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mmu_circUsp9x_1246
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp9x_1246
mm39_Chr. Position ID:
chrX|13020330|13025183|+
Gene name:
Usp9x
Transcript:
ENSMUST00000089302.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
34,35,36,37
Exon/intron offsets:
0,1902,3577,4627
Genomic length:
4853
Exon/intron sizes in nt:
1,42,75,41,24,226
Flanking exon/introns:
chrX:13017682-13020330|chrX:13025183-13026012
Splice length:
1246
Other database IDs:
CIRCpedia: MMU_CIRCpedia_7717, circAtlas: mmu-Usp9x_0073
Human Ortholog IDs:
Mature spliced Sequence:
GTACGAATGTGAAGAATCTTTTACGACTCTGAATGTAGACATTAGAAACCACCAAAATCTTCTGGATTCTTTGGAACAGTATGTCAAAGGAGACTTACTAGAAGGAGCAAATGCTTATCATTGTGAAAAATGCAATAAAAAGGTTGATACTGTAAAGCGCTTGCTAATTAAAAAATTGCCTCCTGTTCTTGCTATCCAACTAAAACGATTCGATTATGACTGGGAAAGAGAATGTGCAATCAAGTTCAATGATTACTTTGAATTTCCTCGAGAGTTAGACATGGAACCTTACACAGTGGCAGGTGTTGCTAAACTGGAGGGAGATAATGTCAACCCAGAAAGTCAGCTGATACAACAGAATGAGCAGTCTGAAAGCGAGAAAGCAGGAAGCACAAAATACAGACTTGTGGGTGTGCTTGTGCACAGTGGTCAAGCAAGTGGCGGACATTACTATTCTTACATCATTCAGAGGAATGGAGGGGATGGTGAAAAAAATCGTTGGTATAAATTTGATGATGGAGATGTAACGGAATGTAAAATGGATGACGATGAAGAAATGAAAAACCAGTGTTTTGGGGGAGAGTACATGGGAGAAGTATTTGATCACATGATGAAGCGCATGTCGTACAGGCGTCAGAAAAGATGGTGGAATGCATATATACTTTTTTATGAACGAATGGACACAATAGGTCATGATGATGAGGTGATAAGATACATATCAGAGATTGCTATCACCACAAGGCCCCATCAGATTGTCATGCCATCCGCCATTGAAAGAAGTGTTCGGAAGCAGAATGTTCAGTTCATGCACAACCGAATGCAGTACAGTCTGGAATATTTTCAGTTTATGAAAAAGCTACTGACATGTAATGGTGTTTACTTAAACCCTCCTCCAGGGCAAGATCACCTGTCTCCTGAAGCAGAAGAAATCACTATGATTAGTATTCAGCTTGCTGCTAGGTTCCTTTTTACTACAGGATTTCACACAAAGAAAATAGTCCGAGGATCTGCCAGTGATTGGTATGATGCATTGTGTATTCTCCTGCGTCACAGCAAGAACGTGCGGTTTTGGTTTGCTCACAATGTCCTTTTTAATGTTTCAAATCGATTCTCTGAGTACCTTTTGGAATGCCCTAGTGCAGAAGTGAGAGGTGCATTTGCAAAGCTCATAGTTTTCATTGCACATTTTTCCTTACAAGACGGGCCTTGTCCTTCACCTTTTGCATCTCCTGGACCTTCTAGTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGGCCTTGTCCTTCACCTTT
60.18
AGTCTCCTTTGACATACTGTTCCA
59.41
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTTACAAGACGGGCCTTG
59.68
AGTCTCCTTTGACATACTGTTCCA
59.41
152
PCR template sequence:
GAGAGGTGCATTTGCAAAGCTCATAGTTTTCATTGCACATTTTTCCTTACAAGACGGGCCTTGTCCTTCACCTTTTGCATCTCCTGGACCTTCTAGTCAGGTACGAATGTGAAGAATCTTTTACGACTCTGAATGTAGACATTAGAAACCACCAAAATCTTCTGGATTCTTTGGAACAGTATGTCAAAGGAGACTTACTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
18
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-32-5p(1), mmu-miR-181a-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-494-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-190b-5p(1), mmu-miR-207(1), mmu-miR-335-3p(1), mmu-miR-1904(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACCTTCTAGTCAGGTACGAATGTGAA
siRNA sets
TTCACATTCGTACCTGACT,TTCGTACCTGACTAGAAGG,ATTCGTACCTGACTAGAAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP9X_1246_ORF_1
0.9158
0.082670417
0.978060492
978
ORF sequence:
ATGGAACCTTACACAGTGGCAGGTGTTGCTAAACTGGAGGGAGATAATGTCAACCCAGAAAGTCAGCTGATACAACAGAATGAGCAGTCTGAAAGCGAGAAAGCAGGAAGCACAAAATACAGACTTGTGGGTGTGCTTGTGCACAGTGGTCAAGCAAGTGGCGGACATTACTATTCTTACATCATTCAGAGGAATGGAGGGGATGGTGAAAAAAATCGTTGGTATAAATTTGATGATGGAGATGTAACGGAATGTAAAATGGATGACGATGAAGAAATGAAAAACCAGTGTTTTGGGGGAGAGTACATGGGAGAAGTATTTGATCACATGATGAAGCGCATGTCGTACAGGCGTCAGAAAAGATGGTGGAATGCATATATACTTTTTTATGAACGAATGGACACAATAGGTCATGATGATGAGGTGATAAGATACATATCAGAGATTGCTATCACCACAAGGCCCCATCAGATTGTCATGCCATCCGCCATTGAAAGAAGTGTTCGGAAGCAGAATGTTCAGTTCATGCACAACCGAATGCAGTACAGTCTGGAATATTTTCAGTTTATGAAAAAGCTACTGACATGTAATGGTGTTTACTTAAACCCTCCTCCAGGGCAAGATCACCTGTCTCCTGAAGCAGAAGAAATCACTATGATTAGTATTCAGCTTGCTGCTAGGTTCCTTTTTACTACAGGATTTCACACAAAGAAAATAGTCCGAGGATCTGCCAGTGATTGGTATGATGCATTGTGTATTCTCCTGCGTCACAGCAAGAACGTGCGGTTTTGGTTTGCTCACAATGTCCTTTTTAATGTTTCAAATCGATTCTCTGAGTACCTTTTGGAATGCCCTAGTGCAGAAGTGAGAGGTGCATTTGCAAAGCTCATAGTTTTCATTGCACATTTTTCCTTACAAGACGGGCCTTGTCCTTCACCTTTTGCATCTCCTGGACCTTCTAGTCAGGTACGAATGTGA
Peptide sequence:
MEPYTVAGVAKLEGDNVNPESQLIQQNEQSESEKAGSTKYRLVGVLVHSGQASGGHYYSYIIQRNGGDGEKNRWYKFDDGDVTECKMDDDEEMKNQCFGGEYMGEVFDHMMKRMSYRRQKRWWNAYILFYERMDTIGHDDEVIRYISEIAITTRPHQIVMPSAIERSVRKQNVQFMHNRMQYSLEYFQFMKKLLTCNGVYLNPPPGQDHLSPEAEEITMISIQLAARFLFTTGFHTKKIVRGSASDWYDALCILLRHSKNVRFWFAHNVLFNVSNRFSEYLLECPSAEVRGAFAKLIVFIAHFSLQDGPCPSPFASPGPSSQVRM
IRESfinder result
IRESfinder score
0.559469437
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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