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mmu_circSil1_408
Basic information of circular RNA
PanCircBase ID:
mmu_circSil1_408
mm39_Chr. Position ID:
chr18|35458336|35481808|-
Gene name:
Sil1
Transcript:
ENSMUST00000235619.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
5,4,3
Exon/intron offsets:
0,15814,23356
Genomic length:
23472
Exon/intron sizes in nt:
19,21,00,116
Flanking exon/introns:
chr18:35451016-35458336|chr18:35481808-35571319
Splice length:
408
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GCTGTTCCTGCAGGATCCCATGTGCGAATGAACCTACAGACTGGAGTAAACGAGGTGAAGCTCCAACAAGAAGACAAATTTCAAAATAATCTGAAAGGATTTAAAAGAGGCAGAAGGCTGGACATCAACGCCAACACATACACATCTCAGGACCTCAAGAGTGCGCTGGCCAAATTCAAGGAGGGGACCGAGATGGAGAATTCAAAGGATGAACTGGCGAGACAGGCCACAGTCAAGCAGCTCTTCCGCCCCATTGAGGAGCTGAAGAAGGAATTTGATGAGCTGAACGTTGTTCTTGAGACTGACATGCAGATTATGGTTCGGCTGATAAACAAGTTCAACAGCTCCAGCTCCAGCCTAGAAGAGAAGGTTGCTGCGCTCTTTGATCTTGAGTACTATGTCCATCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACAAGTTCAACAGCTCCAGC
58.69
TGTTGGAGCTTCACCTCGTT
59.53
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACAAGTTCAACAGCTCCAGC
58.69
TTGTTGGAGCTTCACCTCGT
59.53
146
PCR template sequence:
GCAGATTATGGTTCGGCTGATAAACAAGTTCAACAGCTCCAGCTCCAGCCTAGAAGAGAAGGTTGCTGCGCTCTTTGATCTTGAGTACTATGTCCATCAGGCTGTTCCTGCAGGATCCCATGTGCGAATGAACCTACAGACTGGAGTAAACGAGGTGAAGCTCCAACAAGAAGACAAATTTCAAAATAATCTGAAAGGAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-297a-5p(1), mmu-miR-1187(1), mmu-miR-452-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTATGTCCATCAGGCTGTTCCTGCAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSIL1_408_ORF_1
1.2676
0.422505445
0.989188005
789
ORF sequence:
ATGAACCTACAGACTGGAGTAAACGAGGTGAAGCTCCAACAAGAAGACAAATTTCAAAATAATCTGAAAGGATTTAAAAGAGGCAGAAGGCTGGACATCAACGCCAACACATACACATCTCAGGACCTCAAGAGTGCGCTGGCCAAATTCAAGGAGGGGACCGAGATGGAGAATTCAAAGGATGAACTGGCGAGACAGGCCACAGTCAAGCAGCTCTTCCGCCCCATTGAGGAGCTGAAGAAGGAATTTGATGAGCTGAACGTTGTTCTTGAGACTGACATGCAGATTATGGTTCGGCTGATAAACAAGTTCAACAGCTCCAGCTCCAGCCTAGAAGAGAAGGTTGCTGCGCTCTTTGATCTTGAGTACTATGTCCATCAGGCTGTTCCTGCAGGATCCCATGTGCGAATGAACCTACAGACTGGAGTAAACGAGGTGAAGCTCCAACAAGAAGACAAATTTCAAAATAATCTGAAAGGATTTAAAAGAGGCAGAAGGCTGGACATCAACGCCAACACATACACATCTCAGGACCTCAAGAGTGCGCTGGCCAAATTCAAGGAGGGGACCGAGATGGAGAATTCAAAGGATGAACTGGCGAGACAGGCCACAGTCAAGCAGCTCTTCCGCCCCATTGAGGAGCTGAAGAAGGAATTTGATGAGCTGAACGTTGTTCTTGAGACTGACATGCAGATTATGGTTCGGCTGATAAACAAGTTCAACAGCTCCAGCTCCAGCCTAGAAGAGAAGGTTGCTGCGCTCTTTGATCTTGAGTACTATGTCCATCAG
Peptide sequence:
MNLQTGVNEVKLQQEDKFQNNLKGFKRGRRLDINANTYTSQDLKSALAKFKEGTEMENSKDELARQATVKQLFRPIEELKKEFDELNVVLETDMQIMVRLINKFNSSSSSLEEKVAALFDLEYYVHQAVPAGSHVRMNLQTGVNEVKLQQEDKFQNNLKGFKRGRRLDINANTYTSQDLKSALAKFKEGTEMENSKDELARQATVKQLFRPIEELKKEFDELNVVLETDMQIMVRLINKFNSSSSSLEEKVAALFDLEYYVHQ
IRESfinder result
IRESfinder score
0.401552833
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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