top of page
mmu_ciSmc3_1252
Basic information of circular RNA
PanCircBase ID:
mmu_ciSmc3_1252
mm39_Chr. Position ID:
chr19|53602284|53603536|+
Gene name:
Smc3
Transcript:
ENSMUST00000025930.10
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
3
Exon/intron offsets:
0
Genomic length:
1252
Exon/intron sizes in nt:
1252
Flanking exon/introns:
chr19:53602284-53603536
Splice length:
1252
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTATAGATTTCTGGATTTTTTAACTATGAATTCAAGTGTCTTTAAGATGGTTTATTAAATAATTGATTTCTGAAATGATGTTTGTATGAAACCTAAGAAGTCATACATGGTTGTTGTTTAGTGTAGCAGGTTAGATCTGAATTGTGTGTGTTCAGTCTGTCTTTGAGACAGCAGAGACACTTGTTGAAATTATTTATGCTGTAATAATGGCAGTGTCTATCTTAGATAGAGTCTAAGAAATGATAGAGCAGTGTAGCAAAAAATATTGATACCTATTTGAAGATGATAGAGATTTGAAAATTCTCTAAGGATGGAAATATAAGATGCCTTTGTTAAATTCTTTGTGGAGAAAAAAATGAGGCAAGTTGGGCTGTAGTCTAAGGAGGGGTTAAAATGTTAACTTAGTTGGTGGTGCTCATGGAAACCAGCGCTTAGTAGGAGGAAAGGGTCTGTGTCTTTACACATGTGTCTGAGGGATGCAGAAACAAACTCCTGTAATGGCTGTGACTCGGTGCTGGTCAGAGAGCAGATAGAAGGAAAGCGTACAGCTCAAAATCCCAGAGAAAGGAGGGCAGTTTCAATCCACCCATCCCATGAGGAGGAGGAGACCAGTCTCTCAGAGCAGGTAGCACTGTACATGAGTGTTGCCTCCCTGTGTTCTCAGGCTGACTTGTAGTTTAGAGATCTCTTAGGACCTGGACCAGAATAGCTGAATTAAAGCATTCTGTACCTTGACAGTGGCCCACTAATTAGGTATTTTGTGTGTAATGAGGACATAAGCAGTGCGGCAGGAGCTGGGAATTTAGAACGGTTCCCTGTATTTCTTAGTTAGTAGAAATGTGTTCAGGTGTAGCAGTGTGTTGTACATTATTAGGCAAAAATATTTTTTTAGGATTAAAACCTTACGTGGCCTTTTTATGTAGTTTGTTGTTATGTAGCAGTACATAACTTTATAGTAGTGACCTAGTTAATCGGTGTAAGCTTTTATTAGGGAGAGGACCTGCCTTCTGCATCTCTCTTAGTTCTTGTGATACTTGATGTCCTTTTCAGCAGAAGCTCAATTTCTTGATTTCCCTACCAGTGATTATTAGTCTGATGTACTGATGCATTGTCTACAGTCATTATGTGTGAAACAACTTATCTGCAGTGTTTGTTACATTGCATGTGGTATTCTTAAGTTATGGAGTTGTGAATAAGCCCTAAGTTCTCCTTTAGGGTGTGCTAATAACCTTATTTTTGTGTTTCTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTTCTCCTTTAGGGTGTGCT
58.66
AGGTTTCATACAAACATCATTTCAGA
57.59
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTTCTCCTTTAGGGTGTGCT
58.66
GGTTTCATACAAACATCATTTCAGA
56.35
143
PCR template sequence:
GTTTGTTACATTGCATGTGGTATTCTTAAGTTATGGAGTTGTGAATAAGCCCTAAGTTCTCCTTTAGGGTGTGCTAATAACCTTATTTTTGTGTTTCTAGGTAAGTATAGATTTCTGGATTTTTTAACTATGAATTCAAGTGTCTTTAAGATGGTTTATTAAATAATTGATTTCTGAAATGATGTTTGTATGAAACCTAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
19
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-26a-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-324-5p(1), mmu-miR-185-5p(1), mmu-miR-139-5p(1), mmu-miR-495-3p(1), mmu-miR-26b-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-411-3p(1), mmu-miR-511-3p(1), mmu-miR-340-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-3061-5p(1), mmu-miR-3105-3p(1), mmu-miR-338-3p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTGTGTTTCTAGGTAAGTATAGATT
siRNA sets
ATACTTACCTAGAAACACA, TATACTTACCTAGAAACAC, CTATACTTACCTAGAAACA
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
0.825417376
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page