ENSG00000107829_ENSG00000224817:-:10:101667885:101673673

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000107829_ENSG00000224817:-:10:101667885:101673673 ENSG00000107829_ENSG00000224817 MSTRG.4529.1 - 10 101667886 101673673 414 UCAGAUGCCCUGGAUGCAGCUAGAGGAUGAUUCUCUGUACAUAUCCCAGGCUAAUUUCAUCCUGGCCUACCAGUUCCGUCCAGAUGGUGCCAGCUUGAAUCGUCGGCCUCUGGGAGUCUUUGCUGGGCAUGAUGAGGACGUUUGCCACUUUGUGCUGGCCAACUCGCAUAUUGUUAGUGCAGGAGGGGAUGGGAAGAUUGGCAUUCAUAAGAUUCACAGCACCUUCACUGUCAAGUACUCGGCUCAUGAACAGGAGGUGAACUGUGUGGAUUGCAAAGGGGGCAUCAUUGUGAGUGGCUCCAGGGACAGGACGGCCAAGGUGUGGCCUUUGGCCUCAGGCCGGCUGGGGCAGUGCUUACACACCAUCCAGACUGAAGACCGAGUCUGGUCCAUUGCUAUCAGCCCAUUACUCAGUCAGAUGCCCUGGAUGCAGCUAGAGGAUGAUUCUCUGUACAUAUCCCAGG circ
ENSG00000107829_ENSG00000224817:-:10:101667885:101673673 ENSG00000107829_ENSG00000224817 MSTRG.4529.1 - 10 101667886 101673673 22 CCAUUACUCAGUCAGAUGCCCU bsj
ENSG00000107829_ENSG00000224817:-:10:101667885:101673673 ENSG00000107829_ENSG00000224817 MSTRG.4529.1 - 10 101673664 101673873 210 AUCACCACAAGGCUCAGUUACUCUAGUUUUCUGAGGAUAGCUGAUGGGCAGGUAAUUUUGAAGGAGGGUAUCAAGUAUAGAUAAUAAGCCUUGUUGGUUAUCCUUACUAAGUUGGGGAUUGGUCAGCUUCUUCAAAGAUUGGAGUUGAGUUUUCAUACUGUAUCUUGAUGACUUUUAAAUUUUCUUUUCCAUCAUUUCAGUCAGAUGCCC ie_up
ENSG00000107829_ENSG00000224817:-:10:101667885:101673673 ENSG00000107829_ENSG00000224817 MSTRG.4529.1 - 10 101667686 101667895 210 CAUUACUCAGGUAAGGGAGACAUAUUUGGAUGUGGUUUUGUCCUGUAUAAUAAUGCUUUUAUUUUACUAGAUCAGGUGAGCUAGAAAAUCUUCCUGUUGUGUAUUCUAGGUUGCUUUGAGUCACUGUCUUGGAGAUUUUUUAAUCCUCCAGAGAUUUGAGUUAUUUAGGCCACUUCAUAUAUGCGUGGGAUUGAGAUAACCUUCUAAAUG 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 0.004830918 0.0004927293 3.293430 GACGUU AGACGA,AGACGU,GACGAA,GACGAU,GACGUA,GACGUU
G3BP2 4 1644 0.012077295 0.0023839405 2.340877 AGGAUG,GGAUGA,GGAUGG,GGAUUG AGGAUA,AGGAUG,AGGAUU,GGAUAA,GGAUAG,GGAUGA,GGAUGG,GGAUUA,GGAUUG
RBM6 2 1054 0.007246377 0.0015289102 2.244756 AUCCAG,CAUCCA AAUCCA,AUCCAA,AUCCAG,CAUCCA,UAUCCA
CELF5 3 1415 0.009661836 0.0020520728 2.235215 GUGUGG,UGUGUG GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU
CELF4 4 1782 0.012077295 0.0025839306 2.224658 GGUGUG,GUGUGG,UGUGUG GGUGUG,GGUGUU,GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU
RBM24 5 2357 0.014492754 0.0034172229 2.084435 GAGUGG,GUGUGG,UGAGUG,UGUGUG AGAGUG,AGUGUG,GAGUGA,GAGUGG,GAGUGU,GUGUGA,GUGUGG,GUGUGU,UGAGUG,UGUGUG
IGF2BP1 1 831 0.004830918 0.0012057377 2.002381 AGCACC AAGCAC,ACCCGU,AGCACC,CACCCG,CCCGUU,GCACCC
PUM2 3 1890 0.009661836 0.0027404447 1.817887 GUACAU,UACAUA,UGUACA GUAAAU,GUACAU,GUAGAU,GUAUAU,UAAAUA,UACAUA,UACAUC,UAGAUA,UAUAUA,UGUAAA,UGUACA,UGUAGA,UGUAUA
SNRPB2 1 991 0.004830918 0.0014376103 1.748625 AUUGCA AUUGCA,GUAUUG,UAUUGC,UGCAGU,UUGCAG
ESRP2 3 2150 0.009661836 0.0031172377 1.632029 GGGAAG,GGGGAU,UGGGAA GGGAAA,GGGAAG,GGGAAU,GGGGAA,GGGGAG,GGGGAU,UGGGAA,UGGGGA
RBFOX1 1 1077 0.004830918 0.0015622419 1.628680 GCAUGA AGCAUG,GCAUGA,GCAUGC,GCAUGU,UGACUG,UGCAUG
CELF6 4 2997 0.012077295 0.0043447134 1.474964 GUGUGG,UGUGAG,UGUGUG GUGAGG,GUGAUG,GUGGGG,GUGGUG,GUGUGG,GUGUUG,UGUGAG,UGUGAU,UGUGGG,UGUGGU,UGUGUG,UGUGUU
NELFE 4 3028 0.012077295 0.0043896388 1.460123 CUCUGG,GGCUAA,UCUCUG,UCUGGU CUCUCU,CUCUGG,CUGGCU,CUGGUU,GCUAAC,GGCUAA,GGUCUC,GGUUAG,GUCUCU,UCUCUC,UCUCUG,UCUGGC,UCUGGU,UGGCUA,UGGUUA
AGO2 2 1830 0.007246377 0.0026534924 1.449367 AGUGCU,GUGCUU AAAAAA,AAAGUG,AAGUGC,AGUGCU,GUGCUU,UAAAGU
ACO1 1 1283 0.004830918 0.0018607779 1.376391 CAGUGC CAGUGA,CAGUGC,CAGUGG,CAGUGU
NOVA1 5 3872 0.014492754 0.0056127669 1.368548 AGCACC,AUUCAU,CAGUCA,CAUUCA,UCAGUC AACACC,ACCACC,AGCACC,AGUCAC,AUCAAC,AUCACC,AUCAUC,AUUCAU,CAGUCA,CAUUCA,CCCCCC,GGGGGG,UCAGUC,UCAUUC,UUCAUU,UUUUUU
HNRNPA3 2 2140 0.007246377 0.0031027457 1.223714 CCAAGG,GCCAAG AAGGAG,AGGAGC,CAAGGA,CCAAGG,GCCAAG,GGAGCC
NONO 1 1498 0.004830918 0.0021723567 1.153036 AGAGGA AGAGGA,AGGAAC,GAGAGG,GAGGAA
HNRNPF 13 10561 0.033816425 0.0153064921 1.143580 AAGGGG,AAGGUG,AGGGGA,AUGGGA,CUGGGG,GAGGGG,GAUGGG,GGAGGG,GGAUGG,GGGAAG,GGGAUG,GGGGGC,UGGGAA 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
SAMD4A 4 3992 0.012077295 0.0057866714 1.061492 CUGGCC,CUGGUC,GCUGGC CGGGAA,CGGGAC,CGGGCA,CGGGCC,CGGGUA,CGGGUC,CUGGAA,CUGGAC,CUGGCA,CUGGCC,CUGGUA,CUGGUC,GCGGGA,GCGGGC,GCGGGU,GCUGGA,GCUGGC,GCUGGU

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
NOVA1 2 5 0.13636364 0.0003929788 8.438792 CAGUCA,UCAGUC ACCACC,CAGUCA,CAUUCA,UCAGUC
SF1 1 24 0.09090909 0.0016374116 5.794936 CAGUCA ACAGAC,ACAGUC,AGUAAG,AUACUA,CACAGA,CACUGA,CAGUCA,GCUGAC,GCUGCC,UACUGA,UGCUAA,UGCUGA,UGCUGC

RBP on BSJ (Exon and Intron)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
RBM42 1 103 0.004761905 0.0005239823 3.183949 ACUAAG AACUAA,AACUAC,ACUAAG,ACUACG
MATR3 2 216 0.007142857 0.0010933091 2.707800 AAUCUU,AUCUUG AAUCUU,AUCUUA,AUCUUG,CAUCUU
G3BP2 4 490 0.011904762 0.0024738009 2.266737 AGGAUA,GGAUAG,GGAUUG AGGAUA,AGGAUG,AGGAUU,GGAUAA,GGAUAG,GGAUGA,GGAUGG,GGAUUA,GGAUUG
SRP14 1 218 0.004761905 0.0011033857 2.109602 CCUGUA CCUGUA,CGCCUG,CUGUAG,GCCUGU
AKAP1 1 221 0.004761905 0.0011185006 2.089973 AUAUAU AUAUAU,UAUAUA
HNRNPM 1 222 0.004761905 0.0011235389 2.083489 GAAGGA AAGGAA,GAAGGA,GGGGGG
EIF4B 1 226 0.004761905 0.0011436921 2.057840 CUUGGA CUCGGA,CUUGGA,GUCGGA,GUUGGA,UCGGAA,UCGGAC,UUGGAA,UUGGAC
ERI1 1 228 0.004761905 0.0011537686 2.045185 UUUCAG UUCAGA,UUUCAG
SNRNP70 1 253 0.004761905 0.0012797259 1.895704 AUCAAG AAUCAA,AUCAAG,AUUCAA,GAUCAA,GUUCAA,UUCAAG
RBMS3 3 562 0.009523810 0.0028365578 1.747397 AUAUAU,CAUAUA,UAUAGA AAUAUA,AUAUAG,AUAUAU,CAUAUA,CUAUAG,CUAUAU,UAUAGA,UAUAGC,UAUAUA,UAUAUC
ZFP36L2 4 774 0.011904762 0.0039046755 1.608264 UAUUUA,UUAUUU,UUUAUU AUUUAU,UAUUUA,UUAUUU,UUUAUU
NOVA2 8 1434 0.021428571 0.0072299476 1.567479 AGACAU,AGAUCA,AUCACC,CUAGAU,GAGACA,GAGUCA,UAGAUC,UUUUUU AACACC,ACCACC,AGACAU,AGAUCA,AGCACC,AGGCAU,AGUCAU,AUCAAC,AUCACC,AUCAUC,CCUAGA,CUAGAU,GAGACA,GAGGCA,GAGUCA,GAUCAC,GGGGGG,UAGAUC,UUUUUU
ZNF638 3 646 0.009523810 0.0032597743 1.546767 GUUGGU,UGUUGG,UGUUGU CGUUCG,CGUUCU,CGUUGG,CGUUGU,GGUUCG,GGUUCU,GGUUGG,GGUUGU,GUUCGU,GUUCUU,GUUGGU,GUUGUU,UGUUCG,UGUUCU,UGUUGG,UGUUGU
HNRNPA3 1 349 0.004761905 0.0017634019 1.433177 AAGGAG AAGGAG,AGGAGC,CAAGGA,CCAAGG,GCCAAG,GGAGCC
HNRNPAB 1 351 0.004761905 0.0017734784 1.424957 CAAAGA AAAGAC,AAGACA,ACAAAG,AGACAA,AUAGCA,CAAAGA,GACAAA
LIN28A 4 900 0.011904762 0.0045395002 1.390933 GGAGAU,GGAGGG,UGGAGA,UGGAGU AGGAGA,AGGAGU,CGGAGA,CGGAGG,CGGAGU,GGAGAA,GGAGAU,GGAGGA,GGAGGG,GGAGUA,UGGAGA,UGGAGG,UGGAGU
TIAL1 30 5597 0.073809524 0.0282043531 1.387889 AAAUUU,AAUUUU,AGUUUU,AUUUUA,AUUUUC,AUUUUG,AUUUUU,CUUUUA,CUUUUC,GUUUUC,UAAAUU,UAUUUU,UCAGUU,UUAAAU,UUAUUU,UUCAGU,UUUAAA,UUUAUU,UUUCAG,UUUUAA,UUUUAU,UUUUCA,UUUUUA,UUUUUU AAAUUU,AAUUUU,AGUUUU,AUUUUA,AUUUUC,AUUUUG,AUUUUU,CAGUUU,CUUUUA,CUUUUC,CUUUUG,CUUUUU,GUUUUC,GUUUUU,UAAAUU,UAUUUU,UCAGUU,UUAAAU,UUAUUU,UUCAGU,UUUAAA,UUUAUU,UUUCAG,UUUUAA,UUUUAU,UUUUCA,UUUUUA,UUUUUC,UUUUUG,UUUUUU
PABPC5 2 596 0.007142857 0.0030078597 1.247764 AGAAAA,GAAAAU AGAAAA,AGAAAG,AGAAAU,GAAAAU,GAAAGU,GAAAUU
A1CF 2 598 0.007142857 0.0030179363 1.242939 AGUAUA,GAUCAG AGUAUA,AUAAUU,AUCAGU,CAGUAU,GAUCAG,UAAUUA,UAAUUG,UCAGUA,UGAUCA,UUAAUU
CELF1 4 1097 0.011904762 0.0055320435 1.105654 CUGUCU,GUUGUG,UGUUGU,UUGUGU CUGUCU,GUGUGU,GUGUUG,GUUGUG,GUUUGU,UGUCUG,UGUGUG,UGUGUU,UGUUGU,UGUUUG,UUGUGU
SRSF3 16 3825 0.040476190 0.0192765014 1.070230 ACUUCA,AGAGAU,AUCUUC,CACCAC,CACUUC,CAGAGA,CAUCAU,CUUCAA,CUUCAU,CUUCUU,GAGAUU,UAUCAA,UCUUCA,UCUUCC,UUCUUC AACGAC,AACGAU,AACUUU,ACAUCA,ACAUCG,ACAUUC,ACCACC,ACGACG,ACGACU,ACGAUC,ACGAUU,ACUACA,ACUACG,ACUUCA,ACUUCG,ACUUCU,ACUUUA,AGAGAU,AUCAAC,AUCAUC,AUCGAC,AUCGAU,AUCGCU,AUCGUU,AUCUUC,AUUCAU,CAACGA,CACAAC,CACAUC,CACCAC,CACUAC,CACUUC,CAGAGA,CAUCAA,CAUCAC,CAUCAU,CAUCGA,CAUCGC,CAUCGU,CAUUCA,CCACCA,CCUCGU,CCUCUU,CGAUCG,CGCUUC,CUACAA,CUACAC,CUACAG,CUACGA,CUCCAA,CUCGUC,CUCUUC,CUUCAA,CUUCAC,CUUCAG,CUUCAU,CUUCGA,CUUCUU,CUUUAU,GACUUC,GAGAUU,GAUCAA,GAUCGA,GCUUCA,GUCAAC,UACAAA,UACAAC,UACAAU,UACAGC,UACAUC,UACGAU,UACUUC,UAUCAA,UCAACG,UCACAA,UCAGAG,UCAUCA,UCAUCC,UCAUCG,UCAUCU,UCGACA,UCGACU,UCGAUA,UCGAUC,UCGAUU,UCGCUU,UCGUCC,UCGUUC,UCUCCA,UCUUCA,UCUUCC,UCUUCG,UGUCAA,UUACGA,UUCAAC,UUCAUC,UUCGAC,UUCGAU,UUCUCC,UUCUUC
QKI 3 904 0.009523810 0.0045596534 1.062615 UAACCU,UACUCA,UCAUAU AAUCAU,ACACAC,ACACUA,ACUAAC,ACUAAU,ACUCAU,ACUUAU,AUCAUA,AUCUAA,AUCUAC,AUUAAC,CACACU,CACUAA,CUAACA,CUAACC,CUAACG,CUAAUC,CUACUC,CUCAUA,UAACCU,UAAUCA,UACUCA,UCAUAU,UCUAAU,UCUACU

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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