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mmu_circUsp9x_480_1
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp9x_480_1
mm39_Chr. Position ID:
chrX|12960162|12966751|+
Gene name:
Usp9x
Transcript:
ENSMUST00000169594.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
3,4,5
Exon/intron offsets:
0,4526,6509
Genomic length:
6589
Exon/intron sizes in nt:
254,146,80
Flanking exon/introns:
chrX:12938564-12960162|chrX:12966751-12969566
Splice length:
480
Other database IDs:
CIRCpedia: MMU_CIRCpedia_7628, circAtlas: mmu-Usp9x_0004
circAtlas: hsa-USP9X_0009, CIRCpedia: HSA_CIRCpedia_65803
Human Ortholog IDs:
Mature spliced Sequence:
GTTATGCAATGGTCTCTGCAAGATGTTTTATTCTTGAATTGGAACCTTTTACGACTGACAAATGCTGGTACTTTATCTCCTATAAGTGGACTATAATTTCTTTTCTTAAGACAACTACATAAGCAGACAAAATTGCAAAGATCTGCCCTGTGTCGAGTATGACAGCCACGACTCGTGGCTCTCCAGTTGGAGGGAATGACAACCAGGGCCAAGCCCCTGATGGACAGTCTCAGCCCCCCCTCCAACAGAATCAGACTTCATCGCCTGATTCGTCCAATGAAAATTCCCCTGCAACTCCTCCTGATGAGCAAGGTCAAGGTGATGCTCCTCCACAGATTGAAGATGAGGAACCTGCATTTCCACACACTGACTTGGCAAAGTTAGATGATATGATCAACAGGCCTCGATGGGTTGTTCCAGTTTTGCCGAAAGGGGAATTAGAAGTGCTTTTAGAAGCTGCTATTGATCTTAGTAAGAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGATCAACAGGCCTCGATGG
59.82
AGTACCAGCATTTGTCAGTCGT
59.96
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGTTGTTCCAGTTTTGCCG
60.25
AGTACCAGCATTTGTCAGTCGT
59.96
144
PCR template sequence:
TTAGATGATATGATCAACAGGCCTCGATGGGTTGTTCCAGTTTTGCCGAAAGGGGAATTAGAAGTGCTTTTAGAAGCTGCTATTGATCTTAGTAAGAAAGGTTATGCAATGGTCTCTGCAAGATGTTTTATTCTTGAATTGGAACCTTTTACGACTGACAAATGCTGGTACTTTATCTCCTATAAGTGGACTATAATTTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-328-3p(1), mmu-miR-3105-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTTAGTAAGAAAGGTTATGCAATGGT
siRNA sets
TTGCATAACCTTTCTTACT, ATTGCATAACCTTTCTTAC, CATAACCTTTCTTACTAAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP9X_480_1_ORF_1
1.0803
0.057554909
0.545572607
444
ORF sequence:
ATGACAGCCACGACTCGTGGCTCTCCAGTTGGAGGGAATGACAACCAGGGCCAAGCCCCTGATGGACAGTCTCAGCCCCCCCTCCAACAGAATCAGACTTCATCGCCTGATTCGTCCAATGAAAATTCCCCTGCAACTCCTCCTGATGAGCAAGGTCAAGGTGATGCTCCTCCACAGATTGAAGATGAGGAACCTGCATTTCCACACACTGACTTGGCAAAGTTAGATGATATGATCAACAGGCCTCGATGGGTTGTTCCAGTTTTGCCGAAAGGGGAATTAGAAGTGCTTTTAGAAGCTGCTATTGATCTTAGTAAGAAAGGTTATGCAATGGTCTCTGCAAGATGTTTTATTCTTGAATTGGAACCTTTTACGACTGACAAATGCTGGTACTTTATCTCCTATAAGTGGACTATAATTTCTTTTCTTAAGACAACTACATAA
Peptide sequence:
MTATTRGSPVGGNDNQGQAPDGQSQPPLQQNQTSSPDSSNENSPATPPDEQGQGDAPPQIEDEEPAFPHTDLAKLDDMINRPRWVVPVLPKGELEVLLEAAIDLSKKGYAMVSARCFILELEPFTTDKCWYFISYKWTIISFLKTTT
IRESfinder result
IRESfinder score
0.574995042
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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