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mmu_circPkn2_656
Basic information of circular RNA
PanCircBase ID:
mmu_circPkn2_656
mm39_Chr. Position ID:
chr3|142526297|142535090|-
Gene name:
Pkn2
Transcript:
ENSMUST00000043812.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
8,7,6,5
Exon/intron offsets:
0,982,8344,8647
Genomic length:
8793
Exon/intron sizes in nt:
110,186,214,146
Flanking exon/introns:
chr3:142517818-142526297|chr3:142535090-142536257
Splice length:
656
Other database IDs:
CIRCpedia: MMU_CIRCpedia_9244, circAtlas: mmu-Pkn2_0010
circAtlas: hsa-PKN2_0010, CIRCpedia: HSA_CIRCpedia_33100
Human Ortholog IDs:
Mature spliced Sequence:
CAAAACCTGTGATAAGCCCTCTTGAGCTTCGGATGGAAGAATTAAGACATCATTTTAAGATAGAATTTGCAGTAGCCGAAGGTGCAAAGAATGTCATGAAGTTACTTGGCTCAGGAAAAGTAACAGACAGAAAAGCGCTTTCAGAAGCACAAGCGAGATTTAATGAATCAAGTCAGAAGTTGGACCTTTTAAAGTATTCACTAGAGCAAAGGTTAAATGAGCTCCCCAGGAATCACCCCAAAAGCAGTGTCGTCATTGAGGAGCTTTCACTGGTTGCGTCACCAACCCTGAGTCCACGGCAGAGCATGCTGTCCACGCAGAACCAGTATAGCACACTGTCCAAGCCAGCGGCGCTAACCGGTACTTTGGAAGTTCGTCTTATGGGGTGCCAAGATATCCTAGAGAATGTACCTGGACGGTCAAAAGCAACGTCGGTAGCACTACCTGGGTGGAGTCCAAGTGACAACAGATCGTCTTTTATGAGCAGAACCAGCAAGAGTAAAAGTGGGAGTAGTCGCAACCTCCTGAAAACGGATGACTTGTCCAATGATGTTTGTGCTGTTTTGAAGCTAGATAATACTGTGGTTGGTCAAACTAGCTGGAAACCCATTTCAAATCAGTCGTGGGACCAGAAGTTTACACTGGAACTAGACAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTCAAATCAGTCGTGGGACCA
59.58
ACATTCTTTGCACCTTCGGC
59.4
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGTTGGTCAAACTAGCTGGA
59.23
ACATTCTTTGCACCTTCGGC
59.4
168
PCR template sequence:
TGCTGTTTTGAAGCTAGATAATACTGTGGTTGGTCAAACTAGCTGGAAACCCATTTCAAATCAGTCGTGGGACCAGAAGTTTACACTGGAACTAGACAGGCAAAACCTGTGATAAGCCCTCTTGAGCTTCGGATGGAAGAATTAAGACATCATTTTAAGATAGAATTTGCAGTAGCCGAAGGTGCAAAGAATGTCATGAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-199a-5p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-196a-5p(1), mmu-miR-26b-5p(1), mmu-miR-127-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGAACTAGACAGGCAAAACCTGTGAT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPKN2_656_ORF_1
0.6349
0.049314297
0.667764568
636
ORF sequence:
ATGGAAGAATTAAGACATCATTTTAAGATAGAATTTGCAGTAGCCGAAGGTGCAAAGAATGTCATGAAGTTACTTGGCTCAGGAAAAGTAACAGACAGAAAAGCGCTTTCAGAAGCACAAGCGAGATTTAATGAATCAAGTCAGAAGTTGGACCTTTTAAAGTATTCACTAGAGCAAAGGTTAAATGAGCTCCCCAGGAATCACCCCAAAAGCAGTGTCGTCATTGAGGAGCTTTCACTGGTTGCGTCACCAACCCTGAGTCCACGGCAGAGCATGCTGTCCACGCAGAACCAGTATAGCACACTGTCCAAGCCAGCGGCGCTAACCGGTACTTTGGAAGTTCGTCTTATGGGGTGCCAAGATATCCTAGAGAATGTACCTGGACGGTCAAAAGCAACGTCGGTAGCACTACCTGGGTGGAGTCCAAGTGACAACAGATCGTCTTTTATGAGCAGAACCAGCAAGAGTAAAAGTGGGAGTAGTCGCAACCTCCTGAAAACGGATGACTTGTCCAATGATGTTTGTGCTGTTTTGAAGCTAGATAATACTGTGGTTGGTCAAACTAGCTGGAAACCCATTTCAAATCAGTCGTGGGACCAGAAGTTTACACTGGAACTAGACAGGCAAAACCTGTGA
Peptide sequence:
MEELRHHFKIEFAVAEGAKNVMKLLGSGKVTDRKALSEAQARFNESSQKLDLLKYSLEQRLNELPRNHPKSSVVIEELSLVASPTLSPRQSMLSTQNQYSTLSKPAALTGTLEVRLMGCQDILENVPGRSKATSVALPGWSPSDNRSSFMSRTSKSKSGSSRNLLKTDDLSNDVCAVLKLDNTVVGQTSWKPISNQSWDQKFTLELDRQNL
IRESfinder result
IRESfinder score
0.530716637
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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