ENSG00000033867:-:3:27383152:27452498

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000033867:-:3:27383152:27452498 ENSG00000033867 ENST00000454389 - 3 27383153 27452498 3530 GGUCCUGAUGAAGAAGCUGUUGUGGAUCUUGGCAAAACUAGCUCAACUGUGAACACCAAGUUUGAAAAAGAAGAACUAGAAAGUCAUAGAGCUGUAUAUAUUGGUGUUCACGUCCCGUUUAGUAAAGAGAGUCGUCGGCGUCAUAGGCAUCGCGGACACAAACAUCACCACCGGAGAAGAAAAGAUAAAGAAUCAGAUAAAGAAGAUGGACGGGAAUCUCCUUCUUAUGAUACACCAUCCCAGAGAGUUCAGUUUAUCCUUGGUACUGAAGAUGAUGAUGAAGAACAUAUUCCCCAUGAUCUCUUCACGGAAAUGGAUGAACUGUGUUACAGAGAUGGAGAAGAAUAUGAAUGGAAAGAAACUGCUAGAUGGCUGAAAUUUGAAGAGGAUGUUGAAGAUGGCGGUGACCGAUGGAGUAAACCUUAUGUGGCAACUCUCUCUUUGCACAGUCUUUUUGAACUAAGGAGUUGCAUCCUCAAUGGAACAGUCAUGCUGGAUAUGAGAGCAAGCACUCUAGAUGAAAUAGCAGAUAUGGUAUUAGACAACAUGAUAGCUUCUGGCCAAUUAGACGAGUCCAUACGAGAGAAUGUCAGAGAAGCUCUUCUGAAGAGACAUCAUCAUCAGAAUGAGAAAAGAUUCACCAGUCGGAUUCCUCUUGUUCGAUCUUUUGCAGAUAUAGGCAAGAAACAUUCUGACCCUCACUUGCUUGAAAGGAAUGGGGAAGGCCUUUCAGCCUCCCGCCACUCUUUGCGAACAGGUCUGUCUGCCUCAAACCUUUCCUUGAGAGGAGAAUCACCUUUAUCUCUUCUUCUUGGUCAUCUUCUUCCUUCUUCAAGAGCUGGAACCCCUGCAGGCUCAAGGUGUACAACCCCAGUACCCACCCCUCAAAACAGUCCUCCUUCUAGCCCUAGCAUCAGCCGCCUGACCUCCAGAAGUUCCCAAGAGAGUCAGCGUCAGGCCCCAGAACUACUGGUUUCACCUGCCAGUGAUGAUAUUCCCACAGUAGUAAUUCAUCCGCCUGAGGAAGACUUAGAAGCAGCGCUGAAAGGCGAGGAGCAGAAGAAUGAGGAAAAUGUUGACUUAACUCCAGGUAUUUUGGCCUCUCCCCAGUCUGCUCCUGGAAACUUGGACAAUAGUAAAAGUGGAGAAAUUAAAGGUAAUGGAAGUGGUGGAAGCAGAGAAAAUAGUACUGUUGACUUCAGCAAGGUUGAUAUGAAUUUCAUGAGAAAAAUUCCUACGGGUGCUGAGGCAUCCAACGUCCUGGUGGGCGAAGUAGACUUUUUGGAAAGGCCAAUAAUUGCAUUUGUGAGACUGGCUCCUGCUGUCCUCCUUACAGGGUUGACUGAGGUCCCUGUUCCAACCAGGUUUUUGUUUUUGUUAUUGGGUCCAGCGGGCAAGGCACCACAGUACCAUGAAAUUGGACGAUCAAUAGCCACUCUCAUGACAGAUGAGAUUUUCCAUGAUGUAGCUUAUAAAGCAAAAGACAGAAAUGACCUCUUAUCUGGAAUUGAUGAAUUUUUAGAUCAAGUAACUGUCCUACCUCCAGGAGAGUGGGAUCCUUCUAUACGCAUAGAACCACCAAAAAGUGUCCCUUCUCAGGAAAAGAGAAAGAUUCCUGUGUUUCACAAUGGAUCUACCCCCACACUGGGUGAGACUCCUAAAGAGGCCGCUCAUCAUGCUGGGCCUGAGCUACAGAGGACUGGACGGCUUUUUGGUGGUUUGAUACUUGACAUCAAAAGGAAAGCACCUUUUUUCUUGAGUGACUUCAAGGAUGCAUUAAGCCUGCAGUGCCUGGCCUCGAUUCUUUUCCUAUACUGUGCCUGUAUGUCUCCUGUAAUCACUUUUGGAGGGCUGCUUGGAGAAGCUACAGAAGGCAGAAUAAGUGCAAUAGAGUCUCUUUUUGGAGCAUCAUUAACUGGGAUUGCCUAUUCAUUGUUUGCUGGGCAACCUCUAACAAUAUUGGGGAGCACAGGUCCAGUUCUAGUGUUUGAAAAAAUUUUAUAUAAAUUCUGCAGAGAUUAUCAACUUUCUUAUCUGUCUUUAAGAACCAGUAUUGGUCUGUGGACUUCUUUUUUGUGCAUUGUUUUGGUUGCAACAGAUGCAAGCAGCCUUGUGUGUUAUAUUACUCGAUUUACAGAAGAGGCUUUUGCAGCCCUUAUUUGCAUCAUAUUCAUCUACGAGGCUUUGGAGAAGCUCUUUGAUUUAGGAGAAACAUAUGCAUUUAAUAUGCACAACAACUUAGAUAAACUGACCAGCUACUCAUGUGUAUGUACUGAACCUCCAAACCCCAGCAAUGAAACUCUAGCACAAUGGAAGAAAGAUAAUAUAACAGCACACAAUAUUUCCUGGAGAAAUCUUACUGUUUCUGAAUGUAAAAAACUUCGUGGUGUAUUCUUGGGGUCAGCUUGUGGUCAUCAUGGACCUUAUAUUCCAGAUGUGCUCUUUUGGUGUGUCAUCUUGUUUUUCACAACAUUUUUUCUGUCUUCAUUCCUCAAGCAAUUUAAGACCAAGCGUUACUUUCCUACCAAGGUGCGAUCGACAAUCAGUGAUUUUGCUGUAUUUCUCACAAUAGUAAUAAUGGUUACAAUUGACUACCUUGUAGGAGUUCCAUCUCCUAAACUUCAUGUUCCUGAAAAAUUUGAGCCUACUCAUCCAGAGAGAGGGUGGAUCAUAAGCCCACUGGGAGAUAAUCCUUGGUGGACCUUAUUAAUAGCUGCUAUUCCUGCUUUGCUUUGUACCAUUCUCAUCUUUAUGGAUCAACAAAUCACAGCUGUAAUUAUAAACAGAAAGGAACACAAAUUGAAGAAAGGAGCUGGCUAUCACCUUGAUUUGCUCAUGGUUGGCGUUAUGUUGGGAGUUUGCUCUGUCAUGGGACUUCCAUGGUUUGUGGCUGCAACAGUGUUGUCAAUAAGUCAUGUCAACAGCUUAAAAGUUGAAUCUGAAUGUUCUGCUCCAGGGGAACAACCCAAGUUUUUGGGAAUUCGUGAACAGCGGGUUACAGGGCUAAUGAUUUUUAUUCUAAUGGGCCUCUCUGUGUUCAUGACUUCAGUCCUAAAGUUUAUUCCAAUGCCUGUUCUGUAUGGUGUUUUCCUUUAUAUGGGAGUUUCCUCAUUAAAAGGAAUCCAGUUAUUUGACCGUAUAAAAUUAUUUGGAAUGCCUGCUAAGCAUCAGCCUGAUUUGAUAUACCUCCGUUAUGUGCCGCUCUGGAAGGUCCAUAUUUUCACAGUCAUUCAGCUUACUUGUUUGGUCCUUUUAUGGGUGAUAAAAGUUUCAGCUGCUGCAGUGGUUUUUCCCAUGAUGGUUCUUGCAUUAGUGUUUGUGCGCAAACUCAUGGACCUGUGUUUCACGAAGAGAGAACUUAGUUGGCUUGAUGAUCUUAUGCCAGAAAGUAAGAAAAAGAAAGAAGAUGACAAAAAGAAAAAAGAGAAAGAGGAAGCUGAACGGAUGCUUCAAGAUGAUGAUGAUACUGUGCACCUUCCAUUUGAAGGGGGAAGUCUCUUGCAAAUUCCAGUCAAGGCCCUAAAAUAUAGGGUCCUGAUGAAGAAGCUGUUGUGGAUCUUGGCAAAACUAGCUCAACUGU circ
ENSG00000033867:-:3:27383152:27452498 ENSG00000033867 ENST00000454389 - 3 27383153 27452498 22 CUAAAAUAUAGGGUCCUGAUGA bsj
ENSG00000033867:-:3:27383152:27452498 ENSG00000033867 ENST00000454389 - 3 27452489 27452698 210 CUCUGGGAUUUUUGAAUGGUCUUCUGUGGAUUUAAAAAGCUUGUAAACAUAAUUUUAAAAGAAUGCAAUUAGCUGUAAUGAGUUCAGUUAUUUGAGAGAAAGCAGUCUGUUUUAUAUUUUGUUGCCAUUUCAAAGGAUGCAUAUAAUAGGUCCUCAAUAGAUUGUGAUCUCAUGAGUCAAUGAGAAUAAUUUGUUUUUAGGGUCCUGAUG ie_up
ENSG00000033867:-:3:27383152:27452498 ENSG00000033867 ENST00000454389 - 3 27382953 27383162 210 UAAAAUAUAGGUGAGAUAUGACUUUAUGCUCUAAAACUUUUAUAUGCAUGUCAAAUGUAUUAAUAAGUCAUAUAAUGCUUCUUUAAAGUGAUGAUUUCUAUUUUAUAAAAGAUGAUACAAUCUGCAUAUGGUGUAUCAACUAAAGGAGGGCUUCACACAAUUUGAAAAGGAAGUCCCUUGCUCCUUUCCCACCCAAGCUGGACUUGGACU 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
RBMS1 7 497 0.002266289 0.0007217036 1.650854 AUAUAC,AUAUAG,GAUAUA,UAUAUA AUAUAC,AUAUAG,GAUAUA,UAUAUA
PTBP2 3 267 0.001133144 0.0003883867 1.544766 CUCUCU CUCUCU
PABPN1 15 1222 0.004532578 0.0017723764 1.354647 AAAAGA,AGAAGA AAAAGA,AGAAGA
CSTF2 23 1967 0.006798867 0.0028520334 1.253303 GUGUGU,GUGUUG,GUGUUU,GUUUUG,UGUGUG,UGUGUU,UGUUUG,UGUUUU GUGUGU,GUGUUG,GUGUUU,GUUUUG,UGUGUG,UGUGUU,UGUUUG,UGUUUU
MATR3 8 739 0.002549575 0.0010724109 1.249399 AAUCUU,AUCUUA,AUCUUG,CAUCUU AAUCUU,AUCUUA,AUCUUG,CAUCUU
CELF5 14 1415 0.004249292 0.0020520728 1.050141 GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU GUGUGG,GUGUGU,GUGUUG,GUGUUU,UGUGUG,UGUGUU
RBM4 31 3065 0.009065156 0.0044432593 1.028713 CCUCUU,CCUUCC,CCUUCU,CUCUUU,CUUCCU,CUUCUU,UCCUUC,UUCCUU,UUCUUG CCUCUU,CCUUCC,CCUUCU,CGCGCG,CGCGGG,CGCGGU,CUCUUU,CUUCCU,CUUCUU,GCGCGA,GCGCGC,GCGCGG,UCCUUC,UUCCUU,UUCUUG
PABPC5 24 2400 0.007082153 0.0034795387 1.025292 AGAAAA,AGAAAG,AGAAAU,GAAAAU,GAAAGU,GAAAUU AGAAAA,AGAAAG,AGAAAU,GAAAAU,GAAAGU,GAAAUU
RALY 15 1553 0.004532578 0.0022520629 1.009085 UUUUUC,UUUUUG,UUUUUU UUUUUC,UUUUUG,UUUUUU

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
HNRNPA1L2 2 3 0.1363636 0.0002619859 9.023754 AUAGGG,UAGGGU AUAGGG,UUAGGG
HNRNPA2B1 2 49 0.1363636 0.0032748232 5.379898 AUAGGG,UAGGGU AAGGAA,AAGGGG,AAUUUA,AGAAGC,AGAUAU,AGGAAC,AGGAGC,AGGGGC,AGUAGG,AUAGGG,AUUUAA,CAAGAA,CAAGGA,CAAGGG,CCAAGA,CCAAGG,GAAGCC,GAAGGA,GCCAAG,GCGAAG,GGAACC,GGGGCC,UAGACA,UUAGGG
HNRNPA1 2 119 0.1363636 0.0078595756 4.116864 AUAGGG,UAGGGU AAAAAA,AAAGAG,AAGAGG,AAGGUG,AAUUUA,AGAGGA,AGAUAU,AGAUUA,AGGAAG,AGGAGC,AGGGAC,AGGGCA,AGGGUU,AGUAGG,AGUGAA,AUAGGG,AUUAGA,AUUUAA,CAAAGA,CAAGGA,CAGGGA,CCAAGG,GAAGGU,GACUUA,GAGGAA,GAGGAG,GAGUGG,GAUUAG,GCAGGC,GCCAAG,GGAAGG,GGACUU,GGAGGA,GGCAGG,GGGACU,GGGCAG,GGUGCG,GUUAGG,UAGACA,UAGAGA,UAGAGU,UAGAUU,UAGGAA,UAGGCU,UAGGGC,UAGUGA,UAGUUA,UCGGGC,UGGUGC,UUAGAU,UUAGGG,UUUAGA

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 AACUAA AACUAA,AACUAC,ACUAAG,ACUACG
PABPN1 2 178 0.007142857 0.0009018541 2.985535 AAAAGA AAAAGA,AGAAGA
RBFOX2 1 124 0.004761905 0.0006297864 2.918604 UGCAUG UGACUG,UGCAUG
HNRNPA1L2 2 188 0.007142857 0.0009522370 2.907109 UAGGGU,UUAGGG AUAGGG,GUAGGG,UAGGGA,UAGGGU,UUAGGG
EIF4B 2 226 0.007142857 0.0011436921 2.642803 CUUGGA,UUGGAC CUCGGA,CUUGGA,GUCGGA,GUUGGA,UCGGAA,UCGGAC,UUGGAA,UUGGAC
RBFOX1 2 287 0.007142857 0.0014510278 2.299426 GCAUGU,UGCAUG AGCAUG,GCAUGA,GCAUGC,GCAUGU,UGACUG,UGCAUG
HNRNPA0 1 200 0.004761905 0.0010126965 2.233337 AGAUAU AAUUUA,AGAUAU,AGUAGG
RBMS1 1 217 0.004761905 0.0010983474 2.116204 AUAUAG AUAUAC,AUAUAG,GAUAUA,UAUAUA
HNRNPM 1 222 0.004761905 0.0011235389 2.083489 AAGGAA AAGGAA,GAAGGA,GGGGGG
RBMS3 4 562 0.011904762 0.0028365578 2.069326 AAUAUA,AUAUAG,CAUAUA AAUAUA,AUAUAG,AUAUAU,CAUAUA,CUAUAG,CUAUAU,UAUAGA,UAUAGC,UAUAUA,UAUAUC
RC3H1 4 631 0.011904762 0.0031841999 1.902536 CUUCUG,UCCCUU,UCUGUG,UUCUGU CCCUUC,CCUUCU,CUUCUG,UCCCUU,UCUGUG,UUCUGU
SSB 3 505 0.009523810 0.0025493753 1.901395 CUGUUU,UGUUUU CUGUUU,GCUGUU,UGCUGU,UGUUUU
HNRNPA3 1 349 0.004761905 0.0017634019 1.433177 AAGGAG AAGGAG,AGGAGC,CAAGGA,CCAAGG,GCCAAG,GGAGCC
PPIE 47 9262 0.114285714 0.0466696896 1.292087 AAAAUA,AAAUAU,AAUAAU,AAUAUA,AAUUUU,AUAAAA,AUAAUA,AUAAUU,AUAUAA,AUAUUU,AUUAAU,AUUUAA,AUUUUA,AUUUUU,UAAAAA,UAAAAU,UAAUAA,UAAUUU,UAUAAA,UAUAAU,UAUAUU,UAUUAA,UAUUUU,UUAAAA,UUAAUA,UUAUAA,UUAUAU,UUAUUU,UUUAAA,UUUAUA,UUUUAA,UUUUAU,UUUUUA AAAAAA,AAAAAU,AAAAUA,AAAAUU,AAAUAA,AAAUAU,AAAUUA,AAAUUU,AAUAAA,AAUAAU,AAUAUA,AAUAUU,AAUUAA,AAUUAU,AAUUUA,AAUUUU,AUAAAA,AUAAAU,AUAAUA,AUAAUU,AUAUAA,AUAUAU,AUAUUA,AUAUUU,AUUAAA,AUUAAU,AUUAUA,AUUAUU,AUUUAA,AUUUAU,AUUUUA,AUUUUU,UAAAAA,UAAAAU,UAAAUA,UAAAUU,UAAUAA,UAAUAU,UAAUUA,UAAUUU,UAUAAA,UAUAAU,UAUAUA,UAUAUU,UAUUAA,UAUUAU,UAUUUA,UAUUUU,UUAAAA,UUAAAU,UUAAUA,UUAAUU,UUAUAA,UUAUAU,UUAUUA,UUAUUU,UUUAAA,UUUAAU,UUUAUA,UUUAUU,UUUUAA,UUUUAU,UUUUUA,UUUUUU
KHDRBS1 9 1945 0.023809524 0.0098045143 1.280021 AUAAAA,AUUUAA,CUAAAA,UAAAAA,UAAAAC,UAAAAG,UUAAAA AUAAAA,AUUUAA,AUUUAC,CAAAAU,CUAAAA,CUAAAU,GAAAAC,UAAAAA,UAAAAC,UAAAAG,UUAAAA,UUAAAU,UUUUAC,UUUUUU
A1CF 2 598 0.007142857 0.0030179363 1.242939 AUAAUU AGUAUA,AUAAUU,AUCAGU,CAGUAU,GAUCAG,UAAUUA,UAAUUG,UCAGUA,UGAUCA,UUAAUU
HNRNPA2B1 9 2033 0.023809524 0.0102478839 1.216213 AAGGAA,AAGGAG,AGAUAU,AUUUAA,UAGGGU,UUAGGG,UUUAUA AAGAAG,AAGGAA,AAGGAG,AAGGGG,AAUUUA,ACUAGA,AGAAGC,AGACUA,AGAUAU,AGGAAC,AGGAGC,AGGGGC,AGUAGG,AUAGCA,AUAGGG,AUUUAA,CAAGAA,CAAGGA,CAAGGG,CCAAGA,CCAAGG,CGAAGG,CUAGAC,GAAGCC,GAAGGA,GACUAG,GCCAAG,GCGAAG,GGAACC,GGAGCC,GGGGCC,GUAGGG,UAGACA,UAGACU,UAGGGA,UAGGGU,UUAGGG,UUUAUA
RBM46 4 1091 0.011904762 0.0055018138 1.113560 AUGAUA,AUGAUU,GAUGAU AAUCAA,AAUCAU,AAUGAA,AAUGAU,AUCAAA,AUCAAG,AUCAAU,AUCAUA,AUCAUG,AUCAUU,AUGAAA,AUGAAG,AUGAAU,AUGAUA,AUGAUG,AUGAUU,GAUCAA,GAUCAU,GAUGAA,GAUGAU
ZCRB1 2 666 0.007142857 0.0033605401 1.087808 AUUUAA,GAUUUA AAUUAA,ACUUAA,AUUUAA,GAAUUA,GACUUA,GAUUAA,GAUUUA,GCUUAA,GGAUUA,GGCUUA,GGUUUA,GUUUAA
AGO2 2 677 0.007142857 0.0034159613 1.064210 AAAGUG,UAAAGU AAAAAA,AAAGUG,AAGUGC,AGUGCU,GUGCUU,UAAAGU
PABPC4 1 462 0.004761905 0.0023327287 1.029520 AAAAAG AAAAAA,AAAAAG

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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