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mmu_circUbe3b_742
Basic information of circular RNA
PanCircBase ID:
mmu_circUbe3b_742
mm39_Chr. Position ID:
chr5|114522375|114530244|+
Gene name:
Ube3b
Transcript:
ENSMUST00000074002.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
2,3,4,5,6,7,8
Exon/intron offsets:
0,2779,3066,4408,4750,6075,7783
Genomic length:
7869
Exon/intron sizes in nt:
88,185,121,60,105,97,86
Flanking exon/introns:
chr5:114519036-114522375|chr5:114530244-114531137
Splice length:
742
Other database IDs:
circAtlas: mmu-Ube3b_0009
Human Ortholog IDs:
Mature spliced Sequence:
GCCAGAAAACCCAACTCCTCGGAAGCCAGAGGCTGCAGGAGGTCACTGATGGTCACCTAGCATCTCCGCTGCACAGGCAGGTCCTCAGGCTTCGTCGTGTCAGTTTGCAAACATGTTCACTGTATCTCAGACCTCCAGAGCATGGTTCATCGACAGAGCCCGGCAGGCACGAGAAGAGAGGCTGGTGCAGAAGGAGCGGGAGCGCTCAGCGGTGACGATCCAGGCCCTAGTCCGCAGTTTCCTCTGCCGGAGGCGACTGCACAGAGACATCAGGAAAGAGATTGATGAGTTTTTTAGTGCTGATGAGTCTGGGTCCAGTAAAAGAAGTGCACTTTGTATTTTTAAGATTGCCAGGAGACTGCTGTTTATATGCAAAACTACCGAGGACAGCGAGAGACTGGAGAAGTTGTGTCGAAGCATCCTGAACAGCATGGATGCCGAGAATGAGCCAAAGGTGTGGTACGTGTCCCTGGCTCTCTCCAAGGACCTCACGCTGCTGTGGATTAAGCAGATCAAGAGCATCCTGTGGCACTGCTGTGAGCTTCTGGGGCAGCTCAAGCCAGAGATCTTACAGGACTCCAGGCTCATCACGCTGTACCTCACCATGCTTGTGACCTTCACAGACACTTCAACATGGAAGATTCTCCGGGGAAAAGGTGAGAGCCTTCGGCCAGCCCTGAACCACATTTGCGCAAATATAATGGGCCATCTCAACCAGCGTGGACTTTACTCTGTATTGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTCCGGGGAAAAGGTGAGA
60.18
CCATCAGTGACCTCCTGCAG
60.11
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTCCGGGGAAAAGGTGAGA
60.18
GACCATCAGTGACCTCCTGC
60.11
154
PCR template sequence:
TCTCCGGGGAAAAGGTGAGAGCCTTCGGCCAGCCCTGAACCACATTTGCGCAAATATAATGGGCCATCTCAACCAGCGTGGACTTTACTCTGTATTGCAGGCCAGAAAACCCAACTCCTCGGAAGCCAGAGGCTGCAGGAGGTCACTGATGGTCACCTAGCATCTCCGCTGCACAGGCAGGTCCTCAGGCTTCGTCGTGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-298-5p(1), mmu-miR-139-5p(1), mmu-miR-182-5p(1), mmu-miR-207(1), mmu-miR-452-3p(1), mmu-miR-296-3p(1), mmu-miR-202-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTCTGTATTGCAGGCCAGAAAACCCA
siRNA sets
TTTTCTGGCCTGCAATACA, GTTTTCTGGCCTGCAATAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUBE3B_742_ORF_1
1.1257
0.271221514
0.948033073
690
ORF sequence:
ATGTTCACTGTATCTCAGACCTCCAGAGCATGGTTCATCGACAGAGCCCGGCAGGCACGAGAAGAGAGGCTGGTGCAGAAGGAGCGGGAGCGCTCAGCGGTGACGATCCAGGCCCTAGTCCGCAGTTTCCTCTGCCGGAGGCGACTGCACAGAGACATCAGGAAAGAGATTGATGAGTTTTTTAGTGCTGATGAGTCTGGGTCCAGTAAAAGAAGTGCACTTTGTATTTTTAAGATTGCCAGGAGACTGCTGTTTATATGCAAAACTACCGAGGACAGCGAGAGACTGGAGAAGTTGTGTCGAAGCATCCTGAACAGCATGGATGCCGAGAATGAGCCAAAGGTGTGGTACGTGTCCCTGGCTCTCTCCAAGGACCTCACGCTGCTGTGGATTAAGCAGATCAAGAGCATCCTGTGGCACTGCTGTGAGCTTCTGGGGCAGCTCAAGCCAGAGATCTTACAGGACTCCAGGCTCATCACGCTGTACCTCACCATGCTTGTGACCTTCACAGACACTTCAACATGGAAGATTCTCCGGGGAAAAGGTGAGAGCCTTCGGCCAGCCCTGAACCACATTTGCGCAAATATAATGGGCCATCTCAACCAGCGTGGACTTTACTCTGTATTGCAGGCCAGAAAACCCAACTCCTCGGAAGCCAGAGGCTGCAGGAGGTCACTGATGGTCACCTAG
Peptide sequence:
MFTVSQTSRAWFIDRARQAREERLVQKERERSAVTIQALVRSFLCRRRLHRDIRKEIDEFFSADESGSSKRSALCIFKIARRLLFICKTTEDSERLEKLCRSILNSMDAENEPKVWYVSLALSKDLTLLWIKQIKSILWHCCELLGQLKPEILQDSRLITLYLTMLVTFTDTSTWKILRGKGESLRPALNHICANIMGHLNQRGLYSVLQARKPNSSEARGCRRSLMVT
IRESfinder result
IRESfinder score
0.459471489
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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