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mmu_circUsp6nl_472
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp6nl_472
mm39_Chr. Position ID:
chr2|6341178|6419851|+
Gene name:
Usp6nl
Transcript:
ENSMUST00000114937.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
2,3,4,5,6,7
Exon/intron offsets:
0,54687,58105,63912,72561,78565
Genomic length:
78673
Exon/intron sizes in nt:
92,68,83,40,81,108
Flanking exon/introns:
chr2:6327765-6341178|chr2:6419851-6425713
Splice length:
472
Other database IDs:
CIRCpedia: MMU_CIRCpedia_25576, circAtlas: mmu-Usp6nl_0026
Human Ortholog IDs:
Mature spliced Sequence:
AACAGGATATGTATTCCTCTGAGAAACCCTGGACAGCAGATCTTGGTTTAATACTGGATTGGAACAACACCCACAGAGGTTTGCAGTCATGAATTCCGACCAGGATGTAGCACTCAAACTTGCTCAAGAACGAGCTGAAATAGTTGCTAAATATGACAGAGGGCGGGAAGGTGCAGAGATCGAGCCCTGGGAAGATGCTGATTATCTTGTTTACAAAGTCACCGATAGATTTGGCTTTTTACATGAGGAGGAGCTCCCATACCATAATGCAGCTGCGGACCGGCAAAAGCAACTGGAAATCGAAAGGACTTCCAAGTGGCTGAAAATGCTGAAAAAATGGGAGAGATACAAGAACACCGAGAAGTTTCATCGACGAATTTACAAAGGAATTCCACTCCAGCTCCGAGGTGAAGTCTGGGCTCTTCTTCTTGAGATCCCTAAAATGAAAGAAGAAACAAGAGACCTTTATAGT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCTCCGAGGTGAAGTCTG
60.11
TGCAAACCTCTGTGGGTGTT
60.03
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCTCCGAGGTGAAGTCTG
60.11
GACTGCAAACCTCTGTGGGT
60.18
163
PCR template sequence:
ACGAATTTACAAAGGAATTCCACTCCAGCTCCGAGGTGAAGTCTGGGCTCTTCTTCTTGAGATCCCTAAAATGAAAGAAGAAACAAGAGACCTTTATAGTAACAGGATATGTATTCCTCTGAGAAACCCTGGACAGCAGATCTTGGTTTAATACTGGATTGGAACAACACCCACAGAGGTTTGCAGTCATGAATTCCGAC
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-221-3p(1), mmu-miR-222-3p(1), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
AGACCTTTATAGTAACAGGATATGTA
siRNA sets
ATATCCTGTTACTATAAAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP6NL_472_ORF_1
1.16
0.150131866
0.655870911
435
ORF sequence:
ATGAATTCCGACCAGGATGTAGCACTCAAACTTGCTCAAGAACGAGCTGAAATAGTTGCTAAATATGACAGAGGGCGGGAAGGTGCAGAGATCGAGCCCTGGGAAGATGCTGATTATCTTGTTTACAAAGTCACCGATAGATTTGGCTTTTTACATGAGGAGGAGCTCCCATACCATAATGCAGCTGCGGACCGGCAAAAGCAACTGGAAATCGAAAGGACTTCCAAGTGGCTGAAAATGCTGAAAAAATGGGAGAGATACAAGAACACCGAGAAGTTTCATCGACGAATTTACAAAGGAATTCCACTCCAGCTCCGAGGTGAAGTCTGGGCTCTTCTTCTTGAGATCCCTAAAATGAAAGAAGAAACAAGAGACCTTTATAGTAACAGGATATGTATTCCTCTGAGAAACCCTGGACAGCAGATCTTGGTTTAA
Peptide sequence:
MNSDQDVALKLAQERAEIVAKYDRGREGAEIEPWEDADYLVYKVTDRFGFLHEEELPYHNAAADRQKQLEIERTSKWLKMLKKWERYKNTEKFHRRIYKGIPLQLRGEVWALLLEIPKMKEETRDLYSNRICIPLRNPGQQILV
IRESfinder result
IRESfinder score
0.560497333
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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