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mmu_ciPak4_2762
Basic information of circular RNA
PanCircBase ID:
mmu_ciPak4_2762
mm39_Chr. Position ID:
chr7|28264696|28267458|-
Gene name:
Pak4
Transcript:
ENSMUST00000108283.8
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
3
Exon/intron offsets:
0
Genomic length:
2762
Exon/intron sizes in nt:
2762
Flanking exon/introns:
chr7:28264696-28267458
Splice length:
2762
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAGCCATCACCACACCACTTTAGCCCACAGCCCATACTGCCAGAATGGCCCAGCCCTTCAATTGCTCCTGGCTTCTTTGCAGAACCTCCCACCTCTGTAGCCCAGTGGTCGGCCTTCCACCTGCCAGTACAATCCTGGAAGGTCAGCTTCTGACTTCCACTCCTGCCCCAACACCACAACACTACACATTCAACCTTGGTCTCCCAGTGCTTCATGACATGGGAGACAACATGGGAGTGCTCCCAGACAACATCCGGGCTTGGCTAGGGGATGCCTAAGCTGCATTCCAAGGTCCAGGAGCAGCTGAGGCAGATGGGAGCAGGGCAGCAGCCATTCAGTCTTATCATCCTGAGCAAATTGTCAGTTGGAGTGAGACTTGAGGTTTAGATCCAAGATCCTCACACTTCCCCCGCCCCCGTGTACAATGTGAGAATTGTGGTCTCACTGCCTAGGCAGGAACTACAGCCTTGCAGGCCTAGTGGTAAGAGTGCCCCAGCTGGACTCATGCCATGGGTGGTGGGACCCAGAGGAGTACAGCCAGACGTGTCCCCACTTGGTGGAGTTGGGCGTGCCTATGGTCAGCAGGCTGGGTACCCGGCCCTGCAGCTGATTCATCCTCTCCCAGTGACCAGCCAGGGTCTGGCAGGAGAGAGGCAGCGTCATCAGGGCACCCACAGCCGTGGTGCTTGGGTGGAGGCTGGGCTCTTTCTGGTTATTTCTGTGGCCCCGTAGGGTCATGTGAGAGCTTTGACTTCTCTCTGTTGCCTAGAAAGCCCCTCTTGTCATCTGAATCTGTATGGGCTTTTCATGCCCCAGGCCAGCTGGAAGCCAGTAGCAACTGGTTATGAAGTAGGCCCCTCCATAGTCCCCAGACAACCCACCCTAAACACTCCCATGACCCAATGAGCTTTGTGGTCATTTCTCACACATTGTGTGTCCCCAAAATTTCACCACTGCTCTATGCACCCTTGTGTTTCCACACCTTTCCACAGTCCTGCCAGGGGAAGGACACTTGTCCTAATTCCCGTGCAGGCAGGCACCTTAGCTGGGACTGCCTAGATGACAAGCTTCCTGACCACTGACTCAGGTTCTAATAGCAGAGCCTGGCAGGTAGCCCCTGAAGGAAAAAAGAAATGAAAAAGGTAAACATGCCTGCTCCTAGGTGTGGTGGAGGAGGTTATTGTGGGTATGAGGGAGAGCACAGCCAGAGGCAGGGGCATCTGGAAGAGGCCAGAGTGGACATGACTCTGAGCCAGGTGAGGAGAGGGGGAGGGAAGAGCCAGGAGGCCAGGAGGGTAAAAGGCAGCAGAGTCAGCGCAGCCAAAATGGCTGGATTATATAGGGAAAGGCAGCTGGGGGAAGGCAGTCCAGGGGGAAGCAGTGGATGCCGGAAAGAAAGACCCTGTAACAGGTAGGGACTGAGGGATGCTGGGAAATGCTAGAGGCCTGGTCTGCTTTGATATGTCAAATAGGCACCTCAGCCATTTGTCCTGGGTTTGAAACCTAACATCCATCTTTCTTGACTCCCTGGACAAGGCCAGGCTTTCAGGCAGACAGCCAGGGCCCACAAGAGGCTGGGACCACAGCATGCCATTAGGAGCCTTATGGACTCCAGGTCGTTCCCGGGAGCTCAGTATAAACTCAGCCTCAGAGACTATCCAGGCAACTCCCCACCTCTCCTTCTTGCCTTCCTCCTCCCTTCCTTCCTTCTTTTGCAAAGTACCTTGTTCTTGGTGTGGACTCTGATCTAGGTCCAAGACCTGGTAGGCTGTGAATGGTAGAACAAGTGCTCAGCCCCGGGAAGGCCACAGGGTAAAGCAGCATCCTGGGCTCACAGCCTAGTCCGCTGCAGCAGGCCTACAACCCTGGTTCTCAACCTGTGGGTCACGACCCACATAGTGGATATTTACATTACAATTCATAACAGTAGCAGACCACAGTTATGAAGTGGCAATGAAATAATTTTGTGTTTAGGGTCATCACAGCATGAGGAATGGTCGCAGCATTAGAAAGGCTGAGAACCACTGTTCTAGAAGAAAAAAGGAAAGAGCCGGAGACTTGTGGGCTGGCATTTAAACTAGGGGTTAGCAAGTCCTCAGAGAAGGAGGTTTTGATCAGAGACCTCTGGGAGGGGAGTGGGACAGCCATGGAGACATTTGGGAGATGTAGGGCAGGGCAAAGAGCTGATGGACACACATCCAGTGTATTGGAGGAACCGCCTGATGTGCCCAGTGCTCAGGAGGAGCCAAGAAGACCACACCTCAGTGGGGCAGGGAGAGTGGAGGCTTGGTGGTTCAGGGCATGTTTCAGTTGACGCTTGCCACACAGCTCCCAAGCCTCCTAGCTTTAGGCTGTGGGCTTTCTATTCTGCGCCACATCCTCTGCCCTAGGGGATCAGAGCTGCGTGGTTTGAGGGTTAATGATGCTGGCAGCCTGCAGGGGAGGAAGTGCTGAGCCAAGCGGCCTGTAATTTGCAGCTCTTGGGGGCTGATTATAGGCTGAGTTCTCCTCCCTCACCCTAGTCCACAGGGCAGAGCTTGCTGCCAGGCTGGGAGCCAAGGAAAGTCAAGAGGCACTTGTTGGGGGAGCACCAGAGTGGGTGGTGGGCGTGACAGCAGCTCCTGGGGCTCCCACCCATCATCACAGGCTATCACCTCACCTGTCTCTGTCTTGTTTCTGTGTTGTATTGTCTTTCCTGTGTCGGATGCACGACCTGTGTCCCCTCCTTCCTGGCCCTACCCTGCCATTGCCTGGACCCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTTTCCTGTGTCGGATGCA
59.32
GGTGGGAGGTTCTGCAAAGA
59.89
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTTTCCTGTGTCGGATGCA
59.32
GAGGTGGGAGGTTCTGCAAA
59.89
168
PCR template sequence:
GTCTCTGTCTTGTTTCTGTGTTGTATTGTCTTTCCTGTGTCGGATGCACGACCTGTGTCCCCTCCTTCCTGGCCCTACCCTGCCATTGCCTGGACCCCAGGTAGCCATCACCACACCACTTTAGCCCACAGCCCATACTGCCAGAATGGCCCAGCCCTTCAATTGCTCCTGGCTTCTTTGCAGAACCTCCCACCTCTGTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
22
Interacting miRNAs (#binding sites)
mmu-miR-149-5p(2), mmu-miR-338-3p(2), mmu-miR-23b-3p(1), mmu-miR-140-5p(1), mmu-miR-18a-5p(1), mmu-miR-298-5p(1), mmu-miR-324-5p(1), mmu-miR-326-3p(1), mmu-miR-23a-3p(1), mmu-miR-434-3p(1), mmu-miR-494-3p(1), mmu-miR-382-3p(1), mmu-miR-370-3p(1), mmu-miR-34b-5p(1), mmu-miR-705(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1), mmu-miR-207(1), mmu-miR-673-5p(1), mmu-miR-335-3p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCCTGGACCCCAGGTAGCCATCACCA
siRNA sets
NA
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
0.577513333
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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