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mmu_circUbr2_542
Basic information of circular RNA
PanCircBase ID:
mmu_circUbr2_542
mm39_Chr. Position ID:
chr17|47275682|47280227|-
Gene name:
Ubr2
Transcript:
ENSMUST00000113337.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
22,21,20,19,18,17
Exon/intron offsets:
0,1384,2275,2433,3627,4434
Genomic length:
4545
Exon/intron sizes in nt:
53,12,56,41,23,66,111
Flanking exon/introns:
chr17:47274716-47275682|chr17:47280227-47281026
Splice length:
542
Other database IDs:
CIRCpedia: MMU_CIRCpedia_21009
circAtlas: hsa-UBR2_0061
Human Ortholog IDs:
Mature spliced Sequence:
AGTGAACTGAGCCCACCCATGTTGATAGAACATCCTCTTAGATGTCTTGTCTTATGTGCTCAAGTGCATGCTGGGATGTGGAGAAGAAATGGCTTCTCTCTAGTAAATCAGATCTATTACTACCATAATGTGAAATGCAGGCGAGAGATGTTCGACAAGGACATAGTGATGCTTCAGACAGGTGTCTCCATGATGGACCCAAACCACTTCCTGATGATCATGCTCAGCCGCTTTGAACTCTATCAGCTCTTCAGCACGCCTGACTATGGGAAGAGATTCAGTTCTGAGGTTACCCATAAGGACGTCGTTCAGCAGAACAACACTCTGATCGAAGAGATGCTCTACCTCATCATCATGCTTGTGGGAGAAAGATTCAACCCTGGGGTTGGACAGGTGGCTGCCACAGATGAAATCAAGAGGGAGATTATCCATCAGTTGAGCATCAAGCCTATGGCTCACAGTGAGCTGGTGAAGTCTCTGCCTGAAGATGAGAACAAGGAGACCGGCATGGAGAGCGTCATCGAGTCCGTTGCACATTTCAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGAGCTGGTGAAGTCTCTGC
59.68
ACATCCCAGCATGCACTTGA
59.96
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGCTGGTGAAGTCTCTGCC
60.39
ACATCCCAGCATGCACTTGA
59.96
159
PCR template sequence:
TCAAGCCTATGGCTCACAGTGAGCTGGTGAAGTCTCTGCCTGAAGATGAGAACAAGGAGACCGGCATGGAGAGCGTCATCGAGTCCGTTGCACATTTCAAAGTGAACTGAGCCCACCCATGTTGATAGAACATCCTCTTAGATGTCTTGTCTTATGTGCTCAAGTGCATGCTGGGATGTGGAGAAGAAATGGCTTCTCTC
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-140-5p(1), mmu-miR-203-3p(1), mmu-miR-24-3p(1), mmu-miR-188-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTGCACATTTCAAAGTGAACTGAGCC
siRNA sets
GTTCACTTTGAAATGTGCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUBR2_542_ORF_1
1.2664
0.316989825
0.903450792
534
ORF sequence:
ATGTTGATAGAACATCCTCTTAGATGTCTTGTCTTATGTGCTCAAGTGCATGCTGGGATGTGGAGAAGAAATGGCTTCTCTCTAGTAAATCAGATCTATTACTACCATAATGTGAAATGCAGGCGAGAGATGTTCGACAAGGACATAGTGATGCTTCAGACAGGTGTCTCCATGATGGACCCAAACCACTTCCTGATGATCATGCTCAGCCGCTTTGAACTCTATCAGCTCTTCAGCACGCCTGACTATGGGAAGAGATTCAGTTCTGAGGTTACCCATAAGGACGTCGTTCAGCAGAACAACACTCTGATCGAAGAGATGCTCTACCTCATCATCATGCTTGTGGGAGAAAGATTCAACCCTGGGGTTGGACAGGTGGCTGCCACAGATGAAATCAAGAGGGAGATTATCCATCAGTTGAGCATCAAGCCTATGGCTCACAGTGAGCTGGTGAAGTCTCTGCCTGAAGATGAGAACAAGGAGACCGGCATGGAGAGCGTCATCGAGTCCGTTGCACATTTCAAAGTGAACTGA
Peptide sequence:
MLIEHPLRCLVLCAQVHAGMWRRNGFSLVNQIYYYHNVKCRREMFDKDIVMLQTGVSMMDPNHFLMIMLSRFELYQLFSTPDYGKRFSSEVTHKDVVQQNNTLIEEMLYLIIMLVGERFNPGVGQVAATDEIKREIIHQLSIKPMAHSELVKSLPEDENKETGMESVIESVAHFKVN
IRESfinder result
IRESfinder score
0.491558401
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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