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mmu_ciDdx39b_2334
Basic information of circular RNA
PanCircBase ID:
mmu_ciDdx39b_2334
mm39_Chr. Position ID:
chr17|35463524|35465858|+
Gene name:
Ddx39b
Transcript:
ENSMUST00000068056.12
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
4
Exon/intron offsets:
0
Genomic length:
2334
Exon/intron sizes in nt:
2334
Flanking exon/introns:
chr17:35463524-35465912
Splice length:
2334
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGGGGGGAAAGAAACCTGGGACAGGAGGCTGTGGGGAGACAGGCACTGGGAGGGAGGTTGGCTGTCCTCGGGCATCCCTGTGCTGTCAGTGGTGTGGTCACATGAGAGACTTCAGTTAGTGCCACACCCTTCTGTGGCTGCCCTTCCAGGTTCCATACTGTGAATACACCTGTGTGTTCCTGAGAGTTCGTAGCTTTAGGTGATACCACCGCAACACTTTGTGGTTAGTTGGTTTTGGTATTGCAGATTCCATTCCAGAGCCTTGAGCTACTATGTGTGGGACTGAGCCACCCCTGGGTCCTTTGTTTTTATGTTCACGACTGTCTCTTAACCACCACGTTGTCCTGGTAGGCCTTGAACTCACCTTAGTCTAGAGATAGGAGGCCTTGAACCTGAGGCTCCTGCCACAGGTTCCTGAGTAGTTGGGGCAGGCCTTTGCCACCTGGCTTGGCCAGAGCCTCTGTTCTGTTCTCCTGAATTGCTTGGTAGATTGTTTGAGAGTTGGGTTGTATGTGGCAAGAGGAAGCTAGATGCTCTTAAAACAGCCCTGGTGTGGACTTTAACTCTAGAGTGGTTAAAGCTTTCCGGGGGTCATAACAAGTGGCCTGTGTCCTCTGTGAAGGAACGTGGTGTGGCCTCACAGTTGGCATCCTTTGGAACTTTTGAGATTATATATTTCCATGCTTGGGTGAGTGGCCTGCTGGGTTTGAAAGGCCTTGTAAGCTGGCCCTGTGAGTAGAGAGATGTGTGCAGACTTCCTATTCTGGTTAGGGTGGGGAAAGAGCAGCTTGGATCAGTCTGGGCTGACCTTTGAGTCAAATCCACCTTCCTCTGCCTCTACTGGGATTAAAGGCGAGCATCTCCACAACCGCCCAGCATGACAGATTTAAAAGGGGGAATTCTAGAAGAAGAAAAGGAAAGGCAGTATGTGCAAAATGCTAAAGGAGGCCAGAGATCTTGTGATCTCTGAGGTTTCCATTGCTCGGCATAACCAAGCATTAGACATTGTTTTCCTAACCTGTCTGTGTGCAAGCTTACTGGCCTCTGAAACATTTTAGCGTATTTATATATCTTTTTCCTAGGATTTTGAAAATAGTTTGTAATCTGGAGGCATTGTCTATGTCTGTGTGCCTGTGCCTCTGGCTGTATGTCATTATACCTTGCCAAAAAACTAATAGACTTTCAGTTCCTTGGCTGACCGGTCCCTTGTGGTGGATTTAATAGTTGGGAACTGAAGCTGGATCAGTGGCTCATTCCTGTATTCCCATGGCCTGGGAGGTTGAGGTGGGCGTTTGCTGGAGTTGAAGGCTGCCCGGGGCTAAGGTCTCAAAACAAAGAGGGAGGGTGGCAAAGCTGCAGTCCTTCTCTGCAGGACCCACAGCACCCTTGTGCTACTCAAAATGCTCTGAGAGTTGGGATCAAGTCTGAGGTTGGGTTTGGTGTAGGAGCCTGCAGATTAGCTGGTTAGGTCCCCCCCCCCATCATAAAATCAGAATCATCTGTACTTCTCCTTGGCTGTGCAGCACAGTGTCCTCTAGGGGGCTGTCTAGTCCCTCCCTTAGTTTTAGCTCGCTTTTCCCTCAGTATTTGTAACTATGTCTGAAAGCTTAACTGATACCAGTAAACCATCGTGAACAGGAGTGGAGTGCTCCTGTGTGCATGTGTTAGCCATTGTGGTTCAGGATTGAGAAGAGGAAGAGGTTTACTGTAGAGTAAGCGTCCTGGTTATTTCTTTCCCCTTGAAATTGGACAAGTCCACGTGTCACAGCTCACACATCCAGCACTCACCTGGTGTCACAGCTCACACACTCACCTAGTGGGTTGCACATGGTGTGACTTTTATCTCAGGCACCGAGGAAGCAAAGGCTCCAGGCCAGGGAGACTGTCTGACAGTTCAGTTAGGAAAGCTTGCTTGTGGTTTGATCGTTGGGTGGCGCCTCACACTTGCTGGTGGCTTCTTGCTTTCTTCATCTGTGTAAGGAAGCTGTGACTTTGGAGTCACACGTGCCTCGTTGTGTAGATCAGCTAGGGCTGTGCAGAGCGATCCTGTCGTGGAGTTTGAGTGGAGGCGGAGAAGCTGAGTGTTCATCCCTTCCTCCATCCCCCTTGGCCCCCTGGTGCTGAGGGGGTCGCTTTGTTTCTTATGGGAGGCACAGGAGCCACTGCAGGCCTGAAAGCTAAGAGTTGGTTTACAGTCAACCACAGAATGGACACACTGGTATTGGCAAGATGGCCCACTGCCTTTAATCTGTACTTGGTGCCAGACAGGCTGATCTACAAAGTGAGTTCTAGGCCAACCAGGGCTATACAGTGAGGCCTCTCAAACCAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGTTCTAGGCCAACCAGGG
59.75
CCACTGACAGCACAGGGATG
60.68
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTACTTGGTGCCAGACAGG
59.6
CCACTGACAGCACAGGGATG
60.68
177
PCR template sequence:
GGCCCACTGCCTTTAATCTGTACTTGGTGCCAGACAGGCTGATCTACAAAGTGAGTTCTAGGCCAACCAGGGCTATACAGTGAGGCCTCTCAAACCAAAGGTAAGGGGGGAAAGAAACCTGGGACAGGAGGCTGTGGGGAGACAGGCACTGGGAGGGAGGTTGGCTGTCCTCGGGCATCCCTGTGCTGTCAGTGGTGTGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
23
Interacting miRNAs (#binding sites)
mmu-miR-298-5p(2), mmu-miR-673-5p(2), mmu-miR-9-5p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-200c-3p(1), mmu-miR-709(1), mmu-miR-203-3p(1), mmu-miR-139-5p(1), mmu-miR-214-3p(1), mmu-miR-24-3p(1), mmu-miR-136-5p(1), mmu-miR-26b-5p(1), mmu-miR-182-5p(1), mmu-miR-34b-5p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1), mmu-miR-207(1), mmu-miR-188-3p(1), mmu-miR-490-3p(1), mmu-miR-3061-5p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCTCAAACCAAAGGTAAGGGGGGAAA
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
0.724061935
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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