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mmu_circUbe2k_242
Basic information of circular RNA
PanCircBase ID:
mmu_circUbe2k_242
mm39_Chr. Position ID:
chr5|65728874|65749318|+
Gene name:
Ube2k
Transcript:
ENSMUST00000142407.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
3,4,5
Exon/intron offsets:
0,9854,20344
Genomic length:
20444
Exon/intron sizes in nt:
59,83,100
Flanking exon/introns:
chr5:65723425-65728874|chr5:65749318-65751762
Splice length:
242
Other database IDs:
circBase: hsa_circ_0069494, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_48549
Human Ortholog IDs:
Mature spliced Sequence:
GTGGAAGATATCAACTAGAGATAAAAATACCAGAAACATATCCATTTAACCCCCCTAAGGTCCGGTTTATCACTAAAATATGGCACCCTAATATTAGTTCCGTCACAGGGGCTATTTGTTTGGATATCCTGAAAGATCAATGGGCAGCAGCAATGACTCTGCGCACGGTATTATTGTCATTGCAAGCGCTGTTGGCGGCTGCAGAACCAGATGACCCCCAAGATGCAGTAGTAGCGAATCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGACTCTGCGCACGGTATT
59.82
GATAAACCGGACCTTAGGGGG
59.58
161
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AATGACTCTGCGCACGGTAT
59.82
GATAAACCGGACCTTAGGGGG
59.58
162
PCR template sequence:
GGCAGCAGCAATGACTCTGCGCACGGTATTATTGTCATTGCAAGCGCTGTTGGCGGCTGCAGAACCAGATGACCCCCAAGATGCAGTAGTAGCGAATCAGGTGGAAGATATCAACTAGAGATAAAAATACCAGAAACATATCCATTTAACCCCCCTAAGGTCCGGTTTATCACTAAAATATGGCACCCTAATATTAGTTC
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-190b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGTAGCGAATCAGGTGGAAGATATCA
siRNA sets
ATATCTTCCACCTGATTCG, TATCTTCCACCTGATTCGC, ATCTTCCACCTGATTCGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUBE2K_242_ORF_1
1.2102
0.217219935
0.208103292
108
ORF sequence:
ATGACTCTGCGCACGGTATTATTGTCATTGCAAGCGCTGTTGGCGGCTGCAGAACCAGATGACCCCCAAGATGCAGTAGTAGCGAATCAGGTGGAAGATATCAACTAG
Peptide sequence:
MTLRTVLLSLQALLAAAEPDDPQDAVVANQVEDIN
IRESfinder result
IRESfinder score
0.365560187
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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