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mmu_ciPls3_783
Basic information of circular RNA
PanCircBase ID:
mmu_ciPls3_783
mm39_Chr. Position ID:
chrX|74845347|74846130|-
Gene name:
Pls3
Transcript:
ENSMUST00000114059.10
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
6
Exon/intron offsets:
0
Genomic length:
783
Exon/intron sizes in nt:
783
Flanking exon/introns:
chrX:74845347-74846130
Splice length:
783
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGCGCGGTGTTCTCTGCTCTCTCTTCCATGAACTGTGATTTGAAACAGAGGCTATAGACTGTCTGCTGGCCTCTAATCCTCAGAGCAGCTCTGAGTGTAGAATGTCCATTGATGTTTTAGACCATGAGCTGGGACTCAGAAAGGCTTGCGGTTGTGGGTCTTGTTGGAGAAGTTCACACTGGCACTGAGGTGTTGTTCCATATTGAACTCAAAGCCCTGTGTGCCTTTCATTGCCTATTGAGTTAAGATATGACCAAAGTGATCAAAAGGATTTAAGCGCTTTCTTAGCTGGTGTGCTTAAAGGATGGAGTGTGTTTGTTTTCCACTGAATGAGTAAGTATAGTACAGCAAAATCCCATCACGCAGCAGTGTCCTTGAGATGTACAGATTGGTTATTTCTAAAGCCTGGATGTATGCCATACGCTGCTGGATTCCAATTCAGGCAATTTTAGAAAAATCCATTCACATGGATATATTTCCTTTGGTTACTTGACTTTTTTTACTTTAGAATTGACATAATTCAAAAGCAACCAGATAAAAAGAAAAGGTCCACTTCCTGTCGAATTGTGGAAAAAAAAAAAGAATACAAGTGAGACTGAGAATTGCTGCCACTTTGCTACTTAACGCTGAACTCTGCAATTTGTTTTCTGTAAATGTGGGTGGATGAAATTAATACCTCGTATTAATTTCTCAGCTTACTGGTATTTTTCAGTGAAGGCTGAAGTGGACTGGGTGTGGAAAAAGGAAAAGGTCAAGAAGTGCATAATTTGGCTGTCTTGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGAAGTGGACTGGGTGTGG
60.25
TAGAGGCCAGCAGACAGTCT
59.96
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAAGGCTGAAGTGGACTGGG
60.32
AGAGGCCAGCAGACAGTCTA
59.96
144
PCR template sequence:
TTAATTTCTCAGCTTACTGGTATTTTTCAGTGAAGGCTGAAGTGGACTGGGTGTGGAAAAAGGAAAAGGTCAAGAAGTGCATAATTTGGCTGTCTTGCAGGTGCGCGGTGTTCTCTGCTCTCTCTTCCATGAACTGTGATTTGAAACAGAGGCTATAGACTGTCTGCTGGCCTCTAATCCTCAGAGCAGCTCTGAGTGTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-124-3p(1), mmu-miR-9-5p(1), mmu-miR-26a-5p(1), mmu-miR-132-3p(1), mmu-miR-495-3p(1), mmu-miR-26b-5p(1), mmu-miR-539-5p(1), mmu-miR-452-3p(1), mmu-miR-1199-5p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGCTGTCTTGCAGGTGCGCGGTGTTC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIPLS3_783_ORF_1
0.9652
-0.116863696
0.063847018
177
ORF sequence:
ATGAAATTAATACCTCGTATTAATTTCTCAGCTTACTGGTATTTTTCAGTGAAGGCTGAAGTGGACTGGGTGTGGAAAAAGGAAAAGGTCAAGAAGTGCATAATTTGGCTGTCTTGCAGGTGCGCGGTGTTCTCTGCTCTCTCTTCCATGAACTGTGATTTGAAACAGAGGCTATAG
Peptide sequence:
MKLIPRINFSAYWYFSVKAEVDWVWKKEKVKKCIIWLSCRCAVFSALSSMNCDLKQRL
IRESfinder result
IRESfinder score
0.758343098
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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