ENSG00000172943:-:X:53984913:54002682

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000172943:-:X:53984913:54002682 ENSG00000172943 ENST00000686349 - X 53984914 54002682 2085 GGUGGAUCCAUGCUGUGCUGACGCCUGUGGACUGCCUUGCCUUUGGAGGGAACUUCUUACACAGCCUUAACAUCGAGAUGCAGCUCAAAGCCUAUGAGAUUGAGAAGCGGCUGAGCACAGCAGACCUCUUCAGAUUCCCCAACUUUGAGACCAUCUGUUGGUAUGUGGGAAAGCACAUCCUGGACAUCUUUCGCGGUUUGCGAGAGAACAGGAGACACCCUGCCUCCUACCUGGUCCAUGGUGGCAAAGCCUUGAACUUGGCCUUUAGAGCCUGGACAAGGAAAGAAGCUCUGCCAGACCAUGAGGAUGAGAUCCCGGAGACAGUGCGAACCGUACAGCUCAUUAAAGAUCUGGCCAGGGAGAUCCGCCUGGUGGAAGACAUCUUCCAACAGAACGUUGGGAAGACGAGCAAUAUCUUUGGGCUGCAGAGGAUCUUCCCAGCCGGCUCCAUUCCCCUAACCAGGCCAGCCCAUUCCACUUCAGUGUCCAUGUCCAGGCUGUCACUGCCCUCCAAAAAUGGUUCAAAGAAGAAAGGCCUGAAGCCCAAGGAACUCUUCAAGAAGGCAGAGCGAAAGGGCAAGGAGAGUUCAGCCUUGGGGCCUGCUGGCCAGUUGAGCUAUAAUCUCAUGGACACAUACAGUCAUCAGGCACUGAAGACAGGCUCUUUCCAGAAAGCAAAGUUCAACAUCACUGGUGCCUGCUUGAAUGACUCAGAUGACGACUCACCAGACUUGGACCUUGAUGGAAAUGAGAGCCCAUUGGCCCUAUUGAUGUCUAACGGCAGUACGAAAAGGGUGAAGAGUUUAUCCAAAUCUCGGCGAACCAAGAUAGCAAAGAAGGUAGACAAGGCUAGGCUGAUGGCAGAACAGGUGAUGGAAGACGAAUUUGACUUGGAUUCAGAUGAUGAGCUGCAGAUUGACGAGAGAUUGGGAAAGGAGAAGGCGACCCUGAUAAUAAGACCAAAAUUUCCCCGGAAAUUGCCCCGUGCGAAGCCUUGCUCUGACCCCAACCGAGUUCGUGAACCAGGAGAAGUUGAGUUUGACAUUGAGGAGGACUAUACAACAGAUGAGGACAUGGUGGAAGGGGUUGAAGGCAAGCUUGGGAAUGGUAGUGGCGCUGGUGGCAUUCUUGAUCUGCUCAAGGCCAGCAGGCAGGUGGGGGGACCUGACUAUGCUGCCCUCACGUGAGUACUGGCUUUUAUCUCCCCUUUCCAGGCUAUCAGACAGCAACCCCCGCUCCCGCCCAAGGUGCCAGGUCAGCCAAUCAGUAGAUAUUUAUAGAGCUAUUUAAAGGGACAAAGAAUUAUCCAGGGCAUUUGGGUGAAAGAAUAAAGUAGGCAUGAAACCACUCCUAAGGAACUUAAGAUCUGAUGGCAAUAAGAUGUAUAGACUUCAAGAGGAAUCAAUUUUGGGCACUUAGGAAGUUGGGAAGAGGGGCUGGAAGAGUCAAGCAAGGAGAAUUGUUACAAAAACAAUGAAAGGAAAGAAUGCAGCAUGCCUAAACAGGGAGGGAAGUGUGCCCCUUUUUUGCCACCUUGCCUGCUGUCUGUGGAGAGACAACACAAAAAGGACUGGCUUUUCGUGAAAGCAAUCUAUGAUACUGUCUUGAUCCUUAAACUUAAUUCCAAAUUUUUCACUUUGGAUGAUUCUCCCCUUUUUCCUCCCACUUUGAUCCUCAUAGCUAUCAUCCCUCCUCCCUGAGUAUUCUGAUGACCGAUUUACUCUGACAGCUAAAAACAACUCUCUCAGUAUUUCUCCUCUGUUCCUUGCAGCGAGGCCCCAGCUUCUCCCAGCACUCAGGAGGCCAUCCAGGGCAUGCUGUGCAUGGCCAACCUGCAGUCCUCAUCGUCCUCACCGGCUACCUCUAGCCUGCAGGCCUGGUGGACUGGGGGACAGGAUCGAAGCAGUGGGAGCUCCAGCAGUGGGCUGGGCACAGUGUCUAACAGUCCUGCUUCCCAGCGCACCCCAGGGAAGCGGCCCAUCAAGCGGCCAGCAUACUGGAGAACCGAGAGCGAGGAGGAGGAGGAGAACGCCAGUCUGGAUGAACAGGACAGCUUGGGAGCGUGCUUCAAGGAUGCAGAGUAUAGGUGGAUCCAUGCUGUGCUGACGCCUGUGGACUGCCUUGCCUUUGGAGGG circ
ENSG00000172943:-:X:53984913:54002682 ENSG00000172943 ENST00000686349 - X 53984914 54002682 22 UGCAGAGUAUAGGUGGAUCCAU bsj
ENSG00000172943:-:X:53984913:54002682 ENSG00000172943 ENST00000686349 - X 54002673 54002882 210 AGUGGCAUCUCAGCUUCUCUCAAAGAGUCUCAGGGAGCCUAAGGAUUCCUUGGACCACACCUUGAGAACAUCUGGUGUUGGGAAGCCAGUUUGGAGGCUAACUGCUCUUAAGGAGUUGGGUUUGAGAUGAGUAGGUAGUGGAGAUAAUCAGAGGAAGAAAGGCCCUCUUCCAGCUUUGAUUUUGCCUUGUUACACUGCAGGGUGGAUCCA ie_up
ENSG00000172943:-:X:53984913:54002682 ENSG00000172943 ENST00000686349 - X 53984714 53984923 210 GCAGAGUAUAGUAAGGGCAGCUAAGCACAUGGGUUCAGGCCAGAAGGGGUCUCCUCAGUCCCAGUCUCCAUCCUAGUCCCAAUAGAGGACAGCUUGUAGUGAACAAAGUCCUGGUCUUAAGCCUGAUACUUAGUUUCUCUAAGCCAUAUUUUCCUAAUUUGUAAAAUGGGAAUAUCUCACAGGUUAAUGUUAAGAAUUUGAGAUUAUGCU 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 3 339 0.0019184652 0.0004927293 1.961085 AGACGA,GACGAA AGACGA,AGACGU,GACGAA,GACGAU,GACGUA,GACGUU
SUPV3L1 1 199 0.0009592326 0.0002898408 1.726620 CCGCCC CCGCCC
ZC3H10 7 1053 0.0038369305 0.0015274610 1.328817 CAGCGA,CAGCGC,CCAGCG,GAGCGA,GCAGCG,GGAGCG CAGCGA,CAGCGC,CCAGCG,CGAGCG,GAGCGA,GAGCGC,GCAGCG,GGAGCG
PTBP2 1 267 0.0009592326 0.0003883867 1.304387 CUCUCU CUCUCU
YBX2 10 1480 0.0052757794 0.0021462711 1.297552 AACAAC,AACAUC,ACAACA,ACAACU,ACAUCA,ACAUCG,ACAUCU AACAAC,AACAUC,ACAACA,ACAACG,ACAACU,ACAUCA,ACAUCG,ACAUCU
SRSF11 4 688 0.0023980815 0.0009985015 1.264044 AAGAAG AAGAAG
NXF1 1 286 0.0009592326 0.0004159215 1.205569 AACCUG AACCUG
FXR2 22 3434 0.0110311751 0.0049780156 1.147944 AGACAA,AGACAG,AGACGA,GACAAA,GACAAG,GACAGG,GACGAA,GACGAG,GGACAA,GGACAG,UGACAG,UGACGA AGACAA,AGACAG,AGACGA,AGACGG,GACAAA,GACAAG,GACAGA,GACAGG,GACGAA,GACGAG,GACGGA,GACGGG,GGACAA,GGACAG,GGACGA,GGACGG,UGACAA,UGACAG,UGACGA,UGACGG
RBM6 6 1054 0.0033573141 0.0015289102 1.134804 AUCCAA,AUCCAG,CAUCCA,UAUCCA AAUCCA,AUCCAA,AUCCAG,CAUCCA,UAUCCA
HNRNPA0 2 453 0.0014388489 0.0006579386 1.128890 AGAUAU,AGUAGG AAUUUA,AGAUAU,AGUAGG
SNRNP70 7 1237 0.0038369305 0.0017941145 1.096681 AAUCAA,AUCAAG,GUUCAA,UUCAAG AAUCAA,AUCAAG,AUUCAA,GAUCAA,GUUCAA,UUCAAG
ENOX1 19 3195 0.0095923261 0.0046316558 1.050353 AAGACA,AGACAG,AGGACA,AUACAG,CAGACA,CAUACA,CGUACA,GGACAG,GUACAG,UAGACA,UAUACA,UGGACA AAGACA,AAUACA,AGACAG,AGGACA,AGUACA,AUACAG,CAGACA,CAUACA,CGGACA,CGUACA,GGACAG,GUACAG,UAGACA,UAUACA,UGGACA,UGUACA
HNRNPAB 10 1782 0.0052757794 0.0025839306 1.029817 AAGACA,ACAAAG,AGACAA,AUAGCA,CAAAGA,GACAAA AAAGAC,AAGACA,ACAAAG,AGACAA,AUAGCA,CAAAGA,GACAAA
ESRP2 12 2150 0.0062350120 0.0031172377 1.000124 GGGAAA,GGGAAG,GGGAAU,UGGGAA GGGAAA,GGGAAG,GGGAAU,GGGGAA,GGGGAG,GGGGAU,UGGGAA,UGGGGA

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
MSI1 2 23 0.1363636 0.001571915 6.438792 AGGUGG,UAGGUG AGGAAG,AGGAGG,AGGUAG,AGGUGG,AGUAAG,AGUAGG,AGUUGG,UAGGAA,UAGGAG,UAGGUG,UAGUUA,UAGUUG

RBP on BSJ (Exon and Intron)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
IFIH1 1 146 0.004761905 0.0007406288 2.684716 GGCCCU CCGCGG,CGCGGA,GCCGCG,GCGGAU,GGCCCU,GGCCGC,GGGCCG
EIF4B 2 226 0.007142857 0.0011436921 2.642803 CUUGGA,UUGGAC CUCGGA,CUUGGA,GUCGGA,GUUGGA,UCGGAA,UCGGAC,UUGGAA,UUGGAC
RBM28 3 340 0.009523810 0.0017180572 2.470761 AGUAGG,GAGUAG,UGUAGU AGUAGA,AGUAGG,AGUAGU,GAGUAG,GUGUAG,UGUAGA,UGUAGG,UGUAGU
IGF2BP1 1 173 0.004761905 0.0008766626 2.441445 AAGCAC 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
NONO 3 364 0.009523810 0.0018389762 2.372636 AGAGGA,GAGGAA AGAGGA,AGGAAC,GAGAGG,GAGGAA
AGO1 2 283 0.007142857 0.0014308746 2.319604 AGGUAG,GGUAGU AGGUAG,GAGGUA,GGUAGU,GUAGUA,UGAGGU
HNRNPA0 1 200 0.004761905 0.0010126965 2.233337 AGUAGG AAUUUA,AGAUAU,AGUAGG
SRSF4 4 558 0.011904762 0.0028164047 2.079612 AGGAAG,GAAGAA,GAGGAA,GGAAGA AAGAAG,AGAAGA,AGGAAG,GAAGAA,GAGGAA,GGAAGA
TUT1 1 230 0.004761905 0.0011638452 2.032640 GAUACU AAAUAC,AAUACU,AGAUAC,CAAUAC,CGAUAC,GAUACU
HNRNPA3 2 349 0.007142857 0.0017634019 2.018140 AAGGAG,GGAGCC AAGGAG,AGGAGC,CAAGGA,CCAAGG,GCCAAG,GGAGCC
HNRNPAB 2 351 0.007142857 0.0017734784 2.009919 ACAAAG,CAAAGA AAAGAC,AAGACA,ACAAAG,AGACAA,AUAGCA,CAAAGA,GACAAA
MSI1 7 961 0.019047619 0.0048468360 1.974496 AGGAAG,AGGUAG,AGUAAG,AGUAGG,AGUUGG,UAGGUA,UAGUAA AGGAAG,AGGAGG,AGGUAG,AGGUGG,AGUAAG,AGUAGG,AGUUAG,AGUUGG,UAGGAA,UAGGAG,UAGGUA,UAGGUG,UAGUAA,UAGUAG,UAGUUA,UAGUUG
TRA2A 7 1133 0.019047619 0.0057134220 1.737184 AAGAAA,AGAAAG,AGAGGA,AGGAAG,GAAGAA,GAGGAA AAAGAA,AAGAAA,AAGAAG,AAGAGG,AGAAAG,AGAAGA,AGAGGA,AGGAAG,GAAAGA,GAAGAA,GAAGAG,GAGGAA
ESRP2 4 731 0.011904762 0.0036880290 1.690617 GGGAAG,GGGAAU,UGGGAA GGGAAA,GGGAAG,GGGAAU,GGGGAA,GGGGAG,GGGGAU,UGGGAA,UGGGGA
HNRNPLL 4 748 0.011904762 0.0037736800 1.657495 ACCACA,ACUGCA,CACACC,CACUGC ACAAAC,ACACAC,ACACCA,ACAUAC,ACCACA,ACCGCA,ACGACA,ACUGCA,AGACGA,CAAACA,CACACA,CACACC,CACCAC,CACCGC,CACUGC,CAGACG,CAUACA,GACGAC,GCAAAC,GCACAC,GCAUAC
YBX1 7 1321 0.019047619 0.0066606207 1.515882 AACAUC,ACAUCU,ACCACA,CACACC,CAUCUG,CCACAC,UCCAGC 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 5 1059 0.014285714 0.0053405885 1.419503 GCUAAC,GGCUAA,GGUCUC,UCUCUC,UCUGGU CUCUCU,CUCUGG,CUGGCU,CUGGUU,GCUAAC,GGCUAA,GGUCUC,GGUUAG,GUCUCU,UCUCUC,UCUCUG,UCUGGC,UCUGGU,UGGCUA,UGGUUA
LIN28A 4 900 0.011904762 0.0045395002 1.390933 AGGAGU,GGAGAU,UGGAGA,UGGAGG AGGAGA,AGGAGU,CGGAGA,CGGAGG,CGGAGU,GGAGAA,GGAGAU,GGAGGA,GGAGGG,GGAGUA,UGGAGA,UGGAGG,UGGAGU
SNRPA 8 1947 0.021428571 0.0098145909 1.126536 AGUAGG,AUUCCU,GAUUCC,GGAGAU,GUAGUG,UAUGCU,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
PUM1 9 2172 0.023809524 0.0109482064 1.120844 AAUGUU,AGAAUU,AGAUAA,CCAGAA,CUUGUA,UAAUGU,UGUAAA,UUAAUG,UUGUAG 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
RBM5 9 2359 0.023809524 0.0118903668 1.001746 AAGGAG,AAGGGG,AGGGAG,AGGGUG,CUCUUC,CUUCUC,GAAGGG,UUCUCU AAAAAA,AAGGAA,AAGGAG,AAGGGG,AAGGUA,AAGGUG,AGGGAA,AGGGAG,AGGGUA,AGGGUG,AGGUAA,CAAGGA,CAAGGG,CCCCCC,CUCUUC,CUUCUC,GAAGGA,GAAGGG,GAAGGU,GAGGGA,GAGGGU,GGGGGG,GGUGGU,UCUUCU,UUCUCU

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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