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mmu_circPard3b_853
Basic information of circular RNA
PanCircBase ID:
mmu_circPard3b_853
mm39_Chr. Position ID:
chr1|62383092|62518954|+
Gene name:
Pard3b
Transcript:
ENSMUST00000075374.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
17,18,19,20
Exon/intron offsets:
0,936,96077,135565
Genomic length:
135862
Exon/intron sizes in nt:
2,07,23,81,11,297
Flanking exon/introns:
chr1:62315086-62383092|chr1:62518954-62571803
Splice length:
853
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
ACTCTCCAGGCAAAGATTTTGGTCCAACTTTGGGTCTGAAAAAGTCCAGTTCCTTGGAGAGCCTACAGACGGCTGTGGCTGAAGTCAGGAAGAATGATCTGCCCTTCCACAGGCCCAGACCACACATGGTGCGGGGCCGAGGCTGCAACGAGAGCTTCCGAGCAGCCATCGACAAATCGTACGATGGGCCAGAAGAGGCAGACGCGGATGGTCTGTCTGATAAGAGCTCTCGCTCAGGCCACACAGCTCTGAATTGTGAGTCTGCCCCTCAGGGAAACCCCGAGCTAGACAATGTGGAAAATAAAGCCAAAAACATCAAAAAAACAAAAGAGAAGGAGAAGAAAAAAGGAAAGGGCAAGCTGAAAGTCAAGGAAAAAAAGCTGAAGGAGGAACATGAGGACGCAGAGAGGAAAATGAAGAGGAAGGGCTTCGGTGCCATGCTGAGATTTGGAAAGAAGAAAGATGATAAGGTCGGAAAGGCTGAGCAGAAAGGTGCGCAGAAGTCCGGCCACCCGGAGGAAGAGGAGCTGGAAAGAATGAAAGAAGAGAGAGAGAGGATTGGAGCAAAACATCAGGAGCTGAGAGAAAAGCAGGCAAGAGGCCTTGTTGATTATGCCACGGCAGTGACTGGACCAGTGCACGATATGGACGATGACGAAATGGACCCCAATTATGCCAGAGTGAACCACTTTCGGGAACCATGTGCATCAGCAAATGTCTTTAGATCTCCATCTCCCCTTCGAGCTGGACCACTTGCTTACCCTCGGGATGGGCGTCCACTGTCTCCAGACCACTTAGAGGGTCTCTATGCCAAGGTCAACAAGCCATATCATCCACCAGCCCTAGCTGACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCACTGTCTCCAGACCACT
59.81
GGCTCTCCAAGGAACTGGAC
60.04
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTCCACTGTCTCCAGACCAC
59.68
GGCTCTCCAAGGAACTGGAC
60.04
142
PCR template sequence:
TTGCTTACCCTCGGGATGGGCGTCCACTGTCTCCAGACCACTTAGAGGGTCTCTATGCCAAGGTCAACAAGCCATATCATCCACCAGCCCTAGCTGACAGACTCTCCAGGCAAAGATTTTGGTCCAACTTTGGGTCTGAAAAAGTCCAGTTCCTTGGAGAGCCTACAGACGGCTGTGGCTGAAGTCAGGAAGAATGATCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-216a-5p(1), mmu-miR-351-5p(1), mmu-miR-1187(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
CCCTAGCTGACAGACTCTCCAGGCAA
siRNA sets
GAGAGTCTGTCAGCTAGGG, TTGCCTGGAGAGTCTGTCA, GGAGAGTCTGTCAGCTAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPARD3B_853_ORF_1
0.943
0.342720097
0.976272429
810
ORF sequence:
ATGGTGCGGGGCCGAGGCTGCAACGAGAGCTTCCGAGCAGCCATCGACAAATCGTACGATGGGCCAGAAGAGGCAGACGCGGATGGTCTGTCTGATAAGAGCTCTCGCTCAGGCCACACAGCTCTGAATTGTGAGTCTGCCCCTCAGGGAAACCCCGAGCTAGACAATGTGGAAAATAAAGCCAAAAACATCAAAAAAACAAAAGAGAAGGAGAAGAAAAAAGGAAAGGGCAAGCTGAAAGTCAAGGAAAAAAAGCTGAAGGAGGAACATGAGGACGCAGAGAGGAAAATGAAGAGGAAGGGCTTCGGTGCCATGCTGAGATTTGGAAAGAAGAAAGATGATAAGGTCGGAAAGGCTGAGCAGAAAGGTGCGCAGAAGTCCGGCCACCCGGAGGAAGAGGAGCTGGAAAGAATGAAAGAAGAGAGAGAGAGGATTGGAGCAAAACATCAGGAGCTGAGAGAAAAGCAGGCAAGAGGCCTTGTTGATTATGCCACGGCAGTGACTGGACCAGTGCACGATATGGACGATGACGAAATGGACCCCAATTATGCCAGAGTGAACCACTTTCGGGAACCATGTGCATCAGCAAATGTCTTTAGATCTCCATCTCCCCTTCGAGCTGGACCACTTGCTTACCCTCGGGATGGGCGTCCACTGTCTCCAGACCACTTAGAGGGTCTCTATGCCAAGGTCAACAAGCCATATCATCCACCAGCCCTAGCTGACAGACTCTCCAGGCAAAGATTTTGGTCCAACTTTGGGTCTGAAAAAGTCCAGTTCCTTGGAGAGCCTACAGACGGCTGTGGCTGA
Peptide sequence:
MVRGRGCNESFRAAIDKSYDGPEEADADGLSDKSSRSGHTALNCESAPQGNPELDNVENKAKNIKKTKEKEKKKGKGKLKVKEKKLKEEHEDAERKMKRKGFGAMLRFGKKKDDKVGKAEQKGAQKSGHPEEEELERMKEERERIGAKHQELREKQARGLVDYATAVTGPVHDMDDDEMDPNYARVNHFREPCASANVFRSPSPLRAGPLAYPRDGRPLSPDHLEGLYAKVNKPYHPPALADRLSRQRFWSNFGSEKVQFLGEPTDGCG
IRESfinder result
IRESfinder score
0.221495489
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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