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mmu_ciUsp9x_804
Basic information of circular RNA
PanCircBase ID:
mmu_ciUsp9x_804
mm39_Chr. Position ID:
chrX|13026142|13026946|+
Gene name:
Usp9x
Transcript:
ENSMUST00000089302.11
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
38
Exon/intron offsets:
0
Genomic length:
804
Exon/intron sizes in nt:
804
Flanking exon/introns:
chrX:13026142-13026985
Splice length:
804
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGAATTAAATTTTTCATAATCTCTGTTAAAGTATCATGTTAAATGATAGTCATTCAGAAGGTCCAATGATGAAATAATGTTTTTTCTTTTTTCTTTATATGAAACTGTCTCTAAATACAGAATATCCTTTGCCCGAACCCCTGTGCACTTTATAATTTTTTACATAATACTTCTGTGGTAAACACAAGTGAGATTCTATTGTCTTAAGTTTTGCTTCCAAAAAGCAATACTACATCTACCTGCTTTATTAATATACTCATTCCCAGGCGCCATCCAATTCACTAACTGAATCAGAATTACCACAGTTAGTGCAAAAAAAATTCCATGTTTTTACTGTGAAGAGTCATCAATTTTGGAATAAGGTCTAGAAAAGAAGTAAAATAAATTAAAATTAGAGGAAATAATGTCCATTCAATTAGTGCTAGCAGTATAGGAGAGCACTTTTCTCATACTAATTCCAGGTTTGATTTCCAGCATCCCTAATAATTTTTTAAACTAAGAATTGACTTAAATTACTCCTTGATCTTTCTAATACTACCTGCTCATTCCTGTTATGTTACTACTAGAACTGTACCTAAATATCATGCACAATTGTCTTCCACTGTTTTATTTTGTTGCAAAAGATTAGATTGGGGGACAATAGTTGTCTAACATGGACATTTTCAGCATCAAAGGATGGGGTACGCCTTTAGTTTCAGTACTAAGAGAGGCAGACAGATCTCTGAGTTAATTTCAAATATTTGTCCTTTTTGTTTTGTTCACAAAGTTCATTCCATCCTAATGTTTTCTTTCTCTGTTTTC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGAGGCAGACAGATCTCTGAGT
60.03
TCATTGGACCTTCTGAATGACT
57.08
168
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGAGGCAGACAGATCTCTGAGT
60.03
TCATCATTGGACCTTCTGAATGACT
60.05
171
PCR template sequence:
TAAGAGAGGCAGACAGATCTCTGAGTTAATTTCAAATATTTGTCCTTTTTGTTTTGTTCACAAAGTTCATTCCATCCTAATGTTTTCTTTCTCTGTTTTCGTAAGAATTAAATTTTTCATAATCTCTGTTAAAGTATCATGTTAAATGATAGTCATTCAGAAGGTCCAATGATGAAATAATGTTTTTTCTTTTTTCTTTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(2), mmu-miR-93-5p(2), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-7b-5p(1), mmu-miR-7a-5p(1), mmu-miR-340-5p(1), mmu-miR-98-5p(1), mmu-miR-335-3p(1), mmu-miR-669d-5p(1), mmu-miR-3065-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTCTCTGTTTTCGTAAGAATTAAAT
siRNA sets
TTAATTCTTACGAAAACAG, TAATTCTTACGAAAACAGA, TTTAATTCTTACGAAAACA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIUSP9X_804_ORF_1
0.768
-0.473485624
0.010411688
171
ORF sequence:
ATGGGGTACGCCTTTAGTTTCAGTACTAAGAGAGGCAGACAGATCTCTGAGTTAATTTCAAATATTTGTCCTTTTTGTTTTGTTCACAAAGTTCATTCCATCCTAATGTTTTCTTTCTCTGTTTTCGTAAGAATTAAATTTTTCATAATCTCTGTTAAAGTATCATGTTAA
Peptide sequence:
MGYAFSFSTKRGRQISELISNICPFCFVHKVHSILMFSFSVFVRIKFFIISVKVSC
IRESfinder result
IRESfinder score
0.952174479
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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