ENSG00000114316:-:3:49276426:49327816

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000114316:-:3:49276426:49327816 ENSG00000114316 MSTRG.22947.1 - 3 49276427 49327816 3151 AUCCUGAGAGUCAGACCUUGAAAGAACACUUAAUUGAUGAAUUGGACUAUGUAUUGGUCCCUACCGAGGCGUGGAAUAAACUACUAAACUGGUACGGCUGUGUAGAAGGCCAGCAACCCAUCGUCAGAAAAGUUGUGGAGCAUGGCCUGUUUGUCAAGCACUGCAAAGUCGAGGUGUAUUUGCUGGAACUGAAGCUCUGUGAGAACAGUGACCCCACCAAUGUGCUGAGUUGCCAUUUCAGCAAGGCAGACACCAUUGCAACCAUCGAGAAAGAGAUGCGGAAGCUAUUCAACAUCCCUGCGGAGCGUGAAACACGGCUCUGGAACAAAUACAUGAGCAACACCUACGAGCAGUUGAGCAAGCUAGACAACACUGUCCAGGAUGCUGGGCUAUACCAGGGUCAGGUGCUAGUAAUUGAGCCUCAAAAUGAAGAUGGCACAUGGCCCAGGCAGACCUUGCAGUCAAAUGGAUCUGGCUUUUCUGCUUCGUAUAAUUGUCAGGAGCCACCAUCCUCUCAUAUACAACCUGGGCUCUGUGGACUUGGAAACCUGGGAAACACCUGCUUCAUGAACUCCGCUUUGCAGUGUUUGAGCAACACUGCACCACUGACUGACUACUUUCUCAAAGAUGAGUAUGAAGCCGAAAUCAACAGAGACAACCCUCUGGGGAUGAAAGGGGAAAUUGCAGAAGCCUAUGCUGAACUCAUUAAGCAGAUGUGGUCUGGAAGGGACGCCCAUGUGGCACCUCGCAUGUUCAAAACUCAAGUAGGACGUUUUGCUCCUCAAUUUUCUGGCUACCAGCAACAAGAUUCUCAGGAGCUGCUGGCCUUUCUUCUAGAUGGAUUGCAUGAAGAUCUGAACCGGGUAAAGAAAAAGCCCUACUUGGAGCUGAAGGAUGCCAAUGGGCGGCCAGAUGCGGUGGUGGCAAAGGAAGCCUGGGAGAAUCACAGGUUGAGGAAUGAUUCUGUGAUUGUGGAUACUUUCCAUGGCCUCUUCAAAUCUACUUUGGUUUGCCCAGAAUGUGCUAAGGUUUCUGUGACCUUUGACCCAUUUUGCUAUCUAACGCUGCCACUGCCCUUGAAGAAAGAUCGAGUUAUGGAGGUUUUCCUGGUUCCUGCUGACCCUCACUGCAGACCUACUCAGUACCGUGUGACUGUGCCGCUGAUGGGGGCUGUGUCCGACCUGUGCGAGGCUCUCUCCAGGCUGUCUGGCAUUGCUGCAGAAAAUAUGGUGGUCGCAGAUGUGUAUAAUCACCGAUUCCACAAAAUUUUCCAAAUGGAUGAAGGUUUAAACCACAUCAUGCCUCGGGAUGACAUUUUCGUGUACGAGGUCUGCAGCACUUCCGUGGAUGGCUCGGAAUGUGUCACGCUUCCAGUCUACUUCAGGGAGAGGAAGUCCAGGCCAUCAAGCACUUCCUCCGCAUCAGCGCUAUAUGGGCAGCCACUAUUGCUUUCUGUCCCCAAGCACAAGUUAACCCUUGAGUCUUUGUACCAGGCUGUUUGUGAUCGUAUCAGCCGCUAUGUGAAACAGCCUUUACCUGAUGAGUUUGGCAGCUCACCCUUGGAGCCAGGGGCCUGCAAUGGCUCCAGGAACAGCUGUGAAGGAGAAGAUGAGGAAGAAAUGGAGCAUCAGGAAGAAGGCAAAGAGCAGCUUUCAGAAACAGAAGGCAGUGGGGAAGAUGAGCCAGGAAAUGACCCCAGUGAGACCACCCAAAAGAAGAUCAAAGGCCAGCCCUGCCCAAAAAGGCUUUUUACCUUCAGUCUUGUGAACUCCUAUGGAACAGCUGACAUAAAUUCACUUGCAGCUGAUGGAAAACUACUUAAACUCAACUCUCGAUCUACACUGGCCAUGGAUUGGGACAGUGAAACUCGGAGACUUUACUAUGAUGAGCAAGAAUCUGAGGCCUACGAGAAGCAUGUGAGCAUGUUGCAGCCUCAGAAGAAGAAGAAGACCACAGUGGCCCUGAGAGACUGCAUCGAGCUCUUCACCACCAUGGAGACCCUUGGGGAGCAUGACCCCUGGUACUGUCCCAACUGUAAGAAGCAUCAACAGGCCACAAAAAAGUUUGACCUAUGGUCCUUGCCCAAGAUCCUGGUGGUCCACCUCAAACGUUUCUCCUACAACAGAUACUGGAGGGAUAAGCUCGACACAGUCGUAGAAUUCCCAAUCAGAGGGCUGAACAUGUCCGAGUUUGUCUGUAACCUGUCAGCAAGGCCUUAUGUGUACGACCUCAUUGCCGUGUCCAAUCAUUAUGGAGCCAUGGGGGUUGGCCACUACACUGCAUAUGCGAAGAACAAACUGAAUGGUAAAUGGUAUUACUUUGAUGAUAGCAACGUGUCCCUGGCCUCUGAGGAUCAGAUAGUGACUAAAGCAGCUUAUGUGCUAUUUUACCAACGUCGAGAUGAUGAAUUUUAUAAGACACCUUCACUUAGCAGUUCUGGUUCCUCUGAUGGAGGGACACGACCAAGCAGCUCUCAGCAGGGCUUUGGGGAUGAUGAGGCUUGCAGCAUGGACACCAACUAAUGCUGACUCCACGAUCCUGCCACCCUGUAGCGCCAGUGUAAUCCCCCAGGAGAACAUCUUUGACACUCUGCAGACUGCUAGUGUUCUGUCUAAAAACCAGACAAGGAAAUACCCUUCUUUUAUGAGCAGAAGGAAACAAAAAAAAAAAAAGAAGACCGUUUACCUAGAAGAAGCUAUGUCAAGAGGCUGAAUUAUUUUUAUUUUUAAACAGGUGGAGAAAUGUCUGAAAAACUAAGAAGAUGCAGAAAGGAACUGACUGCAGCCAUUGACCGGGCCUUUGAAGGAGUUAGUUAUUCCCAGGAGUGCACAGGCCAGCAGAGGCUGGAACUGAGCGCCGCGCCGCUCUCCUUCUCGCUGCCCGUGCACAGGCUCCUCUGCAGAAGACAUCCUCUGGCAGCCUGCUCUUCUGCUGCUCCUUUUGCUGCUGUCCCAUGUGCUCCUGAGAAUGAGAACCCUGCCUUUGCAACAAACCAUGCCCCGGUAAAUGCAAAACCACAUGCUCUGUGCCCCGAGAGAAAACCUCUAACCAGCAAGGAAAAUGUAUUGAUGCAUUCCUCCAUUUUGGCACCUGAAAGAGAGUCUUGGAGAACUGCAGGAGAGGGGGAAAACUGGAGAAAAGAAAAUUUAAGAUCCUGAGAGUCAGACCUUGAAAGAACACUUAAUUGAUGAAUUGGACUAU circ
ENSG00000114316:-:3:49276426:49327816 ENSG00000114316 MSTRG.22947.1 - 3 49276427 49327816 22 GAAAAUUUAAGAUCCUGAGAGU bsj
ENSG00000114316:-:3:49276426:49327816 ENSG00000114316 MSTRG.22947.1 - 3 49327807 49328016 210 AAAAUCUUCAUGGAUAAAGAGAAAACAUGGAUAAAGACAAAAGUCUGCUCUGUAUAAUGACCAGUGACAGAAUUUUGGAAUUUCAUUCCUGUUUCUUUCUGUAAAUAAUUUUCUUAUUUCUGAAAAGUACAUGGAAAUCAUGUAAAACCAUCAUUUCUGGGGUAAAGAGCAGUGACUUAUGUGCUCUUUUCCUUUUUUAGAUCCUGAGAG ie_up
ENSG00000114316:-:3:49276426:49327816 ENSG00000114316 MSTRG.22947.1 - 3 49276227 49276436 210 AAAAUUUAAGGUGAUUCUAAUUUUGAUGGUUUAACAGCUACAAUUAAGGGGAUUCUUGUUUCUGAAAAAGUUGUUGAAGAUCCUAGAUUUAGUUCAUGACAGUGCUCUUGCCUCCUCUUGGCAGCUCUGUGACUGCAUUUGGGGAGUUGACAGACAUUCUUCAGAAUCUGGCCUAGGAAACAGUUAUAUUUUGUGUAUAUGUUCCAGUUG 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
SNRPB2 14 991 0.0047603935 0.0014376103 1.727408 AUUGCA,GUAUUG,UAUUGC,UGCAGU,UUGCAG AUUGCA,GUAUUG,UAUUGC,UGCAGU,UUGCAG
RBM42 5 407 0.0019041574 0.0005912752 1.687251 AACUAA,AACUAC,ACUAAG AACUAA,AACUAC,ACUAAG,ACUACG
SRSF11 9 688 0.0031735957 0.0009985015 1.668282 AAGAAG AAGAAG
NXF1 3 286 0.0012694383 0.0004159215 1.609807 AACCUG AACCUG
RBFOX1 14 1077 0.0047603935 0.0015622419 1.607463 AGCAUG,GCAUGA,GCAUGU,UGACUG,UGCAUG AGCAUG,GCAUGA,GCAUGC,GCAUGU,UGACUG,UGCAUG
ESRP1 1 156 0.0006347191 0.0002275250 1.480093 AGGGAU AGGGAU
IGHMBP2 9 813 0.0031735957 0.0011796520 1.427757 AAAAAA AAAAAA
PABPN1 13 1222 0.0044430340 0.0017723764 1.325860 AAAAGA,AGAAGA AAAAGA,AGAAGA
PABPC4 13 1251 0.0044430340 0.0018144033 1.292050 AAAAAA,AAAAAG AAAAAA,AAAAAG
RBFOX2 4 452 0.0015867978 0.0006564894 1.273275 UGACUG,UGCAUG UGACUG,UGCAUG
SRSF4 37 3740 0.0120596636 0.0054214720 1.153433 AAGAAG,AGAAGA,AGGAAG,GAAGAA,GAGGAA,GGAAGA AAGAAG,AGAAGA,AGGAAG,GAAGAA,GAGGAA,GGAAGA
HNRNPM 9 999 0.0031735957 0.0014492040 1.130858 AAGGAA,GAAGGA AAGGAA,GAAGGA,GGGGGG

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
SRSF2 1 479 0.09090909 0.0314383 1.531901 AGAUCC AAAAGA,AAAGAG,AAGAGA,AAGCAG,AAGCUG,AAGGCG,AAUACC,AAUGCU,ACCACC,ACCACU,ACCAGC,ACCAGU,ACCCCC,ACCCCU,ACUCAA,AGAAGA,AGAAGC,AGAAUA,AGAAUG,AGAGAA,AGAGAU,AGAGGA,AGAGGU,AGAGUA,AGAGUG,AGAGUU,AGAUAA,AGAUCC,AGAUGC,AGCACU,AGCAGA,AGCAGU,AGCCGA,AGCCUC,AGCGGA,AGCUGU,AGGAAG,AGGAGA,AGGAGC,AGGAGG,AGGAGU,AGGCAG,AGGCGU,AGGCUG,AGGGUA,AGUAGG,AGUAGU,AGUGAC,AGUGUU,AUGAUG,AUGCUG,AUGGAG,AUUAGU,AUUCCU,AUUGAU,CAGAGA,CAGAGG,CAGAGU,CAGUAG,CAGUGG,CCACCA,CCAGAU,CCAGCC,CCAGCU,CCAGGG,CCAGGU,CCAGUC,CCAGUG,CCAGUU,CCCGCU,CCCGUG,CCGCUA,CCGGUG,CCUCCG,CCUGCG,CCUGCU,CCUGUU,CGAACG,CGAGGA,CGAGUA,CGAGUG,CGAGUU,CGCAGU,CGCUGC,CGUAAG,CGUGCG,CUACCG,CUAGAA,CUCAAG,CUCCAA,CUCCUG,CUCGUG,CUGAUG,GAAAGG,GAAGAA,GAAGCG,GAAGGC,GAAUAC,GAAUCC,GACCCC,GACGGA,GACUCA,GACUGU,GAGAAG,GAGAAU,GAGAGA,GAGAGU,GAGAUA,GAGAUG,GAGCAC,GAGCAG,GAGCUG,GAGGAA,GAGGAC,GAGGAG,GAGUGA,GAUCCC,GAUCCG,GAUGAU,GAUGCU,GAUGGA,GAUUAG,GAUUGA,GCACUG,GCAGAG,GCAGGG,GCAGGU,GCAGUA,GCAGUG,GCCACC,GCCACU,GCCCAC,GCCGAG,GCCGCC,GCCGUU,GCCUCA,GCCUCC,GCGUGU,GCUGUU,GGAACC,GGAAGG,GGAAUG,GGACCG,GGACGC,GGAGAA,GGAGAG,GGAGAU,GGAGCG,GGAGGA,GGAGUG,GGAGUU,GGAUCC,GGAUGG,GGCAGU,GGCCAC,GGCCGC,GGCCUC,GGCGUG,GGCUCC,GGCUCG,GGCUGA,GGCUGC,GGGAAU,GGGAGC,GGGCAG,GGGUAA,GGGUAC,GGGUAG,GGGUAU,GGGUGA,GGUACG,GGUAGG,GGUCAG,GGUUAC,GGUUCC,GGUUGG,GUAAGC,GUAGGC,GUCAGU,GUCGCC,GUCUAA,GUGCAG,GUUAAU,GUUCCC,GUUCCU,GUUCGA,GUUCUG,GUUGGC,GUUUCG,UAAGCU,UACGAG,UACGUG,UAGGCU,UAUGCU,UCACCG,UCAGUG,UCCAGA,UCCAGC,UCCAGG,UCCAGU,UCCUGC,UCCUGU,UCGAGU,UCGUGC,UGAGCU,UGAUCG,UGAUGG,UGCAGA,UGCAGU,UGCCGU,UGCGGU,UGCUGU,UGGAGA,UGGAGG,UGGAGU,UGGCAG,UGUUCC,UUAAUG,UUACUG,UUAGUG,UUCCAG,UUCCCG,UUCCUA,UUCCUG,UUCGAG,UUGUUG

RBP on BSJ (Exon and Intron)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
CNOT4 2 65 0.007142857 0.0003325272 4.424957 GACAGA GACAGA
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
HNRNPAB 4 351 0.011904762 0.0017734784 2.746885 AAAGAC,AAGACA,AGACAA,GACAAA AAAGAC,AAGACA,ACAAAG,AGACAA,AUAGCA,CAAAGA,GACAAA
PABPC3 3 310 0.009523810 0.0015669085 2.603618 AAAACA,AAAACC,GAAAAC AAAAAC,AAAACA,AAAACC,GAAAAC
ACO1 3 325 0.009523810 0.0016424829 2.535660 CAGUGA,CAGUGC CAGUGA,CAGUGC,CAGUGG,CAGUGU
PUM2 8 764 0.021428571 0.0038542926 2.474998 GUAAAU,GUACAU,GUAUAU,UAAAUA,UGUAAA,UGUAUA GUAAAU,GUACAU,GUAGAU,GUAUAU,UAAAUA,UACAUA,UACAUC,UAGAUA,UAUAUA,UGUAAA,UGUACA,UGUAGA,UGUAUA
FXR2 7 730 0.019047619 0.0036829907 2.370661 AGACAA,GACAAA,GACAGA,UGACAG AGACAA,AGACAG,AGACGA,AGACGG,GACAAA,GACAAG,GACAGA,GACAGG,GACGAA,GACGAG,GACGGA,GACGGG,GGACAA,GGACAG,GGACGA,GGACGG,UGACAA,UGACAG,UGACGA,UGACGG
ZCRB1 6 666 0.016666667 0.0033605401 2.310201 AAUUAA,AUUUAA,GACUUA,GAUUUA,GGUUUA,GUUUAA AAUUAA,ACUUAA,AUUUAA,GAAUUA,GACUUA,GAUUAA,GAUUUA,GCUUAA,GGAUUA,GGCUUA,GGUUUA,GUUUAA
HNRNPA0 1 200 0.004761905 0.0010126965 2.233337 AAUUUA AAUUUA,AGAUAU,AGUAGG
MATR3 1 216 0.004761905 0.0010933091 2.122837 AAUCUU AAUCUU,AUCUUA,AUCUUG,CAUCUU
EIF4B 1 226 0.004761905 0.0011436921 2.057840 UUGGAA CUCGGA,CUUGGA,GUCGGA,GUUGGA,UCGGAA,UCGGAC,UUGGAA,UUGGAC
ERI1 1 228 0.004761905 0.0011537686 2.045185 UUCAGA UUCAGA,UUUCAG
RBFOX1 1 287 0.004761905 0.0014510278 1.714464 UGACUG AGCAUG,GCAUGA,GCAUGC,GCAUGU,UGACUG,UGCAUG
G3BP2 2 490 0.007142857 0.0024738009 1.529772 GGAUAA AGGAUA,AGGAUG,AGGAUU,GGAUAA,GGAUAG,GGAUGA,GGAUGG,GGAUUA,GGAUUG
CELF2 4 881 0.011904762 0.0044437727 1.421682 GUUGUU,UAUGUG,UAUGUU,UUGUGU AUGUGU,GUAUGU,GUCUGU,GUGUGU,GUUGUU,UAUGUG,UAUGUU,UGUGUG,UGUUGU,UUGUGU
PUM1 11 2172 0.028571429 0.0109482064 1.383879 AGAAUU,CAGAAU,GUAAAU,GUACAU,GUAUAU,UAAAUA,UGUAAA,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
ESRP2 3 731 0.009523810 0.0036880290 1.368689 GGGGAG,GGGGAU,UGGGGA GGGAAA,GGGAAG,GGGAAU,GGGGAA,GGGGAG,GGGGAU,UGGGAA,UGGGGA
KHDRBS3 8 1646 0.021428571 0.0082980653 1.368689 AAAUAA,AUAAAG,GAUAAA,UAAAAC,UAAAUA,UUUUUU AAAUAA,AAUAAA,AGAUAA,AUAAAA,AUAAAC,AUAAAG,AUUAAA,GAUAAA,UAAAAC,UAAAUA,UUAAAC,UUUUUU
ENOX1 3 756 0.009523810 0.0038139863 1.320239 AAGACA,AGUACA,CAGACA AAGACA,AAUACA,AGACAG,AGGACA,AGUACA,AUACAG,CAGACA,CAUACA,CGGACA,CGUACA,GGACAG,GUACAG,UAGACA,UAUACA,UGGACA,UGUACA
SART3 3 777 0.009523810 0.0039197904 1.280762 AGAAAA,GAAAAA,GAAAAC AAAAAA,AAAAAC,AGAAAA,GAAAAA,GAAAAC
RC3H1 2 631 0.007142857 0.0031841999 1.165570 UCUGUG,UUCUGU CCCUUC,CCUUCU,CUUCUG,UCCCUU,UCUGUG,UUCUGU
RBM4 4 1094 0.011904762 0.0055169287 1.109602 CCUCUU,CUCUUU,UUCCUU,UUCUUG CCUCUU,CCUUCC,CCUUCU,CGCGCG,CGCGGG,CGCGGU,CUCUUU,CUUCCU,CUUCUU,GCGCGA,GCGCGC,GCGCGG,UCCUUC,UUCCUU,UUCUUG
QKI 3 904 0.009523810 0.0045596534 1.062615 AAUCAU,ACUUAU,UCUAAU AAUCAU,ACACAC,ACACUA,ACUAAC,ACUAAU,ACUCAU,ACUUAU,AUCAUA,AUCUAA,AUCUAC,AUUAAC,CACACU,CACUAA,CUAACA,CUAACC,CUAACG,CUAAUC,CUACUC,CUCAUA,UAACCU,UAAUCA,UACUCA,UCAUAU,UCUAAU,UCUACU
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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