top of page
mmu_circRubcn_857
Basic information of circular RNA
PanCircBase ID:
mmu_circRubcn_857
mm39_Chr. Position ID:
chr16|32645933|32649692|-
Gene name:
Rubcn
Transcript:
ENSMUST00000115105.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
18,17,16,15,14,13,12
Exon/intron offsets:
0,571,1121,1724,2295,3105,3701
Genomic length:
3759
Exon/intron sizes in nt:
154,62,239,65,146,133,58
Flanking exon/introns:
chr16:32644842-32645933|chr16:32649692-32656283
Splice length:
857
Other database IDs:
circAtlas: mmu-1700021K19Rik_0013
Human Ortholog IDs:
Mature spliced Sequence:
ACGCTGACATCCGGAGGAGTGCAGTCTCAAACGGCAAATCATCCTTCTCCCAGAATCTCTCGCACTGCTTCCTGCACTCCACATCGGCTGAGGCAGTGGCCATGGGGCTTCTGAAGCAGTTTGAGGGGATGCAGCTTCCAGCTGCCTCGGAGCTCGAGTGGCTAGTCCCAGAGCATGATGCTCCACAGAAGCTCCTACCCATCCCCGACTCCCTGCCCATCTCACCAGATGACGGGCAGCACGCGGACATCTACAAGCTGCGAATCCGCGTCCGTGGCAACCTGGAGTGGGCTCCGCCCCGGCCGCAGATCATTTTTAATGTTCATCCAGCCCCCACGAGGAAGATTGCCGTGGCCAAGCAGAATTACCGCTGTGCGGGATGTGGCATCCGGACGGACCCCGACTATATCAAGCGGCTGCGGTACTGTGAGTACCTAGGCAAGTACTTCTGCCAGTGCTGCCACGAGAACGCCCAGATGGTCGTCCCCAGCCGCATTCTGCGCAAATGGGACTTCAGCAAGTACTATGTCAGCAACTTCTCCAAGGACCTGCTCCTGAAGATCTGGAATGATCCTCTCTTCAATGTGCAGGACATCAATAGCGCACTCTACAGGAAGGTCAAGCTGCTTAACCAAGTCCGGCTGCTGCGGGTTCAGCTGTACCACATGAAGAACATGTTTAAGACATGCCGACTGGCCAAAGAGCTCCTGGATTCCTTTGACGTGGTTCCAGGCCACCTGACAGAGGACCTCCATCTGTACTCGCTGAGTGACCTGACTGCAACCAAGAAGGGAGAACTGGGGCCCCGGCTGGCGGAGCTCACTAGAGCGGGAGCCGCCCACGTGGAGAGATGCATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGTGACCTGACTGCAACCA
59.89
AGCAGTGCGAGAGATTCTGG
59.82
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGTGACCTGACTGCAACCA
59.89
CAGGAAGCAGTGCGAGAGAT
59.82
165
PCR template sequence:
GTACTCGCTGAGTGACCTGACTGCAACCAAGAAGGGAGAACTGGGGCCCCGGCTGGCGGAGCTCACTAGAGCGGGAGCCGCCCACGTGGAGAGATGCATGACGCTGACATCCGGAGGAGTGCAGTCTCAAACGGCAAATCATCCTTCTCCCAGAATCTCTCGCACTGCTTCCTGCACTCCACATCGGCTGAGGCAGTGGC
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-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-101a-3p(1), mmu-miR-324-5p(1), mmu-miR-324-3p(1), mmu-miR-99a-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGAGAGATGCATGACGCTGACATCCG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRUBCN_857_ORF_1
1.2149
0.412447293
0.99290073
870
ORF sequence:
ATGGGGCTTCTGAAGCAGTTTGAGGGGATGCAGCTTCCAGCTGCCTCGGAGCTCGAGTGGCTAGTCCCAGAGCATGATGCTCCACAGAAGCTCCTACCCATCCCCGACTCCCTGCCCATCTCACCAGATGACGGGCAGCACGCGGACATCTACAAGCTGCGAATCCGCGTCCGTGGCAACCTGGAGTGGGCTCCGCCCCGGCCGCAGATCATTTTTAATGTTCATCCAGCCCCCACGAGGAAGATTGCCGTGGCCAAGCAGAATTACCGCTGTGCGGGATGTGGCATCCGGACGGACCCCGACTATATCAAGCGGCTGCGGTACTGTGAGTACCTAGGCAAGTACTTCTGCCAGTGCTGCCACGAGAACGCCCAGATGGTCGTCCCCAGCCGCATTCTGCGCAAATGGGACTTCAGCAAGTACTATGTCAGCAACTTCTCCAAGGACCTGCTCCTGAAGATCTGGAATGATCCTCTCTTCAATGTGCAGGACATCAATAGCGCACTCTACAGGAAGGTCAAGCTGCTTAACCAAGTCCGGCTGCTGCGGGTTCAGCTGTACCACATGAAGAACATGTTTAAGACATGCCGACTGGCCAAAGAGCTCCTGGATTCCTTTGACGTGGTTCCAGGCCACCTGACAGAGGACCTCCATCTGTACTCGCTGAGTGACCTGACTGCAACCAAGAAGGGAGAACTGGGGCCCCGGCTGGCGGAGCTCACTAGAGCGGGAGCCGCCCACGTGGAGAGATGCATGACGCTGACATCCGGAGGAGTGCAGTCTCAAACGGCAAATCATCCTTCTCCCAGAATCTCTCGCACTGCTTCCTGCACTCCACATCGGCTGAGGCAGTGGCCATGGGGCTTCTGA
Peptide sequence:
MGLLKQFEGMQLPAASELEWLVPEHDAPQKLLPIPDSLPISPDDGQHADIYKLRIRVRGNLEWAPPRPQIIFNVHPAPTRKIAVAKQNYRCAGCGIRTDPDYIKRLRYCEYLGKYFCQCCHENAQMVVPSRILRKWDFSKYYVSNFSKDLLLKIWNDPLFNVQDINSALYRKVKLLNQVRLLRVQLYHMKNMFKTCRLAKELLDSFDVVPGHLTEDLHLYSLSDLTATKKGELGPRLAELTRAGAAHVERCMTLTSGGVQSQTANHPSPRISRTASCTPHRLRQWPWGF
IRESfinder result
IRESfinder score
0.335186215
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page