ENSG00000031823:-:19:5941620:5957973

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000031823:-:19:5941620:5957973 ENSG00000031823 MSTRG.16270.6 - 19 5941621 5957973 180 AAAAGCCUGCCAUUGCUCCGCCCGUCUUUGUGUUUCAGAAGGAUAAAGGACAAAAGAGGUCAGCUGGCGGCUCCAGUCCUGAAGGCGGAGAAGAUUCUGACAGAGAAGAUGGAAAUUACUGCCCUCCUGUCAAGCGAGAAAGAACAUCCUCUUUAACCCAGUUCCCACCCUCACAGUCAGAAAAGCCUGCCAUUGCUCCGCCCGUCUUUGUGUUUCAGAAGGAUAAAGGA circ
ENSG00000031823:-:19:5941620:5957973 ENSG00000031823 MSTRG.16270.6 - 19 5941621 5957973 22 CUCACAGUCAGAAAAGCCUGCC bsj
ENSG00000031823:-:19:5941620:5957973 ENSG00000031823 MSTRG.16270.6 - 19 5957964 5958173 210 UCAUUCUGGGUGCAUUUCACAAACCCAGCACACCUGUGCCUCCAGGCAUCCGAGUCAAGACGCUGUUCUAAGUGAUUUGAUGUUCUCUGGAGUUACUAGUUUCAUUUAUAUAUAUGUUUAACAUAUUACAAACAAGUGUAGCUUUGUUUACUGUAUGCAUAUAGUGUUGGGGGGAAAAAAACUAAUUUUUCUUUUUGCAGAAAAGCCUGC ie_up
ENSG00000031823:-:19:5941620:5957973 ENSG00000031823 MSTRG.16270.6 - 19 5941421 5941630 210 UCACAGUCAGGUAAAAUAUGCAAACUUACGGAAUGGUGAAAGCGUUUAUGCUUACAAACCCGCCAUUCCCCUCAGUGCCGCGCAUCCGUCUGCUGUGUCCUUCCUGCCCAGCUCCGGUUAGAGUCGAUCUGAGGCUCGGGCUCUGUCAGGAGUGAGGUGAGAGCUUGUCCAGAGUGCAGCAUCAGGGGUCCUCGUCUCGAAUCAGUGACA 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
SUPV3L1 1 199 0.01111111 0.0002898408 5.260599 CCGCCC CCGCCC
CNOT4 1 314 0.01111111 0.0004564992 4.605247 GACAGA GACAGA
ERI1 2 632 0.01666667 0.0009173461 4.183356 UUCAGA,UUUCAG UUCAGA,UUUCAG
PABPN1 3 1222 0.02222222 0.0017723764 3.648246 AAAAGA,AGAAGA AAAAGA,AGAAGA
CELF5 3 1415 0.02222222 0.0020520728 3.436849 GUGUUU,UGUGUU GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU
CELF4 3 1782 0.02222222 0.0025839306 3.104364 GUGUUU,UGUGUU GGUGUG,GGUGUU,GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU
CSTF2 3 1967 0.02222222 0.0028520334 2.961940 GUGUUU,UGUGUU GUGUGU,GUGUUG,GUGUUU,GUUUUG,UGUGUG,UGUGUU,UGUUUG,UGUUUU
HNRNPM 1 999 0.01111111 0.0014492040 2.938671 GAAGGA AAGGAA,GAAGGA,GGGGGG
G3BP2 2 1644 0.01666667 0.0023839405 2.805545 AGGAUA,GGAUAA AGGAUA,AGGAUG,AGGAUU,GGAUAA,GGAUAG,GGAUGA,GGAUGG,GGAUUA,GGAUUG
PABPC5 3 2400 0.02222222 0.0034795387 2.675035 AGAAAA,AGAAAG,GAAAUU AGAAAA,AGAAAG,AGAAAU,GAAAAU,GAAAGU,GAAAUU
FXR2 4 3434 0.02777778 0.0049780156 2.480289 GACAAA,GACAGA,GGACAA,UGACAG AGACAA,AGACAG,AGACGA,AGACGG,GACAAA,GACAAG,GACAGA,GACAGG,GACGAA,GACGAG,GACGGA,GACGGG,GGACAA,GGACAG,GGACGA,GGACGG,UGACAA,UGACAG,UGACGA,UGACGG
YBX2 1 1480 0.01111111 0.0021462711 2.372099 AACAUC AACAAC,AACAUC,ACAACA,ACAACG,ACAACU,ACAUCA,ACAUCG,ACAUCU
CELF1 2 2391 0.01666667 0.0034664959 2.265416 UGUGUU,UUGUGU CUGUCU,GUGUGU,GUGUUG,GUUGUG,GUUUGU,UGUCUG,UGUGUG,UGUGUU,UGUUGU,UGUUUG,UUGUGU
HNRNPAB 1 1782 0.01111111 0.0025839306 2.104364 GACAAA AAAGAC,AAGACA,ACAAAG,AGACAA,AUAGCA,CAAAGA,GACAAA
TRA2B 7 7329 0.04444444 0.0106226650 2.064857 AAAGAA,AAGAAC,AGAAGA,AGAAGG,GAAAGA,GAAGGA AAAGAA,AAGAAC,AAGAAG,AAGAAU,AAGGAA,AAUAAG,AGAAGA,AGAAGG,AGGAAA,AGGAAG,AUAAGA,GAAAGA,GAAGAA,GAAGGA,GAAUUA,GGAAGG,UAAGAA
KHDRBS2 1 1858 0.01111111 0.0026940701 2.044144 GAUAAA AAUAAA,AUAAAA,AUAAAC,GAUAAA,UUUUUU
CELF2 1 1886 0.01111111 0.0027346479 2.022576 UUGUGU AUGUGU,GUAUGU,GUCUGU,GUGUGU,GUUGUU,UAUGUG,UAUGUU,UGUGUG,UGUUGU,UUGUGU
TRA2A 6 6871 0.03888889 0.0099589296 1.965295 AAAGAA,AAGAGG,AGAAAG,AGAAGA,GAAAGA AAAGAA,AAGAAA,AAGAAG,AAGAGG,AGAAAG,AGAAGA,AGAGGA,AGGAAG,GAAAGA,GAAGAA,GAAGAG,GAGGAA
RBM4 2 3065 0.01666667 0.0044432593 1.907275 CCUCUU,CUCUUU CCUCUU,CCUUCC,CCUUCU,CGCGCG,CGCGGG,CGCGGU,CUCUUU,CUUCCU,CUUCUU,GCGCGA,GCGCGC,GCGCGG,UCCUUC,UUCCUU,UUCUUG
KHDRBS3 2 3429 0.01666667 0.0049707696 1.745424 AUAAAG,GAUAAA AAAUAA,AAUAAA,AGAUAA,AUAAAA,AUAAAC,AUAAAG,AUUAAA,GAUAAA,UAAAAC,UAAAUA,UUAAAC,UUUUUU
SRSF10 11 13860 0.06666667 0.0200874160 1.730674 AAAAGA,AAAGAA,AAAGAG,AAAGGA,AAGAGG,AGAGAA,GAAAGA,GACAAA,GAGAAA,GAGAAG AAAAGA,AAAGAA,AAAGAC,AAAGAG,AAAGGA,AAAGGG,AAGAAA,AAGAAG,AAGACA,AAGAGA,AAGAGG,AAGGAA,AAGGAG,AAGGGA,AAGGGG,ACAAAG,AGACAA,AGAGAA,AGAGAC,AGAGAG,AGAGGA,AGAGGG,CAAAGA,GAAAGA,GACAAA,GAGAAA,GAGAAC,GAGAAG,GAGACA,GAGACC,GAGACG,GAGAGA,GAGAGC,GAGAGG,GAGGAA,GAGGAG,GAGGGA,GAGGGG
SRSF7 11 14481 0.06666667 0.0209873716 1.667444 AAAGGA,AAGGAC,AAGGCG,AGAAGA,AGAGAA,AGGACA,CAGAGA,GAAGGC,GACAAA,GGACAA AAAGGA,AAGAAG,AAGGAC,AAGGCG,AAUGAU,ACGAAU,ACGACG,ACGAGA,ACGAUA,ACGAUU,ACUACG,ACUAGA,AGAAGA,AGACGA,AGACUA,AGAGAA,AGAGAC,AGAGAG,AGAGAU,AGAGGA,AGAUCA,AGAUCU,AGGAAG,AGGACA,AGGCGA,AUAGAA,AUAGAC,AUUGAC,AUUGAU,CAGAGA,CCGAGA,CGAAUG,CGACGA,CGAGAC,CGAGAG,CGAGAU,CGAUAG,CGAUUG,CUACGA,CUAGAG,CUCUUC,CUGAGA,CUUCAC,GAAGAA,GAAGGC,GAAUGA,GACAAA,GACGAC,GACGAG,GACGAU,GACUAC,GAGACU,GAGAGA,GAGAUC,GAGGAA,GAUAGA,GAUUGA,GGAAGG,GGACAA,GGACGA,UACGAC,UACGAU,UAGAGA,UCAACA,UCGAGA,UCGAUU,UCUCCG,UCUUCA,UGAGAG,UGGACA
SRSF4 2 3740 0.01666667 0.0054214720 1.620209 AGAAGA AAGAAG,AGAAGA,AGGAAG,GAAGAA,GAGGAA,GGAAGA
SART3 1 2634 0.01111111 0.0038186524 1.540868 AGAAAA AAAAAA,AAAAAC,AGAAAA,GAAAAA,GAAAAC
LIN28A 2 4315 0.01666667 0.0062547643 1.413938 CGGAGA,GGAGAA AGGAGA,AGGAGU,CGGAGA,CGGAGG,CGGAGU,GGAGAA,GGAGAU,GGAGGA,GGAGGG,GGAGUA,UGGAGA,UGGAGG,UGGAGU
PCBP1 8 13384 0.05000000 0.0193975949 1.366050 AAAUUA,AAUUAC,ACCCUC,CACCCU,CCACCC,CCCACC,CCCUCC,CCUCUU AAAAAA,AAACCA,AAAUUA,AAAUUC,AACCAA,AAUUAA,AAUUAC,AAUUCA,AAUUCC,ACAUUA,ACCAAA,ACCCUC,ACCUUA,AUUAAA,AUUACC,AUUCAC,AUUCCA,AUUCCC,CAAACC,CAACCC,CAAUCC,CAAUUA,CACCCU,CAUACC,CAUCCC,CAUUAA,CAUUCC,CCAAAC,CCAACC,CCAAUC,CCACCC,CCAUAC,CCAUCC,CCAUUA,CCAUUC,CCCACC,CCCCAA,CCCCAC,CCCCCC,CCCUCC,CCCUCU,CCCUUA,CCCUUC,CCUAAC,CCUACC,CCUAUC,CCUCCC,CCUCUU,CCUUAA,CCUUAC,CCUUCC,CCUUUC,CUAACC,CUACCC,CUAUCC,CUUAAA,CUUACC,CUUCCC,CUUUCC,GGGGGG,UCCCCA,UUAGAG,UUAGGA,UUAGGG,UUUUUU
CELF6 1 2997 0.01111111 0.0043447134 1.354670 UGUGUU GUGAGG,GUGAUG,GUGGGG,GUGGUG,GUGUGG,GUGUUG,UGUGAG,UGUGAU,UGUGGG,UGUGGU,UGUGUG,UGUGUU
ZRANB2 1 3173 0.01111111 0.0045997733 1.272368 UAAAGG AAAGGU,AGGGAA,AGGUAA,AGGUAC,AGGUAG,AGGUAU,AGGUCU,AGGUUA,AGGUUU,CGGUAA,CGGUAG,CGGUAU,CGGUCU,GAGGUU,GGGUAA,GGGUGA,GGUAAA,GGUGGU,GUAAAG,GUGGUG,UAAAGG,UGGUAA,UGGUGG
ENOX1 1 3195 0.01111111 0.0046316558 1.262403 AGGACA AAGACA,AAUACA,AGACAG,AGGACA,AGUACA,AUACAG,CAGACA,CAUACA,CGGACA,CGUACA,GGACAG,GUACAG,UAGACA,UAUACA,UGGACA,UGUACA
RBMX 2 4925 0.01666667 0.0071387787 1.223216 AGAAGG,GAAGGA AAGAAG,AAGGAA,AAGUAA,AAGUGU,ACCAAA,AGAAGG,AGGAAG,AGUAAC,AGUGUU,AUCAAA,AUCCCA,AUCCCC,GAAGGA,GGAAGG,GUAACA,UAACAA,UAAGAC,UCAAAA
SF1 2 4931 0.01666667 0.0071474739 1.221460 ACAGUC,CAGUCA 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
SRSF5 4 8869 0.02777778 0.0128544391 1.111665 AGAAGA,AUAAAG,UAAAGG AACAGC,AAGAAG,AGAAGA,AGGAAG,AUAAAG,CAACAG,CACAGA,CACAGC,CACAUA,CACAUC,CACGGA,CACGGC,CACGUA,CACGUC,CCGCAG,CGCAGA,CGCAGC,CGCAGG,CGCAUA,CGCAUC,CGCGGA,CGCGGC,CGCGUA,CGCGUC,GAAGAA,GAGGAA,GGAAGA,UAAAGG,UACAGA,UACAGC,UACAUA,UACAUC,UACGGA,UACGGC,UACGUA,UACGUC,UGCAGA,UGCAGC,UGCAUA,UGCAUC,UGCGGA,UGCGGC,UGCGUA,UGCGUC
PCBP2 5 11045 0.03333333 0.0160079069 1.058181 AAAUUA,AAUUAC,CCCUCC,CCUCCU,UAACCC AAACCA,AAAUUA,AAAUUC,AACCAA,AACCCU,AAUUAA,AAUUAC,AAUUCA,AAUUCC,ACAUUA,ACCAAA,ACCCUA,ACCUUA,AUUAAA,AUUACC,AUUCAC,AUUCCA,AUUCCC,CAAUUA,CAUUAA,CCAUUA,CCAUUC,CCCCCA,CCCCCC,CCCCCU,CCCUAA,CCCUCC,CCCUUA,CCCUUC,CCUCCA,CCUCCC,CCUCCU,CCUUAA,CCUUCC,CUAACC,CUCCCA,CUCCCC,CUCCCU,CUUAAA,CUUCCA,CUUCCC,CUUCCU,GGGGGG,UAACCC,UCCCCA,UUAGAG,UUAGGA,UUAGGG,UUUUUU
YTHDC1 2 5576 0.01666667 0.0080822104 1.044144 GCCUGC,UACUGC GAAUAC,GAAUGC,GACUAC,GACUGC,GAGUAC,GAGUGC,GCAUAC,GCAUGC,GCCUAC,GCCUGC,GCGUAC,GCGUGC,GGAUAC,GGAUGC,GGCUAC,GGCUGC,GGGUAC,GGGUGC,UAAUAC,UAAUGC,UACUAC,UACUGC,UAGUAC,UAGUGC,UCAUAC,UCAUGC,UCCUAC,UCCUGC,UCGUAC,UCGUGC,UGAUAC,UGAUGC,UGCUAC,UGCUGC,UGGUAC,UGGUGC

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
SART3 1 12 0.09090909 0.000851454 6.738352 AGAAAA AAAAAA,AGAAAA,GAAAAA,GAAAAC
PABPC5 1 18 0.09090909 0.001244433 6.190864 AGAAAA AGAAAA,AGAAAG,AGAAAU,GAAAAU,GAAAGU,GAAAUU
PABPC1 1 19 0.09090909 0.001309929 6.116864 AGAAAA AAAAAA,ACAAAC,ACGAAU,AGAAAA,CAAACC,CAAAUA,CGAACA,CUAAUA,GAAAAA,GAAAAC

RBP on BSJ (Exon and Intron)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
RBM25 1 53 0.004761905 0.0002720677 4.129501 UCGGGC AUCGGG,CGGGCA,UCGGGC
AKAP1 4 221 0.011904762 0.0011185006 3.411901 AUAUAU,UAUAUA AUAUAU,UAUAUA
RBMY1A1 1 95 0.004761905 0.0004836759 3.299426 CAAGAC ACAAGA,CAAGAC
RBM42 1 103 0.004761905 0.0005239823 3.183949 AACUAA AACUAA,AACUAC,ACUAAG,ACUACG
RBMS1 3 217 0.009523810 0.0010983474 3.116204 AUAUAG,UAUAUA AUAUAC,AUAUAG,GAUAUA,UAUAUA
PPRC1 1 127 0.004761905 0.0006449012 2.884389 CCGCGC CCGCGC,CGCGCC,CGCGCG,CGGCGC,GCGCGC,GGCGCC,GGCGCG,GGGCGC
IFIH1 1 146 0.004761905 0.0007406288 2.684716 GCCGCG CCGCGG,CGCGGA,GCCGCG,GCGGAU,GGCCCU,GGCCGC,GGGCCG
RBMS3 6 562 0.016666667 0.0028365578 2.554752 AUAUAG,AUAUAU,CAUAUA,UAUAUA AAUAUA,AUAUAG,AUAUAU,CAUAUA,CUAUAG,CUAUAU,UAUAGA,UAUAGC,UAUAUA,UAUAUC
HNRNPLL 7 748 0.019047619 0.0037736800 2.335567 ACAAAC,CAAACA,CACACC,GCAAAC,GCACAC ACAAAC,ACACAC,ACACCA,ACAUAC,ACCACA,ACCGCA,ACGACA,ACUGCA,AGACGA,CAAACA,CACACA,CACACC,CACCAC,CACCGC,CACUGC,CAGACG,CAUACA,GACGAC,GCAAAC,GCACAC,GCAUAC
PABPC1 13 1321 0.033333333 0.0066606207 2.323237 AAAAAA,AAAAAC,ACAAAC,ACUAAU,AGAAAA,CAAACA,CAAACC,CGAAUC,GAAAAA AAAAAA,AAAAAC,ACAAAC,ACAAAU,ACGAAC,ACGAAU,ACUAAC,ACUAAU,AGAAAA,CAAACA,CAAACC,CAAAUA,CAAAUC,CGAACA,CGAACC,CGAAUA,CGAAUC,CUAACA,CUAACC,CUAAUA,CUAAUC,GAAAAA,GAAAAC
ACO1 2 325 0.007142857 0.0016424829 2.120623 CAGUGA,CAGUGC CAGUGA,CAGUGC,CAGUGG,CAGUGU
HNRNPM 1 222 0.004761905 0.0011235389 2.083489 GGGGGG AAGGAA,GAAGGA,GGGGGG
IGHMBP2 2 350 0.007142857 0.0017684401 2.014024 AAAAAA AAAAAA
SART3 5 777 0.014285714 0.0039197904 1.865725 AAAAAA,AAAAAC,AGAAAA,GAAAAA AAAAAA,AAAAAC,AGAAAA,GAAAAA,GAAAAC
RBM3 3 541 0.009523810 0.0027307537 1.802240 AAAACU,AAACUA,AAGACG AAAACG,AAAACU,AAACGA,AAACUA,AAGACG,AAGACU,AAUACG,AAUACU,AGACGA,AGACUA,AUACGA,AUACUA,GAAACG,GAAACU,GAGACG,GAGACU,GAUACG,GAUACU
AGO1 1 283 0.004761905 0.0014308746 1.734641 UGAGGU AGGUAG,GAGGUA,GGUAGU,GUAGUA,UGAGGU
SNRPB2 1 288 0.004761905 0.0014560661 1.709463 UUGCAG AUUGCA,GUAUUG,UAUUGC,UGCAGU,UUGCAG
PABPC4 2 462 0.007142857 0.0023327287 1.614483 AAAAAA AAAAAA,AAAAAG
PABPC3 1 310 0.004761905 0.0015669085 1.603618 AAAAAC AAAAAC,AAAACA,AAAACC,GAAAAC
ZNF638 3 646 0.009523810 0.0032597743 1.546767 UGUUCU,UGUUGG CGUUCG,CGUUCU,CGUUGG,CGUUGU,GGUUCG,GGUUCU,GGUUGG,GGUUGU,GUUCGU,GUUCUU,GUUGGU,GUUGUU,UGUUCG,UGUUCU,UGUUGG,UGUUGU
SSB 2 505 0.007142857 0.0025493753 1.486358 GCUGUU,UGCUGU CUGUUU,GCUGUU,UGCUGU,UGUUUU
RBM28 1 340 0.004761905 0.0017180572 1.470761 GUGUAG AGUAGA,AGUAGG,AGUAGU,GAGUAG,GUGUAG,UGUAGA,UGUAGG,UGUAGU
YBX1 5 1321 0.014285714 0.0066606207 1.100845 CACACC,CCAGCA,GAUCUG,GCCUGC,GUCUGC 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
IGF2BP3 5 1348 0.014285714 0.0067966546 1.071676 AAAAAC,ACAAAC,CAAACA AAAAAC,AAAACA,AAAAUC,AAACAC,AAACUC,AAAUAC,AAAUCA,AAAUUC,AACACA,AACUCA,AAUACA,AAUUCA,ACAAAC,ACAAUC,ACACAC,ACACUC,ACAUAC,ACAUUC,CAAACA,CAAUCA,CACACA,CACUCA,CAUACA,CAUUCA
AGO2 2 677 0.007142857 0.0034159613 1.064210 AAAAAA 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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