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mmu_ciSmc3_1543
Basic information of circular RNA
PanCircBase ID:
mmu_ciSmc3_1543
mm39_Chr. Position ID:
chr19|53622542|53624085|+
Gene name:
Smc3
Transcript:
ENSMUST00000025930.10
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
19
Exon/intron offsets:
0
Genomic length:
1543
Exon/intron sizes in nt:
1543
Flanking exon/introns:
chr19:53622542-53624101
Splice length:
1543
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATATCCTTCTGTTTGAGCGTGAGCGTGACGGGACTGCAGAGAAAGGCAGCATCGATGGCATGTGCTGTCTGTAATTACATGCTTTCTTTCATGAATATTGGAGGGGAATTGCACATTTCACTTTGCTTTTTATTTAAATACAAGAGCTTGTTTAACTTCTGAAGACTAAGAAAAGATTTAAAAAAGATAATTCTGATTTTTGTTTCACTGTTAAGTAGACAGTACTAGTGCATGCTTTGAAGAAATAGAACTTGAGGAGCAACAGAATTCAAGGTTGTCAGACTAAAGGGGAAATGGAAGGGAAGACCTGGCTGATGGTTCAAGGAGCAGCATCAGTAATGCTACTGTTAAATAGATGTCAGATCTACTTAGTGGATGGAAGCACTGGAAAACGTCATTTAGGGTTTACTCTCGGCAAAAATTGGGGTGGATTTGTTAGTGGAGGTAATGACAACAGCTTTCCAATTGTGAGTATCTGCAGGTCTTCCAAGTGAGTGTACTGCTACGTGGAAGGTGGCAAGTTCAGCTCCAACAGAGCGCTTACACATATGCAATTCTTAAAACCACCATGCTGCTTTTGGTGTGATGTCCTATGTGTAGTACAGAGAAAGACAAATGCCTTAGCTGTGCCCTGCAAGGATCTGTGTAGTACTTTGAGAACTGCTTAAATGTGGCAGGATGTTGGGGCAGGATGTGAGGAAGTTTTAAGGAAAGGAGTGCTTGTGTGCTGGCTCAGTGGGTAGGATGCTTGCAGCACAAGCCTGAACACCCGAGTTTGGATTTCCCAGCACGCGTGTGGAAGGCTGGGTGTGCTGAAAGGATGGGCACAGGTGGAGACTAGGAGACTAGGCTGCTAGTGAGCTTAACCCTCTGGTGCTTTCCAAACTCATGAAGAAATACTGTCTCAAAAAGAAACGTGGAGAAGAGTAAAAGAAAACAACAAATGTCAACCCCTGCCCTTCACCCACACTTGTCCATGCACACAGATGCGTGAGAGAGGATGTTGACAGCTTCCAGCTATCTGCATATTTGACCGTCTGTTTAGGTTCATTATTTCACATTAGGCAAGGCTGTTCTTCATACCTGAGTCACCAAAGCAGTGCCTTCTGCATATTTAGTTTTTTAATAAAAATGAATTTCAGTATATATGTGTATATGTTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATATATATATATATATATATATATAATATGTATGTATAATATATATACACACACATGCTGTTACTTGATTTTGCTTAACATTCTTTAATAATTTCTATGATGTTTTGTTCAACTGTAAGTTAAATAAGTATGCATATTTTAGAGTAAAATGTGTGGCAAAATGCTTCAAGTTTCTCTTATGATTGAACATTTTTAGTGGTAGTATTTAATTCAACATTGGTGTAGTCCCGTAAGTCTGGGGGAATTACTTGGGAATAAAGGAGAGGATTCATGATGATGTATTTATAAGAAATGAAGAAAATCTAGAATATATTTACAACCTTAAGAGAATTTC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGGGGGAATTACTTGGGA
57.63
TTTCTCTGCAGTCCCGTCAC
59.97
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGGGGGAATTACTTGGGA
57.63
AGACAGCACATGCCATCGAT
59.82
170
PCR template sequence:
TCTGGGGGAATTACTTGGGAATAAAGGAGAGGATTCATGATGATGTATTTATAAGAAATGAAGAAAATCTAGAATATATTTACAACCTTAAGAGAATTTCATATCCTTCTGTTTGAGCGTGAGCGTGACGGGACTGCAGAGAAAGGCAGCATCGATGGCATGTGCTGTCTGTAATTACATGCTTTCTTTCATGAATATTG
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-466d-3p(4), mmu-miR-466b-3p(4), mmu-miR-1187(2), mmu-miR-124-3p(1), mmu-miR-9-5p(1), mmu-miR-15a-5p(1), mmu-miR-106a-5p(1), mmu-miR-7b-5p(1), mmu-miR-200c-3p(1), mmu-miR-26a-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-7a-5p(1), mmu-miR-203-3p(1), mmu-miR-434-3p(1), mmu-miR-26b-5p(1), mmu-miR-194-5p(1), mmu-miR-125b-1-3p(1), mmu-miR-466a-5p(1), mmu-miR-466p-5p(1), mmu-miR-669d-5p(1), mmu-miR-697(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTAAGAGAATTTCATATCCTTCTGTT
siRNA sets
ACAGAAGGATATGAAATTC
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
0.782723272
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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