ENSG00000144040:-:2:73020238:73040931

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000144040:-:2:73020238:73040931 ENSG00000144040 ENST00000474528 - 2 73020239 73040931 186 AGACGUCUCAGAGAGGCUGUGCAGCUGCUGGAGGACUAUAAGCAUGGGACCCUGCGCCCGGGGGUCACCAAUGAACAGCUCUGGAGUGCACAGAAAAUCAAGCAGGCUAUUCUACAUCCGGACACCAAUGAGAAGAUCUUCAUGCCAUUUAGAAUGUCAGGUUAUAUUCCUUUUGGGACGCCAAUUAGACGUCUCAGAGAGGCUGUGCAGCUGCUGGAGGACUAUAAGCAUGGGAC circ
ENSG00000144040:-:2:73020238:73040931 ENSG00000144040 ENST00000474528 - 2 73020239 73040931 22 GGACGCCAAUUAGACGUCUCAG bsj
ENSG00000144040:-:2:73020238:73040931 ENSG00000144040 ENST00000474528 - 2 73040922 73041131 210 UAGCUCUACUUCAUUUUUUAAACUGCCGAGUAAGAACAUUUAGGUGGUAUUUCUAUAUGAUUUUGUGUGUGUCCCAUGAACUGAGGGCAGGCCCAAAGCCUUGCACUGGCAGUAUUUGAUACUGAUGUAAUCCCACAAAAGAAAAAUUUGCGGGAGCCCUGGAUCUGUGCCCCUCAAUGUCUCUUUUCUUUCUUCUGCAGAGACGUCUCA ie_up
ENSG00000144040:-:2:73020238:73040931 ENSG00000144040 ENST00000474528 - 2 73020039 73020248 210 GACGCCAAUUGUAAGUGUUACCUUCAAAGGAUUUCCUUUUCUAAAAAAUUAUUUUAAAUGUCUAACUUUAUGUUAUUGCUCACGGGUAUUUGACUGAAUUGUUGAUUUAGGAUAAGUCAAUUCCUGGAGGGAAAUUACCAAAUAAAAUGAUAUGUAUUUCUUACCACAUCUCUUGAUGCUGAUUGGCAAACCUCUUUUCAUAAAAAGCCU 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
ANKHD1 1 339 0.01075269 0.0004927293 4.447758 AGACGU AGACGA,AGACGU,GACGAA,GACGAU,GACGUA,GACGUU
RBM8A 1 611 0.01075269 0.0008869128 3.599761 UGCGCC ACGCGC,AUGCGC,CGCGCC,CGCGCG,CGCGCU,GCGCGC,GUGCGC,UGCGCC,UGCGCG,UGCGCU
SNRNP70 2 1237 0.01612903 0.0017941145 3.168316 AAUCAA,AUCAAG AAUCAA,AUCAAG,AUUCAA,GAUCAA,GUUCAA,UUCAAG
RBFOX1 1 1077 0.01075269 0.0015622419 2.783008 AGCAUG AGCAUG,GCAUGA,GCAUGC,GCAUGU,UGACUG,UGCAUG
PABPN1 1 1222 0.01075269 0.0017723764 2.600940 AGAAGA AAAAGA,AGAAGA
NONO 1 1498 0.01075269 0.0021723567 2.307364 GAGAGG AGAGGA,AGGAAC,GAGAGG,GAGGAA
PABPC5 2 2400 0.01612903 0.0034795387 2.212692 AGAAAA,GAAAAU AGAAAA,AGAAAG,AGAAAU,GAAAAU,GAAAGU,GAAAUU
LIN28A 4 4315 0.02688172 0.0062547643 2.103598 GGAGGA,UGGAGG,UGGAGU AGGAGA,AGGAGU,CGGAGA,CGGAGG,CGGAGU,GGAGAA,GGAGAU,GGAGGA,GGAGGG,GGAGUA,UGGAGA,UGGAGG,UGGAGU
PUM2 1 1890 0.01075269 0.0027404447 1.972215 UACAUC GUAAAU,GUACAU,GUAGAU,GUAUAU,UAAAUA,UACAUA,UACAUC,UAGAUA,UAUAUA,UGUAAA,UGUACA,UGUAGA,UGUAUA
CPEB2 1 2261 0.01075269 0.0032780993 1.713766 CCUUUU AUUUUU,CAUUUU,CCUUUU,CUUUUU,UUUUUU
RBM46 3 4554 0.02150538 0.0066011240 1.703914 AAUCAA,AAUGAA,AUCAAG AAUCAA,AAUCAU,AAUGAA,AAUGAU,AUCAAA,AUCAAG,AUCAAU,AUCAUA,AUCAUG,AUCAUU,AUGAAA,AUGAAG,AUGAAU,AUGAUA,AUGAUG,AUGAUU,GAUCAA,GAUCAU,GAUGAA,GAUGAU
SART3 1 2634 0.01075269 0.0038186524 1.493562 AGAAAA AAAAAA,AAAAAC,AGAAAA,GAAAAA,GAAAAC
TARDBP 1 2654 0.01075269 0.0038476365 1.482653 GAAUGU GAAUGA,GAAUGG,GAAUGU,GUGAAU,GUGUGU,GUUGUG,GUUGUU,GUUUUG,UGAAUG,UGUGUG,UUGUGC,UUGUUC,UUUUGC
SRSF5 5 8869 0.03225806 0.0128544391 1.327393 AACAGC,AGAAGA,CACAGA,UACAUC,UGCAGC 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
NELFE 1 3028 0.01075269 0.0043896388 1.292523 CUCUGG CUCUCU,CUCUGG,CUGGCU,CUGGUU,GCUAAC,GGCUAA,GGUCUC,GGUUAG,GUCUCU,UCUCUC,UCUCUG,UCUGGC,UCUGGU,UGGCUA,UGGUUA
RBM4 1 3065 0.01075269 0.0044432593 1.275007 UUCCUU CCUCUU,CCUUCC,CCUUCU,CGCGCG,CGCGGG,CGCGGU,CUCUUU,CUUCCU,CUUCUU,GCGCGA,GCGCGC,GCGCGG,UCCUUC,UUCCUU,UUCUUG
HNRNPH3 4 7688 0.02688172 0.0111429292 1.270497 CGGGGG,GAAUGU,GGAGGA 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
ZRANB2 1 3173 0.01075269 0.0045997733 1.225063 AGGUUA 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 0.01075269 0.0046316558 1.215097 CGGACA AAGACA,AAUACA,AGACAG,AGGACA,AGUACA,AUACAG,CAGACA,CAUACA,CGGACA,CGUACA,GGACAG,GUACAG,UAGACA,UAUACA,UGGACA,UGUACA
IGF2BP3 2 4815 0.01612903 0.0069793662 1.208492 AAAAUC,AAAUCA AAAAAC,AAAACA,AAAAUC,AAACAC,AAACUC,AAAUAC,AAAUCA,AAAUUC,AACACA,AACUCA,AAUACA,AAUUCA,ACAAAC,ACAAUC,ACACAC,ACACUC,ACAUAC,ACAUUC,CAAACA,CAAUCA,CACACA,CACUCA,CAUACA,CAUUCA
HNRNPF 5 10561 0.03225806 0.0153064921 1.075516 AUGGGA,CGGGGG,GAAUGU,GGAGGA AAGGCG,AAGGGA,AAGGGG,AAGGUG,AAUGUG,AGGAAG,AGGCGA,AGGGAA,AGGGAU,AGGGGA,AUGGGA,AUGGGG,AUGUGG,CGAUGG,CGGGAU,CGGGGG,CUGGGG,GAAGGG,GAAGGU,GAAUGU,GAGGAA,GAGGGG,GAUGGG,GGAAGG,GGAAUG,GGAGGA,GGAGGG,GGAUGG,GGCGAA,GGGAAG,GGGAAU,GGGAGG,GGGAUG,GGGCUG,GGGGAA,GGGGAG,GGGGCU,GGGGGC,GGGGGG,GGGGUA,UGGGAA,UGGGGU,UGUGGG
HNRNPLL 1 3534 0.01075269 0.0051229360 1.069655 ACACCA ACAAAC,ACACAC,ACACCA,ACAUAC,ACCACA,ACCGCA,ACGACA,ACUGCA,AGACGA,CAAACA,CACACA,CACACC,CACCAC,CACCGC,CACUGC,CAGACG,CAUACA,GACGAC,GCAAAC,GCACAC,GCAUAC
YBX1 3 7119 0.02150538 0.0103183321 1.059488 ACACCA,CCCUGC,CCUGCG 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

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
PCBP2 1 26 0.09090909 0.001768405 5.683904 CAAUUA AAACCA,AAAUUA,AAAUUC,AAUUAA,ACCAAA,AUUAAA,CCAUUC,CCCCCU,CCCUCC,CCCUUA,CCUCCC,CUCCCU,CUUCCA,UAACCC,UUAGAG,UUAGGA,UUAGGG
PCBP1 1 35 0.09090909 0.002357873 5.268867 CAAUUA AAAAAA,AAACCA,AAAUUA,AAAUUC,AAUUAA,ACCAAA,ACCCUC,AUUAAA,CAAACC,CAUACC,CCAACC,CCACCC,CCAUAC,CCAUUC,CCCACC,CCCCAC,CCCUCC,CCCUUA,CCUCCC,CCUCUU,UUAGAG,UUAGGA,UUAGGG
HNRNPA1 1 119 0.09090909 0.007859576 3.531901 AUUAGA AAAAAA,AAAGAG,AAGAGG,AAGGUG,AAUUUA,AGAGGA,AGAUAU,AGAUUA,AGGAAG,AGGAGC,AGGGAC,AGGGCA,AGGGUU,AGUAGG,AGUGAA,AUAGGG,AUUAGA,AUUUAA,CAAAGA,CAAGGA,CAGGGA,CCAAGG,GAAGGU,GACUUA,GAGGAA,GAGGAG,GAGUGG,GAUUAG,GCAGGC,GCCAAG,GGAAGG,GGACUU,GGAGGA,GGCAGG,GGGACU,GGGCAG,GGUGCG,GUUAGG,UAGACA,UAGAGA,UAGAGU,UAGAUU,UAGGAA,UAGGCU,UAGGGC,UAGUGA,UAGUUA,UCGGGC,UGGUGC,UUAGAU,UUAGGG,UUUAGA

RBP on BSJ (Exon and Intron)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
ANKHD1 1 56 0.004761905 0.0002871826 4.051499 AGACGU AGACGA,AGACGU,GACGAA,GACGAU,GACGUA,GACGUU
RBFOX2 1 124 0.004761905 0.0006297864 2.918604 UGACUG UGACUG,UGCAUG
PABPN1 1 178 0.004761905 0.0009018541 2.400573 AAAAGA AAAAGA,AGAAGA
TUT1 1 230 0.004761905 0.0011638452 2.032640 GAUACU AAAUAC,AAUACU,AGAUAC,CAAUAC,CGAUAC,GAUACU
G3BP2 3 490 0.009523810 0.0024738009 1.944809 AGGAUA,AGGAUU,GGAUAA AGGAUA,AGGAUG,AGGAUU,GGAUAA,GGAUAG,GGAUGA,GGAUGG,GGAUUA,GGAUUG
CELF2 6 881 0.016666667 0.0044437727 1.907109 GUGUGU,UAUGUU,UGUGUG,UUGUGU AUGUGU,GUAUGU,GUCUGU,GUGUGU,GUUGUU,UAUGUG,UAUGUU,UGUGUG,UGUUGU,UUGUGU
YBX2 1 263 0.004761905 0.0013301088 1.839994 ACAUCU AACAAC,AACAUC,ACAACA,ACAACG,ACAACU,ACAUCA,ACAUCG,ACAUCU
CELF5 4 669 0.011904762 0.0033756550 1.818299 GUGUGU,UGUGUG GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU
RBFOX1 1 287 0.004761905 0.0014510278 1.714464 UGACUG AGCAUG,GCAUGA,GCAUGC,GCAUGU,UGACUG,UGCAUG
SNRPB2 1 288 0.004761905 0.0014560661 1.709463 UAUUGC AUUGCA,GUAUUG,UAUUGC,UGCAGU,UUGCAG
PABPC4 2 462 0.007142857 0.0023327287 1.614483 AAAAAA,AAAAAG AAAAAA,AAAAAG
CELF4 4 776 0.011904762 0.0039147521 1.604546 GUGUGU,UGUGUG GGUGUG,GGUGUU,GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU
HNRNPA3 1 349 0.004761905 0.0017634019 1.433177 GGAGCC AAGGAG,AGGAGC,CAAGGA,CCAAGG,GCCAAG,GGAGCC
IGHMBP2 1 350 0.004761905 0.0017684401 1.429061 AAAAAA AAAAAA
RBM24 4 888 0.011904762 0.0044790407 1.410277 GUGUGU,UGUGUG AGAGUG,AGUGUG,GAGUGA,GAGUGG,GAGUGU,GUGUGA,GUGUGG,GUGUGU,UGAGUG,UGUGUG
RBM3 2 541 0.007142857 0.0027307537 1.387202 GAGACG,GAUACU AAAACG,AAAACU,AAACGA,AAACUA,AAGACG,AAGACU,AAUACG,AAUACU,AGACGA,AGACUA,AUACGA,AUACUA,GAAACG,GAAACU,GAGACG,GAGACU,GAUACG,GAUACU
CELF1 5 1097 0.014285714 0.0055320435 1.368689 GUGUGU,UGUGUG,UUGUGU CUGUCU,GUGUGU,GUGUUG,GUUGUG,GUUUGU,UGUCUG,UGUGUG,UGUGUU,UGUUGU,UGUUUG,UUGUGU
SART3 3 777 0.009523810 0.0039197904 1.280762 AAAAAA,AGAAAA,GAAAAA AAAAAA,AAAAAC,AGAAAA,GAAAAA,GAAAAC
SNRPA 9 1947 0.023809524 0.0098145909 1.278539 AUGCUG,AUUCCU,GCAGUA,GGGUAU,GUUACC,UUACCU,UUCCUG,UUGCAC,UUUCCU ACCUGC,AGCAGU,AGGAGA,AGUAGG,AGUAGU,AUACCU,AUGCAC,AUGCUG,AUUCCU,AUUGCA,CAGUAG,CCUGCU,CUGCUA,GAGCAG,GAUACC,GAUUCC,GCAGUA,GGAGAU,GGGUAU,GGUAUG,GUAGGC,GUAGGG,GUAGUC,GUAGUG,GUAUGC,GUUACC,GUUUCC,UACCUG,UAUGCU,UCCUGC,UGCACA,UGCACC,UGCACG,UUACCU,UUCCUG,UUGCAC,UUUCCU
SAMD4A 3 790 0.009523810 0.0039852882 1.256855 CGGGUA,CUGGCA,GCGGGA CGGGAA,CGGGAC,CGGGCA,CGGGCC,CGGGUA,CGGGUC,CUGGAA,CUGGAC,CUGGCA,CUGGCC,CUGGUA,CUGGUC,GCGGGA,GCGGGC,GCGGGU,GCUGGA,GCUGGC,GCUGGU
PABPC5 2 596 0.007142857 0.0030078597 1.247764 AGAAAA,GAAAUU AGAAAA,AGAAAG,AGAAAU,GAAAAU,GAAAGU,GAAAUU
CSTF2 4 1022 0.011904762 0.0051541717 1.207726 GUGUGU,UGUGUG GUGUGU,GUGUUG,GUGUUU,GUUUUG,UGUGUG,UGUGUU,UGUUUG,UGUUUU
TARDBP 4 1034 0.011904762 0.0052146312 1.190902 GUGUGU,UGUGUG GAAUGA,GAAUGG,GAAUGU,GUGAAU,GUGUGU,GUUGUG,GUUGUU,GUUUUG,UGAAUG,UGUGUG,UUGUGC,UUGUUC,UUUUGC
KHDRBS2 4 1051 0.011904762 0.0053002821 1.167398 AAUAAA,AUAAAA,UUUUUU AAUAAA,AUAAAA,AUAAAC,GAUAAA,UUUUUU
RC3H1 2 631 0.007142857 0.0031841999 1.165570 CUUCUG,UCUGUG CCCUUC,CCUUCU,CUUCUG,UCCCUU,UCUGUG,UUCUGU
RBM4 4 1094 0.011904762 0.0055169287 1.109602 CCUCUU,CUCUUU,UUCCUU CCUCUU,CCUUCC,CCUUCU,CGCGCG,CGCGGG,CGCGGU,CUCUUU,CUUCCU,CUUCUU,GCGCGA,GCGCGC,GCGCGG,UCCUUC,UUCCUU,UUCUUG
PABPC1 5 1321 0.014285714 0.0066606207 1.100845 AAAAAA,AGAAAA,CAAACC,CAAAUA,GAAAAA AAAAAA,AAAAAC,ACAAAC,ACAAAU,ACGAAC,ACGAAU,ACUAAC,ACUAAU,AGAAAA,CAAACA,CAAACC,CAAAUA,CAAAUC,CGAACA,CGAACC,CGAAUA,CGAAUC,CUAACA,CUAACC,CUAAUA,CUAAUC,GAAAAA,GAAAAC
KHDRBS3 6 1646 0.016666667 0.0082980653 1.006119 AAAUAA,AAUAAA,AUAAAA,UUAAAC,UUUUUU AAAUAA,AAUAAA,AGAUAA,AUAAAA,AUAAAC,AUAAAG,AUUAAA,GAUAAA,UAAAAC,UAAAUA,UUAAAC,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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