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mmu_circJmjd1c_2558
Basic information of circular RNA
PanCircBase ID:
mmu_circJmjd1c_2558
mm39_Chr. Position ID:
chr10|67059787|67065828|+
Gene name:
Jmjd1c
Transcript:
ENSMUST00000174408.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
9,10,11
Exon/intron offsets:
0,728,5839
Genomic length:
6041
Exon/intron sizes in nt:
1,73,21,83,202
Flanking exon/introns:
chr10:67056414-67059787|chr10:67065828-67067750
Splice length:
2558
Other database IDs:
circAtlas: mmu-Jmjd1c_0043
Human Ortholog IDs:
Mature spliced Sequence:
AATTCTCCCAGTCCTTGGCTACATCAACCCACTCCTGTGACCTCAGCGGATGGTATTGGATTACTTAGTCACATTCCTGTCAGACCTTCCAGTGCAGAGCCTCATCGACCTCACAAGATTACAGTGCATTCCAGTCCCCCACTGACAAAGACATTAGCAGATCACCACAAAGAAGAATTGGAGAGGAAAGCTTTTATGGAACCATTACGGTCTAATGCATCCACATCAGTAAAAGGTGACCTGGATCTTAATAGGTCACAGGCAGGAAAAGATTGTCACTTGCATAGGCATTTTGTGGGTCCAAGGCCACCCCAGGAGACTGGAGAGAGACTGAACAAATACAAGGAGGAACATCGTCGGATTCTTCAGGAGAGTATTGATGTGGCTCCATTTACAACCAAAATCAAGGGTCATGAGGTTGAAAGAGAGAATTACTCCAGAGTAGTACCATCATCTTCTAGTCCTAAAAGCCATGCTATCAAACAAGATAAAGACGTAGACCGCTCCGTGTCAGAGATTTATAAGATGAAGCACTCAGTGCCTCAGAGTTTGCCCCAGAGTAACTACTTCACTACTTTATCTAATAGTGTGGTCAATGAGCCACCAAGATCCTACCCATCCAAAGAAGTTTCCAACATTTACACTGAGAAACAAAATAATAACCTTTCTGCAACAGCCAATCCTCAAACTCATTCTTTTATATCATCTCTTTCGAAGCCTCCACCTTTGATTAAACACCAACCAGAAAGTGAAAGTTTAGTGGGCAAGATACCAGACCATCTTCCCCATCAGAGTGCATCTCACTCAGTAACAACGTTCAGAAGTGATTGTCGGAGCCCTACCCATCTGACTGTTTCTTCTACTAATGCACTCCGCAGCATGCCTGCTCTGCACAGGGCACCAGTATTCCATCCACCAATCCACCACAGTTTGGAAAGAAAGGAAAGCAGCTACAGTAGCCTTTCCCCTCCAACACTGACACCGGTGATGCCAGTAAATGCTGGTGGCAAAGTTCAAGAATCTCAGAAGCCTCCAACTCTAATTCCTGAGCCAAAAGACTCTCAGTCAAATTTTAAGAATTCTTCTGATCAGAGTCTAACGGAAATGTGGAGATCTAATAACAACCTCAACAGAGAGAAAGCTGAGTGGCCCGTGGAAAAGAGTAGTGGAAAGTCCCAGGCTGCTGTGGCATCTGTCATTGTTCGTCCACCTTCTAGTACAAAAGTTGATAGTGTGCCATCTGTACCATTAGCTTCCAAAGATCGAGTTTGTGAAAGATCTTCATCTGGGGCAAATAAAACAGATTACCTCAAACCAGAAGCCGGAGAGACTGGAAGAATTATTCTACCAAATGTGAATTTAGAAAGTGCTCATGTGAAATCTGAAAAAAACTTTGAAGCTGTCTCCCAGGGCAACGTTCCTGTTTCAGTCATGTCTGCTGTAAATGTAGTCTCTACTACCAAAGCAGATGTGTTCACATCTGCTGCCACTACCACCAGTGTCTCCAGCTTGAGTAGTGCAGAAACAAGTTATTCTTTATCAAATACCATTTCGGCCTCTACACCCTTCGAATGTACTTCTTCAAAAAGTGTTGTTAGTCAGGCAGTGGCGCAAGCAAAGGACTGCACAGTCAGCACCGCGGTTCCAGGCACTCTGGCCTGTAGTAAGACAGGAAGTGCTGTTCAGCCCGGCTCTGGCTTCTCAGGCACAACTGATTTTATTCATTTAAAAAAGCACAAGGCAGCGTTGGCTGCAGCTCAGTTTAAAAATAGTAGTGTCAGTGAGGCTGAACTTAATACTGTGAGAAATCAGACAGTGGCAGCCTCTCTTCCCCTGGATAGCACCATGACCTGCACTGCAAGTAACAAAGCAATCTCTGTAGGAAATGGGCCAGCAGCCCAGTCCAGTCAGCCCAACTACCACACTAAACTGAAGAAGGCCTGGCTCACCAGACATTCAGAAGAAGATAAAAATACTAATAAAATGGAAAATTCAGGGAATTCTGTATCCGAAATTATTAAGCCATGTTCTGTCAACTTAATAGCCTCTACATCTAATGATATAGAAAATCGTGCAGATGGCAGAGTCGCTGTAGATAAATATGGAAGAGATGAGAAAGTCAGCAGGAGAAAAGCCAAAAGAACTTACGAATCTGGCTCTGAAAGTGGAGACTCAGATGAGAGCGAAAGCAAGTCGGAGCAGAGGACTAAACGGCAGCCGAAGCCAACTTATAAAAAGAAGCAGAACGACCTGCAGAAGAGGAAAGGCGAGGTCGAAGAGGACTCGAAGCCTAATGGAGTTCTCAGCAGGAGCGCCAAGGACAAAAGTAAACTGAAGTTGCAGAACAGTAATAGCGCTGGCGTTCCTCGTTCCGTGCTGAAAGACTGGCGGAAGGTCAAGAAGCTGAAGCAAACTGGAGAATCATTTCTGCAGGATGACTCCTGCTGTGAGATAGGTCCCAACTTACAGAAGTGCCGAGAGTGCAGACTTATCCGGAGTAAGAAGGGGGAAGAATCAACTCACTCACCGGTGTTTTGTAGATTTTACTACTTTAGGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGCCGAGAGTGCAGACTTA
59.76
CCAATACCATCCGCTGAGGT
59.53
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TACAGAAGTGCCGAGAGTGC
59.76
CCAATACCATCCGCTGAGGT
59.53
153
PCR template sequence:
CCAACTTACAGAAGTGCCGAGAGTGCAGACTTATCCGGAGTAAGAAGGGGGAAGAATCAACTCACTCACCGGTGTTTTGTAGATTTTACTACTTTAGGAGAATTCTCCCAGTCCTTGGCTACATCAACCCACTCCTGTGACCTCAGCGGATGGTATTGGATTACTTAGTCACATTCCTGTCAGACCTTCCAGTGCAGAGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
19
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(2), mmu-miR-452-3p(2), mmu-miR-9-5p(1), mmu-let-7a-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-1a-3p(1), mmu-miR-206-3p(1), mmu-let-7c-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-136-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-192-5p(1), mmu-miR-340-5p(1), mmu-miR-383-5p(1), mmu-miR-98-5p(1), mmu-miR-300-3p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTACTTTAGGAGAATTCTCCCAGTC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCJMJD1C_2558_ORF_1
0.9312
0.093021724
0.99999924
2403
ORF sequence:
ATGGAACCATTACGGTCTAATGCATCCACATCAGTAAAAGGTGACCTGGATCTTAATAGGTCACAGGCAGGAAAAGATTGTCACTTGCATAGGCATTTTGTGGGTCCAAGGCCACCCCAGGAGACTGGAGAGAGACTGAACAAATACAAGGAGGAACATCGTCGGATTCTTCAGGAGAGTATTGATGTGGCTCCATTTACAACCAAAATCAAGGGTCATGAGGTTGAAAGAGAGAATTACTCCAGAGTAGTACCATCATCTTCTAGTCCTAAAAGCCATGCTATCAAACAAGATAAAGACGTAGACCGCTCCGTGTCAGAGATTTATAAGATGAAGCACTCAGTGCCTCAGAGTTTGCCCCAGAGTAACTACTTCACTACTTTATCTAATAGTGTGGTCAATGAGCCACCAAGATCCTACCCATCCAAAGAAGTTTCCAACATTTACACTGAGAAACAAAATAATAACCTTTCTGCAACAGCCAATCCTCAAACTCATTCTTTTATATCATCTCTTTCGAAGCCTCCACCTTTGATTAAACACCAACCAGAAAGTGAAAGTTTAGTGGGCAAGATACCAGACCATCTTCCCCATCAGAGTGCATCTCACTCAGTAACAACGTTCAGAAGTGATTGTCGGAGCCCTACCCATCTGACTGTTTCTTCTACTAATGCACTCCGCAGCATGCCTGCTCTGCACAGGGCACCAGTATTCCATCCACCAATCCACCACAGTTTGGAAAGAAAGGAAAGCAGCTACAGTAGCCTTTCCCCTCCAACACTGACACCGGTGATGCCAGTAAATGCTGGTGGCAAAGTTCAAGAATCTCAGAAGCCTCCAACTCTAATTCCTGAGCCAAAAGACTCTCAGTCAAATTTTAAGAATTCTTCTGATCAGAGTCTAACGGAAATGTGGAGATCTAATAACAACCTCAACAGAGAGAAAGCTGAGTGGCCCGTGGAAAAGAGTAGTGGAAAGTCCCAGGCTGCTGTGGCATCTGTCATTGTTCGTCCACCTTCTAGTACAAAAGTTGATAGTGTGCCATCTGTACCATTAGCTTCCAAAGATCGAGTTTGTGAAAGATCTTCATCTGGGGCAAATAAAACAGATTACCTCAAACCAGAAGCCGGAGAGACTGGAAGAATTATTCTACCAAATGTGAATTTAGAAAGTGCTCATGTGAAATCTGAAAAAAACTTTGAAGCTGTCTCCCAGGGCAACGTTCCTGTTTCAGTCATGTCTGCTGTAAATGTAGTCTCTACTACCAAAGCAGATGTGTTCACATCTGCTGCCACTACCACCAGTGTCTCCAGCTTGAGTAGTGCAGAAACAAGTTATTCTTTATCAAATACCATTTCGGCCTCTACACCCTTCGAATGTACTTCTTCAAAAAGTGTTGTTAGTCAGGCAGTGGCGCAAGCAAAGGACTGCACAGTCAGCACCGCGGTTCCAGGCACTCTGGCCTGTAGTAAGACAGGAAGTGCTGTTCAGCCCGGCTCTGGCTTCTCAGGCACAACTGATTTTATTCATTTAAAAAAGCACAAGGCAGCGTTGGCTGCAGCTCAGTTTAAAAATAGTAGTGTCAGTGAGGCTGAACTTAATACTGTGAGAAATCAGACAGTGGCAGCCTCTCTTCCCCTGGATAGCACCATGACCTGCACTGCAAGTAACAAAGCAATCTCTGTAGGAAATGGGCCAGCAGCCCAGTCCAGTCAGCCCAACTACCACACTAAACTGAAGAAGGCCTGGCTCACCAGACATTCAGAAGAAGATAAAAATACTAATAAAATGGAAAATTCAGGGAATTCTGTATCCGAAATTATTAAGCCATGTTCTGTCAACTTAATAGCCTCTACATCTAATGATATAGAAAATCGTGCAGATGGCAGAGTCGCTGTAGATAAATATGGAAGAGATGAGAAAGTCAGCAGGAGAAAAGCCAAAAGAACTTACGAATCTGGCTCTGAAAGTGGAGACTCAGATGAGAGCGAAAGCAAGTCGGAGCAGAGGACTAAACGGCAGCCGAAGCCAACTTATAAAAAGAAGCAGAACGACCTGCAGAAGAGGAAAGGCGAGGTCGAAGAGGACTCGAAGCCTAATGGAGTTCTCAGCAGGAGCGCCAAGGACAAAAGTAAACTGAAGTTGCAGAACAGTAATAGCGCTGGCGTTCCTCGTTCCGTGCTGAAAGACTGGCGGAAGGTCAAGAAGCTGAAGCAAACTGGAGAATCATTTCTGCAGGATGACTCCTGCTGTGAGATAGGTCCCAACTTACAGAAGTGCCGAGAGTGCAGACTTATCCGGAGTAAGAAGGGGGAAGAATCAACTCACTCACCGGTGTTTTGTAGATTTTACTACTTTAGGAGAATTCTCCCAGTCCTTGGCTACATCAACCCACTCCTGTGA
Peptide sequence:
MEPLRSNASTSVKGDLDLNRSQAGKDCHLHRHFVGPRPPQETGERLNKYKEEHRRILQESIDVAPFTTKIKGHEVERENYSRVVPSSSSPKSHAIKQDKDVDRSVSEIYKMKHSVPQSLPQSNYFTTLSNSVVNEPPRSYPSKEVSNIYTEKQNNNLSATANPQTHSFISSLSKPPPLIKHQPESESLVGKIPDHLPHQSASHSVTTFRSDCRSPTHLTVSSTNALRSMPALHRAPVFHPPIHHSLERKESSYSSLSPPTLTPVMPVNAGGKVQESQKPPTLIPEPKDSQSNFKNSSDQSLTEMWRSNNNLNREKAEWPVEKSSGKSQAAVASVIVRPPSSTKVDSVPSVPLASKDRVCERSSSGANKTDYLKPEAGETGRIILPNVNLESAHVKSEKNFEAVSQGNVPVSVMSAVNVVSTTKADVFTSAATTTSVSSLSSAETSYSLSNTISASTPFECTSSKSVVSQAVAQAKDCTVSTAVPGTLACSKTGSAVQPGSGFSGTTDFIHLKKHKAALAAAQFKNSSVSEAELNTVRNQTVAASLPLDSTMTCTASNKAISVGNGPAAQSSQPNYHTKLKKAWLTRHSEEDKNTNKMENSGNSVSEIIKPCSVNLIASTSNDIENRADGRVAVDKYGRDEKVSRRKAKRTYESGSESGDSDESESKSEQRTKRQPKPTYKKKQNDLQKRKGEVEEDSKPNGVLSRSAKDKSKLKLQNSNSAGVPRSVLKDWRKVKKLKQTGESFLQDDSCCEIGPNLQKCRECRLIRSKKGEESTHSPVFCRFYYFRRILPVLGYINPLL
IRESfinder result
IRESfinder score
0.624667049
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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