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mmu_circUsp40_755
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp40_755
mm39_Chr. Position ID:
chr1|87877880|87890210|-
Gene name:
Usp40
Transcript:
ENSMUST00000189409.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
11,10,9,8,7,6,5
Exon/intron offsets:
0,1484,2181,3992,7052,9630,12265
Genomic length:
12330
Exon/intron sizes in nt:
211,66,119,95,124,75,65
Flanking exon/introns:
chr1:87877749-87877880|chr1:87890210-87893027
Splice length:
755
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GAGAGATTTGGCACTTAAGGAAAATGGATTGGTGCTATGAAGCTGGTGAACCTTTATGTGAAGAGGATGCAACACTGAAAGAGCTTATGATACGTTCTGGGGATACTTTGCTTTTAACTGAAGGGAAACTTCCTCCTCCGGGTCACTTGAAGATGCCCATCTGGTGGTACCAGCCTGCAAGGCTGTCAGGACACTGTGAGAGTCGGGACCACTTAAACTGTGCCTTTTCTCAAGATAGCACCTGGAGGGCTGCTCCCACCCAAGGTGCTCCTGGCCCCGAGCCTGCAGAAGTCTCTCTCCTCTACTTGGGGGATATGGAGATCTCAGAAGAGGCCACATTGGTGGAACTGAAGTCTCAGGCCTTGGCCTTGCCTTCTGTTTCGAAGCTCGCTGTCCAGTCCACAGCCCTGCTCAGAGTCTGGACAGTGGAGAGCAAGCGCCCCAGCAGACTCTTGCGCACTAACTGGCGGCAGCTCAAGGAGTACAGACTGGGCCGGAGAGCAGAGCTCTGCCTAGAGCTCCTTCAAAAAGAGGAGGACTTGGGGCCCCGAGATGTACTGCTGAGGACACAGCTACGCATCCCTGGTGAGAGAGCCTACTCCCTGGCGACAGACCTGATATGGGACACCACCAGAGGATGGACTGCTGGCTCCTTGAGGCAGAGAGTAGCTGACTTCTATTCTCTTCCTGTGGAGAAAATTGAAATTGCCAAATATTTTCCTGAAAAGTTTGAGTGGCTTCCAATATCTAGCTGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGCAGAGAGTAGCTGACTTCT
58.9
TCAGTGTTGCATCCTCTTCACA
59.9
176
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCAGAGAGTAGCTGACTTCT
58.9
CAGTGTTGCATCCTCTTCACA
58.5
175
PCR template sequence:
GAGGCAGAGAGTAGCTGACTTCTATTCTCTTCCTGTGGAGAAAATTGAAATTGCCAAATATTTTCCTGAAAAGTTTGAGTGGCTTCCAATATCTAGCTGGGAGAGATTTGGCACTTAAGGAAAATGGATTGGTGCTATGAAGCTGGTGAACCTTTATGTGAAGAGGATGCAACACTGAAAGAGCTTATGATACGTTCTGG
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-124-3p(1), mmu-miR-182-5p(1), mmu-miR-680(1)
siRNAs for circular RNA silencing
Junction sequence
AATATCTAGCTGGGAGAGATTTGGCA
siRNA sets
AAATCTCTCCCAGCTAGAT, AATCTCTCCCAGCTAGATA, TGCCAAATCTCTCCCAGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP40_755_ORF_1
0.6626
0.137067764
0.872852952
750
ORF sequence:
ATGGATTGGTGCTATGAAGCTGGTGAACCTTTATGTGAAGAGGATGCAACACTGAAAGAGCTTATGATACGTTCTGGGGATACTTTGCTTTTAACTGAAGGGAAACTTCCTCCTCCGGGTCACTTGAAGATGCCCATCTGGTGGTACCAGCCTGCAAGGCTGTCAGGACACTGTGAGAGTCGGGACCACTTAAACTGTGCCTTTTCTCAAGATAGCACCTGGAGGGCTGCTCCCACCCAAGGTGCTCCTGGCCCCGAGCCTGCAGAAGTCTCTCTCCTCTACTTGGGGGATATGGAGATCTCAGAAGAGGCCACATTGGTGGAACTGAAGTCTCAGGCCTTGGCCTTGCCTTCTGTTTCGAAGCTCGCTGTCCAGTCCACAGCCCTGCTCAGAGTCTGGACAGTGGAGAGCAAGCGCCCCAGCAGACTCTTGCGCACTAACTGGCGGCAGCTCAAGGAGTACAGACTGGGCCGGAGAGCAGAGCTCTGCCTAGAGCTCCTTCAAAAAGAGGAGGACTTGGGGCCCCGAGATGTACTGCTGAGGACACAGCTACGCATCCCTGGTGAGAGAGCCTACTCCCTGGCGACAGACCTGATATGGGACACCACCAGAGGATGGACTGCTGGCTCCTTGAGGCAGAGAGTAGCTGACTTCTATTCTCTTCCTGTGGAGAAAATTGAAATTGCCAAATATTTTCCTGAAAAGTTTGAGTGGCTTCCAATATCTAGCTGGGAGAGATTTGGCACTTAA
Peptide sequence:
MDWCYEAGEPLCEEDATLKELMIRSGDTLLLTEGKLPPPGHLKMPIWWYQPARLSGHCESRDHLNCAFSQDSTWRAAPTQGAPGPEPAEVSLLYLGDMEISEEATLVELKSQALALPSVSKLAVQSTALLRVWTVESKRPSRLLRTNWRQLKEYRLGRRAELCLELLQKEEDLGPRDVLLRTQLRIPGERAYSLATDLIWDTTRGWTAGSLRQRVADFYSLPVEKIEIAKYFPEKFEWLPISSWERFGT
IRESfinder result
IRESfinder score
0.632413483
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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