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mmu_ciPclo_1738
Basic information of circular RNA
PanCircBase ID:
mmu_ciPclo_1738
mm39_Chr. Position ID:
chr5|14842106|14843844|+
Gene name:
Pclo
Transcript:
ENSMUST00000182407.8
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
19
Exon/intron offsets:
0
Genomic length:
1738
Exon/intron sizes in nt:
1738
Flanking exon/introns:
chr5:14842106-14843845
Splice length:
1738
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAGGAGATATTTCATGTAGAGCACCGTTGTTTTTCTATTTGTTCAGTCAGTAGCTTCTCGAACGTGAGTGTCTCTATGTTTAATATACACTGTAAAGTTGGGTTCTGTTGGAAAATAGTGTGATATAATGAAAAGTGTGCTCCTGGTTAGGAAGAAAGGGGCTTTAGGCAAATACCAGCACATACTTAGGTGTTAGTCTTGCCAGCTTCATTTCCTTACTTTGTAAAAGTCATACTGGCCTACATAAGGTAATCCTATTTCATGAAACACATAACAGTAGAATTTCAGAGAATTCACTGATCTATCTCAAAAAAGAGTATAAAGTTCCTTCTGCTATCTTTACTAGAAATATGGCCATCATTACTATTAAGTATATTCTTTTTAATTTTTTTCAATCTCTGAATTCTCATATTGCCAGTCTATAACTAAAATTCTGCATCCTGTTTTTACTTGTCCTTTGAAGAACATTTTCCCCACATTACCAAAACCAACAGCAACTCAAATTCTTCAAGTCTTTCCTAAATGTTGGATCCCAACTAAAAATCGTGTTACACATCCACATGGTGCTTAGCAATATGCACCACATTTCTATAATGAGCTCTCCCTTTAGCTTTTTAAACCACTGTTCTACAAGATAACCAATCCTCCCATCAGTGATAAATCCACAAACCTGTATGAGATAAACGTGTGGTGACAGCATGCATTAATATTTGTAAATATTAAAGACGATTAGTGAGCACTGTTGCCTTCTGGAAGTGCTTCCATGTGCACCAGAAGCAGGCAGACTGTGTCACAGTGTTCTGGAGGGTGAAAAACTAGGGTCACCTCTAATAGTCCGACCACAGAAAAAGTACTGAAGATGTTTTCTGAGGATGTATGATAGACTGGGTTCGAATTCGACTTAGCCATTTAAACTTCGCCATGCTAAACATTCTGAAAGATAATTGACATGTAGATCTCTCTGTCTCTCTCTGTCCCACTGTCTCTGTGTCTCTGTCTCTCTTTATTTATGTATGTGTCTGGGTGTGGGTGTGGGTGTAGTTCTCGCCATCTACAGTCTCAGTTTCCTGAGACAATGATTCTATAACATTATTTAGATTCTAATAAGTTCTACTGCTAACCCAGAATCCACTCTGTTTTTACTTAAGCATGCCCCATATCTCTGTAGACGCATTGTGTTGTACTAGCCTCTACTAGAATAAGCAGAGCTGTAGGGAAGATGGGGCTGAGACATCTGTTCCCTGAGGCTTCTGAGAACTCATTTTCCTTTTTTCTTTTCTTAATAATTAGTTATTGATTATTTGGGAATTTCACATAATATACCCCATCCCACTTCCAGTCCTCCCAGGTCCAGCCCCTTGTACACTCTCCCACAAAAAAAGCAGAAAGATGAAAAAAGAAATAAAGGAAGGAAGGAAGGAAGGAAGGAAAGAAGGAGGGAAGGAGGGAAGGAGGGAAGGAGGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAGGGAAGGAAGGAAGAAGTTTCTTCTCCAGACTGGCCTCCCTTACTTCCTTTCCTGACTTGTTCTTTAAATGCTTAATACCATTACTCAATTGTGTGGAGTGGCACAAATGGCACAAAAAGACAGCATTGATGTAAAAGACTGTTTCCAGTTACATGTAGACTAGACTTTCACAGCAAGGCACTGGGCAGCAACTTTAACTCACTTTTTTATTCCTTTGTAACCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTTTCACAGCAAGGCACTGG
59.69
AACATAGAGACACTCACGTTCGA
59.5
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTAGACTTTCACAGCAAGGCA
59.9
AGAGACACTCACGTTCGAGA
58.12
141
PCR template sequence:
CATTGATGTAAAAGACTGTTTCCAGTTACATGTAGACTAGACTTTCACAGCAAGGCACTGGGCAGCAACTTTAACTCACTTTTTTATTCCTTTGTAACCAGTAGGAGATATTTCATGTAGAGCACCGTTGTTTTTCTATTTGTTCAGTCAGTAGCTTCTCGAACGTGAGTGTCTCTATGTTTAATATACACTGTAAAGTT
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-137-3p(1), mmu-miR-141-3p(1), mmu-miR-7b-5p(1), mmu-miR-31-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-146a-5p(1), mmu-miR-132-3p(1), mmu-miR-709(1), mmu-miR-127-5p(1), mmu-miR-182-5p(1), mmu-miR-511-3p(1), mmu-miR-340-5p(1), mmu-miR-335-3p(1), mmu-miR-1904(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCCTTTGTAACCAGTAGGAGATATTT
siRNA sets
AAATATCTCCTACTGGTTA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.879593586
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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