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mmu_circUsp16_990
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp16_990
mm39_Chr. Position ID:
chr16|87272304|87277857|+
Gene name:
Usp16
Transcript:
ENSMUST00000026710.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
12,13,14,15
Exon/intron offsets:
0,1297,3709,5458
Genomic length:
5553
Exon/intron sizes in nt:
57,174,664,95
Flanking exon/introns:
chr16:87271561-87272304|chr16:87277857-87278601
Splice length:
990
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_168590
Human Ortholog IDs:
Mature spliced Sequence:
GTCTCCTTAGTGCATGAATCGTTCCTTGATTTGTCTCTTCCAGTTTTAGATGATCAGAGTGGTAAGAAAAGTATAAATGATAAAAATGTGAAAATGACAATGGAGGAAGAAGATAAAGACAGTGAGGAAGAGAAAGATGACAGCTACATGAAATCAAGGAGCGATCTTCCGTCAGGGACAAGCAAGCACCTACAGAAAAAGGCAAAGAAGCAGGCCAAAAAGCAGGCCAAGAACCAACGAAGGCAACAAAAAATTCAAGAAAGATTTCTTCACTTCAATGAGCTCTGCGCCACTGACTACACGGAAGACAATGAACGTGAAGCTGACACAGCACTTGCGGGAGAAGTGGAAGTGGATACCGACTCCACCCATGGTTCTCAAGAGGAGGCCACACAGATAGAGCTGTCTGTTAACCAGAAGGATTTGGATGGCCAAGAGAGCATGATAGAAAGGACACCTGATGTGCAGGAAAGCCCAGAGGACCTAGGAGTGAAAAGTGCTAACACCGAGAGTGATCTGGGGATTGTGACGCCTGCTCCTGAATGTCCTAGGGATTTCAATGGTGCCTTCCTGGAAGAAAGGACCAGTGGAGAACTAGACATTATCAATGGTTTAAAAAACCTTAATTTGAATGCTGCTGTTGATCCTGATGAAATAAATATAGAGATTCCGAATGACAGTCATTCTGCACCCAAGGTATATGAGGTCATGAACGAGGACCCAGAAACTGCTTTCTGTACCCTCGCGAACCGAGAAGCGTTTAGTACTGATGAGTGTTCCATTCAACATTGCTTATATCAGTTCACCCGGAATGAGAAACTTCAAGATGCCAATAAACTGCTTTGTGAAGTGTGTTCAAGACGGCAGTGTAATGGACCAAAGGCAAATATAAAAGGTGACAGGAGACATGTTTACACCAATGCCAAGAAGCAGATGCTGGTCTCCCTCGCGCCTCCTGTCCTCACTCTGCATTTAAAGCGATTCCAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGGTGACAGGAGACATGTT
56.37
TGGAAGAGACAAATCAAGGAACG
58.93
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAAGGTGACAGGAGACATGT
56.37
TGGAAGAGACAAATCAAGGAACG
58.93
141
PCR template sequence:
AAAAGGTGACAGGAGACATGTTTACACCAATGCCAAGAAGCAGATGCTGGTCTCCCTCGCGCCTCCTGTCCTCACTCTGCATTTAAAGCGATTCCAGCAGGTCTCCTTAGTGCATGAATCGTTCCTTGATTTGTCTCTTCCAGTTTTAGATGATCAGAGTGGTAAGAAAAGTATAAATGATAAAAATGTGAAAATGACAA
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-124-3p(1), mmu-miR-9-5p(1), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-30a-5p(1), mmu-miR-30c-5p(1), mmu-miR-326-3p(1), mmu-miR-30b-5p(1), mmu-miR-136-5p(1), mmu-miR-532-5p(1), mmu-miR-350-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCGATTCCAGCAGGTCTCCTTAGTGC
siRNA sets
ACTAAGGAGACCTGCTGGA, CACTAAGGAGACCTGCTGG, TAAGGAGACCTGCTGGAAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP16_990_ORF_1
1.1304
0.246378964
0.999989215
1887
ORF sequence:
ATGACAATGGAGGAAGAAGATAAAGACAGTGAGGAAGAGAAAGATGACAGCTACATGAAATCAAGGAGCGATCTTCCGTCAGGGACAAGCAAGCACCTACAGAAAAAGGCAAAGAAGCAGGCCAAAAAGCAGGCCAAGAACCAACGAAGGCAACAAAAAATTCAAGAAAGATTTCTTCACTTCAATGAGCTCTGCGCCACTGACTACACGGAAGACAATGAACGTGAAGCTGACACAGCACTTGCGGGAGAAGTGGAAGTGGATACCGACTCCACCCATGGTTCTCAAGAGGAGGCCACACAGATAGAGCTGTCTGTTAACCAGAAGGATTTGGATGGCCAAGAGAGCATGATAGAAAGGACACCTGATGTGCAGGAAAGCCCAGAGGACCTAGGAGTGAAAAGTGCTAACACCGAGAGTGATCTGGGGATTGTGACGCCTGCTCCTGAATGTCCTAGGGATTTCAATGGTGCCTTCCTGGAAGAAAGGACCAGTGGAGAACTAGACATTATCAATGGTTTAAAAAACCTTAATTTGAATGCTGCTGTTGATCCTGATGAAATAAATATAGAGATTCCGAATGACAGTCATTCTGCACCCAAGGTATATGAGGTCATGAACGAGGACCCAGAAACTGCTTTCTGTACCCTCGCGAACCGAGAAGCGTTTAGTACTGATGAGTGTTCCATTCAACATTGCTTATATCAGTTCACCCGGAATGAGAAACTTCAAGATGCCAATAAACTGCTTTGTGAAGTGTGTTCAAGACGGCAGTGTAATGGACCAAAGGCAAATATAAAAGGTGACAGGAGACATGTTTACACCAATGCCAAGAAGCAGATGCTGGTCTCCCTCGCGCCTCCTGTCCTCACTCTGCATTTAAAGCGATTCCAGCAGGTCTCCTTAGTGCATGAATCGTTCCTTGATTTGTCTCTTCCAGTTTTAGATGATCAGAGTGGTAAGAAAAGTATAAATGATAAAAATGTGAAAATGACAATGGAGGAAGAAGATAAAGACAGTGAGGAAGAGAAAGATGACAGCTACATGAAATCAAGGAGCGATCTTCCGTCAGGGACAAGCAAGCACCTACAGAAAAAGGCAAAGAAGCAGGCCAAAAAGCAGGCCAAGAACCAACGAAGGCAACAAAAAATTCAAGAAAGATTTCTTCACTTCAATGAGCTCTGCGCCACTGACTACACGGAAGACAATGAACGTGAAGCTGACACAGCACTTGCGGGAGAAGTGGAAGTGGATACCGACTCCACCCATGGTTCTCAAGAGGAGGCCACACAGATAGAGCTGTCTGTTAACCAGAAGGATTTGGATGGCCAAGAGAGCATGATAGAAAGGACACCTGATGTGCAGGAAAGCCCAGAGGACCTAGGAGTGAAAAGTGCTAACACCGAGAGTGATCTGGGGATTGTGACGCCTGCTCCTGAATGTCCTAGGGATTTCAATGGTGCCTTCCTGGAAGAAAGGACCAGTGGAGAACTAGACATTATCAATGGTTTAAAAAACCTTAATTTGAATGCTGCTGTTGATCCTGATGAAATAAATATAGAGATTCCGAATGACAGTCATTCTGCACCCAAGGTATATGAGGTCATGAACGAGGACCCAGAAACTGCTTTCTGTACCCTCGCGAACCGAGAAGCGTTTAGTACTGATGAGTGTTCCATTCAACATTGCTTATATCAGTTCACCCGGAATGAGAAACTTCAAGATGCCAATAAACTGCTTTGTGAAGTGTGTTCAAGACGGCAGTGTAATGGACCAAAGGCAAATATAAAAGGTGACAGGAGACATGTTTACACCAATGCCAAGAAGCAGATGCTGGTCTCCCTCGCGCCTCCTGTCCTCACTCTGCATTTAAAGCGATTCCAGCAG
Peptide sequence:
MTMEEEDKDSEEEKDDSYMKSRSDLPSGTSKHLQKKAKKQAKKQAKNQRRQQKIQERFLHFNELCATDYTEDNEREADTALAGEVEVDTDSTHGSQEEATQIELSVNQKDLDGQESMIERTPDVQESPEDLGVKSANTESDLGIVTPAPECPRDFNGAFLEERTSGELDIINGLKNLNLNAAVDPDEINIEIPNDSHSAPKVYEVMNEDPETAFCTLANREAFSTDECSIQHCLYQFTRNEKLQDANKLLCEVCSRRQCNGPKANIKGDRRHVYTNAKKQMLVSLAPPVLTLHLKRFQQVSLVHESFLDLSLPVLDDQSGKKSINDKNVKMTMEEEDKDSEEEKDDSYMKSRSDLPSGTSKHLQKKAKKQAKKQAKNQRRQQKIQERFLHFNELCATDYTEDNEREADTALAGEVEVDTDSTHGSQEEATQIELSVNQKDLDGQESMIERTPDVQESPEDLGVKSANTESDLGIVTPAPECPRDFNGAFLEERTSGELDIINGLKNLNLNAAVDPDEINIEIPNDSHSAPKVYEVMNEDPETAFCTLANREAFSTDECSIQHCLYQFTRNEKLQDANKLLCEVCSRRQCNGPKANIKGDRRHVYTNAKKQMLVSLAPPVLTLHLKRFQQ
IRESfinder result
IRESfinder score
0.461211773
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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