ENSG00000147403:+:X:154399337:154399941

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000147403:+:X:154399337:154399941 ENSG00000147403 MSTRG.35107.3 + X 154399338 154399941 306 UUACCGGUAUUGUAAGAACAAGCCGUACCCAAAGUCUCGCUUCUGCCGAGGUGUCCCUGAUGCCAAGAUUCGCAUUUUUGACCUGGGGCGGAAAAAGGCAAAAGUGGAUGAGUUUCCGCUUUGUGGCCACAUGGUGUCAGAUGAAUAUGAGCAGCUGUCCUCUGAAGCCCUGGAGGCUGCCCGAAUUUGUGCCAAUAAGUACAUGGUAAAAAGUUGUGGCAAAGAUGGCUUCCAUAUCCGGGUGCGGCUCCACCCCUUCCACGUCAUCCGCAUCAACAAGAUGUUGUCCUGUGCUGGGGCUGACAGUUACCGGUAUUGUAAGAACAAGCCGUACCCAAAGUCUCGCUUCUGCCGAG circ
ENSG00000147403:+:X:154399337:154399941 ENSG00000147403 MSTRG.35107.3 + X 154399338 154399941 22 GGGGCUGACAGUUACCGGUAUU bsj
ENSG00000147403:+:X:154399337:154399941 ENSG00000147403 MSTRG.35107.3 + X 154399138 154399347 210 UUCUAGUCUUGGGUGUUGUCUGUGUUGCAGCAGCCAACUGUUGCUUUGUAGUUUAUUUCCCCGAAUGGAAACGGUUUAGAAGUGGACGUGCAUUCCCCACCCUUUUCCCGUCCCUCGUUUGGGUUGUUCCUUGAGGGGCAAAGUGCCUGUUGGGCUUUCUGUGAACCUCACCUAACCUGUGUUUUUUCACUCCCCUGCAGUUACCGGUAU ie_up
ENSG00000147403:+:X:154399337:154399941 ENSG00000147403 MSTRG.35107.3 + X 154399932 154400141 210 GGGCUGACAGGUGAGCUUGGUCUGGGCCUUUUAAGGCAGUUGGAGUCUCUACAUUAUUAGGCUUGCAUUAUUUUAUCAGAGCAUAGAGGUGGCCCCAGUGACUCAGCCACUAUGGCUACUAGAAAAGCCAGGCUGGCAAGUGACUUUCAGUGGUCACUCAGGACCCCUUCCUGCAGAUACAAACAAAGCAUGAGUAAGUCUUAGCAAGCU 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
RBMY1A1 1 489 0.006535948 0.0007101099 3.202282 ACAAGA ACAAGA,CAAGAC
PABPC4 2 1251 0.009803922 0.0018144033 2.433864 AAAAAG AAAAAA,AAAAAG
SNRPB2 1 991 0.006535948 0.0014376103 2.184724 GUAUUG AUUGCA,GUAUUG,UAUUGC,UGCAGU,UUGCAG
RC3H1 2 1786 0.009803922 0.0025897275 1.920559 CCCUUC,CUUCUG CCCUUC,CCUUCU,CUUCUG,UCCCUU,UCUGUG,UUCUGU
RBM41 1 1318 0.006535948 0.0019115000 1.773691 UACAUG AUACAU,AUACUU,UACAUG,UACAUU,UACUUG,UACUUU,UUACAU,UUACUU
HNRNPCL1 2 2062 0.009803922 0.0029897078 1.713354 AUUUUU,UUUUUG AUUUUU,CUUUUU,UUUUUG,UUUUUU
CPEB2 2 2261 0.009803922 0.0032780993 1.580499 AUUUUU,CAUUUU AUUUUU,CAUUUU,CCUUUU,CUUUUU,UUUUUU
RALY 1 1553 0.006535948 0.0022520629 1.537149 UUUUUG UUUUUC,UUUUUG,UUUUUU
ZRANB2 3 3173 0.013071895 0.0045997733 1.506834 CGGUAU,GGUAAA,UGGUAA AAAGGU,AGGGAA,AGGUAA,AGGUAC,AGGUAG,AGGUAU,AGGUCU,AGGUUA,AGGUUU,CGGUAA,CGGUAG,CGGUAU,CGGUCU,GAGGUU,GGGUAA,GGGUGA,GGUAAA,GGUGGU,GUAAAG,GUGGUG,UAAAGG,UGGUAA,UGGUGG
CELF1 2 2391 0.009803922 0.0034664959 1.499881 GUUGUG,UGUUGU CUGUCU,GUGUGU,GUGUUG,GUUGUG,GUUUGU,UGUCUG,UGUGUG,UGUGUU,UGUUGU,UGUUUG,UUGUGU
G3BP2 1 1644 0.006535948 0.0023839405 1.455048 GGAUGA AGGAUA,AGGAUG,AGGAUU,GGAUAA,GGAUAG,GGAUGA,GGAUGG,GGAUUA,GGAUUG
TARDBP 2 2654 0.009803922 0.0038476365 1.349386 GUUGUG,UUGUGC GAAUGA,GAAUGG,GAAUGU,GUGAAU,GUGUGU,GUUGUG,GUUGUU,GUUUUG,UGAAUG,UGUGUG,UUGUGC,UUGUUC,UUUUGC
ZNF638 1 1773 0.006535948 0.0025708878 1.346130 UGUUGU CGUUCG,CGUUCU,CGUUGG,CGUUGU,GGUUCG,GGUUCU,GGUUGG,GGUUGU,GUUCGU,GUUCUU,GUUGGU,GUUGUU,UGUUCG,UGUUCU,UGUUGG,UGUUGU
HNRNPAB 1 1782 0.006535948 0.0025839306 1.338829 CAAAGA AAAGAC,AAGACA,ACAAAG,AGACAA,AUAGCA,CAAAGA,GACAAA
MBNL1 14 13372 0.049019608 0.0193802045 1.338775 AUGCCA,CCGCUU,CGCUUC,CGCUUU,CUCGCU,CUGCCC,CUGCCG,GUCUCG,GUGCUG,UCCGCU,UCGCUU,UCUCGC,UGCGGC,UUGUGC ACGCUA,ACGCUC,ACGCUG,ACGCUU,AUGCCA,AUGCCC,AUGCCG,AUGCUC,AUGCUU,CCCGCU,CCGCUA,CCGCUC,CCGCUG,CCGCUU,CCUGCU,CGCUGC,CGCUGU,CGCUUC,CGCUUG,CGCUUU,CUCGCU,CUGCCA,CUGCCC,CUGCCG,CUGCCU,CUGCGG,CUGCUA,CUGCUC,CUGCUG,CUGCUU,CUUGCU,CUUGUG,GCGCUC,GCGCUG,GCGCUU,GCUGCG,GCUGCU,GCUUGC,GCUUGU,GCUUUU,GGCUUU,GUCUCG,GUGCUA,GUGCUC,GUGCUG,GUGCUU,UCCGCU,UCGCUA,UCGCUC,UCGCUG,UCGCUU,UCUCGC,UCUGCU,UGCGGC,UGCUGC,UGCUGU,UGCUUC,UGCUUU,UGUCUC,UUCGCU,UUGCCA,UUGCCC,UUGCCG,UUGCCU,UUGCUA,UUGCUC,UUGCUG,UUGCUU,UUGUGC,UUUGCU
AGO2 1 1830 0.006535948 0.0026534924 1.300504 AAAGUG AAAAAA,AAAGUG,AAGUGC,AGUGCU,GUGCUU,UAAAGU
CELF2 1 1886 0.006535948 0.0027346479 1.257041 UGUUGU AUGUGU,GUAUGU,GUCUGU,GUGUGU,GUUGUU,UAUGUG,UAUGUU,UGUGUG,UGUUGU,UUGUGU
PUM2 1 1890 0.006535948 0.0027404447 1.253986 GUACAU GUAAAU,GUACAU,GUAGAU,GUAUAU,UAAAUA,UACAUA,UACAUC,UAGAUA,UAUAUA,UGUAAA,UGUACA,UGUAGA,UGUAUA
HNRNPA3 1 2140 0.006535948 0.0031027457 1.074851 GCCAAG AAGGAG,AGGAGC,CAAGGA,CCAAGG,GCCAAG,GGAGCC

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
SNRPA 1 39 0.09090909 0.002619859 5.116864 GUUACC AGCAGU,AGGAGA,AGUAGG,AGUAGU,AUACCU,AUGCUG,AUUCCU,AUUGCA,CAGUAG,CCUGCU,GAGCAG,GAUACC,GCAGUA,GGAGAU,GGGUAU,GUAGGC,GUAGUG,UAUGCU,UCCUGC,UGCACG,UUCCUG,UUGCAC
SRSF2 1 479 0.09090909 0.031438302 1.531901 GUUACC 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
RBFOX1 2 287 0.007142857 0.0014510278 2.299426 AGCAUG,GCAUGA AGCAUG,GCAUGA,GCAUGC,GCAUGU,UGACUG,UGCAUG
SNRPB2 2 288 0.007142857 0.0014560661 2.294425 UGCAGU,UUGCAG AUUGCA,GUAUUG,UAUUGC,UGCAGU,UUGCAG
ACO1 2 325 0.007142857 0.0016424829 2.120623 CAGUGA,CAGUGG CAGUGA,CAGUGC,CAGUGG,CAGUGU
SRP14 1 218 0.004761905 0.0011033857 2.109602 GCCUGU CCUGUA,CGCCUG,CUGUAG,GCCUGU
CELF4 6 776 0.016666667 0.0039147521 2.089973 GGUGUU,GUGUUG,GUGUUU,UGUGUU GGUGUG,GGUGUU,GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU
CELF5 5 669 0.014285714 0.0033756550 2.081334 GUGUUG,GUGUUU,UGUGUU GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU
EIF4B 1 226 0.004761905 0.0011436921 2.057840 GUUGGA CUCGGA,CUUGGA,GUCGGA,GUUGGA,UCGGAA,UCGGAC,UUGGAA,UUGGAC
ERI1 1 228 0.004761905 0.0011537686 2.045185 UUUCAG UUCAGA,UUUCAG
TUT1 1 230 0.004761905 0.0011638452 2.032640 AGAUAC AAAUAC,AAUACU,AGAUAC,CAAUAC,CGAUAC,GAUACU
RC3H1 4 631 0.011904762 0.0031841999 1.902536 CCCUUC,UCUGUG,UUCUGU CCCUUC,CCUUCU,CUUCUG,UCCCUU,UCUGUG,UUCUGU
ZNF638 4 646 0.011904762 0.0032597743 1.868695 GGUUGU,GUUGUU,UGUUGG,UGUUGU CGUUCG,CGUUCU,CGUUGG,CGUUGU,GGUUCG,GGUUCU,GGUUGG,GGUUGU,GUUCGU,GUUCUU,GUUGGU,GUUGUU,UGUUCG,UGUUCU,UGUUGG,UGUUGU
CSTF2 6 1022 0.016666667 0.0051541717 1.693153 GUGUUG,GUGUUU,UGUGUU,UGUUUU GUGUGU,GUGUUG,GUGUUU,GUUUUG,UGUGUG,UGUGUU,UGUUUG,UGUUUU
CELF1 6 1097 0.016666667 0.0055320435 1.591081 GUGUUG,UGUCUG,UGUGUU,UGUUGU CUGUCU,GUGUGU,GUGUUG,GUUGUG,GUUUGU,UGUCUG,UGUGUG,UGUGUU,UGUUGU,UGUUUG,UUGUGU
RBM28 1 340 0.004761905 0.0017180572 1.470761 UGUAGU AGUAGA,AGUAGG,AGUAGU,GAGUAG,GUGUAG,UGUAGA,UGUAGG,UGUAGU
HNRNPAB 1 351 0.004761905 0.0017734784 1.424957 ACAAAG AAAGAC,AAGACA,ACAAAG,AGACAA,AUAGCA,CAAAGA,GACAAA
ZFP36L2 3 774 0.009523810 0.0039046755 1.286336 UUAUUU,UUUAUU AUUUAU,UAUUUA,UUAUUU,UUUAUU
CELF2 3 881 0.009523810 0.0044437727 1.099754 GUCUGU,GUUGUU,UGUUGU AUGUGU,GUAUGU,GUCUGU,GUGUGU,GUUGUU,UAUGUG,UAUGUU,UGUGUG,UGUUGU,UUGUGU
AGO2 2 677 0.007142857 0.0034159613 1.064210 AAAGUG,AAGUGC AAAAAA,AAAGUG,AAGUGC,AGUGCU,GUGCUU,UAAAGU

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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