ENSG00000089154:-:12:120134290:120153909

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000089154:-:12:120134290:120153909 ENSG00000089154 ENST00000300648 - 12 120134291 120153909 3616 GUGUGGCUUGGCGUUGGCCCUCAACAAGCUCUCCCAGUAUUUGGACAGCUCUCAGGUGAAGCCACUCUUUCAGUUUUUUGUCCCUGAUGCCCUCAAUGACCGACACCCAGAUGUCCGGAAGUGCAUGUUGGAUGCAGCCCUCGCAACGCUCAACACUCAUGGGAAGGAGAACGUCAACUCGCUGUUGCCAGUAUUCGAGGAGUUCCUGAAGAACGCGCCCAAUGAUGCCAGCUAUGAUGCUGUGCGACAGAGUGUGGUGGUCCUGAUGGGCUCUCUGGCCAAGCACCUGGACAAGAGUGACCCCAAAGUGAAGCCCAUUGUUGCCAAGCUCAUCGCUGCCCUCUCCACCCCCUCCCAGCAGGUCCAGGAGUCCGUAGCCAGCUGCUUGCCACCCCUUGUGCCAGCCAUCAAGGAGGAUGCUGGAGGGAUGAUCCAGAGGCUUAUGCAGCAGCUGCUGGAGUCAGACAAGUACGCAGAGCGCAAAGGGGCCGCCUAUGGCCUGGCGGGCCUGGUGAAGGGCCUGGGCAUCCUCUCGCUGAAGCAACAGGAGAUGAUGGCGGCACUGACUGAUGCCAUCCAAGAUAAGAAGAACUUCCGCCGGCGAGAGGGAGCCCUCUUUGCCUUCGAGAUGCUCUGCACCAUGCUGGGGAAACUUUUUGAGCCGUAUGUGGUUCACGUGCUGCCCCAUCUGCUCCUGUGCUUUGGGGAUGGAAACCAGUAUGUGCGUGAGGCUGCAGAUGACUGUGCCAAGGCUGUGAUGAGCAACUUGAGUGCUCACGGGGUGAAGCUGGUGCUCCCCUCCUUACUGGCUGCCCUGGAGGAGGAAUCGUGGCGGACCAAAGCUGGGUCAGUGGAGCUUCUUGGGGCAAUGGCGUACUGUGCUCCUAAGCAGCUGUCAUCCUGUCUACCCAACAUUGUGCCCAAGCUUACGGAGGUGCUGACCGACUCCCAUGUCAAAGUCCAGAAGGCUGGACAGCAGGCGCUCAGGCAGAUCGGCUCCGUUAUCAGGAACCCGGAGAUCCUGGCCAUUGCUCCAGUCCUCCUGGAUGCCCUGACGGAUCCCUCCAGGAAGACCCAGAAGUGCUUGCAGACCCUGCUGGACACCAAGUUUGUCCACUUCAUUGAUGCCCCAUCCCUGGCCCUCAUCAUGCCCAUUGUCCAGAGAGCCUUCCAGGACCGUUCCACGGACACGCGGAAGAUGGCAGCCCAGAUUAUUGGCAACAUGUACUCCCUGACAGACCAGAAGGACUUGGCUCCGUACCUGCCCAGCGUGACGCCUGGCCUGAAAGCAUCGCUUUUGGACCCUGUGCCUGAGGUGCGGACCGUAUCUGCAAAGGCCCUUGGGGCCAUGGUGAAGGGCAUGGGGGAGUCGUGCUUUGAGGACUUGCUGCCGUGGCUGAUGGAGACACUGACCUAUGAGCAGAGCUCUGUGGAUCGCUCAGGCGCUGCACAGGGGUUGGCUGAGGUCAUGGCCGGUUUGGGGGUGGAGAAGUUGGAGAAGUUGAUGCCAGAAAUCGUGGCUACAGCCAGCAAAGUGGACAUUGCACCCCAUGUCCGAGAUGGCUACAUUAUGAUGUUUAACUACCUGCCCAUCACCUUUGGAGACAAGUUUACUCCUUAUGUGGGGCCCAUCAUCCCCUGUAUCCUCAAAGCUCUUGCUGAUGAGAAUGAGUUUGUGCGUGACACCGCCCUGCGCGCGGGCCAGCGGGUUAUCUCCAUGUACGCUGAGACAGCCAUCGCCCUGCUGCUGCCCCAGCUAGAGCAAGGCCUCUUUGAUGACCUUUGGAGAAUCAGGUUCAGCUCUGUUCAGCUCCUUGGGGAUCUCCUGUUUCACAUCUCAGGAGUCACUGGGAAGAUGACCACAGAAACUGCCUCUGAGGAUGAUAACUUUGGAACUGCCCAGUCCAACAAGGCGAUCAUCACUGCCCUGGGGGUAGAGCGGCGGAACCGGGUGUUGGCAGGGCUGUACAUGGGCCGCUCAGACACCCAGCUGGUGGUGCGGCAGGCGUCCCUGCAUGUCUGGAAGAUUGUUGUCUCCAAUACCCCCCGCACCUUGCGUGAGAUCCUACCCACUCUCUUUGGGCUCCUGCUGGGUUUCCUGGCCAGCACGUGUGCAGAUAAGAGAACGAUUGCAGCGAGAACAUUGGGAGAUCUUGUGCGGAAGUUAGGGGAGAAAAUCCUCCCCGAGAUCAUCCCCAUCCUUGAGGAAGGCCUGAGGUCUCAGAAGAGCGAUGAGAGGCAGGGUGUGUGCAUUGGCCUAAGUGAGAUCAUGAAGUCCACCAGCCGGGAUGCCGUGCUGUAUUUCUCUGAAUCCCUCGUGCCCACGGCAAGGAAGGCUUUGUGUGACCCACUGGAGGAGGUCAGAGAGGCGGCAGCCAAGACUUUCGAGCAGCUGCAUUCCACCAUCGGCCACCAGGCUCUGGAGGACAUUCUCCCAUUUUUACUAAAGCAGCUGGAUGACGAGGAGGUGUCAGAGUUUGCCUUGGAUGGUCUGAAGCAAGUCAUGGCUAUUAAGAGUCGUGUGGUGCUGCCCUACCUUGUGCCCAAGCUGACAACGCCACCUGUCAACACCCGGGUGCUGGCUUUCCUUUCGUCAGUGGCUGGUGAUGCCCUCACCCGUCAUCUUGGCGUGAUCCUCCCAGCGGUCAUGCUGGCCCUGAAGGAAAAGCUUGGGACCCCAGAUGAGCAGCUGGAGAUGGCCAAUUGUCAGGCUGUGAUCCUCUCCGUAGAGGAUGACACAGGGCACCGGAUCAUCAUCGAGGAUCUGCUGGAGGCCACCCGCAGCCCUGAGGUGGGCAUGAGGCAAGCUGCUGCCAUCAUCCUCAACAUCUACUGUUCCCGCUCAAAGGCUGACUACACCAGCCACCUGCGGAGCCUGGUCUCGGGCCUGAUCCGCCUCUUCAAUGACUCCAGCCCUGUGGUUCUGGAGGAGAGCUGGGAUGCCCUAAAUGCCAUCACUAAGAAGCUGGAUGCUGGCAACCAGUUGGCACUCAUUGAAGAGCUGCACAAGGAAAUCCGGCUCAUAGGGAACGAGAGCAAAGGCGAGCAUGUGCCAGGAUUCUGCCUCCCGAAGAAGGGAGUGACCUCCAUCCUUCCAGUGUUGCGGGAAGGAGUCCUGACUGGCAGCCCUGAGCAGAAGGAGGAGGCAGCCAAAGCCUUAGGCUUGGUAAUCCGCCUGACCUCGGCUGACGCCCUGAGGCCCUCCGUGGUCAGCAUCACUGGCCCUCUGAUCCGCAUCCUGGGGGACAGGUUCAGCUGGAAUGUGAAGGCGGCUCUGCUCGAGACACUCAGCCUCUUGUUGGCUAAGGUUGGGAUUGCCCUGAAGCCCUUCCUGCCCCAGCUGCAGACCACUUUCACCAAAGCCCUGCAGGACUCCAACCGGGGGGUGCGCCUGAAGGCCGCAGAUGCUCUGGGGAAGCUCAUUUCCAUCCACAUUAAGGUGGACCCCCUCUUCACAGAGCUGCUCAAUGGCAUCCGCGCCAUGGAGGACCCAGGUGUCAGGGACACCAUGCUGCAGGCCCUGAGGUUUGUGAUUCAGGGAGCAGGGGCCAAAGUGGAUGCCGUCAUCCGGAAAAACAUCGUCUCACUCCUGCUGAGCAUGCUGGGACACGAUGAGGUGUGGCUUGGCGUUGGCCCUCAACAAGCUCUCCCAGUAUUUGGACAGCU circ
ENSG00000089154:-:12:120134290:120153909 ENSG00000089154 ENST00000300648 - 12 120134291 120153909 22 GACACGAUGAGGUGUGGCUUGG bsj
ENSG00000089154:-:12:120134290:120153909 ENSG00000089154 ENST00000300648 - 12 120153900 120154109 210 AUGGCAAGUCUCCAUAUGACAAGUGGGUUGUUCCAGAACAUUGGGUGAGCACUGGGUGGUGGGCUUCAGGCUGUUCUCUGCCCCCAAAACAGUGUUUGCCUCAGGCAAGCUCCCUCUCCUUGCCGUGCACCAGCAGAGGUUCCACUGGCAGAGGAGGCCCCCUGACUGCCCCUCCUGAUGUGCUCCCACUUCUUUCCCAGGUGUGGCUUG ie_up
ENSG00000089154:-:12:120134290:120153909 ENSG00000089154 ENST00000300648 - 12 120134091 120134300 210 ACACGAUGAGGUACGGCUGCAGGCAGGACUAGUGGCAGCACUGGACCACUGGUUUCCCUCCUCCUCCUUAGGUUGAGUUCUUCACUUUGUGUUAGAACCAGUACAGCUCAGUAGUAAUAAGCAUUCCUGACAUUUCUAUCACCCUGUAUGCUUCACCAACAUUUCCUCGGGUUUCAAGGGAAACGGGGCAGGUAUUGUGGAUAUAUUGGU 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
DDX58 1 71 0.0005530973 0.0001043427 2.406204 GCGCGC GCGCGC
IFIH1 13 904 0.0038716814 0.0013115296 1.561710 CGCGGA,GGCCCU,GGCCGC,GGGCCG CCGCGG,CGCGGA,GCCGCG,GCGGAU,GGCCCU,GGCCGC,GGGCCG
RBM8A 8 611 0.0024889381 0.0008869128 1.488666 ACGCGC,CGCGCC,CGCGCG,GCGCGC,GUGCGC,UGCGCC,UGCGCG ACGCGC,AUGCGC,CGCGCC,CGCGCG,CGCGCU,GCGCGC,GUGCGC,UGCGCC,UGCGCG,UGCGCU
RBM14 6 478 0.0019358407 0.0006941687 1.479602 CGCGCC,CGCGCG,CGCGGG,GCGCGC,GCGCGG CGCGCC,CGCGCG,CGCGGC,CGCGGG,GCGCGC,GCGCGG
RBFOX2 5 452 0.0016592920 0.0006564894 1.337724 UGACUG,UGCAUG UGACUG,UGCAUG
AGO1 6 548 0.0019358407 0.0007956130 1.282822 UGAGGU AGGUAG,GAGGUA,GGUAGU,GUAGUA,UGAGGU
ESRP1 1 156 0.0005530973 0.0002275250 1.281508 AGGGAU AGGGAU
HNRNPA1L2 3 314 0.0011061947 0.0004564992 1.276921 AUAGGG,UAGGGA,UUAGGG AUAGGG,GUAGGG,UAGGGA,UAGGGU,UUAGGG
RBFOX1 12 1077 0.0035951327 0.0015622419 1.202427 AGCAUG,GCAUGA,GCAUGC,GCAUGU,UGACUG,UGCAUG AGCAUG,GCAUGA,GCAUGC,GCAUGU,UGACUG,UGCAUG
PTBP2 2 267 0.0008296460 0.0003883867 1.095002 CUCUCU CUCUCU

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
CELF4 1 4 0.09090909 0.0003274823 8.116864 GGUGUG GGUGUG,GUGUUG,UGUGUG
AGO1 1 6 0.09090909 0.0004584752 7.631437 UGAGGU AGGUAG,GAGGUA,UGAGGU

RBP on BSJ (Exon and Intron)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
FXR1 1 69 0.004761905 0.0003526804 3.755106 AUGACA ACGACA,ACGACG,AUGACA,AUGACG
RBFOX2 1 124 0.004761905 0.0006297864 2.918604 UGACUG UGACUG,UGCAUG
AGO1 3 283 0.009523810 0.0014308746 2.734641 GAGGUA,GUAGUA,UGAGGU AGGUAG,GAGGUA,GGUAGU,GUAGUA,UGAGGU
RBMS1 1 217 0.004761905 0.0010983474 2.116204 GAUAUA AUAUAC,AUAUAG,GAUAUA,UAUAUA
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
SNRNP70 1 253 0.004761905 0.0012797259 1.895704 UUCAAG AAUCAA,AUCAAG,AUUCAA,GAUCAA,GUUCAA,UUCAAG
ZNF638 4 646 0.011904762 0.0032597743 1.868695 GGUUGU,GUUCUU,GUUGUU,UGUUCU CGUUCG,CGUUCU,CGUUGG,CGUUGU,GGUUCG,GGUUCU,GGUUGG,GGUUGU,GUUCGU,GUUCUU,GUUGGU,GUUGUU,UGUUCG,UGUUCU,UGUUGG,UGUUGU
RBFOX1 1 287 0.004761905 0.0014510278 1.714464 UGACUG AGCAUG,GCAUGA,GCAUGC,GCAUGU,UGACUG,UGCAUG
SNRPB2 1 288 0.004761905 0.0014560661 1.709463 GUAUUG AUUGCA,GUAUUG,UAUUGC,UGCAGU,UUGCAG
ZRANB2 8 1360 0.021428571 0.0068571141 1.643862 AGGGAA,AGGUAC,AGGUAU,GAGGUU,GGGUGA,GGUGGU,GUGGUG,UGGUGG AAAGGU,AGGGAA,AGGUAA,AGGUAC,AGGUAG,AGGUAU,AGGUCU,AGGUUA,AGGUUU,CGGUAA,CGGUAG,CGGUAU,CGGUCU,GAGGUU,GGGUAA,GGGUGA,GGUAAA,GGUGGU,GUAAAG,GUGGUG,UAAAGG,UGGUAA,UGGUGG
CELF4 4 776 0.011904762 0.0039147521 1.604546 GGUGUG,GUGUGG,GUGUUU,UGUGUU GGUGUG,GGUGUU,GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU
PABPC3 1 310 0.004761905 0.0015669085 1.603618 AAAACA AAAAAC,AAAACA,AAAACC,GAAAAC
ACO1 1 325 0.004761905 0.0016424829 1.535660 CAGUGU CAGUGA,CAGUGC,CAGUGG,CAGUGU
CELF5 3 669 0.009523810 0.0033756550 1.496371 GUGUGG,GUGUUU,UGUGUU GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU
RBM28 1 340 0.004761905 0.0017180572 1.470761 AGUAGU AGUAGA,AGUAGG,AGUAGU,GAGUAG,GUGUAG,UGUAGA,UGUAGG,UGUAGU
NONO 1 364 0.004761905 0.0018389762 1.372636 AGAGGA AGAGGA,AGGAAC,GAGAGG,GAGGAA
SNRPA 9 1947 0.023809524 0.0098145909 1.278539 AGUAGU,AUUCCU,CAGUAG,GUAUGC,GUUUCC,UAUGCU,UGCACC,UUCCUG,UUUCCU ACCUGC,AGCAGU,AGGAGA,AGUAGG,AGUAGU,AUACCU,AUGCAC,AUGCUG,AUUCCU,AUUGCA,CAGUAG,CCUGCU,CUGCUA,GAGCAG,GAUACC,GAUUCC,GCAGUA,GGAGAU,GGGUAU,GGUAUG,GUAGGC,GUAGGG,GUAGUC,GUAGUG,GUAUGC,GUUACC,GUUUCC,UACCUG,UAUGCU,UCCUGC,UGCACA,UGCACC,UGCACG,UUACCU,UUCCUG,UUGCAC,UUUCCU

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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