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mmu_circUsp40_767
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp40_767
mm39_Chr. Position ID:
chr1|87921895|87932036|-
Gene name:
Usp40
Transcript:
ENSMUST00000040783.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
8,7,6,5,4,3
Exon/intron offsets:
0,1537,3639,5566,8235,10073
Genomic length:
10141
Exon/intron sizes in nt:
129,144,147,165,114,68
Flanking exon/introns:
chr1:87917879-87921895|chr1:87932036-87934946
Splice length:
767
Other database IDs:
circAtlas: mmu-Usp40_0026
Human Ortholog IDs:
Mature spliced Sequence:
AAGCTTTATTTTCTCTTGGTCCGGAAGAGCTGGGTTCTTTAGAGGATAAAGATAAACCTGATGCAAAGGTTCGGATCATACCTTTGCAGTTGCAGCGCTTGTTTGCCCAGCTTCTGCTCTTGGACCAGGAGGCTGCATCTACCATAGACCTCACCGACAGCTTCGGGTGGACCAACGATGAGGAAATGAGGCAACATGATGTGCAGGAACTCAACCGAATTCTCTTCAGTGCTTTGGAAACTTCTTTAGTTGGGACCTCTGGCCATGACCTCATTCATCGTCTATACCATGGCACCATTGTGAACCAGATTGTTTGCAAAGAGTGTAAGAACATCAGTGAGAGGCAGGAAGACTTCTTGGATTTGACAGTAGCAGTCAAAAATGTATCTGGTTTAGAAGATGAACTCTGCAACATGTATGTGGAGGAAGAAATTTTTGACTATGACAACCTGTACCACTGTGGAACCTGTGACCGACTGGTTAAAGCAGCAAAGTCTGCCAAATTGCGTAAGCTGCCTCCTTTTCTTACTATTTCATTACTAAGATTTAATTTTGATTTTGTGAAATGTGAACGCTACAAGGATACTAGCTGTTATACATTCCCCCTCCGGATCAATCTCAAGCCTTTCTGTGAACAGAGTGAACTGGATGACATGGAATATATGTATGACCTCTTCTCCGTCATTATCCACAAAGGTGGCTGCTATGGAGGTCATTACCATGTGTACATTAAAGATGTTGATCATCTTGGCAACTGGCAATGTCAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAAGGTGGCTGCTATGGAGG
59.74
GATCCGAACCTTTGCATCAGG
59.33
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAAGGTGGCTGCTATGGAGG
59.74
ATCCGAACCTTTGCATCAGG
58.24
151
PCR template sequence:
TGACCTCTTCTCCGTCATTATCCACAAAGGTGGCTGCTATGGAGGTCATTACCATGTGTACATTAAAGATGTTGATCATCTTGGCAACTGGCAATGTCAAAAGCTTTATTTTCTCTTGGTCCGGAAGAGCTGGGTTCTTTAGAGGATAAAGATAAACCTGATGCAAAGGTTCGGATCATACCTTTGCAGTTGCAGCGCTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(1), mmu-miR-1a-3p(1), mmu-miR-206-3p(1), mmu-miR-23a-3p(1), mmu-miR-128-3p(1), mmu-miR-3470b(1)
siRNAs for circular RNA silencing
Junction sequence
CTGGCAATGTCAAAAGCTTTATTTTC
siRNA sets
ATAAAGCTTTTGACATTGC, AATAAAGCTTTTGACATTG, GAAAATAAAGCTTTTGACA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP40_767_ORF_1
1.0376
0.201642596
0.955232351
774
ORF sequence:
ATGTCAAAAGCTTTATTTTCTCTTGGTCCGGAAGAGCTGGGTTCTTTAGAGGATAAAGATAAACCTGATGCAAAGGTTCGGATCATACCTTTGCAGTTGCAGCGCTTGTTTGCCCAGCTTCTGCTCTTGGACCAGGAGGCTGCATCTACCATAGACCTCACCGACAGCTTCGGGTGGACCAACGATGAGGAAATGAGGCAACATGATGTGCAGGAACTCAACCGAATTCTCTTCAGTGCTTTGGAAACTTCTTTAGTTGGGACCTCTGGCCATGACCTCATTCATCGTCTATACCATGGCACCATTGTGAACCAGATTGTTTGCAAAGAGTGTAAGAACATCAGTGAGAGGCAGGAAGACTTCTTGGATTTGACAGTAGCAGTCAAAAATGTATCTGGTTTAGAAGATGAACTCTGCAACATGTATGTGGAGGAAGAAATTTTTGACTATGACAACCTGTACCACTGTGGAACCTGTGACCGACTGGTTAAAGCAGCAAAGTCTGCCAAATTGCGTAAGCTGCCTCCTTTTCTTACTATTTCATTACTAAGATTTAATTTTGATTTTGTGAAATGTGAACGCTACAAGGATACTAGCTGTTATACATTCCCCCTCCGGATCAATCTCAAGCCTTTCTGTGAACAGAGTGAACTGGATGACATGGAATATATGTATGACCTCTTCTCCGTCATTATCCACAAAGGTGGCTGCTATGGAGGTCATTACCATGTGTACATTAAAGATGTTGATCATCTTGGCAACTGGCAATGTCAA
Peptide sequence:
MSKALFSLGPEELGSLEDKDKPDAKVRIIPLQLQRLFAQLLLLDQEAASTIDLTDSFGWTNDEEMRQHDVQELNRILFSALETSLVGTSGHDLIHRLYHGTIVNQIVCKECKNISERQEDFLDLTVAVKNVSGLEDELCNMYVEEEIFDYDNLYHCGTCDRLVKAAKSAKLRKLPPFLTISLLRFNFDFVKCERYKDTSCYTFPLRINLKPFCEQSELDDMEYMYDLFSVIIHKGGCYGGHYHVYIKDVDHLGNWQCQ
IRESfinder result
IRESfinder score
0.588747824
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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