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mmu_ciPkp4_2690
Basic information of circular RNA
PanCircBase ID:
mmu_ciPkp4_2690
mm39_Chr. Position ID:
chr2|59175337|59178027|+
Gene name:
Pkp4
Transcript:
ENSMUST00000168631.8
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
17
Exon/intron offsets:
0
Genomic length:
2690
Exon/intron sizes in nt:
2690
Flanking exon/introns:
chr2:59175337-59178063
Splice length:
2690
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GCAAGTGTGAGGGCCTGGGGCCTGGGGTGAGAGAAGGAGCCATGCCGGAAGCGGGGATTTATTTCTGTTTCTCACATGTTGTCTACACCAGCTAAGACTTGTAATGGTGTGGGCTGCTTTTTGTCATATGCGGGCATTTCCTTTATTATAGTGTGCCTCACTCCTTCACTCTGTCCTCTGAGGTTACTGTAACAAAATACTGTGGGCTAGGGAGCTTATGAACAATAGAAGTTTATTTCCCACAATTGTGGCACCTGTGAAATCCAGGATCAAGGTCCCAACAGATTTTATGTCTGGTCTAAGTCCCTTTCCGGTCTTAGAGAGAGTGAGCTTTGCCCTCACATGGAACAGTCTCTTCCAGGTGACTCTTCTCAAAGGCTGCCCCTCCCAGCACTGCCGCTTTGAGTTAGGACTTGTACTTAGGAATGTTGGAGAGACTCAGGTGTCCAGGCTGTAACCATCCCTAAAGCTACATTTGTTCATGTCCGCTCCTAGAAGAACCAAAAGCACCAGGGTGGTGACAATCTTAGGGCCACTGTCGCCTTTGCAGTTTGGGCTCTGTTCCATGCCTACAGCCTATTCTGCAAGAATGTCTTTAAATCCTCACTTTTGAGATTGATTCTGCTGCCAAGTGCCCAGAGAGCATGAAAACCAGCACTCCGCGTGAGTGCTCTGGGCTCAGTCCCTTTGCTTTTGGACGACAGTAAAAGATGAAGCAGCACCAGTGGGCAGAGAAGATCGTAGCAAAATAGAGGTTTCTTGTCGCGGGGCTGCAGCTGTGACTAAATCTGCCTTAGTGTCAGATCAGCGAAATGGAACTGGGAATGCCAAGTACCTTCTTCAAAACGTAGGTCAGCAGCGCTCTCCCATGCCCGCGCTCTCCCATGCCCGCGCTCGCGCGCGCATACACAGTTCCCACTAAGTTCTCCCTGGCACTGACTGTTTTGAGTTGTCTGCTAGCATCTCACTCCCAAGGTCCTGGGACTTTGTCCCTTATCTGCTGTTGTATCCTTAACAACAAAAGCTTGGTCCTGGTACATGCATAAGGACAATTTATTAATCAGCTGAATGCCAATGCTGAGTTTGACATTACAGCTCTTCAAGTCTTTCCAGTTGATACCACTGAAGGAATTCTTAAAGTATAGAAACAGTGCAAAAAGCCATCACCTTACCCACGAGAAGCCCCAGCTGTCAGCATAGACAGCGTAGCACATCGGCGTTTTTATTTATTGTATTTTTAAATTTTCATTAGTAACAAATGCATACAGTATATTTGTTTGTTTTGATTATTTTTTTTTCTCTTTCAAATAAGGCCCCATCGTGTAGCCCGGGCTCACTGTGTAGCCCGGGCTGGTCTCAAAATTCATAGCAGTCCTCCCAACTCAGTCTACTGAGTTCTAGGATTACAAGAGTAAGCTACCTGCCCTGCCTCTGCTGTTTTGTGCTCCACTCACTGCATGTCCGCGTGCTGTCCCGGTACAGGCTTACAGCAGTGAGTGGAGCACAAAACAGTGCTCCAGGGCTGAGGCAGACAAGGCGCCCAATGAGTAACAGCAGCAGAGCCTGGCAGATGGCACTCACAGGCACAGATGACAAACGCAGAGAATGCGGCAAGCATGTCAGGGAAGGAGAAGTGTCAGGGAAGGCCTCCTGGTGATGGCAGGAAGCTGACCTGAGGGAGGAAGTGTGTGGGATGAGGGCGGGAGGAAACTGCGCCCCTCTGGGGCAGAAGCATGTGAGCAGAGTCCAGCAAGAGGCTGCCGGGCGGGCGAGGAAAAGCAGAACATGGTGCAGGAGGAAGAAAGGGAGTTTGGGGGAGCAATAGGACCGAGAAGCAGTAGGACCTTATAGTCGGTTCTCAGTCTCTGAATGACACCAGAGCCTCTGGAGAGCAGTGAGCAGAGGAGTACCATGGCCAGTTTCCCACACGCACACTGAAGGCTAGGGTGCAGTGGCTGCGGTGACGTCAGCAGCATTGCTGATGGGGTTGAAAAGCAATTCAACAGGTTTTACTAATGAGTGAGCGGCAGGAGAGGAGAGGATTGTGAATGACGCCAAAGTGGTTGTCCAAGAGGCCACATCTAGGCAGGGAAGCTTATGGGAGGACCGTCCTGAGTTTGCTCTGGACTTGGGTGCGTGGGGATAACTATTAAACATCCAGTGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGCGCGTGCATGAGTGTGGTAGGTCAACAGGAGAGAGGTACAAGGCCAATACTCAAACTGGAAAAATATACCTGGGCGGTCAGTCAGCATTTAAATGGCTCATTTATAGAAGTGAAGGTTGACAGGTATCAGGGAGATTAGGACCCCAAAATAAACGCAGAAAGGAGCAGCCAGAACCCGGGAGCATGTGGTAACTTGGAATCCAAACGGAAGGAGATGACGAGAGTTAGGCTGGAGTCAGAAGCCCTGCTTACTCGGGTAGAACAAGCTTGAGGCCTGACCATCGGATACGACAGTCATACAGAGGCTGTGAATTGAAGAGGAGATGGGATGGGAGAAATCAGAGGTGTGAGTGGCTGCTTTCAGGGGCTTCTTGTGTGCTGCAAAGGTTAGAGGGCACTCTTGCCTTTCCCAGGATTCTGGTTCTGCCCACAGAATCTGGTAGCCTCCATCCTGCTCCTTTGGCTGCTGGTTTGCAGCCTGAGTCTCTCCATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGATTCTGGTTCTGCCCACA
59.96
CAGAAATAAATCCCCGCTTCCG
59.71
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TAGCCTCCATCCTGCTCCTT
60.03
AGCTGGTGTAGACAACATGTGA
59.63
146
PCR template sequence:
GGCACTCTTGCCTTTCCCAGGATTCTGGTTCTGCCCACAGAATCTGGTAGCCTCCATCCTGCTCCTTTGGCTGCTGGTTTGCAGCCTGAGTCTCTCCATGGCAAGTGTGAGGGCCTGGGGCCTGGGGTGAGAGAAGGAGCCATGCCGGAAGCGGGGATTTATTTCTGTTTCTCACATGTTGTCTACACCAGCTAAGACTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
28
Interacting miRNAs (#binding sites)
mmu-miR-666-5p(2), mmu-miR-673-5p(2), mmu-miR-670-5p(2), mmu-miR-210-3p(1), mmu-miR-135a-5p(1), mmu-miR-31-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-298-5p(1), mmu-miR-196a-5p(1), mmu-miR-132-3p(1), mmu-miR-709(1), mmu-miR-326-3p(1), mmu-miR-138-5p(1), mmu-miR-495-3p(1), mmu-miR-128-3p(1), mmu-miR-149-5p(1), mmu-miR-382-3p(1), mmu-miR-192-5p(1), mmu-miR-215-5p(1), mmu-miR-297a-5p(1), mmu-miR-466d-3p(1), mmu-miR-499-5p(1), mmu-miR-129-5p(1), mmu-miR-207(1), mmu-miR-466b-3p(1), mmu-miR-574-5p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAGTCTCTCCATGGCAAGTGTGAGGG
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
0.555123368
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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