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mmu_circUbr2_604
Basic information of circular RNA
PanCircBase ID:
mmu_circUbr2_604
mm39_Chr. Position ID:
chr17|47275682|47281088|-
Gene name:
Ubr2
Transcript:
ENSMUST00000113337.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
22,21,20,19,18,17,16
Exon/intron offsets:
0,1384,2275,2433,3627,4434,5344
Genomic length:
5406
Exon/intron sizes in nt:
53,125,64,123,66,111,62
Flanking exon/introns:
chr17:47274716-47275682|chr17:47281088-47283789
Splice length:
604
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GTTTGCATGTATTGTTAAGCAAAAGTGAAGTGGCATATAAATTTCCAGAGCTCCTACCTCTAAGTGAACTGAGCCCACCCATGTTGATAGAACATCCTCTTAGATGTCTTGTCTTATGTGCTCAAGTGCATGCTGGGATGTGGAGAAGAAATGGCTTCTCTCTAGTAAATCAGATCTATTACTACCATAATGTGAAATGCAGGCGAGAGATGTTCGACAAGGACATAGTGATGCTTCAGACAGGTGTCTCCATGATGGACCCAAACCACTTCCTGATGATCATGCTCAGCCGCTTTGAACTCTATCAGCTCTTCAGCACGCCTGACTATGGGAAGAGATTCAGTTCTGAGGTTACCCATAAGGACGTCGTTCAGCAGAACAACACTCTGATCGAAGAGATGCTCTACCTCATCATCATGCTTGTGGGAGAAAGATTCAACCCTGGGGTTGGACAGGTGGCTGCCACAGATGAAATCAAGAGGGAGATTATCCATCAGTTGAGCATCAAGCCTATGGCTCACAGTGAGCTGGTGAAGTCTCTGCCTGAAGATGAGAACAAGGAGACCGGCATGGAGAGCGTCATCGAGTCCGTTGCACATTTCAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGAACAAGGAGACCGGCATG
60.04
ATCAACATGGGTGGGCTCAG
60.03
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGAACAAGGAGACCGGCAT
59.75
ATCAACATGGGTGGGCTCAG
60.03
141
PCR template sequence:
TCAAGCCTATGGCTCACAGTGAGCTGGTGAAGTCTCTGCCTGAAGATGAGAACAAGGAGACCGGCATGGAGAGCGTCATCGAGTCCGTTGCACATTTCAAGTTTGCATGTATTGTTAAGCAAAAGTGAAGTGGCATATAAATTTCCAGAGCTCCTACCTCTAAGTGAACTGAGCCCACCCATGTTGATAGAACATCCTCT
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-140-5p(1), mmu-let-7a-5p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-let-7c-5p(1), mmu-miR-203-3p(1), mmu-let-7d-5p(1), mmu-miR-24-3p(1), mmu-miR-188-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTGCACATTTCAAGTTTGCATGTATT
siRNA sets
AATACATGCAAACTTGAAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUBR2_604_ORF_1
1.2367
0.217117517
0.93446056
657
ORF sequence:
ATGAGAACAAGGAGACCGGCATGGAGAGCGTCATCGAGTCCGTTGCACATTTCAAGTTTGCATGTATTGTTAAGCAAAAGTGAAGTGGCATATAAATTTCCAGAGCTCCTACCTCTAAGTGAACTGAGCCCACCCATGTTGATAGAACATCCTCTTAGATGTCTTGTCTTATGTGCTCAAGTGCATGCTGGGATGTGGAGAAGAAATGGCTTCTCTCTAGTAAATCAGATCTATTACTACCATAATGTGAAATGCAGGCGAGAGATGTTCGACAAGGACATAGTGATGCTTCAGACAGGTGTCTCCATGATGGACCCAAACCACTTCCTGATGATCATGCTCAGCCGCTTTGAACTCTATCAGCTCTTCAGCACGCCTGACTATGGGAAGAGATTCAGTTCTGAGGTTACCCATAAGGACGTCGTTCAGCAGAACAACACTCTGATCGAAGAGATGCTCTACCTCATCATCATGCTTGTGGGAGAAAGATTCAACCCTGGGGTTGGACAGGTGGCTGCCACAGATGAAATCAAGAGGGAGATTATCCATCAGTTGAGCATCAAGCCTATGGCTCACAGTGAGCTGGTGAAGTCTCTGCCTGAAGATGAGAACAAGGAGACCGGCATGGAGAGCGTCATCGAGTCCGTTGCACATTTC
Peptide sequence:
MRTRRPAWRASSSPLHISSLHVLLSKSEVAYKFPELLPLSELSPPMLIEHPLRCLVLCAQVHAGMWRRNGFSLVNQIYYYHNVKCRREMFDKDIVMLQTGVSMMDPNHFLMIMLSRFELYQLFSTPDYGKRFSSEVTHKDVVQQNNTLIEEMLYLIIMLVGERFNPGVGQVAATDEIKREIIHQLSIKPMAHSELVKSLPEDENKETGMESVIESVAHF
IRESfinder result
IRESfinder score
0.526030063
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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