ENSG00000181090_ENSG00000197070:+:9:137754170:137800984

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000181090_ENSG00000197070:+:9:137754170:137800984 ENSG00000181090_ENSG00000197070 MSTRG.33733.4 + 9 137754171 137800984 1464 AGUUCGGAAUCCAGCAUUAAGAAGAAAUUUCUCAAGAGGAAAGGAAAGACCGACAGUCCCUGGAUCAAGCCAGCCAGGAAAAGGAGGCGGAGAAGUAGAAAGAAGCCCAGCGGUGCCCUCGGUUCUGAGUCGUAUAAGUCAUCUGCAGGAAGCGCUGAGCAGACGGCACCAGGAGACAGCACAGGGUACAUGGAAGUUUCUCUGGACUCCCUGGAUCUCCGAGUCAAAGGAAUUCUGUCUUCACAAGCAGAAGGGUUGGCCAACGGUCCAGAUGUGCUGGAGACAGACGGCCUCCAGGAAGUGCCUCUCUGCAGCUGCCGGAUGGAAACACCGAAGAGUCGAGAGAUCACCACACUGGCCAACAACCAGUGCAUGGCUACAGAGAGCGUGGACCAUGAAUUGGGCCGGUGCACAAACAGCGUGGUCAAGUAUGAGCUGAUGCGCCCCUCCAACAAGGCCCCGCUCCUCGUGCUGUGUGAAGACCACCGGGGCCGCAUGGUGAAGCACCAGUGCUGUCCUGGCUGUGGCUACUUCUGCACAGCGGGUAAUUUUAUGGAGUGUCAGCCCGAGAGCAGCAUCUCUCACCGUUUCCACAAAGACUGUGCCUCUCGAGUCAAUAACGCCAGCUAUUGUCCCCACUGUGGGGAGGAGAGCUCCAAGGCCAAAGAGGUGACGAUAGCUAAAGCAGACACCACCUCGACCGUGACACCAGUCCCCGGGCAGGAGAAGGGCUCGGCCCUGGAGGGCAGGGCCGACACCACAACGGGCAGUGCUGCCGGGCCACCACUCUCGGAGGACGACAAGCUGCAGGGUGCAGCCUCCCACGUGCCCGAGGGCUUUGAUCCAACGGGACCUGCUGGGCUUGGGAGGCCAACUCCCGGCCUUUCCCAGGGACCAGGGAAGGAAACCUUGGAGAGCGCUCUCAUCGCCCUCGACUCGGAAAAACCCAAGAAGCUUCGCUUCCACCCAAAGCAGCUGUACUUCUCCGCCAGGCAAGGGGAGCUUCAGAAGGUGCUCCUCAUGCUGGUGGACGGAAUUGACCCCAACUUCAAAAUGGAGCACCAGAAUAAGCGCUCUCCACUGCACGCCGCGGCAGAGGCUGGACACGUGGACAUCUGCCACAUGCUGGUUCAGGCGGGCGCUAAUAUUGACACCUGCUCAGAAGACCAGAGGACCCCGUUGAUGGAAGCAGCCGAAAACAACCAUCUGGAAGCAGUGAAGUACCUCAUCAAGGCUGGGGCCCUGGUGGAUCCCAAGGACGCAGAGGGCUCUACGUGUUUGCACCUGGCUGCCAAGAAAGGCCACUACGAAGUGGUCCAGUACCUGCUUUCAAAUGGACAGAUGGACGUCAACUGUCAGGAUGACGGAGGCUGGACACCCAUGAUCUGGGCCACAGAGUACAAGCACGUGGACCUCGUGAAGCUGCUGCUGUCCAAGGGCUCUGACAUCAACAUCCGAGACAACAGUUCGGAAUCCAGCAUUAAGAAGAAAUUUCUCAAGAGGAAAGGAAAGAC circ
ENSG00000181090_ENSG00000197070:+:9:137754170:137800984 ENSG00000181090_ENSG00000197070 MSTRG.33733.4 + 9 137754171 137800984 22 UCCGAGACAACAGUUCGGAAUC bsj
ENSG00000181090_ENSG00000197070:+:9:137754170:137800984 ENSG00000181090_ENSG00000197070 MSTRG.33733.4 + 9 137753971 137754180 210 UGAGCUGAGAGAGUUAGGGAAAAGCGCAGGGUGCCUUUAAGCGUGUGACCCAGCAAAAUGUCUACAAGUUAAGUUCACCGUUUAAUUGAAGAUCAAGACAUAGCCAGUGUUCUGUUUUGCAAGAAAACACUUGUAGUGCUCUUGCCUUCCGUAGCUUCCUGUGCUUAGUGGUUUAUAUGCCUGCCCGUUUGGUUCUCCAGAGUUCGGAAU ie_up
ENSG00000181090_ENSG00000197070:+:9:137754170:137800984 ENSG00000181090_ENSG00000197070 MSTRG.33733.4 + 9 137800975 137801184 210 CCGAGACAACGUAAGUUCGUCACACCCUCCCCGGGAGCCGUGUCCUGGAGGGGUGGGGACCUCCUCCCCCAGAAGGUUCUUUUCUCAAAAGCAGAACCCUGGCACCUGGUGGCGGCUUUGACCUCUUCCUGUGGCAGCAUCGGCCCGGCACUGUGCUGUGGCUGUCCUGUGCUGGAUGCAGAUGGGGGAUGUGAGGUCCCAGCAGAGGCC 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 2 268 0.002049180 0.0003898359 2.394108 CGGGCA AUCGGG,CGGGCA,UCGGGC
IFIH1 8 904 0.006147541 0.0013115296 2.228759 CCGCGG,GCCGCG,GGCCCU,GGCCGC,GGGCCG CCGCGG,CGCGGA,GCCGCG,GCGGAU,GGCCCU,GGCCGC,GGGCCG
CNOT4 2 314 0.002049180 0.0004564992 2.166363 GACAGA GACAGA
PTBP2 1 267 0.001366120 0.0003883867 1.814519 CUCUCU CUCUCU
FXR1 2 411 0.002049180 0.0005970720 1.779070 ACGACA,AUGACG ACGACA,ACGACG,AUGACA,AUGACG
IGF2BP1 5 831 0.004098361 0.0012057377 1.765131 AAGCAC,AGCACC,CCCGUU AAGCAC,ACCCGU,AGCACC,CACCCG,CCCGUU,GCACCC
ANKHD1 1 339 0.001366120 0.0004927293 1.471217 GACGAU AGACGA,AGACGU,GACGAA,GACGAU,GACGUA,GACGUU
SRSF11 3 688 0.002732240 0.0009985015 1.452248 AAGAAG AAGAAG
YBX2 7 1480 0.005464481 0.0021462711 1.348252 AACAAC,AACAUC,ACAACA,ACAACG,ACAUCA,ACAUCU AACAAC,AACAUC,ACAACA,ACAACG,ACAACU,ACAUCA,ACAUCG,ACAUCU
HNRNPLL 17 3534 0.012295082 0.0051229360 1.263039 ACAAAC,ACACCA,ACCACA,ACGACA,ACUGCA,CAAACA,CACCAC,CACUGC,CAGACG,GACGAC ACAAAC,ACACAC,ACACCA,ACAUAC,ACCACA,ACCGCA,ACGACA,ACUGCA,AGACGA,CAAACA,CACACA,CACACC,CACCAC,CACCGC,CACUGC,CAGACG,CAUACA,GACGAC,GCAAAC,GCACAC,GCAUAC
EIF4B 5 1179 0.004098361 0.0017100607 1.260999 CUCGGA,CUUGGA,UCGGAA CUCGGA,CUUGGA,GUCGGA,GUUGGA,UCGGAA,UCGGAC,UUGGAA,UUGGAC
HNRNPM 4 999 0.003415301 0.0014492040 1.236752 AAGGAA,GAAGGA AAGGAA,GAAGGA,GGGGGG
RBM8A 2 611 0.002049180 0.0008869128 1.208183 AUGCGC,UGCGCC ACGCGC,AUGCGC,CGCGCC,CGCGCG,CGCGCU,GCGCGC,GUGCGC,UGCGCC,UGCGCG,UGCGCU
RBM42 1 407 0.001366120 0.0005912752 1.208183 ACUACG AACUAA,AACUAC,ACUAAG,ACUACG
FXR2 15 3434 0.010928962 0.0049780156 1.134514 AGACAA,AGACAG,AGACGG,GACAAG,GACAGA,GACGGA,GGACAG,GGACGA,GGACGG,UGACGA,UGACGG AGACAA,AGACAG,AGACGA,AGACGG,GACAAA,GACAAG,GACAGA,GACAGG,GACGAA,GACGAG,GACGGA,GACGGG,GGACAA,GGACAG,GGACGA,GGACGG,UGACAA,UGACAG,UGACGA,UGACGG
SAMD4A 17 3992 0.012295082 0.0057866714 1.087276 CGGGAC,CGGGCA,CGGGCC,CGGGUA,CUGGAA,CUGGAC,CUGGCC,GCGGGC,GCGGGU,GCUGGA,GCUGGU CGGGAA,CGGGAC,CGGGCA,CGGGCC,CGGGUA,CGGGUC,CUGGAA,CUGGAC,CUGGCA,CUGGCC,CUGGUA,CUGGUC,GCGGGA,GCGGGC,GCGGGU,GCUGGA,GCUGGC,GCUGGU
RBFOX2 1 452 0.001366120 0.0006564894 1.057241 UGCAUG UGACUG,UGCAUG

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
YBX2 1 2 0.09090909 0.0001964894 8.853829 ACAACA ACAACA,ACAUCU
SRSF5 1 44 0.09090909 0.0029473408 4.946939 CAACAG AACAGC,AGAAGA,AGGAAG,AUAAAG,CAACAG,CACAGA,CACAGC,CACAUC,CACGGA,CGCAGC,GAAGAA,GAGGAA,GGAAGA,UAAAGG,UACAGA,UACAGC,UACGUA,UGCAGA,UGCAGC,UGCGGC

RBP on BSJ (Exon and Intron)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
RBMY1A1 1 95 0.004761905 0.0004836759 3.299426 CAAGAC ACAAGA,CAAGAC
HNRNPA1L2 2 188 0.007142857 0.0009522370 2.907109 UAGGGA,UUAGGG AUAGGG,GUAGGG,UAGGGA,UAGGGU,UUAGGG
SNRNP70 2 253 0.007142857 0.0012797259 2.480666 AUCAAG,GAUCAA AAUCAA,AUCAAG,AUUCAA,GAUCAA,GUUCAA,UUCAAG
IGF2BP1 1 173 0.004761905 0.0008766626 2.441445 CCCGUU AAGCAC,ACCCGU,AGCACC,CACCCG,CCCGUU,GCACCC
PABPC3 2 310 0.007142857 0.0015669085 2.188580 AAAACA,GAAAAC AAAAAC,AAAACA,AAAACC,GAAAAC
ZNF638 5 646 0.014285714 0.0032597743 2.131729 GGUUCU,GUUCGU,GUUCUU,UGUUCU CGUUCG,CGUUCU,CGUUGG,CGUUGU,GGUUCG,GGUUCU,GGUUGG,GGUUGU,GUUCGU,GUUCUU,GUUGGU,GUUGUU,UGUUCG,UGUUCU,UGUUGG,UGUUGU
EIF4B 1 226 0.004761905 0.0011436921 2.057840 UCGGAA CUCGGA,CUUGGA,GUCGGA,GUUGGA,UCGGAA,UCGGAC,UUGGAA,UUGGAC
HNRNPAB 2 351 0.007142857 0.0017734784 2.009919 AAGACA,AGACAA AAAGAC,AAGACA,ACAAAG,AGACAA,AUAGCA,CAAAGA,GACAAA
SSB 3 505 0.009523810 0.0025493753 1.901395 CUGUUU,UGCUGU,UGUUUU CUGUUU,GCUGUU,UGCUGU,UGUUUU
YBX2 1 263 0.004761905 0.0013301088 1.839994 ACAACG AACAAC,AACAUC,ACAACA,ACAACG,ACAACU,ACAUCA,ACAUCG,ACAUCU
AGO1 1 283 0.004761905 0.0014308746 1.734641 UGAGGU AGGUAG,GAGGUA,GGUAGU,GUAGUA,UGAGGU
ACO1 1 325 0.004761905 0.0016424829 1.535660 CAGUGU CAGUGA,CAGUGC,CAGUGG,CAGUGU
RBM28 1 340 0.004761905 0.0017180572 1.470761 UGUAGU AGUAGA,AGUAGG,AGUAGU,GAGUAG,GUGUAG,UGUAGA,UGUAGG,UGUAGU
HNRNPA3 1 349 0.004761905 0.0017634019 1.433177 GGAGCC AAGGAG,AGGAGC,CAAGGA,CCAAGG,GCCAAG,GGAGCC
ESRP2 3 731 0.009523810 0.0036880290 1.368689 GGGAAA,GGGGAU,UGGGGA GGGAAA,GGGAAG,GGGAAU,GGGGAA,GGGGAG,GGGGAU,UGGGAA,UGGGGA
A1CF 2 598 0.007142857 0.0030179363 1.242939 UAAUUG,UUAAUU AGUAUA,AUAAUU,AUCAGU,CAGUAU,GAUCAG,UAAUUA,UAAUUG,UCAGUA,UGAUCA,UUAAUU
RBM4 4 1094 0.011904762 0.0055169287 1.109602 CCUCUU,CCUUCC,CUUCCU CCUCUU,CCUUCC,CCUUCU,CGCGCG,CGCGGG,CGCGGU,CUCUUU,CUUCCU,CUUCUU,GCGCGA,GCGCGC,GCGCGG,UCCUUC,UUCCUU,UUCUUG
YBX1 5 1321 0.014285714 0.0066606207 1.100845 CACACC,CAGCAA,CCAGCA,GCCUGC 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
ZCRB1 2 666 0.007142857 0.0033605401 1.087808 GGUUUA,GUUUAA AAUUAA,ACUUAA,AUUUAA,GAAUUA,GACUUA,GAUUAA,GAUUUA,GCUUAA,GGAUUA,GGCUUA,GGUUUA,GUUUAA
AGO2 2 677 0.007142857 0.0034159613 1.064210 AGUGCU,GUGCUU AAAAAA,AAAGUG,AAGUGC,AGUGCU,GUGCUU,UAAAGU

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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