ENSG00000159140:+:21:33567156:33569087

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000159140:+:21:33567156:33569087 ENSG00000159140 MSTRG.21290.1 + 21 33567157 33569087 228 CCUGUGGACAUCUCUACAGCAAUGAGUGAACGGGCACUUGCUCAGAAAAGACUCAGUGAGAAUGCAUUUGAUCUUGAAGCCAUGAGCAUGUUAAAUAGAGCUCAGGAAAGGAUUGAUGCCUGGGCUCAGCUGAACUCUAUUCCUGGCCAGUUCACAGGAAGUACAGGAGUACAGGUUUUGACACAAGAACAGUUGGCCAAUACUGGUGCCCAAGCCUGGAUUAAAAAGCCUGUGGACAUCUCUACAGCAAUGAGUGAACGGGCACUUGCUCAGAAAAG circ
ENSG00000159140:+:21:33567156:33569087 ENSG00000159140 MSTRG.21290.1 + 21 33567157 33569087 22 GGAUUAAAAAGCCUGUGGACAU bsj
ENSG00000159140:+:21:33567156:33569087 ENSG00000159140 MSTRG.21290.1 + 21 33566957 33567166 210 AUACUUUGUAAUUUAUCUUAAUCCUCUUCUGUUUUCCAAGAUUACUUUCUCUUUCUGAGUCUUCUCCCUGUUUUCCAAGAUUAUUAGUAUUAUAAGACUAUUAUUUUGUUUUUGAUAUGUAGCAACUAAAGAUAUGAGUACUUUUCAGAAUUUAGGGGACUAUGGUAAUUUGAGAUAAUUAUCUCUGUUUUCUUUCUUAGCCUGUGGACA ie_up
ENSG00000159140:+:21:33567156:33569087 ENSG00000159140 MSTRG.21290.1 + 21 33569078 33569287 210 GAUUAAAAAGGUACACAGUAUAUGCACAUAUGAAAGUGUCGAACAAAAAGUUUAAAUUUUUUGGAAACUGUUUAUUAAAACUGCAUGAAAAGACCAGUGACUCUAACCAAAGUUCCAAGUAAAUUUGCUAUGUGUAUAUGCUCCAGGGCGGACACUGAAGACGGACUGGAUUCAUGAGAAAAUGGCAAAUGUAUAAAUGUGGCUCAAGAG 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
RBM25 1 268 0.00877193 0.0003898359 4.491956 CGGGCA AUCGGG,CGGGCA,UCGGGC
TUT1 2 678 0.01315789 0.0009840095 3.741113 AAUACU,CAAUAC AAAUAC,AAUACU,AGAUAC,CAAUAC,CGAUAC,GAUACU
RBMY1A1 1 489 0.00877193 0.0007101099 3.626780 ACAAGA ACAAGA,CAAGAC
RBFOX1 2 1077 0.01315789 0.0015622419 3.074239 AGCAUG,GCAUGU AGCAUG,GCAUGA,GCAUGC,GCAUGU,UGACUG,UGCAUG
MATR3 1 739 0.00877193 0.0010724109 3.032036 AUCUUG AAUCUU,AUCUUA,AUCUUG,CAUCUU
G3BP2 3 1644 0.01754386 0.0023839405 2.879546 AGGAUU,GGAUUA,GGAUUG AGGAUA,AGGAUG,AGGAUU,GGAUAA,GGAUAG,GGAUGA,GGAUGG,GGAUUA,GGAUUG
SRP14 1 847 0.00877193 0.0012289250 2.835497 GCCUGU CCUGUA,CGCCUG,CUGUAG,GCCUGU
ENOX1 5 3195 0.02631579 0.0046316558 2.506329 AGUACA,GUACAG,UGGACA AAGACA,AAUACA,AGACAG,AGGACA,AGUACA,AUACAG,CAGACA,CAUACA,CGGACA,CGUACA,GGACAG,GUACAG,UAGACA,UAUACA,UGGACA,UGUACA
ZCRB1 2 1605 0.01315789 0.0023274215 2.499124 GAUUAA,GGAUUA AAUUAA,ACUUAA,AUUUAA,GAAUUA,GACUUA,GAUUAA,GAUUUA,GCUUAA,GGAUUA,GGCUUA,GGUUUA,GUUUAA
PABPN1 1 1222 0.00877193 0.0017723764 2.307209 AAAAGA AAAAGA,AGAAGA
PABPC4 1 1251 0.00877193 0.0018144033 2.273399 AAAAAG AAAAAA,AAAAAG
ACO1 1 1283 0.00877193 0.0018607779 2.236988 CAGUGA CAGUGA,CAGUGC,CAGUGG,CAGUGU
RBM3 2 2152 0.01315789 0.0031201361 2.076248 AAGACU,AAUACU AAAACG,AAAACU,AAACGA,AAACUA,AAGACG,AAGACU,AAUACG,AAUACU,AGACGA,AGACUA,AUACGA,AUACUA,GAAACG,GAAACU,GAGACG,GAGACU,GAUACG,GAUACU
YBX2 1 1480 0.00877193 0.0021462711 2.031062 ACAUCU AACAAC,AACAUC,ACAACA,ACAACG,ACAACU,ACAUCA,ACAUCG,ACAUCU
RBM24 2 2357 0.01315789 0.0034172229 1.945032 GAGUGA,UGAGUG AGAGUG,AGUGUG,GAGUGA,GAGUGG,GAGUGU,GUGUGA,GUGUGG,GUGUGU,UGAGUG,UGUGUG
HNRNPAB 1 1782 0.00877193 0.0025839306 1.763327 AAAGAC AAAGAC,AAGACA,ACAAAG,AGACAA,AUAGCA,CAAAGA,GACAAA
MSI1 2 2770 0.01315789 0.0040157442 1.712189 AGGAAG,AGUUGG AGGAAG,AGGAGG,AGGUAG,AGGUGG,AGUAAG,AGUAGG,AGUUAG,AGUUGG,UAGGAA,UAGGAG,UAGGUA,UAGGUG,UAGUAA,UAGUAG,UAGUUA,UAGUUG
PUM2 1 1890 0.00877193 0.0027404447 1.678484 UAAAUA GUAAAU,GUACAU,GUAGAU,GUAUAU,UAAAUA,UACAUA,UACAUC,UAGAUA,UAUAUA,UGUAAA,UGUACA,UGUAGA,UGUAUA
CSTF2 1 1967 0.00877193 0.0028520334 1.620903 GUUUUG GUGUGU,GUGUUG,GUGUUU,GUUUUG,UGUGUG,UGUGUU,UGUUUG,UGUUUU
KHDRBS1 3 4064 0.01754386 0.0058910141 1.574378 UAAAAA,UUAAAA,UUAAAU AUAAAA,AUUUAA,AUUUAC,CAAAAU,CUAAAA,CUAAAU,GAAAAC,UAAAAA,UAAAAC,UAAAAG,UUAAAA,UUAAAU,UUUUAC,UUUUUU
YTHDC1 4 5576 0.02192982 0.0080822104 1.440072 GAAUGC,GAGUAC,UGAUGC,UGGUGC 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
KHDRBS3 2 3429 0.01315789 0.0049707696 1.404388 AUUAAA,UAAAUA AAAUAA,AAUAAA,AGAUAA,AUAAAA,AUAAAC,AUAAAG,AUUAAA,GAUAAA,UAAAAC,UAAAUA,UUAAAC,UUUUUU
PABPC5 1 2400 0.00877193 0.0034795387 1.333998 AGAAAA AGAAAA,AGAAAG,AGAAAU,GAAAAU,GAAAGU,GAAAUU
SART3 1 2634 0.00877193 0.0038186524 1.199831 AGAAAA AAAAAA,AAAAAC,AGAAAA,GAAAAA,GAAAAC
TARDBP 1 2654 0.00877193 0.0038476365 1.188922 GUUUUG GAAUGA,GAAUGG,GAAUGU,GUGAAU,GUGUGU,GUUGUG,GUUGUU,GUUUUG,UGAAUG,UGUGUG,UUGUGC,UUGUUC,UUUUGC
SAMD4A 2 3992 0.01315789 0.0057866714 1.185123 CGGGCA,CUGGCC CGGGAA,CGGGAC,CGGGCA,CGGGCC,CGGGUA,CGGGUC,CUGGAA,CUGGAC,CUGGCA,CUGGCC,CUGGUA,CUGGUC,GCGGGA,GCGGGC,GCGGGU,GCUGGA,GCUGGC,GCUGGU
SRSF9 14 20254 0.06578947 0.0293536261 1.164318 AGGAAA,AUGAGC,CUGGAU,GAAGCC,GAUGCC,GGAAAG,GGUGCC,UGAACG,UGAAGC,UGAGAA,UGAGCA,UGAUGC,UGGAUU,UGGUGC AGGAAA,AGGAAC,AGGACA,AGGACC,AGGAGA,AGGAGC,AUGAAA,AUGAAC,AUGACA,AUGACC,AUGAGA,AUGAGC,CUGGAU,GAAGCA,GAAGCC,GAAGGA,GAAGGC,GAUGCA,GAUGCC,GAUGGA,GAUGGC,GGAAAA,GGAAAG,GGAACA,GGAACG,GGAAGC,GGAAGG,GGACAA,GGACAG,GGACCA,GGACCG,GGAGAA,GGAGAG,GGAGCA,GGAGCC,GGAGCG,GGAGGA,GGAGGC,GGAUGC,GGAUGG,GGGAGC,GGGAGG,GGGUGC,GGGUGG,GGUGCA,GGUGCC,GGUGGA,GGUGGC,UGAAAA,UGAAAG,UGAACA,UGAACG,UGAAGC,UGAAGG,UGACAA,UGACAG,UGACCA,UGACCG,UGAGAA,UGAGAG,UGAGCA,UGAGCG,UGAUGC,UGAUGG,UGGAGC,UGGAGG,UGGAUU,UGGUGC,UGGUGG
LIN28A 2 4315 0.01315789 0.0062547643 1.072901 AGGAGU,GGAGUA AGGAGA,AGGAGU,CGGAGA,CGGAGG,CGGAGU,GGAGAA,GGAGAU,GGAGGA,GGAGGG,GGAGUA,UGGAGA,UGGAGG,UGGAGU

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
SRP14 1 1 0.09090909 0.0001309929 9.438792 GCCUGU GCCUGU
ZFP36 1 126 0.09090909 0.0083180508 3.450107 AAAAGC AAAAAA,AAAAAG,AAAAAU,AAAAGA,AAAAGC,AAAAGG,AAAAGU,AAAAUA,AAAGAA,AAAGCA,AAAUAA,AACAAA,AACAAG,AAGAAA,AAGCAA,AAGGAA,AAGUAA,AAUAAG,ACAAAC,ACAAAG,ACAAGC,ACAAGG,ACAAGU,ACCUGU,AGAAAG,AGGAAA,AGUAAA,AUAAAG,AUAAAU,AUAAGC,AUUUAA,CAAAGA,CAAAUA,CAAGGA,CAAGUA,CCCUCC,CCCUGU,CCUUCU,GCAAAG,GGAAAG,GUAAAG,UAAAGA,UAAAUA,UAAGCA,UAAGGA,UCCUCU,UCCUGC,UCCUGU,UCUUCC,UCUUCU,UCUUGC,UCUUUC,UUGUGC,UUGUGG

RBP on BSJ (Exon and Intron)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
HNRNPA0 3 200 0.009523810 0.0010126965 3.233337 AAUUUA,AGAUAU AAUUUA,AGAUAU,AGUAGG
RBM42 1 103 0.004761905 0.0005239823 3.183949 AACUAA AACUAA,AACUAC,ACUAAG,ACUACG
SSB 8 505 0.021428571 0.0025493753 3.071320 CUGUUU,UGUUUU CUGUUU,GCUGUU,UGCUGU,UGUUUU
RBFOX2 1 124 0.004761905 0.0006297864 2.918604 UGCAUG UGACUG,UGCAUG
ERI1 2 228 0.007142857 0.0011537686 2.630147 UUCAGA,UUUCAG UUCAGA,UUUCAG
RBM41 5 502 0.014285714 0.0025342604 2.494937 AUACUU,UACUUU,UUACUU AUACAU,AUACUU,UACAUG,UACAUU,UACUUG,UACUUU,UUACAU,UUACUU
PABPN1 1 178 0.004761905 0.0009018541 2.400573 AAAAGA AAAAGA,AGAAGA
RBM3 5 541 0.014285714 0.0027307537 2.387202 AAAACU,AAGACG,AAGACU,AGACUA,GAAACU AAAACG,AAAACU,AAACGA,AAACUA,AAGACG,AAGACU,AAUACG,AAUACU,AGACGA,AGACUA,AUACGA,AUACUA,GAAACG,GAAACU,GAGACG,GAGACU,GAUACG,GAUACU
HNRNPA1L2 1 188 0.004761905 0.0009522370 2.322146 UUAGGG AUAGGG,GUAGGG,UAGGGA,UAGGGU,UUAGGG
RBFOX1 2 287 0.007142857 0.0014510278 2.299426 GCAUGA,UGCAUG AGCAUG,GCAUGA,GCAUGC,GCAUGU,UGACUG,UGCAUG
MATR3 1 216 0.004761905 0.0010933091 2.122837 AUCUUA AAUCUU,AUCUUA,AUCUUG,CAUCUU
SRP14 1 218 0.004761905 0.0011033857 2.109602 GCCUGU CCUGUA,CGCCUG,CUGUAG,GCCUGU
EIF4B 1 226 0.004761905 0.0011436921 2.057840 UUGGAA CUCGGA,CUUGGA,GUCGGA,GUUGGA,UCGGAA,UCGGAC,UUGGAA,UUGGAC
A1CF 4 598 0.011904762 0.0030179363 1.979904 AGUAUA,AUAAUU,CAGUAU,UAAUUA AGUAUA,AUAAUU,AUCAGU,CAGUAU,GAUCAG,UAAUUA,UAAUUG,UCAGUA,UGAUCA,UUAAUU
PUM2 5 764 0.014285714 0.0038542926 1.890035 GUAAAU,GUAUAU,UGUAUA GUAAAU,GUACAU,GUAGAU,GUAUAU,UAAAUA,UACAUA,UACAUC,UAGAUA,UAUAUA,UGUAAA,UGUACA,UGUAGA,UGUAUA
PABPC5 3 596 0.009523810 0.0030078597 1.662801 AGAAAA,GAAAAU,GAAAGU AGAAAA,AGAAAG,AGAAAU,GAAAAU,GAAAGU,GAAAUU
PABPC4 2 462 0.007142857 0.0023327287 1.614483 AAAAAG AAAAAA,AAAAAG
ACO1 1 325 0.004761905 0.0016424829 1.535660 CAGUGA CAGUGA,CAGUGC,CAGUGG,CAGUGU
HNRNPAB 1 351 0.004761905 0.0017734784 1.424957 AAAGAC AAAGAC,AAGACA,ACAAAG,AGACAA,AUAGCA,CAAAGA,GACAAA
HNRNPD 7 1488 0.019047619 0.0075020153 1.344261 AAUUUA,AGAUAU,AUUUAU,UUAGGG,UUAUUU,UUUAUU AAAAAA,AAUUUA,AGAUAU,AGUAGG,AUUUAU,UAUUUA,UUAGAG,UUAGGA,UUAGGG,UUAUUU,UUUAUU
ZFP36L2 3 774 0.009523810 0.0039046755 1.286336 AUUUAU,UUAUUU,UUUAUU AUUUAU,UAUUUA,UUAUUU,UUUAUU
CSTF2 4 1022 0.011904762 0.0051541717 1.207726 UGUUUU GUGUGU,GUGUUG,GUGUUU,GUUUUG,UGUGUG,UGUGUU,UGUUUG,UGUUUU
RC3H1 2 631 0.007142857 0.0031841999 1.165570 CUUCUG,UUCUGU CCCUUC,CCUUCU,CUUCUG,UCCCUU,UCUGUG,UUCUGU
PUM1 9 2172 0.023809524 0.0109482064 1.120844 AGAAUU,AGAUAA,CAGAAU,GUAAAU,GUAUAU,UGUAAU,UGUAUA 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
ZCRB1 2 666 0.007142857 0.0033605401 1.087808 GAUUAA,GUUUAA AAUUAA,ACUUAA,AUUUAA,GAAUUA,GACUUA,GAUUAA,GAUUUA,GCUUAA,GGAUUA,GGCUUA,GGUUUA,GUUUAA

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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