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mmu_circUbr2_178
Basic information of circular RNA
PanCircBase ID:
mmu_circUbr2_178
mm39_Chr. Position ID:
chr17|47275682|47277191|-
Gene name:
Ubr2
Transcript:
ENSMUST00000113337.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
22,21
Exon/intron offsets:
0,1384
Genomic length:
1509
Exon/intron sizes in nt:
53,125
Flanking exon/introns:
chr17:47274716-47275682|chr17:47277191-47277957
Splice length:
178
Other database IDs:
CIRCpedia: MMU_CIRCpedia_219595, circAtlas: mmu-Ubr2_0050
Human Ortholog IDs:
Mature spliced Sequence:
GAGAAAGATTCAACCCTGGGGTTGGACAGGTGGCTGCCACAGATGAAATCAAGAGGGAGATTATCCATCAGTTGAGCATCAAGCCTATGGCTCACAGTGAGCTGGTGAAGTCTCTGCCTGAAGATGAGAACAAGGAGACCGGCATGGAGAGCGTCATCGAGTCCGTTGCACATTTCAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGAACAAGGAGACCGGCATG
60.04
GGCTTGATGCTCAACTGATGG
59.6
137
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGAGCTGGTGAAGTCTCTGC
59.68
TGATTTCATCTGTGGCAGCCA
60.27
132
PCR template sequence:
GCTCACAGTGAGCTGGTGAAGTCTCTGCCTGAAGATGAGAACAAGGAGACCGGCATGGAGAGCGTCATCGAGTCCGTTGCACATTTCAAGAGAAAGATTCAACCCTGGGGTTGGACAGGTGGCTGCCACAGATGAAATCAAGAGGGAGATTATCCATCAGTTGAGCATCAAGCCTATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-203-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTGCACATTTCAAGAGAAAGATTCAA
siRNA sets
AATCTTTCTCTTGAAATGT, ATCTTTCTCTTGAAATGTG, TCTTTCTCTTGAAATGTGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUBR2_178_ORF_1
1.1286
0.295183453
0.430748808
231
ORF sequence:
ATGAGAACAAGGAGACCGGCATGGAGAGCGTCATCGAGTCCGTTGCACATTTCAAGAGAAAGATTCAACCCTGGGGTTGGACAGGTGGCTGCCACAGATGAAATCAAGAGGGAGATTATCCATCAGTTGAGCATCAAGCCTATGGCTCACAGTGAGCTGGTGAAGTCTCTGCCTGAAGATGAGAACAAGGAGACCGGCATGGAGAGCGTCATCGAGTCCGTTGCACATTTC
Peptide sequence:
MRTRRPAWRASSSPLHISRERFNPGVGQVAATDEIKREIIHQLSIKPMAHSELVKSLPEDENKETGMESVIESVAHF
IRESfinder result
IRESfinder score
0.380687746
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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