ENSG00000128710:+:2:176108906:176109358

1. Sequences

id gene transcript strand chrom startGR endGR length seq type
ENSG00000128710:+:2:176108906:176109358 ENSG00000128710 MSTRG.19550.2 + 2 176108907 176109358 452 UUGCCCCCCAGCGGUCCCGGAAAAAGCGCUGUCCCUAUACCAAGUACCAGAUCCGCGAACUGGAACGCGAGUUUUUCUUUAACGUGUACAUAAACAAAGAGAAAAGACUUCAACUCUCUCGGAUGCUCAACCUCACUGACCGGCAAGUCAAAAUCUGGUUCCAGAAUCGCAGGAUGAAAGAAAAGAAACUGAACAGAGACCGUCUGCAGUAUUUCACUGGAAACCCCUUAUUUUGAGAGCUCCAGGAAGCGCCCUCACCCCAGCCCCACUCACCCACCCUCCUUCCCACCAGCCUGCUCUCCGCAGGCCCACUGUCCUUGGGUUUAAUGACGUCUCUUCUCUGUGGAACUUCACGAUUCCUUCCCACGGUCAACUCGGGACCUCCCAGCGACCACUGCAGCCUGCGGACGAGGCCGGGACUUGGCCGAGCGGAUCCUAAUAAGGGGAAAAUGUUGCCCCCCAGCGGUCCCGGAAAAAGCGCUGUCCCUAUACCAAGUACCAG circ
ENSG00000128710:+:2:176108906:176109358 ENSG00000128710 MSTRG.19550.2 + 2 176108907 176109358 22 AGGGGAAAAUGUUGCCCCCCAG bsj
ENSG00000128710:+:2:176108906:176109358 ENSG00000128710 MSTRG.19550.2 + 2 176108707 176108916 210 GAACACAUGUCCACGCCCGCACUCUCUCCUGUGCCCGCCCAUAUAUCAUCCCCCACGACGCAGGCAGGGCCUUUCGGCCGCGGCAGAGAACGUCCCCAACGGGGCCAGGGCCUGGCCCUCGCUCAGUGGCCCGGGCGGGCGGGCGGGUGGGGGCUGUCAGGCAGCGGCCUCUCUCACCCCCUGGUCUCUUUGCCUUGCAGUUGCCCCCCA ie_up
ENSG00000128710:+:2:176108906:176109358 ENSG00000128710 MSTRG.19550.2 + 2 176109349 176109558 210 GGGGAAAAUGGUAAAUGCAAACGUCCCGUUACAAUUUUACCGCCAGUGUGCUGUCGUUCCCCCUCCCCCUCUCCGAGUCCUCGUGGGGACACGGCGGGGUCUGUAGGAAGUUGGGCCGGGUUGGGGGUUGCUAGAAGGCGCUGGUGUUUUGCUCUGAGUUUUAAGAGAUCCCUUCCUUCCUCUUCGGUGAAUGCAGGUUAUUUAAACUUU 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
PTBP2 1 267 0.004424779 0.0003883867 3.510040 CUCUCU CUCUCU
FXR1 1 411 0.004424779 0.0005970720 2.889628 AUGACG ACGACA,ACGACG,AUGACA,AUGACG
ZC3H10 4 1053 0.011061947 0.0015274610 2.856398 CAGCGA,CCAGCG,CGAGCG CAGCGA,CAGCGC,CCAGCG,CGAGCG,GAGCGA,GAGCGC,GCAGCG,GGAGCG
PABPN1 2 1222 0.006637168 0.0017723764 1.904883 AAAAGA AAAAGA,AGAAGA
NELFE 6 3028 0.015486726 0.0043896388 1.818858 CUCUCU,CUGGUU,GUCUCU,UCUCUC,UCUCUG,UCUGGU CUCUCU,CUCUGG,CUGGCU,CUGGUU,GCUAAC,GGCUAA,GGUCUC,GGUUAG,GUCUCU,UCUCUC,UCUCUG,UCUGGC,UCUGGU,UGGCUA,UGGUUA
HNRNPAB 3 1782 0.008849558 0.0025839306 1.776038 AAAGAC,ACAAAG,CAAAGA AAAGAC,AAGACA,ACAAAG,AGACAA,AUAGCA,CAAAGA,GACAAA
IFIH1 1 904 0.004424779 0.0013115296 1.754355 GCGGAU CCGCGG,CGCGGA,GCCGCG,GCGGAU,GGCCCU,GGCCGC,GGGCCG
PUM2 3 1890 0.008849558 0.0027404447 1.691195 GUACAU,UACAUA,UGUACA GUAAAU,GUACAU,GUAGAU,GUAUAU,UAAAUA,UACAUA,UACAUC,UAGAUA,UAUAUA,UGUAAA,UGUACA,UGUAGA,UGUAUA
SNRPB2 1 991 0.004424779 0.0014376103 1.621933 UGCAGU AUUGCA,GUAUUG,UAUUGC,UGCAGU,UUGCAG
RBM4 5 3065 0.013274336 0.0044432593 1.578949 CCUUCC,UCCUUC,UUCCUU CCUCUU,CCUUCC,CCUUCU,CGCGCG,CGCGGG,CGCGGU,CUCUUU,CUUCCU,CUUCUU,GCGCGA,GCGCGC,GCGCGG,UCCUUC,UUCCUU,UUCUUG
ZCRB1 2 1605 0.006637168 0.0023274215 1.511835 GGUUUA,GUUUAA AAUUAA,ACUUAA,AUUUAA,GAAUUA,GACUUA,GAUUAA,GAUUUA,GCUUAA,GGAUUA,GGCUUA,GGUUUA,GUUUAA
G3BP2 2 1644 0.006637168 0.0023839405 1.477220 AGGAUG,GGAUGA AGGAUA,AGGAUG,AGGAUU,GGAUAA,GGAUAG,GGAUGA,GGAUGG,GGAUUA,GGAUUG
PUM1 9 5823 0.022123894 0.0084401638 1.390262 AAUGUU,ACAUAA,CAGAAU,CCAGAA,GUACAU,UACAUA,UGUACA,UUAAUG,UUUAAU 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
EIF4B 1 1179 0.004424779 0.0017100607 1.371558 CUCGGA CUCGGA,CUUGGA,GUCGGA,GUUGGA,UCGGAA,UCGGAC,UUGGAA,UUGGAC
PABPC5 3 2400 0.008849558 0.0034795387 1.346709 AGAAAA,GAAAAU AGAAAA,AGAAAG,AGAAAU,GAAAAU,GAAAGU,GAAAUU
PABPC4 1 1251 0.004424779 0.0018144033 1.286110 AAAAAG AAAAAA,AAAAAG
ZFP36L2 1 1277 0.004424779 0.0018520827 1.256457 UUAUUU AUUUAU,UAUUUA,UUAUUU,UUUAUU
G3BP1 21 14282 0.048672566 0.0206989801 1.233549 ACCCAC,ACCCCU,ACCGGC,AGGCCC,AGGCCG,AUCCGC,CAGGCC,CCACCC,CCCACC,CCCACG,CCCCAC,CCCCAG,CCCCCA,CCCCCC,CCCUCC,CCGCAG,CCGGCA,CUCCGC,UCCGCA ACACGC,ACAGGC,ACCCAC,ACCCAU,ACCCCC,ACCCCU,ACCCGC,ACCGGC,ACGCAC,ACGCAG,ACGCCC,ACGCCG,AGGCAC,AGGCAG,AGGCCC,AGGCCG,AUACGC,AUAGGC,AUCCGC,AUCGGC,CACACG,CACAGG,CACCCG,CACCGG,CACGCA,CACGCC,CAGGCA,CAGGCC,CAUACG,CAUAGG,CAUCCG,CAUCGG,CCACAC,CCACAG,CCACCC,CCACCG,CCACGC,CCAGGC,CCAUAC,CCAUAG,CCAUCC,CCAUCG,CCCACA,CCCACC,CCCACG,CCCAGG,CCCAUA,CCCAUC,CCCCAC,CCCCAG,CCCCCA,CCCCCC,CCCCCG,CCCCGC,CCCCGG,CCCCUA,CCCCUC,CCCGCA,CCCGCC,CCCGGC,CCCUAC,CCCUAG,CCCUCC,CCCUCG,CCGCAC,CCGCAG,CCGCCC,CCGCCG,CCGGCA,CCGGCC,CCUACG,CCUAGG,CCUCCG,CCUCGG,CGGCAC,CGGCAG,CGGCCC,CGGCCG,CUACGC,CUAGGC,CUCCGC,CUCGGC,UACGCA,UACGCC,UAGGCA,UAGGCC,UCCGCA,UCCGCC,UCGGCA,UCGGCC
SART3 3 2634 0.008849558 0.0038186524 1.212542 AGAAAA,GAAAAA AAAAAA,AAAAAC,AGAAAA,GAAAAA,GAAAAC
ESRP2 2 2150 0.006637168 0.0031172377 1.090300 GGGAAA,GGGGAA GGGAAA,GGGAAG,GGGAAU,GGGGAA,GGGGAG,GGGGAU,UGGGAA,UGGGGA
RBM3 2 2152 0.006637168 0.0031201361 1.088959 AAGACU,GAAACU AAAACG,AAAACU,AAACGA,AAACUA,AAGACG,AAGACU,AAUACG,AAUACU,AGACGA,AGACUA,AUACGA,AUACUA,GAAACG,GAAACU,GAGACG,GAGACU,GAUACG,GAUACU
SRSF10 18 13860 0.042035398 0.0200874160 1.065313 AAAAGA,AAAGAA,AAAGAC,AAAGAG,AAGAAA,AAGAGA,AAGGGG,ACAAAG,AGAGAA,AGAGAC,CAAAGA,GAAAGA,GAGAAA,GAGACC,GAGAGC AAAAGA,AAAGAA,AAAGAC,AAAGAG,AAAGGA,AAAGGG,AAGAAA,AAGAAG,AAGACA,AAGAGA,AAGAGG,AAGGAA,AAGGAG,AAGGGA,AAGGGG,ACAAAG,AGACAA,AGAGAA,AGAGAC,AGAGAG,AGAGGA,AGAGGG,CAAAGA,GAAAGA,GACAAA,GAGAAA,GAGAAC,GAGAAG,GAGACA,GAGACC,GAGACG,GAGAGA,GAGAGC,GAGAGG,GAGGAA,GAGGAG,GAGGGA,GAGGGG
U2AF2 1 1477 0.004424779 0.0021419234 1.046698 UUUUUC UUUUCC,UUUUUC,UUUUUU

RBP on BSJ (Exon Only)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
PUM1 1 16 0.09090909 0.00111344 6.351329 AAUGUU AAUAUU,AAUGUU,AAUUGU,ACAUAA,AGAUAA,CAGAAU,GUAAAU,GUCCAG,UAAAUA,UAUAUA,UGUAAA,UGUAGA,UGUAUA,UUAAUG

RBP on BSJ (Exon and Intron)

Plot

Spreadsheet

id foreground background foregroundNorm backgroundNorm log2FC motifF motifB
SUPV3L1 1 31 0.004761905 0.0001612253 4.884389 CCGCCC CCGCCC
IFIH1 5 146 0.014285714 0.0007406288 4.269679 CCGCGG,GCCGCG,GGCCCU,GGCCGC,GGGCCG CCGCGG,CGCGGA,GCCGCG,GCGGAU,GGCCCU,GGCCGC,GGGCCG
RBM14 1 53 0.004761905 0.0002720677 4.129501 CGCGGC CGCGCC,CGCGCG,CGCGGC,CGCGGG,GCGCGC,GCGCGG
FXR1 1 69 0.004761905 0.0003526804 3.755106 ACGACG ACGACA,ACGACG,AUGACA,AUGACG
PTBP2 2 146 0.007142857 0.0007406288 3.269679 CUCUCU CUCUCU
ZC3H10 1 140 0.004761905 0.0007103990 2.744837 GCAGCG CAGCGA,CAGCGC,CCAGCG,CGAGCG,GAGCGA,GAGCGC,GCAGCG,GGAGCG
IGF2BP1 1 173 0.004761905 0.0008766626 2.441445 CCCGUU AAGCAC,ACCCGU,AGCACC,CACCCG,CCCGUU,GCACCC
SNRPB2 2 288 0.007142857 0.0014560661 2.294425 UGCAGU,UUGCAG AUUGCA,GUAUUG,UAUUGC,UGCAGU,UUGCAG
ACO1 2 325 0.007142857 0.0016424829 2.120623 CAGUGG,CAGUGU CAGUGA,CAGUGC,CAGUGG,CAGUGU
SRP14 1 218 0.004761905 0.0011033857 2.109602 CUGUAG CCUGUA,CGCCUG,CUGUAG,GCCUGU
AKAP1 1 221 0.004761905 0.0011185006 2.089973 AUAUAU AUAUAU,UAUAUA
SAMD4A 6 790 0.016666667 0.0039852882 2.064210 CUGGCC,CUGGUC,GCGGGC,GCGGGU,GCUGGU CGGGAA,CGGGAC,CGGGCA,CGGGCC,CGGGUA,CGGGUC,CUGGAA,CUGGAC,CUGGCA,CUGGCC,CUGGUA,CUGGUC,GCGGGA,GCGGGC,GCGGGU,GCUGGA,GCUGGC,GCUGGU
RBM4 8 1094 0.021428571 0.0055169287 1.957598 CCUCUU,CCUUCC,CUCUUU,CUUCCU,UCCUUC,UUCCUU CCUCUU,CCUUCC,CCUUCU,CGCGCG,CGCGGG,CGCGGU,CUCUUU,CUUCCU,CUUCUU,GCGCGA,GCGCGC,GCGCGG,UCCUUC,UUCCUU,UUCUUG
G3BP1 26 3431 0.064285714 0.0172914148 1.894442 ACCCCC,ACGCAG,ACGCCC,AGGCAG,CACGCC,CAGGCA,CCACGC,CCCACG,CCCAUA,CCCCAC,CCCCCA,CCCCCC,CCCCUC,CCCGCA,CCCGCC,CCCUCC,CCCUCG,CCGCAC,CCGCCC,CGGCAG,CGGCCG,UCGGCC ACACGC,ACAGGC,ACCCAC,ACCCAU,ACCCCC,ACCCCU,ACCCGC,ACCGGC,ACGCAC,ACGCAG,ACGCCC,ACGCCG,AGGCAC,AGGCAG,AGGCCC,AGGCCG,AUACGC,AUAGGC,AUCCGC,AUCGGC,CACACG,CACAGG,CACCCG,CACCGG,CACGCA,CACGCC,CAGGCA,CAGGCC,CAUACG,CAUAGG,CAUCCG,CAUCGG,CCACAC,CCACAG,CCACCC,CCACCG,CCACGC,CCAGGC,CCAUAC,CCAUAG,CCAUCC,CCAUCG,CCCACA,CCCACC,CCCACG,CCCAGG,CCCAUA,CCCAUC,CCCCAC,CCCCAG,CCCCCA,CCCCCC,CCCCCG,CCCCGC,CCCCGG,CCCCUA,CCCCUC,CCCGCA,CCCGCC,CCCGGC,CCCUAC,CCCUAG,CCCUCC,CCCUCG,CCGCAC,CCGCAG,CCGCCC,CCGCCG,CCGGCA,CCGGCC,CCUACG,CCUAGG,CCUCCG,CCUCGG,CGGCAC,CGGCAG,CGGCCC,CGGCCG,CUACGC,CUAGGC,CUCCGC,CUCGGC,UACGCA,UACGCC,UAGGCA,UAGGCC,UCCGCA,UCCGCC,UCGGCA,UCGGCC
RBMS3 3 562 0.009523810 0.0028365578 1.747397 AUAUAU,CAUAUA,UAUAUC AAUAUA,AUAUAG,AUAUAU,CAUAUA,CUAUAG,CUAUAU,UAUAGA,UAUAGC,UAUAUA,UAUAUC
NELFE 6 1059 0.016666667 0.0053405885 1.641895 CUCUCU,GGUCUC,GUCUCU,UCUCUC CUCUCU,CUCUGG,CUGGCU,CUGGUU,GCUAAC,GGCUAA,GGUCUC,GGUUAG,GUCUCU,UCUCUC,UCUCUG,UCUGGC,UCUGGU,UGGCUA,UGGUUA
SSB 2 505 0.007142857 0.0025493753 1.486358 UGCUGU,UGUUUU CUGUUU,GCUGUU,UGCUGU,UGUUUU
RBM28 1 340 0.004761905 0.0017180572 1.470761 UGUAGG AGUAGA,AGUAGG,AGUAGU,GAGUAG,GUGUAG,UGUAGA,UGUAGG,UGUAGU
ESRP2 3 731 0.009523810 0.0036880290 1.368689 GGGAAA,GGGGAA,UGGGGA GGGAAA,GGGAAG,GGGAAU,GGGGAA,GGGGAG,GGGGAU,UGGGAA,UGGGGA
HNRNPK 16 3244 0.040476190 0.0163492543 1.307849 ACCCCC,CAUCCC,CCCCAA,CCCCAC,CCCCCA,CCCCCC,CCCCCU,GCCCCC,UCCCCA,UCCCCC,UCCCUU AAAAAA,ACCCAA,ACCCAU,ACCCCA,ACCCCC,ACCCGA,ACCCGC,ACCCGU,ACCCUU,CAAACC,CAACCC,CAUACC,CAUCCC,CCAAAC,CCAACC,CCAUAC,CCAUCC,CCCCAA,CCCCAC,CCCCAU,CCCCCA,CCCCCC,CCCCCU,CCCCUA,CCCCUU,GCCCAA,GCCCAC,GCCCAG,GCCCCC,GCCCCU,GGGGGG,UCCCAA,UCCCAC,UCCCAU,UCCCCA,UCCCCC,UCCCCU,UCCCGA,UCCCUA,UCCCUU,UUUUUU
TARDBP 4 1034 0.011904762 0.0052146312 1.190902 GUGAAU,GUUUUG,UGAAUG,UUUUGC GAAUGA,GAAUGG,GAAUGU,GUGAAU,GUGUGU,GUUGUG,GUUGUU,GUUUUG,UGAAUG,UGUGUG,UUGUGC,UUGUUC,UUUUGC
RC3H1 2 631 0.007142857 0.0031841999 1.165570 CCCUUC,UCCCUU CCCUUC,CCUUCU,CUUCUG,UCCCUU,UCUGUG,UUCUGU

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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