0.004761905 0.0014308746 1.734641 AGGUAG AGGUAG,GAGGUA,GGUAGU,GUAGUA,UGAGGU
A1CF 3 598 0.009523810 0.0030179363 1.657976 AUAAUU,UGAUCA,UUAAUU AGUAUA,AUAAUU,AUCAGU,CAGUAU,GAUCAG,UAAUUA,UAAUUG,UCAGUA,UGAUCA,UUAAUU
CELF4 4 776 0.011904762 0.0039147521 1.604546 GUGUUU,UGUGUU GGUGUG,GGUGUU,GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU
RC3H1 3 631 0.009523810 0.0031841999 1.580608 UCUGUG,UUCUGU CCCUUC,CCUUCU,CUUCUG,UCCCUU,UCUGUG,UUCUGU
RBM28 1 340 0.004761905 0.0017180572 1.470761 UGUAGG AGUAGA,AGUAGG,AGUAGU,GAGUAG,GUGUAG,UGUAGA,UGUAGG,UGUAGU
RBM46 5 1091 0.014285714 0.0055018138 1.376594 AAUGAU,AUCAUA,AUGAUG,GAUCAU AAUCAA,AAUCAU,AAUGAA,AAUGAU,AUCAAA,AUCAAG,AUCAAU,AUCAUA,AUCAUG,AUCAUU,AUGAAA,AUGAAG,AUGAAU,AUGAUA,AUGAUG,AUGAUU,GAUCAA,GAUCAU,GAUGAA,GAUGAU
NONO 1 364 0.004761905 0.0018389762 1.372636 AGGAAC AGAGGA,AGGAAC,GAGAGG,GAGGAA
ESRP2 3 731 0.009523810 0.0036880290 1.368689 GGGAAG,GGGAAU,UGGGAA GGGAAA,GGGAAG,GGGAAU,GGGGAA,GGGGAG,GGGGAU,UGGGAA,UGGGGA
CELF1 5 1097 0.014285714 0.0055320435 1.368689 GUUGUG,UGUCUG,UGUGUU,UUGUGU CUGUCU,GUGUGU,GUGUUG,GUUGUG,GUUUGU,UGUCUG,UGUGUG,UGUGUU,UGUUGU,UGUUUG,UUGUGU
CSTF2 4 1022 0.011904762 0.0051541717 1.207726 GUGUUU,UGUGUU GUGUGU,GUGUUG,GUGUUU,GUUUUG,UGUGUG,UGUGUU,UGUUUG,UGUUUU
QKI 3 904 0.009523810 0.0045596534 1.062615 AUCAUA,CACACU,UAACCU 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
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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