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mmu_circRubcn_238
Basic information of circular RNA
PanCircBase ID:
mmu_circRubcn_238
mm39_Chr. Position ID:
chr16|32670047|32677415|-
Gene name:
Rubcn
Transcript:
ENSMUST00000115105.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,2
Exon/intron offsets:
0,7214
Genomic length:
7368
Exon/intron sizes in nt:
84,154
Flanking exon/introns:
chr16:32668359-32670047|chr16:32677415-32688462
Splice length:
238
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GAGGGAGCACTGGCAGCTGCTGGGTAATTTGAAGACGACTGTGGAAGGTTTGGTGTCAGCCAACTGCCCCAATGTCTGGTCCAAGTATGGTGGCCTGGAGCGGCTGTGCAGGGACATGCAGAACATCCTGTATCATGGGCTCATCCATGACCAGGTGTGTTGCCGCCAGGCTGATTACTGGCAGTTTGTGAAAGACATTCGGTGGCTCAGCCCGCACTCAGCCCTTCACGTGGAGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGGCTGATTACTGGCAGT
59.75
GGCCACCATACTTGGACCAG
60.39
168
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGGCTGATTACTGGCAGT
59.75
CAGGCCACCATACTTGGACC
60.39
170
PCR template sequence:
GCTCATCCATGACCAGGTGTGTTGCCGCCAGGCTGATTACTGGCAGTTTGTGAAAGACATTCGGTGGCTCAGCCCGCACTCAGCCCTTCACGTGGAGAAGGAGGGAGCACTGGCAGCTGCTGGGTAATTTGAAGACGACTGTGGAAGGTTTGGTGTCAGCCAACTGCCCCAATGTCTGGTCCAAGTATGGTGGCCTGGAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-22-3p(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCACGTGGAGAAGGAGGGAGCACTGG
siRNA sets
CAGTGCTCCCTCCTTCTCC, AGTGCTCCCTCCTTCTCCA, GTGCTCCCTCCTTCTCCAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRUBCN_238_ORF_1
1.0714
0.276973417
0.259810849
150
ORF sequence:
ATGCAGAACATCCTGTATCATGGGCTCATCCATGACCAGGTGTGTTGCCGCCAGGCTGATTACTGGCAGTTTGTGAAAGACATTCGGTGGCTCAGCCCGCACTCAGCCCTTCACGTGGAGAAGGAGGGAGCACTGGCAGCTGCTGGGTAA
Peptide sequence:
MQNILYHGLIHDQVCCRQADYWQFVKDIRWLSPHSALHVEKEGALAAAG
IRESfinder result
IRESfinder score
0.282209919
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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