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mmu_circPtprn2_780
Basic information of circular RNA
PanCircBase ID:
mmu_circPtprn2_780
mm39_Chr. Position ID:
chr12|116544018|116822811|+
Gene name:
Ptprn2
Transcript:
ENSMUST00000189009.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
2,3,4,5,6
Exon/intron offsets:
0,141684,243918,260845,278444
Genomic length:
278793
Exon/intron sizes in nt:
5,11,14,10,31,63,349
Flanking exon/introns:
chr12:116449593-116544018|chr12:116822811-116835555
Splice length:
780
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GATGCTTGTTTGAGGATGGCTTGTGTGGATCACTGGAGACCTGTGTGAACGATGGTGTGTTTGGAAGATGTCAAAAGGTTCCGGTGATGGACACTTACCGATATGAGGTACCACCAGGAGCCCTGCTGCACCTGAAGGTCACCTTACAGAAGCTCTCCCGTACAGGTTTCACGTGGCAAGATGACTATACCCAGCGTGTGATTGCCCAGGAGCTTGCAAACCTCCCCAAGGCCTACCTATGGCATGGGGAAGCGTCCGGCCCAGCCAGGTCCTTACAACAGAATGCTGACAATGAAAAATGGTTCAGTCTGGAGAGGGAGGTGGCCCTGGCCAAGACCCTTCGGCGCTATCTGCCCTACCTGGAGCTTCTGTCCCAGACCCCAACAGCAAATGCACACTCTAGGATAGACCATGAGACTCGTCCAGCCAAGGGTGAAGACTCTTCCCCTGAGAACATCCTGACCTACGTGGCCCACACATCAGCACTGACCTATCCTCCTGCAACCCGGGCCAAGTATCCTGATAACCTTCTGCGGCCCTTTAGCCGGCTCCAGCCAGATGAGCTCAGCCCCAAGGTAGACGGTGACATAGACAAACAGAAGCTGATTGCAGCACTGGGCGCCTACACTGCTCAGAGGCTTCCTGGAGAAAATGACCCAGAGCCACGGTACCTTGTACATGGTTCCGCGAGAGCACCAAGGCCATTCTCAGCAACTGCTTTGTCTCAGAGATGGCCTCCACCTCCTGGAGACGCCAAAGACTCCCCGAGTATGGATGATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCTCAGAGATGGCCTCCA
59.96
GTGTCCATCACCGGAACCTT
59.96
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCAAGGCCATTCTCAGCAA
59.89
GTGTCCATCACCGGAACCTT
59.96
180
PCR template sequence:
GGTTCCGCGAGAGCACCAAGGCCATTCTCAGCAACTGCTTTGTCTCAGAGATGGCCTCCACCTCCTGGAGACGCCAAAGACTCCCCGAGTATGGATGATGGATGCTTGTTTGAGGATGGCTTGTGTGGATCACTGGAGACCTGTGTGAACGATGGTGTGTTTGGAAGATGTCAAAAGGTTCCGGTGATGGACACTTACCG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-326-3p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1), mmu-miR-335-3p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGTATGGATGATGGATGCTTGTTTGA
siRNA sets
AACAAGCATCCATCATCCA, CAAACAAGCATCCATCATC, AAACAAGCATCCATCATCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTPRN2_780_ORF_1
0.9367
0.320000956
0.999775259
1473
ORF sequence:
ATGGACACTTACCGATATGAGGTACCACCAGGAGCCCTGCTGCACCTGAAGGTCACCTTACAGAAGCTCTCCCGTACAGGTTTCACGTGGCAAGATGACTATACCCAGCGTGTGATTGCCCAGGAGCTTGCAAACCTCCCCAAGGCCTACCTATGGCATGGGGAAGCGTCCGGCCCAGCCAGGTCCTTACAACAGAATGCTGACAATGAAAAATGGTTCAGTCTGGAGAGGGAGGTGGCCCTGGCCAAGACCCTTCGGCGCTATCTGCCCTACCTGGAGCTTCTGTCCCAGACCCCAACAGCAAATGCACACTCTAGGATAGACCATGAGACTCGTCCAGCCAAGGGTGAAGACTCTTCCCCTGAGAACATCCTGACCTACGTGGCCCACACATCAGCACTGACCTATCCTCCTGCAACCCGGGCCAAGTATCCTGATAACCTTCTGCGGCCCTTTAGCCGGCTCCAGCCAGATGAGCTCAGCCCCAAGGTAGACGGTGACATAGACAAACAGAAGCTGATTGCAGCACTGGGCGCCTACACTGCTCAGAGGCTTCCTGGAGAAAATGACCCAGAGCCACGGTACCTTGTACATGGTTCCGCGAGAGCACCAAGGCCATTCTCAGCAACTGCTTTGTCTCAGAGATGGCCTCCACCTCCTGGAGACGCCAAAGACTCCCCGAGTATGGATGATGGATGCTTGTTTGAGGATGGCTTGTGTGGATCACTGGAGACCTGTGTGAACGATGGTGTGTTTGGAAGATGTCAAAAGGTTCCGGTGATGGACACTTACCGATATGAGGTACCACCAGGAGCCCTGCTGCACCTGAAGGTCACCTTACAGAAGCTCTCCCGTACAGGTTTCACGTGGCAAGATGACTATACCCAGCGTGTGATTGCCCAGGAGCTTGCAAACCTCCCCAAGGCCTACCTATGGCATGGGGAAGCGTCCGGCCCAGCCAGGTCCTTACAACAGAATGCTGACAATGAAAAATGGTTCAGTCTGGAGAGGGAGGTGGCCCTGGCCAAGACCCTTCGGCGCTATCTGCCCTACCTGGAGCTTCTGTCCCAGACCCCAACAGCAAATGCACACTCTAGGATAGACCATGAGACTCGTCCAGCCAAGGGTGAAGACTCTTCCCCTGAGAACATCCTGACCTACGTGGCCCACACATCAGCACTGACCTATCCTCCTGCAACCCGGGCCAAGTATCCTGATAACCTTCTGCGGCCCTTTAGCCGGCTCCAGCCAGATGAGCTCAGCCCCAAGGTAGACGGTGACATAGACAAACAGAAGCTGATTGCAGCACTGGGCGCCTACACTGCTCAGAGGCTTCCTGGAGAAAATGACCCAGAGCCACGGTACCTTGTACATGGTTCCGCGAGAGCACCAAGGCCATTCTCAGCAACTGCTTTGTCTCAGAGATGGCCTCCACCTCCTGGAGACGCCAAAGACTCCCCGAGTATGGATGAT
Peptide sequence:
MDTYRYEVPPGALLHLKVTLQKLSRTGFTWQDDYTQRVIAQELANLPKAYLWHGEASGPARSLQQNADNEKWFSLEREVALAKTLRRYLPYLELLSQTPTANAHSRIDHETRPAKGEDSSPENILTYVAHTSALTYPPATRAKYPDNLLRPFSRLQPDELSPKVDGDIDKQKLIAALGAYTAQRLPGENDPEPRYLVHGSARAPRPFSATALSQRWPPPPGDAKDSPSMDDGCLFEDGLCGSLETCVNDGVFGRCQKVPVMDTYRYEVPPGALLHLKVTLQKLSRTGFTWQDDYTQRVIAQELANLPKAYLWHGEASGPARSLQQNADNEKWFSLEREVALAKTLRRYLPYLELLSQTPTANAHSRIDHETRPAKGEDSSPENILTYVAHTSALTYPPATRAKYPDNLLRPFSRLQPDELSPKVDGDIDKQKLIAALGAYTAQRLPGENDPEPRYLVHGSARAPRPFSATALSQRWPPPPGDAKDSPSMDD
IRESfinder result
IRESfinder score
0.335978314
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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