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mmu_ciDnmt1_2318
Basic information of circular RNA
PanCircBase ID:
mmu_ciDnmt1_2318
mm39_Chr. Position ID:
chr9|20843496|20845814|-
Gene name:
Dnmt1
Transcript:
ENSMUST00000178110.3
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
9
Exon/intron offsets:
0
Genomic length:
2318
Exon/intron sizes in nt:
2318
Flanking exon/introns:
chr9:20843495-20845814
Splice length:
2318
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTGCAGCTGTCATGCCTCCGTGCCCTAAAGTGGTGCTTGCTTGCAGTGTCGCTGCTGTGAACAGGGGCCTGGGACTGAGCACTAGTGTATTTTGTAGCCTGAGAAGTTCCACTGAGAAAACCTAGACCAAGGTGGGCTGGAGAGATGGCTCAGCAGTTGAGAACTCTAGCTCCTTTTGTAAAAGATGCTGGGTTTTGTTCCTGGCATGTGGAAGCCAACTGCTGCCTGTAACTCCAGATCCCAGGGGGTTACTCCTCCGGCACATGTATACAGATGACATGCTGGCGGAACACCCATATACATAAAATACGGATAGCTGAAGAACAGACCCAAGGACCTCACCCAGTGAGGTGGCTCACTGGGTAAAGGTGCTTGTTCGCAAGTCTGACAGTTGAGCTCAACCCTGGAGCCTGCATGATGAAGGTTGTCTTCTGACCTCCATATGTGTCTATACTTGTACATACAGATAACTAAAGTCCAACCAAGCTGGCCATGGTGAGACACATCTGGAACCTCACCTTGTGTTGGAGGCTAAGGCAGGAAGGTTCTCATGAGTTCAAGGCCAGCCTGAGCTAGAGTGAGCCACTGTTTCAAAAAGAAATGAGAAACCATTAAGAAATAAGAGCATTGTGGTGCACACCTTTAATCCTAGCACTCAGGACACAGGTGTATCTCTGAGTTCTGAGTCAACCAGGTTTCAGGACAGCCAGGACTATAGTGAGACACCCTGCTTCAACAACAAAAGGTAGTCTGCCTACCCTAGAAAAGGGTAGCCTGCGACCTTCTCCTTACTCAGACCCTGCCTCAGCAGTCACGTTGCCATCCATCACGTTACTAGTGGCTGTTTAAGTGAGCTTGTGCTCCAAGTGTCTTGGCTGACGGTGTGAAAGCTTAGCAGCCACTGAGCTCGTCATTGAGCCTTGCACCTGGCAGCTGATTCTGGCTGACAGTGGGCTAACTTAATTGTCCACCACTTAGTCCACATGAAGACATCCTTATGTCCATAGAAGGGCACAAGCAACTAGTGCTGGCCTTCAATACTAAGTTTTGATTCTGGTGTTTGTATATATTTTTTGTTTTCGAGACAGGGCTTCTCTATGTAGTCCTGGCTGCCCTGGAACTCGCTCTGTAGATCAAACTGGCTTTGAACTTTGAGCAGAGATTTGCCTGCTTCTGCCTCCCGAGTGCTAGAGATAATGCTGTGCACCACGACCTGGCTTATTTGGAGGTTTTTAATAGATAGGATCTCCTATGTAATTCAGACTTGATCTCTGCTTCAGGATCAAGAATACAAGAATTTCAGGCCTGTTCTATCACATCCAGATAGAGATGATCCTCGTGACATGTCTTAACATGTGGGTGTCTCGAATCCAGACAGGGGATTTCTTACTGGCATGCATCTATGAGTTCAGATGGGAGTCCCAATTGACTCTGGAGGTCACACTAGGGCTAGACTCACACCTCCTAAGCACTGGAGTCACAGGCCCTGCCCAGTCAGTGCTTATGTAGGTGCTGGGCAGTCTGAACTTCAGTCCTTTTCTGAGCTAGTCCAGTCTTGAGATGGTATCGGTGGTGGTTTTCGGGTTTTTTGTTGTTGTTTTTGTTTTTAAAGCTTCTGTTAACACTCACTTGACTCATGCAAATATTGAAGGCCCAAGTGCAGAGGGCAGCCTGGTGCCTGATCCACAGATGCGCAGGGTGGAGGGTAGGGTGCAGAAGAGTAAGACAGTCGGGCTCCTGTGGGATGGAGGCCAGCCTTCTGTGCTTGCTGATGCTGGCCTCGCCACTCATTTCATCACGACAGTCCTGTCTGCCTCCAGGACCGCCAGTGAAGGCCTGCTAGTTGTTTGTCCTAACCTTTGGCATCTCTGATTATCGTTCATTTGAAGAGCTAAGTGGTGTGGTTGATAGACTCGGGGTGTGCACGGGCGCACACCAGTGTGTTTATCTGGTGTATACCCATGCTCCATCTTGCCTGCAGAGGTAAGGGGAGAGCTCCCAGGTTTCACTTCACTCCTCCCATTGTGCATTGTGGGGATGGAACTCGGATCATCAGGCCTACGTGGTAAAATCTTTCCTCTGTTCAGACGTCTGGTGGGCCCCAGCTGAGTGCTTGTTATCGGCTCATGAATGCTGTAGGCTTGAGCCCCAGTTCTGCAAAATGCATAAAATCATGAAGGATAAACAGGTGGCGGGTAGGAAGGGTGACCTGGTCTCGAACTGAGAGGACACATTTAAACCCGCATTTGACTGCCCAGAGCATTGATGATCAGTGTCCATGTGTGAGGTTTTTTTTTTGCTTTTTTACTTGGCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TAAACCCGCATTTGACTGCC
59.11
CACTAGTGCTCAGTCCCAGG
59.47
170
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TAAACCCGCATTTGACTGCC
59.11
CTGTTCACAGCAGCGACACT
60.88
147
PCR template sequence:
CTCGAACTGAGAGGACACATTTAAACCCGCATTTGACTGCCCAGAGCATTGATGATCAGTGTCCATGTGTGAGGTTTTTTTTTTGCTTTTTTACTTGGCAGTAAGTGCAGCTGTCATGCCTCCGTGCCCTAAAGTGGTGCTTGCTTGCAGTGTCGCTGCTGTGAACAGGGGCCTGGGACTGAGCACTAGTGTATTTTGTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
21
Interacting miRNAs (#binding sites)
mmu-miR-709(2), mmu-miR-490-3p(2), mmu-miR-338-3p(2), mmu-miR-9-5p(1), mmu-miR-134-5p(1), mmu-miR-31-5p(1), mmu-miR-205-5p(1), mmu-miR-29b-3p(1), mmu-miR-335-5p(1), mmu-miR-29c-3p(1), mmu-miR-339-5p(1), mmu-miR-214-3p(1), mmu-miR-22-3p(1), mmu-miR-212-3p(1), mmu-miR-297a-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-377-3p(1), mmu-miR-1198-5p(1), mmu-miR-3065-5p(1), mmu-miR-540-3p(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTTTACTTGGCAGTAAGTGCAGCTG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.707003695
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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