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mmu_circUsp40_478
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp40_478
mm39_Chr. Position ID:
chr1|87880061|87890210|-
Gene name:
Usp40
Transcript:
ENSMUST00000189409.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
9,8,7,6,5
Exon/intron offsets:
0,1811,4871,7449,10084
Genomic length:
10149
Exon/intron sizes in nt:
119,95,124,75,65
Flanking exon/introns:
chr1:87879430-87880061|chr1:87890210-87893027
Splice length:
478
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GAGAGATTTGGCACTTAAGGAAAATGGATTGGTGCTATGAAGCTGGTGAACCTTTATGTGAAGAGGATGCAACACTGAAAGAGCTTATGATACGTTCTGGGGATACTTTGCTTTTAACTGAAGGGAAACTTCCTCCTCCGGGTCACTTGAAGATGCCCATCTGGTGGTACCAGCCTGCAAGGCTGTCAGGACACTGTGAGAGTCGGGACCACTTAAACTGTGCCTTTTCTCAAGATAGCACCTGGAGGGCTGCTCCCACCCAAGGTGCTCCTGGCCCCGAGCCTGCAGAAGTCTCTCTCCTCTACTTGGGGGATATGGAGATCTCAGAAGAGGCCACATTGGTGGAACTGAAGTCTCAGGCCTTGGCCTTGCCTTCTGTTTCGAAGCTCGCTGTCCAGTCCACAGCCCTGCTCAGAGTCTGGACAGTGGAGAGCAAGCGCCCCAGCAGACTCTTGCGCACTAACTGGCGGCAGCTCAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTCTGGACAGTGGAGAGCA
60.18
TCAGTGTTGCATCCTCTTCACA
59.9
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTCTGGACAGTGGAGAGCA
60.18
GCTCTTTCAGTGTTGCATCCT
58.84
147
PCR template sequence:
TTTCGAAGCTCGCTGTCCAGTCCACAGCCCTGCTCAGAGTCTGGACAGTGGAGAGCAAGCGCCCCAGCAGACTCTTGCGCACTAACTGGCGGCAGCTCAAGAGAGATTTGGCACTTAAGGAAAATGGATTGGTGCTATGAAGCTGGTGAACCTTTATGTGAAGAGGATGCAACACTGAAAGAGCTTATGATACGTTCTGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-124-3p(1), mmu-miR-680(1)
siRNAs for circular RNA silencing
Junction sequence
GGCGGCAGCTCAAGAGAGATTTGGCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP40_478_ORF_1
0.6752
0.122906853
0.516178888
495
ORF sequence:
ATGGATTGGTGCTATGAAGCTGGTGAACCTTTATGTGAAGAGGATGCAACACTGAAAGAGCTTATGATACGTTCTGGGGATACTTTGCTTTTAACTGAAGGGAAACTTCCTCCTCCGGGTCACTTGAAGATGCCCATCTGGTGGTACCAGCCTGCAAGGCTGTCAGGACACTGTGAGAGTCGGGACCACTTAAACTGTGCCTTTTCTCAAGATAGCACCTGGAGGGCTGCTCCCACCCAAGGTGCTCCTGGCCCCGAGCCTGCAGAAGTCTCTCTCCTCTACTTGGGGGATATGGAGATCTCAGAAGAGGCCACATTGGTGGAACTGAAGTCTCAGGCCTTGGCCTTGCCTTCTGTTTCGAAGCTCGCTGTCCAGTCCACAGCCCTGCTCAGAGTCTGGACAGTGGAGAGCAAGCGCCCCAGCAGACTCTTGCGCACTAACTGGCGGCAGCTCAAGAGAGATTTGGCACTTAAGGAAAATGGATTGGTGCTATGA
Peptide sequence:
MDWCYEAGEPLCEEDATLKELMIRSGDTLLLTEGKLPPPGHLKMPIWWYQPARLSGHCESRDHLNCAFSQDSTWRAAPTQGAPGPEPAEVSLLYLGDMEISEEATLVELKSQALALPSVSKLAVQSTALLRVWTVESKRPSRLLRTNWRQLKRDLALKENGLVL
IRESfinder result
IRESfinder score
0.590151518
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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