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mmu_circSt18_398
Basic information of circular RNA
PanCircBase ID:
mmu_circSt18_398
mm39_Chr. Position ID:
chr1|6807803|6865800|+
Gene name:
St18
Transcript:
ENSMUST00000140079.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
3,4,5,6,7
Exon/intron offsets:
0,15414,31318,33364,57806
Genomic length:
57997
Exon/intron sizes in nt:
78,43,55,31,191
Flanking exon/introns:
chr1:6557965-6807803|chr1:6865800-6872543
Splice length:
398
Other database IDs:
circAtlas: mmu-St18_0042
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
AGACCCCAGTCCTGTGAGATTCTTTGAAGGACTGTGTGAATTCCATTTTATGTGGCTGGGTGCTCATACCAATTTAAGCAATGACATTTCTTCTGTTCAAGTTCAGTAGCTGCTAGAGAAGATGGATGCCGAGGTTGAAGATAAAACGTTGCATACTCTTTCAAAAGGAACTGAAGTTCCAATGGATTCTCTGATCCCAGAGCTCAGGGTTCCATATGATTGCTCTATGGCGAAGAAGAGGAGAGCTGAAGAGCAGGCATCGGGAGTTCCAATTAACAAGAGGAAATCTCTGCTAATGAAACCCCGGCACTACAGCCCAGACATGGGCTGCAAGGAAAGCCCAGACAACAGGAACGAGGATGATGGCCTCCTAGAAACAAACGACCATGCCACTGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGACATGGGCTGCAAGGAAA
59.89
GCACCCAGCCACATAAAATGG
60.13
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GACATGGGCTGCAAGGAAAG
59.47
GCACCCAGCCACATAAAATGG
60.13
142
PCR template sequence:
AAACCCCGGCACTACAGCCCAGACATGGGCTGCAAGGAAAGCCCAGACAACAGGAACGAGGATGATGGCCTCCTAGAAACAAACGACCATGCCACTGCAGAGACCCCAGTCCTGTGAGATTCTTTGAAGGACTGTGTGAATTCCATTTTATGTGGCTGGGTGCTCATACCAATTTAAGCAATGACATTTCTTCTGTTCAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-216a-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CATGCCACTGCAGAGACCCCAGTCCT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCST18_398_ORF_1
1.0874
0.27556622
0.50218134
294
ORF sequence:
ATGGATGCCGAGGTTGAAGATAAAACGTTGCATACTCTTTCAAAAGGAACTGAAGTTCCAATGGATTCTCTGATCCCAGAGCTCAGGGTTCCATATGATTGCTCTATGGCGAAGAAGAGGAGAGCTGAAGAGCAGGCATCGGGAGTTCCAATTAACAAGAGGAAATCTCTGCTAATGAAACCCCGGCACTACAGCCCAGACATGGGCTGCAAGGAAAGCCCAGACAACAGGAACGAGGATGATGGCCTCCTAGAAACAAACGACCATGCCACTGCAGAGACCCCAGTCCTGTGA
Peptide sequence:
MDAEVEDKTLHTLSKGTEVPMDSLIPELRVPYDCSMAKKRRAEEQASGVPINKRKSLLMKPRHYSPDMGCKESPDNRNEDDGLLETNDHATAETPVL
IRESfinder result
IRESfinder score
0.430700001
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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