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mmu_circUsp9x_1070
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp9x_1070
mm39_Chr. Position ID:
chrX|13017508|13022986|+
Gene name:
Usp9x
Transcript:
ENSMUST00000089302.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
33,34,35
Exon/intron offsets:
0,2822,4724
Genomic length:
5478
Exon/intron sizes in nt:
17,41,42,754
Flanking exon/introns:
chrX:13014374-13017508|chrX:13022986-13023907
Splice length:
1070
Other database IDs:
circAtlas: mmu-Usp9x_0058
circAtlas: hsa-USP9X_0085, CIRCpedia: HSA_CIRCpedia_126264
Human Ortholog IDs:
Mature spliced Sequence:
GCTTTGGGGTGAGCCTGTCAATCTTCGTGAACAACATGATGCTTTAGAGTTCTTTAATTCTTTGGTGGATAGTTTAGATGAAGCTTTAAAAGCCTTAGGGCATCCAGCTATGCTAAGTAAAGTCTTGGGAGGTTCCTTTGCTGATCAGAAAATTTGCCAAGGCTGCCCACATAGGTACGAATGTGAAGAATCTTTTACGACTCTGAATGTAGACATTAGAAACCACCAAAATCTTCTGGATTCTTTGGAACAGTATGTCAAAGGAGACTTACTAGAAGGAGCAAATGCTTATCATTGTGAAAAATGCAATAAAAAGGTTGATACTGTAAAGCGCTTGCTAATTAAAAAATTGCCTCCTGTTCTTGCTATCCAACTAAAACGATTCGATTATGACTGGGAAAGAGAATGTGCAATCAAGTTCAATGATTACTTTGAATTTCCTCGAGAGTTAGACATGGAACCTTACACAGTGGCAGGTGTTGCTAAACTGGAGGGAGATAATGTCAACCCAGAAAGTCAGCTGATACAACAGAATGAGCAGTCTGAAAGCGAGAAAGCAGGAAGCACAAAATACAGACTTGTGGGTGTGCTTGTGCACAGTGGTCAAGCAAGTGGCGGACATTACTATTCTTACATCATTCAGAGGAATGGAGGGGATGGTGAAAAAAATCGTTGGTATAAATTTGATGATGGAGATGTAACGGAATGTAAAATGGATGACGATGAAGAAATGAAAAACCAGTGTTTTGGGGGAGAGTACATGGGAGAAGTATTTGATCACATGATGAAGCGCATGTCGTACAGGCGTCAGAAAAGATGGTGGAATGCATATATACTTTTTTATGAACGAATGGACACAATAGGTCATGATGATGAGGTGATAAGATACATATCAGAGATTGCTATCACCACAAGGCCCCATCAGATTGTCATGCCATCCGCCATTGAAAGAAGTGTTCGGAAGCAGAATGTTCAGTTCATGCACAACCGAATGCAGTACAGTCTGGAATATTTTCAGTTTATGAAAAAGCTACTGACATGTAATGGTGTTTACTTAAACCCTCCTCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTTCATGCACAACCGAATGC
60.07
AAGCATCATGTTGTTCACGAAGA
59.19
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTTCAGTTCATGCACAACCGA
59.4
AGCATCATGTTGTTCACGAAGA
58.6
143
PCR template sequence:
GTTCAGTTCATGCACAACCGAATGCAGTACAGTCTGGAATATTTTCAGTTTATGAAAAAGCTACTGACATGTAATGGTGTTTACTTAAACCCTCCTCCAGGCTTTGGGGTGAGCCTGTCAATCTTCGTGAACAACATGATGCTTTAGAGTTCTTTAATTCTTTGGTGGATAGTTTAGATGAAGCTTTAAAAGCCTTAGGG
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-32-5p(1), mmu-miR-181a-5p(1), mmu-miR-150-5p(1), mmu-miR-30e-5p(1), mmu-miR-29b-3p(1), mmu-miR-30a-5p(1), mmu-miR-30c-5p(1), mmu-miR-25-3p(1), mmu-miR-30b-5p(1), mmu-miR-136-5p(1), mmu-miR-363-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-190b-5p(1), mmu-miR-207(1), mmu-miR-335-3p(1), mmu-miR-484(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AACCCTCCTCCAGGCTTTGGGGTGAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP9X_1070_ORF_1
0.9825
0.128096811
0.987026234
1008
ORF sequence:
ATGCTAAGTAAAGTCTTGGGAGGTTCCTTTGCTGATCAGAAAATTTGCCAAGGCTGCCCACATAGGTACGAATGTGAAGAATCTTTTACGACTCTGAATGTAGACATTAGAAACCACCAAAATCTTCTGGATTCTTTGGAACAGTATGTCAAAGGAGACTTACTAGAAGGAGCAAATGCTTATCATTGTGAAAAATGCAATAAAAAGGTTGATACTGTAAAGCGCTTGCTAATTAAAAAATTGCCTCCTGTTCTTGCTATCCAACTAAAACGATTCGATTATGACTGGGAAAGAGAATGTGCAATCAAGTTCAATGATTACTTTGAATTTCCTCGAGAGTTAGACATGGAACCTTACACAGTGGCAGGTGTTGCTAAACTGGAGGGAGATAATGTCAACCCAGAAAGTCAGCTGATACAACAGAATGAGCAGTCTGAAAGCGAGAAAGCAGGAAGCACAAAATACAGACTTGTGGGTGTGCTTGTGCACAGTGGTCAAGCAAGTGGCGGACATTACTATTCTTACATCATTCAGAGGAATGGAGGGGATGGTGAAAAAAATCGTTGGTATAAATTTGATGATGGAGATGTAACGGAATGTAAAATGGATGACGATGAAGAAATGAAAAACCAGTGTTTTGGGGGAGAGTACATGGGAGAAGTATTTGATCACATGATGAAGCGCATGTCGTACAGGCGTCAGAAAAGATGGTGGAATGCATATATACTTTTTTATGAACGAATGGACACAATAGGTCATGATGATGAGGTGATAAGATACATATCAGAGATTGCTATCACCACAAGGCCCCATCAGATTGTCATGCCATCCGCCATTGAAAGAAGTGTTCGGAAGCAGAATGTTCAGTTCATGCACAACCGAATGCAGTACAGTCTGGAATATTTTCAGTTTATGAAAAAGCTACTGACATGTAATGGTGTTTACTTAAACCCTCCTCCAGGCTTTGGGGTGAGCCTGTCAATCTTCGTGAACAACATGATGCTTTAG
Peptide sequence:
MLSKVLGGSFADQKICQGCPHRYECEESFTTLNVDIRNHQNLLDSLEQYVKGDLLEGANAYHCEKCNKKVDTVKRLLIKKLPPVLAIQLKRFDYDWERECAIKFNDYFEFPRELDMEPYTVAGVAKLEGDNVNPESQLIQQNEQSESEKAGSTKYRLVGVLVHSGQASGGHYYSYIIQRNGGDGEKNRWYKFDDGDVTECKMDDDEEMKNQCFGGEYMGEVFDHMMKRMSYRRQKRWWNAYILFYERMDTIGHDDEVIRYISEIAITTRPHQIVMPSAIERSVRKQNVQFMHNRMQYSLEYFQFMKKLLTCNGVYLNPPPGFGVSLSIFVNNMML
IRESfinder result
IRESfinder score
0.518527708
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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