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mmu_circUsp40_1611
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp40_1611
mm39_Chr. Position ID:
chr1|87907736|87930244|-
Gene name:
Usp40
Transcript:
ENSMUST00000040783.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
15,14,13,12,11,10,9,8,7,6,5,4
Exon/intron offsets:
0,956,1994,3739,5887,8870,10047,14159,15696,17798,19725,22394
Genomic length:
22508
Exon/intron sizes in nt:
7,18,51,72,82,29,81,08,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr1:87906355-87907736|chr1:87930244-87931968
Splice length:
1611
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTTCGGATCATACCTTTGCAGTTGCAGCGCTTGTTTGCCCAGCTTCTGCTCTTGGACCAGGAGGCTGCATCTACCATAGACCTCACCGACAGCTTCGGGTGGACCAACGATGAGGAAATGAGGCAACATGATGTGCAGGAACTCAACCGAATTCTCTTCAGTGCTTTGGAAACTTCTTTAGTTGGGACCTCTGGCCATGACCTCATTCATCGTCTATACCATGGCACCATTGTGAACCAGATTGTTTGCAAAGAGTGTAAGAACATCAGTGAGAGGCAGGAAGACTTCTTGGATTTGACAGTAGCAGTCAAAAATGTATCTGGTTTAGAAGATGAACTCTGCAACATGTATGTGGAGGAAGAAATTTTTGACTATGACAACCTGTACCACTGTGGAACCTGTGACCGACTGGTTAAAGCAGCAAAGTCTGCCAAATTGCGTAAGCTGCCTCCTTTTCTTACTATTTCATTACTAAGATTTAATTTTGATTTTGTGAAATGTGAACGCTACAAGGATACTAGCTGTTATACATTCCCCCTCCGGATCAATCTCAAGCCTTTCTGTGAACAGAGTGAACTGGATGACATGGAATATATGTATGACCTCTTCTCCGTCATTATCCACAAAGGTGGCTGCTATGGAGGTCATTACCATGTGTACATTAAAGATGTTGATCATCTTGGCAACTGGCAATGTCAAGAGGAGATAAGTGATACAAATGTGAATGTGAAAGCTCCTCAGAGTGAAGAAGAGGCTAATGATCCATTGGTGGTTCTAAAAACAATCTTATTGCAGGAGGAGGCCAATCAAATTCCTGTTGATCAACTGGGCCAGAAACTCTTGAAAAAAACAGGAATATCTTGGAACAAGAAGTACAGGAAACAGCATGGACCACTGCGAAAGTTCTTACAGCTCCATCCTCAGATATTTCTGCTCAGCACAGATGAAAGTACAGTTAGTCTCCTGAGGAACCATCTTACCCAGGCCCCATCTGACCTACAGAGCTGTGAACAGATTCTACATACACTTGCTTCAGAATCCCCAGGCTTGAATGATGACACCAGTTGCCCACACTGGTTTGATATCAATGATTCCAAAGTCCATCCAATCAGAGAGAAAGATATCACACAGCAGTTCCAGGGTAAAGAAAGTGCCTACATGCTGTTTTATCGGAAAGCCACGTTACAAAGGCCCCCTGAAGCTCGAGCCAATCCAAGATACAGAGTTCCATGTCACTTGCTGAAGGAAATGGATGCAGCCAACATTCTACTGCAGATGAGAAGGGCAGAATGTGACTCTGCAAACAGTACTTTTGAGTTGCATCTTCATTTGGGTCCTCACTACCGTTTCTTCAATGGGGCTCTTCACCCTGCAGTCTCTGAGACAGAAAGCGTGTGGGACTTAACGTTTGATAAAAGAAAAACTTTAGGAGATCTCCGTCAGTCAATATTTCAGCTATTGGAATGTTGGGAAGGAGACATGGTTCTTAGTGTTGCGAAGCGTGTGCCAGCAGGACTTCATGTGTACCACACCCTCGATGGAGATGACTTGACACTGTGTGAAGCTGAGGTTGCTGATGGGGAAGACATCTTTGTATGGAATGGGGTAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCACACCCTCGATGGAGATG
59.89
GCTGTCGGTGAGGTCTATGG
59.9
178
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCACACCCTCGATGGAGATG
59.89
GTAGATGCAGCCTCCTGGTC
59.89
159
PCR template sequence:
AGGACTTCATGTGTACCACACCCTCGATGGAGATGACTTGACACTGTGTGAAGCTGAGGTTGCTGATGGGGAAGACATCTTTGTATGGAATGGGGTAGAGGTTCGGATCATACCTTTGCAGTTGCAGCGCTTGTTTGCCCAGCTTCTGCTCTTGGACCAGGAGGCTGCATCTACCATAGACCTCACCGACAGCTTCGGGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
17
Interacting miRNAs (#binding sites)
mmu-miR-128-3p(2), mmu-miR-23b-3p(1), mmu-miR-93-5p(1), mmu-miR-1a-3p(1), mmu-miR-206-3p(1), mmu-miR-184-3p(1), mmu-miR-23a-3p(1), mmu-miR-138-5p(1), mmu-miR-181b-5p(1), mmu-miR-24-3p(1), mmu-miR-541-5p(1), mmu-miR-297a-5p(1), mmu-miR-377-3p(1), mmu-miR-673-5p(1), mmu-miR-188-3p(1), mmu-miR-3470b(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GAATGGGGTAGAGGTTCGGATCATAC
siRNA sets
TATGATCCGAACCTCTACC, TGATCCGAACCTCTACCCC, GTATGATCCGAACCTCTAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP40_1611_ORF_1
1.0221
0.156544165
0.999999997
3105
ORF sequence:
ATGAGGCAACATGATGTGCAGGAACTCAACCGAATTCTCTTCAGTGCTTTGGAAACTTCTTTAGTTGGGACCTCTGGCCATGACCTCATTCATCGTCTATACCATGGCACCATTGTGAACCAGATTGTTTGCAAAGAGTGTAAGAACATCAGTGAGAGGCAGGAAGACTTCTTGGATTTGACAGTAGCAGTCAAAAATGTATCTGGTTTAGAAGATGAACTCTGCAACATGTATGTGGAGGAAGAAATTTTTGACTATGACAACCTGTACCACTGTGGAACCTGTGACCGACTGGTTAAAGCAGCAAAGTCTGCCAAATTGCGTAAGCTGCCTCCTTTTCTTACTATTTCATTACTAAGATTTAATTTTGATTTTGTGAAATGTGAACGCTACAAGGATACTAGCTGTTATACATTCCCCCTCCGGATCAATCTCAAGCCTTTCTGTGAACAGAGTGAACTGGATGACATGGAATATATGTATGACCTCTTCTCCGTCATTATCCACAAAGGTGGCTGCTATGGAGGTCATTACCATGTGTACATTAAAGATGTTGATCATCTTGGCAACTGGCAATGTCAAGAGGAGATAAGTGATACAAATGTGAATGTGAAAGCTCCTCAGAGTGAAGAAGAGGCTAATGATCCATTGGTGGTTCTAAAAACAATCTTATTGCAGGAGGAGGCCAATCAAATTCCTGTTGATCAACTGGGCCAGAAACTCTTGAAAAAAACAGGAATATCTTGGAACAAGAAGTACAGGAAACAGCATGGACCACTGCGAAAGTTCTTACAGCTCCATCCTCAGATATTTCTGCTCAGCACAGATGAAAGTACAGTTAGTCTCCTGAGGAACCATCTTACCCAGGCCCCATCTGACCTACAGAGCTGTGAACAGATTCTACATACACTTGCTTCAGAATCCCCAGGCTTGAATGATGACACCAGTTGCCCACACTGGTTTGATATCAATGATTCCAAAGTCCATCCAATCAGAGAGAAAGATATCACACAGCAGTTCCAGGGTAAAGAAAGTGCCTACATGCTGTTTTATCGGAAAGCCACGTTACAAAGGCCCCCTGAAGCTCGAGCCAATCCAAGATACAGAGTTCCATGTCACTTGCTGAAGGAAATGGATGCAGCCAACATTCTACTGCAGATGAGAAGGGCAGAATGTGACTCTGCAAACAGTACTTTTGAGTTGCATCTTCATTTGGGTCCTCACTACCGTTTCTTCAATGGGGCTCTTCACCCTGCAGTCTCTGAGACAGAAAGCGTGTGGGACTTAACGTTTGATAAAAGAAAAACTTTAGGAGATCTCCGTCAGTCAATATTTCAGCTATTGGAATGTTGGGAAGGAGACATGGTTCTTAGTGTTGCGAAGCGTGTGCCAGCAGGACTTCATGTGTACCACACCCTCGATGGAGATGACTTGACACTGTGTGAAGCTGAGGTTGCTGATGGGGAAGACATCTTTGTATGGAATGGGGTAGAGGTTCGGATCATACCTTTGCAGTTGCAGCGCTTGTTTGCCCAGCTTCTGCTCTTGGACCAGGAGGCTGCATCTACCATAGACCTCACCGACAGCTTCGGGTGGACCAACGATGAGGAAATGAGGCAACATGATGTGCAGGAACTCAACCGAATTCTCTTCAGTGCTTTGGAAACTTCTTTAGTTGGGACCTCTGGCCATGACCTCATTCATCGTCTATACCATGGCACCATTGTGAACCAGATTGTTTGCAAAGAGTGTAAGAACATCAGTGAGAGGCAGGAAGACTTCTTGGATTTGACAGTAGCAGTCAAAAATGTATCTGGTTTAGAAGATGAACTCTGCAACATGTATGTGGAGGAAGAAATTTTTGACTATGACAACCTGTACCACTGTGGAACCTGTGACCGACTGGTTAAAGCAGCAAAGTCTGCCAAATTGCGTAAGCTGCCTCCTTTTCTTACTATTTCATTACTAAGATTTAATTTTGATTTTGTGAAATGTGAACGCTACAAGGATACTAGCTGTTATACATTCCCCCTCCGGATCAATCTCAAGCCTTTCTGTGAACAGAGTGAACTGGATGACATGGAATATATGTATGACCTCTTCTCCGTCATTATCCACAAAGGTGGCTGCTATGGAGGTCATTACCATGTGTACATTAAAGATGTTGATCATCTTGGCAACTGGCAATGTCAAGAGGAGATAAGTGATACAAATGTGAATGTGAAAGCTCCTCAGAGTGAAGAAGAGGCTAATGATCCATTGGTGGTTCTAAAAACAATCTTATTGCAGGAGGAGGCCAATCAAATTCCTGTTGATCAACTGGGCCAGAAACTCTTGAAAAAAACAGGAATATCTTGGAACAAGAAGTACAGGAAACAGCATGGACCACTGCGAAAGTTCTTACAGCTCCATCCTCAGATATTTCTGCTCAGCACAGATGAAAGTACAGTTAGTCTCCTGAGGAACCATCTTACCCAGGCCCCATCTGACCTACAGAGCTGTGAACAGATTCTACATACACTTGCTTCAGAATCCCCAGGCTTGAATGATGACACCAGTTGCCCACACTGGTTTGATATCAATGATTCCAAAGTCCATCCAATCAGAGAGAAAGATATCACACAGCAGTTCCAGGGTAAAGAAAGTGCCTACATGCTGTTTTATCGGAAAGCCACGTTACAAAGGCCCCCTGAAGCTCGAGCCAATCCAAGATACAGAGTTCCATGTCACTTGCTGAAGGAAATGGATGCAGCCAACATTCTACTGCAGATGAGAAGGGCAGAATGTGACTCTGCAAACAGTACTTTTGAGTTGCATCTTCATTTGGGTCCTCACTACCGTTTCTTCAATGGGGCTCTTCACCCTGCAGTCTCTGAGACAGAAAGCGTGTGGGACTTAACGTTTGATAAAAGAAAAACTTTAGGAGATCTCCGTCAGTCAATATTTCAGCTATTGGAATGTTGGGAAGGAGACATGGTTCTTAGTGTTGCGAAGCGTGTGCCAGCAGGACTTCATGTGTACCACACCCTCGATGGAGATGACTTGACACTGTGTGAAGCTGAGGTTGCTGATGGGGAAGACATCTTTGTATGGAATGGGGTAGAG
Peptide sequence:
MRQHDVQELNRILFSALETSLVGTSGHDLIHRLYHGTIVNQIVCKECKNISERQEDFLDLTVAVKNVSGLEDELCNMYVEEEIFDYDNLYHCGTCDRLVKAAKSAKLRKLPPFLTISLLRFNFDFVKCERYKDTSCYTFPLRINLKPFCEQSELDDMEYMYDLFSVIIHKGGCYGGHYHVYIKDVDHLGNWQCQEEISDTNVNVKAPQSEEEANDPLVVLKTILLQEEANQIPVDQLGQKLLKKTGISWNKKYRKQHGPLRKFLQLHPQIFLLSTDESTVSLLRNHLTQAPSDLQSCEQILHTLASESPGLNDDTSCPHWFDINDSKVHPIREKDITQQFQGKESAYMLFYRKATLQRPPEARANPRYRVPCHLLKEMDAANILLQMRRAECDSANSTFELHLHLGPHYRFFNGALHPAVSETESVWDLTFDKRKTLGDLRQSIFQLLECWEGDMVLSVAKRVPAGLHVYHTLDGDDLTLCEAEVADGEDIFVWNGVEVRIIPLQLQRLFAQLLLLDQEAASTIDLTDSFGWTNDEEMRQHDVQELNRILFSALETSLVGTSGHDLIHRLYHGTIVNQIVCKECKNISERQEDFLDLTVAVKNVSGLEDELCNMYVEEEIFDYDNLYHCGTCDRLVKAAKSAKLRKLPPFLTISLLRFNFDFVKCERYKDTSCYTFPLRINLKPFCEQSELDDMEYMYDLFSVIIHKGGCYGGHYHVYIKDVDHLGNWQCQEEISDTNVNVKAPQSEEEANDPLVVLKTILLQEEANQIPVDQLGQKLLKKTGISWNKKYRKQHGPLRKFLQLHPQIFLLSTDESTVSLLRNHLTQAPSDLQSCEQILHTLASESPGLNDDTSCPHWFDINDSKVHPIREKDITQQFQGKESAYMLFYRKATLQRPPEARANPRYRVPCHLLKEMDAANILLQMRRAECDSANSTFELHLHLGPHYRFFNGALHPAVSETESVWDLTFDKRKTLGDLRQSIFQLLECWEGDMVLSVAKRVPAGLHVYHTLDGDDLTLCEAEVADGEDIFVWNGVE
IRESfinder result
IRESfinder score
0.597978243
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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