ENSG00000004487:+:1:23030468:23059167

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000004487:+:1:23030468:23059167 ENSG00000004487 MSTRG.523.27 + 1 23030469 23059167 816 GUAGAGUACAGAGAGAUGGAUGAAAGCUUGGCCAACCUCUCAGAAGAUGAGUAUUAUUCAGAAGAAGAGAGAAAUGCCAAAGCAGAGAAGGAAAAGAAGCUUCCCCCACCACCCCCUCAAGCCCCACCUGAGGAAGAAAAUGAAAGUGAGCCUGAAGAACCAUCGGGGCAAGCAGGAGGACUUCAAGACGACAGUUCUGGAGGGUAUGGAGACGGCCAAGCAUCAGGUGUGGAGGGCGCAGCUUUCCAGAGCCGACUUCCUCAUGACCGGAUGACUUCUCAAGAAGCAGCCUGUUUUCCAGAUAUUAUCAGUGGACCACAACAGACCCAGAAGGUUUUUCUUUUCAUUAGAAACCGCACACUGCAGUUGUGGUUGGAUAAUCCAAAGAUUCAGCUGACAUUUGAGGCUACUCUCCAACAAUUAGAAGCACCUUAUAACAGUGAUACUGUGCUUGUCCACCGAGUUCACAGUUAUUUAGAGCGUCAUGGUCUUAUCAACUUCGGCAUCUAUAAGAGGAUAAAACCCCUACCAACUAAAAAGACAGGAAAGGUAAUUAUUAUAGGCUCUGGGGUCUCAGGCUUGGCAGCAGCUCGACAGUUACAAAGUUUUGGAAUGGAUGUCACACUUUUGGAAGCCAGGGAUCGUGUGGGUGGACGAGUUGCCACAUUUCGCAAAGGAAACUAUGUAGCUGAUCUUGGAGCCAUGGUGGUAACAGGUCUUGGAGGGAAUCCUAUGGCUGUGGUCAGCAAACAAGUAAAUAUGGAACUGGCCAAGAUCAAGCAAAAAUGCCCACUUUAUGAAGCCAACGGACAAGCUGUAGAGUACAGAGAGAUGGAUGAAAGCUUGGCCAACCUCUCAGAAGAUGA circ
ENSG00000004487:+:1:23030468:23059167 ENSG00000004487 MSTRG.523.27 + 1 23030469 23059167 22 ACGGACAAGCUGUAGAGUACAG bsj
ENSG00000004487:+:1:23030468:23059167 ENSG00000004487 MSTRG.523.27 + 1 23030269 23030478 210 GAACCUGAACUGACACAAGAUUGUUUCAUGAGGGCUUUGUUUUUAAUAACUACCUAUUAUGAGCUGCCUUGUUCCUUGUUGUAUGCUUACUUCCCUUAAAAUGUGAGGUUAACAAUUUACAUUGACUGAUGGUUCCAAAUAGAGUCCCUAAUUUUAAAUGUUCACUGCAUUUAGCUUUCCCUGGUAUGAUCUCCAUAUAGGUAGAGUACA ie_up
ENSG00000004487:+:1:23030468:23059167 ENSG00000004487 MSTRG.523.27 + 1 23059158 23059367 210 CGGACAAGCUGUAAGUCGAGGACAAACAGAACUUUCAACAUUUCUUUGGUUCACUUGAAAACAAUUUUAGGAGAAUGGUAUGGAUGAGCAUAUACAUAUAUACACAUAUAGAGGUGUAUAUAUAUAUAAACUGAGGGUAGAGAUGAUGUGAUGUUAUUCUGGUUGUUUCUUAACUCUUGAGCUAUGUAGGAAAGGAUUAUUGUAUAUAUA 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 0.002450980 0.0002275250 3.429262 AGGGAU AGGGAU
RBM25 1 268 0.002450980 0.0003898359 2.652420 AUCGGG AUCGGG,CGGGCA,UCGGGC
ANKHD1 1 339 0.002450980 0.0004927293 2.314492 AGACGA AGACGA,AGACGU,GACGAA,GACGAU,GACGUA,GACGUU
SRSF11 3 688 0.004901961 0.0009985015 2.295522 AAGAAG AAGAAG
EIF4B 5 1179 0.007352941 0.0017100607 2.104274 CUUGGA,GUUGGA,UUGGAA CUCGGA,CUUGGA,GUCGGA,GUUGGA,UCGGAA,UCGGAC,UUGGAA,UUGGAC
PABPN1 5 1222 0.007352941 0.0017723764 2.052636 AAAAGA,AGAAGA AAAAGA,AGAAGA
RBM42 1 407 0.002450980 0.0005912752 2.051457 AACUAA AACUAA,AACUAC,ACUAAG,ACUACG
FXR1 1 411 0.002450980 0.0005970720 2.037382 ACGACA ACGACA,ACGACG,AUGACA,AUGACG
HNRNPA0 1 453 0.002450980 0.0006579386 1.897334 AGAUAU AAUUUA,AGAUAU,AGUAGG
RBMY1A1 1 489 0.002450980 0.0007101099 1.787245 CAAGAC ACAAGA,CAAGAC
HNRNPM 3 999 0.004901961 0.0014492040 1.758098 AAGGAA,GAAGGA AAGGAA,GAAGGA,GGGGGG
G3BP2 5 1644 0.007352941 0.0023839405 1.624973 AGGAUA,GGAUAA,GGAUGA AGGAUA,AGGAUG,AGGAUU,GGAUAA,GGAUAG,GGAUGA,GGAUGG,GGAUUA,GGAUUG
IGF2BP1 2 831 0.003676471 0.0012057377 1.608405 AAGCAC,AGCACC AAGCAC,ACCCGU,AGCACC,CACCCG,CCCGUU,GCACCC
SRP14 2 847 0.003676471 0.0012289250 1.580925 CUGUAG,GCCUGU CCUGUA,CGCCUG,CUGUAG,GCCUGU
SRSF4 12 3740 0.015931373 0.0054214720 1.555114 AAGAAG,AGAAGA,AGGAAG,GAAGAA,GAGGAA,GGAAGA AAGAAG,AGAAGA,AGGAAG,GAAGAA,GAGGAA,GGAAGA
HNRNPLL 11 3534 0.014705882 0.0051229360 1.521351 ACCACA,ACCGCA,ACGACA,ACUGCA,AGACGA,CAAACA,CACCAC,CACUGC,GACGAC,GCAAAC,GCACAC ACAAAC,ACACAC,ACACCA,ACAUAC,ACCACA,ACCGCA,ACGACA,ACUGCA,AGACGA,CAAACA,CACACA,CACACC,CACCAC,CACCGC,CACUGC,CAGACG,CAUACA,GACGAC,GCAAAC,GCACAC,GCAUAC
RBM3 6 2152 0.008578431 0.0031201361 1.459105 AAACUA,AAGACG,AGACGA,GAAACU,GAGACG,GAUACU AAAACG,AAAACU,AAACGA,AAACUA,AAGACG,AAGACU,AAUACG,AAUACU,AGACGA,AGACUA,AUACGA,AUACUA,GAAACG,GAAACU,GAGACG,GAGACU,GAUACG,GAUACU
SNRNP70 3 1237 0.004901961 0.0017941145 1.450087 AUCAAG,GAUCAA,UUCAAG AAUCAA,AUCAAG,AUUCAA,GAUCAA,GUUCAA,UUCAAG
ERI1 1 632 0.002450980 0.0009173461 1.417821 UUCAGA UUCAGA,UUUCAG
TRA2B 21 7329 0.026960784 0.0106226650 1.343717 AAAGAA,AAGAAC,AAGAAG,AAGGAA,AGAAGA,AGAAGG,AGGAAA,AGGAAG,AUAAGA,GAAGAA,GAAGGA AAAGAA,AAGAAC,AAGAAG,AAGAAU,AAGGAA,AAUAAG,AGAAGA,AGAAGG,AGGAAA,AGGAAG,AUAAGA,GAAAGA,GAAGAA,GAAGGA,GAAUUA,GGAAGG,UAAGAA
TUT1 1 678 0.002450980 0.0009840095 1.316615 GAUACU AAAUAC,AAUACU,AGAUAC,CAAUAC,CGAUAC,GAUACU
RBM6 2 1054 0.003676471 0.0015289102 1.265818 AAUCCA,AUCCAA AAUCCA,AUCCAA,AUCCAG,CAUCCA,UAUCCA
ZRANB2 8 3173 0.011029412 0.0045997733 1.261721 AAAGGU,AGGGAA,AGGUAA,AGGUCU,AGGUUU,GGUGGU,UGGUAA,UGGUGG AAAGGU,AGGGAA,AGGUAA,AGGUAC,AGGUAG,AGGUAU,AGGUCU,AGGUUA,AGGUUU,CGGUAA,CGGUAG,CGGUAU,CGGUCU,GAGGUU,GGGUAA,GGGUGA,GGUAAA,GGUGGU,GUAAAG,GUGGUG,UAAAGG,UGGUAA,UGGUGG
HNRNPAB 4 1782 0.006127451 0.0025839306 1.245720 AAAGAC,AAGACA,ACAAAG,CAAAGA AAAGAC,AAGACA,ACAAAG,AGACAA,AUAGCA,CAAAGA,GACAAA
MATR3 1 739 0.002450980 0.0010724109 1.192501 AUCUUG AAUCUU,AUCUUA,AUCUUG,CAUCUU
FXR2 8 3434 0.011029412 0.0049780156 1.147713 AGACAG,AGACGA,AGACGG,GACAAG,GACAGG,GACGAG,GGACAA,GGACGA AGACAA,AGACAG,AGACGA,AGACGG,GACAAA,GACAAG,GACAGA,GACAGG,GACGAA,GACGAG,GACGGA,GACGGG,GGACAA,GGACAG,GGACGA,GGACGG,UGACAA,UGACAG,UGACGA,UGACGG
PPRC1 1 780 0.002450980 0.0011318283 1.114704 GGGCGC CCGCGC,CGCGCC,CGCGCG,CGGCGC,GCGCGC,GGCGCC,GGCGCG,GGGCGC
TRA2A 16 6871 0.020833333 0.0099589296 1.064831 AAAGAA,AAGAAA,AAGAAG,AAGAGG,AGAAGA,AGAGGA,AGGAAG,GAAGAA,GAAGAG,GAGGAA AAAGAA,AAGAAA,AAGAAG,AAGAGG,AGAAAG,AGAAGA,AGAGGA,AGGAAG,GAAAGA,GAAGAA,GAAGAG,GAGGAA
RBMX 11 4925 0.014705882 0.0071387787 1.042644 AAGAAG,AAGGAA,AAGUAA,AGAAGG,AGGAAG,GAAGGA,GUAACA AAGAAG,AAGGAA,AAGUAA,AAGUGU,ACCAAA,AGAAGG,AGGAAG,AGUAAC,AGUGUU,AUCAAA,AUCCCA,AUCCCC,GAAGGA,GGAAGG,GUAACA,UAACAA,UAAGAC,UCAAAA
RBM28 1 822 0.002450980 0.0011926949 1.039134 UGUAGA AGUAGA,AGUAGG,AGUAGU,GAGUAG,GUGUAG,UGUAGA,UGUAGG,UGUAGU
SSB 2 1260 0.003676471 0.0018274462 1.008493 CUGUUU,UGUUUU CUGUUU,GCUGUU,UGCUGU,UGUUUU

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
SRP14 1 1 0.09090909 0.0001309929 9.438792 CUGUAG GCCUGU
PUM2 1 7 0.09090909 0.0005239717 7.438792 UGUAGA GUAAAU,UAAAUA,UAUAUA,UGUAAA,UGUAGA,UGUAUA
RBM28 1 7 0.09090909 0.0005239717 7.438792 UGUAGA AGUAGG,AGUAGU,UGUAGA,UGUAGG,UGUAGU
PUM1 1 16 0.09090909 0.0011134399 6.351329 UGUAGA AAUAUU,AAUGUU,AAUUGU,ACAUAA,AGAUAA,CAGAAU,GUAAAU,GUCCAG,UAAAUA,UAUAUA,UGUAAA,UGUAGA,UGUAUA,UUAAUG
PTBP1 1 30 0.09090909 0.0020303904 5.484596 AGCUGU AGCUGU,CAUCUU,CCAUCU,CCUCUU,CUAUCU,CUCUUA,CUCUUC,CUCUUG,CUCUUU,CUUUCU,GGCUCC,GUCUUU,UACUUU,UAUUUU,UCCUCU,UCUAUC,UCUCUU,UCUUCU,UCUUUC,UUACUU,UUCUUC,UUCUUG,UUUCUU
SRSF2 2 479 0.13636364 0.0314383023 2.116864 AAGCUG,AGCUGU 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
AKAP1 12 221 0.030952381 0.0011185006 4.790412 AUAUAU,UAUAUA AUAUAU,UAUAUA
RBMS1 11 217 0.028571429 0.0010983474 4.701167 AUAUAC,AUAUAG,UAUAUA AUAUAC,AUAUAG,GAUAUA,UAUAUA
NXF1 1 43 0.004761905 0.0002216848 4.424957 AACCUG AACCUG
RBMS3 19 562 0.047619048 0.0028365578 4.069326 AUAUAG,AUAUAU,CAUAUA,UAUAGA,UAUAUA AAUAUA,AUAUAG,AUAUAU,CAUAUA,CUAUAG,CUAUAU,UAUAGA,UAUAGC,UAUAUA,UAUAUC
RBMY1A1 1 95 0.004761905 0.0004836759 3.299426 ACAAGA ACAAGA,CAAGAC
RBM42 1 103 0.004761905 0.0005239823 3.183949 AACUAC AACUAA,AACUAC,ACUAAG,ACUACG
PUM2 12 764 0.030952381 0.0038542926 3.005512 GUAUAU,UACAUA,UAUAUA,UGUAUA GUAAAU,GUACAU,GUAGAU,GUAUAU,UAAAUA,UACAUA,UACAUC,UAGAUA,UAUAUA,UGUAAA,UGUACA,UGUAGA,UGUAUA
RBFOX2 1 124 0.004761905 0.0006297864 2.918604 UGACUG UGACUG,UGCAUG
AGO1 2 283 0.007142857 0.0014308746 2.319604 AGGUAG,UGAGGU AGGUAG,GAGGUA,GGUAGU,GUAGUA,UGAGGU
HNRNPA0 1 200 0.004761905 0.0010126965 2.233337 AAUUUA AAUUUA,AGAUAU,AGUAGG
RBM41 4 502 0.011904762 0.0025342604 2.231902 AUACAU,UACAUU,UUACAU,UUACUU AUACAU,AUACUU,UACAUG,UACAUU,UACUUG,UACUUU,UUACAU,UUACUU
PABPC3 2 310 0.007142857 0.0015669085 2.188580 AAAACA,GAAAAC AAAAAC,AAAACA,AAAACC,GAAAAC
G3BP2 3 490 0.009523810 0.0024738009 1.944809 AGGAUU,GGAUGA,GGAUUA AGGAUA,AGGAUG,AGGAUU,GGAUAA,GGAUAG,GGAUGA,GGAUGG,GGAUUA,GGAUUG
ENOX1 5 756 0.014285714 0.0038139863 1.905202 AGGACA,AGUACA,CGGACA,UAUACA AAGACA,AAUACA,AGACAG,AGGACA,AGUACA,AUACAG,CAGACA,CAUACA,CGGACA,CGUACA,GGACAG,GUACAG,UAGACA,UAUACA,UGGACA,UGUACA
PUM1 15 2172 0.038095238 0.0109482064 1.798916 AAUGUU,AUUGUA,GUAUAU,UACAUA,UAUAUA,UGUAUA,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
RBFOX1 1 287 0.004761905 0.0014510278 1.714464 UGACUG AGCAUG,GCAUGA,GCAUGC,GCAUGU,UGACUG,UGCAUG
FXR2 4 730 0.011904762 0.0036829907 1.692589 GACAAA,GACAAG,GGACAA AGACAA,AGACAG,AGACGA,AGACGG,GACAAA,GACAAG,GACAGA,GACAGG,GACGAA,GACGAG,GACGGA,GACGGG,GGACAA,GGACAG,GGACGA,GGACGG,UGACAA,UGACAG,UGACGA,UGACGG
HNRNPLL 4 748 0.011904762 0.0037736800 1.657495 ACAAAC,ACUGCA,CAAACA,CACUGC ACAAAC,ACACAC,ACACCA,ACAUAC,ACCACA,ACCGCA,ACGACA,ACUGCA,AGACGA,CAAACA,CACACA,CACACC,CACCAC,CACCGC,CACUGC,CAGACG,CAUACA,GACGAC,GCAAAC,GCACAC,GCAUAC
ZNF638 3 646 0.009523810 0.0032597743 1.546767 GGUUGU,GUUGUU,UGUUGU CGUUCG,CGUUCU,CGUUGG,CGUUGU,GGUUCG,GGUUCU,GGUUGG,GGUUGU,GUUCGU,GUUCUU,GUUGGU,GUUGUU,UGUUCG,UGUUCU,UGUUGG,UGUUGU
RBM28 1 340 0.004761905 0.0017180572 1.470761 UGUAGG AGUAGA,AGUAGG,AGUAGU,GAGUAG,GUGUAG,UGUAGA,UGUAGG,UGUAGU
HNRNPAB 1 351 0.004761905 0.0017734784 1.424957 GACAAA AAAGAC,AAGACA,ACAAAG,AGACAA,AUAGCA,CAAAGA,GACAAA
MSI1 4 961 0.011904762 0.0048468360 1.296424 AGGUAG,UAGGAA,UAGGAG,UAGGUA AGGAAG,AGGAGG,AGGUAG,AGGUGG,AGUAAG,AGUAGG,AGUUAG,AGUUGG,UAGGAA,UAGGAG,UAGGUA,UAGGUG,UAGUAA,UAGUAG,UAGUUA,UAGUUG

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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