ENSG00000141337:+:17:68306942:68401450

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000141337:+:17:68306942:68401450 ENSG00000141337 ENST00000448504 + 17 68306943 68401450 1854 GAAACCUUACAGAAACAUGAAGCCCUCAACCAUCUGCUACUCAGUUAUUCGGGGCUGACGGCGGCUUCUAGAACAUCCAGGUGUUCUGCAGAUGCGAGAACUCAUCCUGUAGUCACCAGAUGGAGUCCCAAACAGCCAAGCAGAUGUAAGGCCUGUGCUGUGGCUCUGAGGCCCUGAAUACAGAAGGGUCACUUUCUUAGUGGCCAAAGAGCAGUUGUUGACAUUGAUGUCUAAUUAUUGAACACGACCAGUCAUUUUACUGAGCUGCGGUGAGGAAACACUGACCAUAGAAGAUCAAGCCAAAUGAGGGAUUGCAAAUUUCCUGAUUCUUUUGAAUUAGGAUUCCAGAUGGGGGCCUCAUUUCUACAGCCCCCAACAUUCCUAUAGCCGUUAUCACUGCCAUCACCACUGCCACCAGCAUCUUCUUGCAGAUUCCACCCCUGCUCCCCAGAGACUUCCUGCUUUGAAAGUGAGCAGAAAGGAAGCUCUCAGAAAAAUCUCUAGUGGUGGCUGCCGUCGCUCCAGACAAUCGGAAUCCUGCCUUCACCACCAUGGGCUGGCUUUUUCUAAAGGUUUUGUUGGCGGGAGUGAGUUUCUCAGGAUUUCUUUAUCCUCUUGUGGAUUUUUGCAUCAGUGGGAAAACAAGAGGACAGAAGCCAAACUUUGUGAUUAUUUUGGCCGAUGACAUGGGGUGGGGUGACCUGGGAGCAAACUGGGCAGAAACAAAGGACACUGCCAACCUUGAUAAGAUGGCUUCGGAGGGAAUGAGGUUUGUGGAUUUCCAUGCAGCUGCCUCCACCUGCUCACCCUCCCGGGCUUCCUUGCUCACCGGCCGGCUUGGCCUUCGCAAUGGAGUCACACGCAACUUUGCAGUCACUUCUGUGGGAGGCCUUCCGCUCAACGAGACCACCUUGGCAGAGGUGCUGCAGCAGGCGGGUUACGUCACUGGGAUAAUAGGCAAAUGGCAUCUUGGACACCACGGCUCUUAUCACCCCAACUUCCGUGGUUUUGAUUACUACUUUGGAAUCCCAUAUAGCCAUGAUAUGGGCUGUACUGAUACUCCAGGCUACAACCACCCUCCUUGUCCAGCGUGUCCACAGGGUGAUGGACCAUCAAGGAACCUUCAAAGAGACUGUUACACUGACGUGGCCCUCCCUCUUUAUGAAAACCUCAACAUUGUGGAGCAGCCGGUGAACUUGAGCAGCCUUGCCCAGAAGUAUGCUGAGAAAGCAACCCAGUUCAUCCAGCGUGCAAGCACCAGCGGGAGGCCCUUCCUGCUCUAUGUGGCUCUGGCCCACAUGCACGUGCCCUUACCUGUGACUCAGCUACCAGCAGCGCCACGGGGCAGAAGCCUGUAUGGUGCAGGGCUCUGGGAGAUGGACAGUCUGGUGGGCCAGAUCAAGGACAAAGUUGACCACACAGUGAAGGAAAACACAUUCCUCUGGUUUACAGGAGACAAUGGCCCGUGGGCUCAGAAGUGUGAGCUAGCGGGCAGUGUGGGUCCCUUCACUGGAUUUUGGCAAACUCGUCAAGGGGGAAGUCCAGCCAAGCAGACGACCUGGGAAGGAGGGCACCGGGUCCCAGCACUGGCUUACUGGCCUGGCAGAGUUCCAGUUAAUGUCACCAGCACUGCCUUGUUAAGCGUGCUGGACAUUUUUCCAACUGUGGUAGCCCUGGCCCAGGCCAGCUUACCUCAAGGACGGCGCUUUGAUGGUGUGGACGUCUCCGAGGUGCUCUUUGGCCGGUCACAGCCUGGGCACAGGGUGCUGUUCCACCCCAACAGCGGGGCAGCUGGAGAGUUUGGAGCCCUGCAGACUGUCCGCCUGGAGCGUUACAAGGCCUUCUACAUUACCGGAAACCUUACAGAAACAUGAAGCCCUCAACCAUCUGCUACUCAGUUAUUC circ
ENSG00000141337:+:17:68306942:68401450 ENSG00000141337 ENST00000448504 + 17 68306943 68401450 22 CUACAUUACCGGAAACCUUACA bsj
ENSG00000141337:+:17:68306942:68401450 ENSG00000141337 ENST00000448504 + 17 68306743 68306952 210 UUCCAACCCUGUCGCUAUAGGUCCAUUGCGAAUAUUAUUAUCAUCACUAUUUUUCAGGUGGAGAAACUGAUGAACCAGUUAAAUAUUUGAAUAAAAACAUCUGUUGGCAUGGAAAAGUGAUUAUUUCCUAAGCUACUGAGUAAAACACAGCUGCACUGGCAGUUUUAACUCUGUUUUCUUGUCAAUUUUUGUUCUUUCAGGAAACCUUAC ie_up
ENSG00000141337:+:17:68306942:68401450 ENSG00000141337 ENST00000448504 + 17 68401441 68401650 210 UACAUUACCGGUGAGUGAGGGGCCACUUAGCCCUGCCUCCCACAGUCACAGCUGCACGGGGACCCCAUGGACUCUCACCCAGGCCUCUGGGAAUGAGUGUGAGUCCCUCCUUUGUGGGGGGUUCUCAGCACCUCUUGACAAGCGUCUCCUCCAAACCCAGGGUCCCUGCACAGGCUCUCUGGAUCCCUCAUAUGCAAAUAAGAUCUUUGU 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 0.001078749 0.0002275250 2.245262 AGGGAU AGGGAU
SRP14 6 847 0.003775620 0.0012289250 1.619317 CCUGUA,CGCCUG,CUGUAG,GCCUGU CCUGUA,CGCCUG,CUGUAG,GCCUGU
RBM25 1 268 0.001078749 0.0003898359 1.468420 CGGGCA AUCGGG,CGGGCA,UCGGGC
ZC3H10 6 1053 0.003775620 0.0015274610 1.305578 CAGCGC,CCAGCG,GCAGCG,GGAGCG CAGCGA,CAGCGC,CCAGCG,CGAGCG,GAGCGA,GAGCGC,GCAGCG,GGAGCG
CNOT4 1 314 0.001078749 0.0004564992 1.240674 GACAGA GACAGA
HNRNPM 5 999 0.003236246 0.0014492040 1.159061 AAGGAA,GAAGGA AAGGAA,GAAGGA,GGGGGG
ANKHD1 1 339 0.001078749 0.0004927293 1.130491 AGACGA AGACGA,AGACGU,GACGAA,GACGAU,GACGUA,GACGUU
PABPC3 6 1234 0.003775620 0.0017897669 1.076942 AAAACA,AAAACC,GAAAAC AAAAAC,AAAACA,AAAACC,GAAAAC
MATR3 3 739 0.002157497 0.0010724109 1.008501 AUCUUG,CAUCUU AAUCUU,AUCUUA,AUCUUG,CAUCUU

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
SRSF1 1 625 0.09090909 0.04100079 1.148773 ACCGGA AAAAGA,AAAGAA,AAAGAC,AAAGAG,AACAGC,AAGAAC,AAGACC,AAGAGA,AAGAGC,AAGAGG,AAGGAC,AAGGCG,AAGGUG,AAUGAC,AAUUUC,ACAAGG,ACAGAG,ACAGCA,ACAGCG,ACAGGA,ACAGGG,ACAGGU,ACAGUG,ACCCGA,ACCGGA,ACGAAU,ACGGAA,ACUGAG,ACUGGA,AGAAGA,AGAAGG,AGACAA,AGACAG,AGACGU,AGAGAA,AGAGAC,AGAGCA,AGAGGA,AGAGGG,AGAGGU,AGAUGG,AGCAGG,AGCCGA,AGCGGA,AGGAAA,AGGAAC,AGGAAG,AGGACA,AGGACC,AGGACG,AGGACU,AGGAGA,AGGAGC,AGGAGG,AGGUAA,AUGAAC,AUGAAG,AUGACA,AUGACU,AUGGAC,AUGGAG,CAAGGA,CAAUGG,CACAGA,CACAGC,CACAGG,CACAGU,CACCCA,CACCCG,CACCGG,CACGCA,CACGGA,CACUGG,CAGAAC,CAGACA,CAGACG,CAGAGA,CAGAGC,CAGAGG,CAGCCG,CAGUCG,CAUGGU,CCAACC,CCAAGG,CCACCA,CCACCC,CCACGG,CCAGCA,CCAGCC,CCAGCG,CCAGGA,CCAGGG,CCCACC,CCCAGC,CCCAGG,CCCCGC,CCCGGG,CCCGUU,CCCUCC,CCCUCG,CCGAGG,CCGCGA,CCGCUA,CCGGAC,CCGGAG,CCGGGA,CCGUCC,CCGUGC,CCGUGG,CCGUUU,CCUAGG,CCUCCG,CCUCGA,CCUGCG,CCUGGA,CCUGGG,CGAACG,CGAAGC,CGAGGA,CGAGGC,CGAGGG,CGAUGG,CGCAGC,CGCCGC,CGCUAU,CGCUGC,CGGAAU,CGGACA,CGGAGC,CGGAGG,CGGCGG,CGGGCA,CGGUGC,CGGUGG,CGUGCG,CGUGGA,CGUGGG,CUCAGG,CUCGUG,CUGAAC,CUGAGU,GAAAGA,GAAAGG,GAACAG,GAAGAA,GAAGAG,GAAGAU,GAAGCA,GAAGCC,GAAGCU,GAAGGA,GAAGGC,GAAGGU,GAAUGA,GACAGA,GACAGG,GACCCA,GACGAA,GACGAC,GACGGA,GACUGA,GAGAAC,GAGAAG,GAGACA,GAGACG,GAGCAG,GAGGAA,GAGGAC,GAGGAG,GAGGAU,GAGGCA,GAGGGA,GAGGGC,GAGGGG,GAGGUA,GAUGAA,GAUGAC,GAUGAU,GAUGCA,GAUGCC,GAUGCU,GAUGGA,GAUGGC,GCACGG,GCAGCA,GCAGCG,GCAGGA,GCAGGC,GCAGGG,GCAGGU,GCCCAC,GCCCGG,GCCCGU,GCGCAA,GCGCCA,GCGCCC,GCGCGG,GCGGAC,GCGGCG,GCGGUU,GCUGGG,GGAAAG,GGAACA,GGAAGA,GGAAGG,GGAAUG,GGACAA,GGACAG,GGACCA,GGACCG,GGACGA,GGAGAA,GGAGAC,GGAGAU,GGAGCA,GGAGCG,GGAGCU,GGAGGA,GGAGGC,GGAGGG,GGAGGU,GGAUAU,GGAUGA,GGAUUC,GGCACA,GGCAGA,GGCCGA,GGCGCA,GGGACG,GGGCCG,GGGGAA,GGGGAG,GGGGCA,GGGGCG,GGGGGA,GGGUAC,GGUCCA,GGUCCG,GGUGAA,GGUGCA,GGUGCC,GGUGCG,GGUGCU,GGUGGA,GGUGGC,GGUGGG,GGUGGU,GUAGGA,GUGACA,UAGACA,UAGGAC,UCAAGA,UCAGGU,UCGGGC,UGAACA,UGAAGA,UGAAGC,UGAAGG,UGACAG,UGACGA,UGACUG,UGAGUU,UGAUGA,UGAUGG,UGGACA,UGGAGA,UGGAGC,UGGAGG,UGGUGC,UGUAGG,UUCAAG

RBP on BSJ (Exon and Intron)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
PTBP2 1 146 0.004761905 0.0007406288 2.684716 CUCUCU CUCUCU
ERI1 2 228 0.007142857 0.0011537686 2.630147 UUUCAG UUCAGA,UUUCAG
PABPC3 3 310 0.009523810 0.0015669085 2.603618 AAAAAC,AAAACA AAAAAC,AAAACA,AAAACC,GAAAAC
IGF2BP1 1 173 0.004761905 0.0008766626 2.441445 AGCACC AAGCAC,ACCCGU,AGCACC,CACCCG,CCCGUU,GCACCC
YBX2 2 263 0.007142857 0.0013301088 2.424957 AACAUC,ACAUCU AACAAC,AACAUC,ACAACA,ACAACG,ACAACU,ACAUCA,ACAUCG,ACAUCU
HNRNPM 1 222 0.004761905 0.0011235389 2.083489 GGGGGG AAGGAA,GAAGGA,GGGGGG
RBM24 6 888 0.016666667 0.0044790407 1.895704 AGUGUG,GAGUGA,GAGUGU,GUGUGA,UGAGUG AGAGUG,AGUGUG,GAGUGA,GAGUGG,GAGUGU,GUGUGA,GUGUGG,GUGUGU,UGAGUG,UGUGUG
ZNF638 4 646 0.011904762 0.0032597743 1.868695 GGUUCU,GUUCUU,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 CUGUUU,UGUUUU CUGUUU,GCUGUU,UGCUGU,UGUUUU
YBX1 6 1321 0.016666667 0.0066606207 1.323237 AACAUC,ACAUCU,AUCAUC,CAUCUG,CCCUGC 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
NELFE 4 1059 0.011904762 0.0053405885 1.156468 CUCUCU,CUCUGG,UCUCUG CUCUCU,CUCUGG,CUGGCU,CUGGUU,GCUAAC,GGCUAA,GGUCUC,GGUUAG,GUCUCU,UCUCUC,UCUCUG,UCUGGC,UCUGGU,UGGCUA,UGGUUA
IGF2BP3 5 1348 0.014285714 0.0067966546 1.071676 AAAAAC,AAAACA,AAACAC,AACACA AAAAAC,AAAACA,AAAAUC,AAACAC,AAACUC,AAAUAC,AAAUCA,AAAUUC,AACACA,AACUCA,AAUACA,AAUUCA,ACAAAC,ACAAUC,ACACAC,ACACUC,ACAUAC,ACAUUC,CAAACA,CAAUCA,CACACA,CACUCA,CAUACA,CAUUCA

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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