ENSG00000141298:-:17:29648143:29672129

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000141298:-:17:29648143:29672129 ENSG00000141298 ENST00000540801 - 17 29648144 29672129 813 GUCUGCACUACAGAGCUUACACAAGGCUUGUGAAGUCGCCAGAGCGCAUAACUACUACCCAGGCAGCCUAUUUCUCACUUGGGUGAGUUAUUAUGAGAGCCAUAUCAACUCAGAUCAAUCCUCAGUCAAUGAAUGGAAUGCAAUGCAAGAUGUACAGUCCCACCGGCCCGACUCUCCAGCUCUCUUCACCGACAUACCUACUGAACGUGAACGAACAGAAAGGCUAAUUAAAACCAAAUUAAGGGAGAUCAUGAUGCAGAAGGAUUUGGAGAAUAUUACAUCCAAAGAGAUAAGAACAGAGUUGGAAAUGCAAAUGGUGUGCAACUUGCGGGAAUUCAAGGAAUUUAUAGACAAUGAAAUGAUAGUGAUCCUUGGUCAAAUGGAUAGCCCUACACAGAUAUUUGAGCAUGUGUUCCUGGGCUCAGAAUGGAAUGCCUCCAACUUAGAGGACUUACAGAACCGAGGGGUACGGUAUAUCUUGAAUGUCACUCGAGAGAUAGAUAACUUCUUCCCAGGAGUCUUUGAGUAUCAUAACAUUCGGGUAUAUGAUGAAGAGGCAACGGAUCUCCUGGCGUACUGGAAUGACACUUACAAAUUCAUCUCUAAAGCAAAGAAACAUGGAUCUAAAUGCCUUGUGCACUGCAAAAUGGGGGUGAGUCGCUCAGCCUCCACCGUGAUUGCCUAUGCAAUGAAGGAAUAUGGCUGGAAUCUGGACCGAGCCUAUGACUAUGUGAAAGAAAGACGAACGGUAACCAAGCCCAACCCAAGCUUCAUGAGACAACUGGAAGAGUAUCAGGGGAUCUUGCUGGCAAGGUCUGCACUACAGAGCUUACACAAGGCUUGUGAAGUCGCCAGAGCGCAUA circ
ENSG00000141298:-:17:29648143:29672129 ENSG00000141298 ENST00000540801 - 17 29648144 29672129 22 UUGCUGGCAAGGUCUGCACUAC bsj
ENSG00000141298:-:17:29648143:29672129 ENSG00000141298 ENST00000540801 - 17 29672120 29672329 210 CUUUCAGCAAAUGUCUUGUCCAUUGCUGUGGAUAGAUAAUAUGGUAUAAUCAGAAUUGGAGAAUCUUGACUUUCAAGGAGUAGAUUGUCCAGAGGACAAAUUCUAUAGAAUUUAAAAAUUAGAAGAGUUUGGAGUACACAGGUUAUUGGCCUUUGGCACCCCACAGUUCUAUGGUGCUCAUUUCCCAGCAUGUCUUUCAGGUCUGCACUA ie_up
ENSG00000141298:-:17:29648143:29672129 ENSG00000141298 ENST00000540801 - 17 29647944 29648153 210 UGCUGGCAAGGUGAGUCAGUGACUUUCUCCAAUUCUCCCUCCUUUUAAGUUCCCUAAAGCAAGAUGAAGUGUCCUUCUCUGUAGCUACUUCUCAAGCUGAUUUGGAUGUGAUAUUUUUUCAAAAAAGACUUAUUUCUCUAUCAAUCCAGUUUUCAAAACAUAAGUGUAAGCAUUUAAGAUUUGCAUGGGCUGGCCGGGCACAGUGGCUCA 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
OAS1 1 77 0.002460025 0.0001130379 4.443794 GCAUAA GCAUAA
ANKHD1 2 339 0.003690037 0.0004927293 2.904768 AGACGA,GACGAA AGACGA,AGACGU,GACGAA,GACGAU,GACGUA,GACGUU
PTBP2 1 267 0.002460025 0.0003883867 2.663107 CUCUCU CUCUCU
HNRNPA0 2 453 0.003690037 0.0006579386 2.487610 AAUUUA,AGAUAU AAUUUA,AGAUAU,AGUAGG
HNRNPM 4 999 0.006150062 0.0014492040 2.085340 AAGGAA,GAAGGA AAGGAA,GAAGGA,GGGGGG
RBM42 1 407 0.002460025 0.0005912752 2.056771 AACUAC AACUAA,AACUAC,ACUAAG,ACUACG
FXR1 1 411 0.002460025 0.0005970720 2.042696 AUGACA ACGACA,ACGACG,AUGACA,AUGACG
MATR3 2 739 0.003690037 0.0010724109 1.782777 AUCUUG AAUCUU,AUCUUA,AUCUUG,CAUCUU
RBM46 17 4554 0.022140221 0.0066011240 1.745886 AAUGAA,AAUGAU,AUCAAU,AUCAUA,AUCAUG,AUGAAA,AUGAAG,AUGAAU,AUGAUA,AUGAUG,GAUCAA,GAUCAU,GAUGAA AAUCAA,AAUCAU,AAUGAA,AAUGAU,AUCAAA,AUCAAG,AUCAAU,AUCAUA,AUCAUG,AUCAUU,AUGAAA,AUGAAG,AUGAAU,AUGAUA,AUGAUG,AUGAUU,GAUCAA,GAUCAU,GAUGAA,GAUGAU
HNRNPAB 5 1782 0.007380074 0.0025839306 1.514068 AAAGAC,AGACAA,CAAAGA AAAGAC,AAGACA,ACAAAG,AGACAA,AUAGCA,CAAAGA,GACAAA
SNRNP70 3 1237 0.004920049 0.0017941145 1.455401 AUUCAA,GAUCAA,UUCAAG AAUCAA,AUCAAG,AUUCAA,GAUCAA,GUUCAA,UUCAAG
PUM2 5 1890 0.007380074 0.0027404447 1.429225 GUAUAU,UACAUC,UAGAUA,UGUACA GUAAAU,GUACAU,GUAGAU,GUAUAU,UAAAUA,UACAUA,UACAUC,UAGAUA,UAUAUA,UGUAAA,UGUACA,UGUAGA,UGUAUA
TARDBP 7 2654 0.009840098 0.0038476365 1.354700 GAAUGA,GAAUGG,GAAUGU,UGAAUG,UUGUGC GAAUGA,GAAUGG,GAAUGU,GUGAAU,GUGUGU,GUUGUG,GUUGUU,GUUUUG,UGAAUG,UGUGUG,UUGUGC,UUGUUC,UUUUGC
RBM6 2 1054 0.003690037 0.0015289102 1.271132 AUCCAA,CAUCCA AAUCCA,AUCCAA,AUCCAG,CAUCCA,UAUCCA
RBFOX1 2 1077 0.003690037 0.0015622419 1.240017 AGCAUG,GCAUGU AGCAUG,GCAUGA,GCAUGC,GCAUGU,UGACUG,UGCAUG
SAMD4A 10 3992 0.013530135 0.0057866714 1.225371 CGGGAA,CGGGUA,CUGGAA,CUGGAC,CUGGCA,GCGGGA,GCUGGA,GCUGGC CGGGAA,CGGGAC,CGGGCA,CGGGCC,CGGGUA,CGGGUC,CUGGAA,CUGGAC,CUGGCA,CUGGCC,CUGGUA,CUGGUC,GCGGGA,GCGGGC,GCGGGU,GCUGGA,GCUGGC,GCUGGU
EIF4B 2 1179 0.003690037 0.0017100607 1.109588 GUUGGA,UUGGAA CUCGGA,CUUGGA,GUCGGA,GUUGGA,UCGGAA,UCGGAC,UUGGAA,UUGGAC
ZCRB1 3 1605 0.004920049 0.0023274215 1.079940 AAUUAA,GACUUA AAUUAA,ACUUAA,AUUUAA,GAAUUA,GACUUA,GAUUAA,GAUUUA,GCUUAA,GGAUUA,GGCUUA,GGUUUA,GUUUAA

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
YBX1 1 19 0.09090909 0.001309929 6.116864 GGUCUG AACCAC,ACACCA,ACAUCU,ACCACC,CACCAC,CAGCAA,CCACCA,CCAGCA,CCUGCG,CUGCGG,GAUCUG,GCCUGC,UCCAGC,UGCGGU
ZRANB2 1 45 0.09090909 0.003012837 4.915230 AGGUCU AAAGGU,AGGGAA,AGGUAA,AGGUAC,AGGUAG,AGGUAU,AGGUCU,AGGUUA,AGGUUU,GAGGUU,GGGUAA,GGGUGA,GGUAAA,GGUGGU,GUAAAG,UAAAGG,UGGUAA
SFPQ 1 153 0.09090909 0.010086455 3.172005 GGUCUG AAGAAC,AAGAGC,AAGAGG,AAGCAA,AAGGAA,AAGGAC,AAGGGA,ACUGGG,AGAGAG,AGAGGA,AGAGGU,AGGAAC,AGGACC,AGGGAU,AGGGGG,AUCGGA,CAGGCA,CUGGAG,CUGGGA,GAAGAA,GAAGAG,GAAGCA,GAAGGA,GAGGAA,GAGGAC,GAGGUA,GCAGGC,GGAAGA,GGAGAG,GGAGGA,GGAGGG,GGGGGA,GUAAGA,GUAAUG,GUAGUG,GUAGUU,GUCUGG,GUGAUU,UAAGAG,UAAGGA,UAAGGG,UAAUGG,UAAUUG,UAGAGA,UAGAUC,UAGUGG,UAGUGU,UAGUUG,UCGGAA,UCUAAG,UGAAGC,UGAUGG,UGAUGU,UGAUUG,UGCAGG,UGGAGA,UGGAGC,UGGAGG,UGGUUU,UUAAUG,UUAGUG,UUAGUU,UUGAAG,UUGGUU

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 CGGGCA AUCGGG,CGGGCA,UCGGGC
PABPN1 2 178 0.007142857 0.0009018541 2.985535 AAAAGA,AGAAGA AAAAGA,AGAAGA
RBFOX2 1 124 0.004761905 0.0006297864 2.918604 UGCAUG UGACUG,UGCAUG
RBM6 2 191 0.007142857 0.0009673519 2.884389 AAUCCA,AUCCAG AAUCCA,AUCCAA,AUCCAG,CAUCCA,UAUCCA
RBFOX1 3 287 0.009523810 0.0014510278 2.714464 AGCAUG,GCAUGU,UGCAUG AGCAUG,GCAUGA,GCAUGC,GCAUGU,UGACUG,UGCAUG
MATR3 2 216 0.007142857 0.0010933091 2.707800 AAUCUU,AUCUUG AAUCUU,AUCUUA,AUCUUG,CAUCUU
ERI1 2 228 0.007142857 0.0011537686 2.630147 UUUCAG UUCAGA,UUUCAG
IGF2BP1 1 173 0.004761905 0.0008766626 2.441445 GCACCC AAGCAC,ACCCGU,AGCACC,CACCCG,CCCGUU,GCACCC
HNRNPA0 1 200 0.004761905 0.0010126965 2.233337 AAUUUA AAUUUA,AGAUAU,AGUAGG
ACO1 2 325 0.007142857 0.0016424829 2.120623 CAGUGA,CAGUGG CAGUGA,CAGUGC,CAGUGG,CAGUGU
SRP14 1 218 0.004761905 0.0011033857 2.109602 CUGUAG CCUGUA,CGCCUG,CUGUAG,GCCUGU
RBM28 2 340 0.007142857 0.0017180572 2.055723 AGUAGA,GAGUAG AGUAGA,AGUAGG,AGUAGU,GAGUAG,GUGUAG,UGUAGA,UGUAGG,UGUAGU
HNRNPA3 2 349 0.007142857 0.0017634019 2.018140 AAGGAG,CAAGGA AAGGAG,AGGAGC,CAAGGA,CCAAGG,GCCAAG,GGAGCC
HNRNPAB 2 351 0.007142857 0.0017734784 2.009919 AAAGAC,GACAAA AAAGAC,AAGACA,ACAAAG,AGACAA,AUAGCA,CAAAGA,GACAAA
SNRNP70 1 253 0.004761905 0.0012797259 1.895704 UUCAAG AAUCAA,AUCAAG,AUUCAA,GAUCAA,GUUCAA,UUCAAG
LIN28A 6 900 0.016666667 0.0045395002 1.876360 AGGAGU,GGAGAA,GGAGUA,UGGAGA,UGGAGU AGGAGA,AGGAGU,CGGAGA,CGGAGG,CGGAGU,GGAGAA,GGAGAU,GGAGGA,GGAGGG,GGAGUA,UGGAGA,UGGAGG,UGGAGU
SAMD4A 5 790 0.014285714 0.0039852882 1.841817 CGGGCA,CUGGCA,CUGGCC,GCUGGC CGGGAA,CGGGAC,CGGGCA,CGGGCC,CGGGUA,CGGGUC,CUGGAA,CUGGAC,CUGGCA,CUGGCC,CUGGUA,CUGGUC,GCGGGA,GCGGGC,GCGGGU,GCUGGA,GCUGGC,GCUGGU
PABPC4 2 462 0.007142857 0.0023327287 1.614483 AAAAAA,AAAAAG AAAAAA,AAAAAG
PABPC3 1 310 0.004761905 0.0015669085 1.603618 AAAACA AAAAAC,AAAACA,AAAACC,GAAAAC
ZCRB1 3 666 0.009523810 0.0033605401 1.502846 AUUUAA,GACUUA AAUUAA,ACUUAA,AUUUAA,GAAUUA,GACUUA,GAUUAA,GAUUUA,GCUUAA,GGAUUA,GGCUUA,GGUUUA,GUUUAA
PUM1 12 2172 0.030952381 0.0109482064 1.499356 ACAUAA,AGAAUU,AGAUAA,CAGAAU,GAAUUG,GUAGAU,GUCCAG,UAAUAU,UAGAUA,UGUCCA 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
IGHMBP2 1 350 0.004761905 0.0017684401 1.429061 AAAAAA AAAAAA
NONO 1 364 0.004761905 0.0018389762 1.372636 AGAGGA AGAGGA,AGGAAC,GAGAGG,GAGGAA
RBMS3 2 562 0.007142857 0.0028365578 1.332360 CUAUAG,UAUAGA AAUAUA,AUAUAG,AUAUAU,CAUAUA,CUAUAG,CUAUAU,UAUAGA,UAUAGC,UAUAUA,UAUAUC

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.

Back to Home