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mmu_circKpna3_702
Basic information of circular RNA
PanCircBase ID:
mmu_circKpna3_702
mm39_Chr. Position ID:
chr14|61620683|61640491|-
Gene name:
Kpna3
Transcript:
ENSMUST00000022496.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
10,9,8,7,6,5,4,3,2
Exon/intron offsets:
0,1353,1868,4189,7929,8164,8313,8521,19763
Genomic length:
19808
Exon/intron sizes in nt:
45,170,87,86,96,53,30,90,45
Flanking exon/introns:
chr14:61611864-61620683|chr14:61640491-61677171
Splice length:
702
Other database IDs:
circAtlas: mmu-Kp3_0001
Human Ortholog IDs:
Mature spliced Sequence:
ACGATGCGAAGACACAGAAATGAAGTGACAGTTGAACTCCGGAAGAACAAAAGAGACGAACACTTACTGAAAAAGAGAAATGTTCCCCAAGAAGAAAGCTTAGAAGATTCAGATGTTGATGCTGATTTTAAAGCACAAAATGTAACACTAGAAGCTATATTACAGAATGCCACAAGTGATAATCCTGTAGTCCAGTTGAGTGCTGTGCAGGCAGCAAGGAAACTATTATCCAGTGACAGAAATCCACCAATTGATGACCTAATAAAATCTGGGATTTTACCAATTCTAGTCAAATGTCTAGAAAGAGATGATAATCCTTCATTACAGTTTGAAGCTGCTTGGGCACTAACTAATATAGCATCGGGAACTTCTGCACAGACTCAAGCTGTTGTACAGTCTAATGCAGTACCACTTTTTCTGCGACTCCTCCATTCCCCACATCAGAATGTTTGTGAACAAGCGGTGTGGGCTTTGGGAAACATTATAGGTGATGGTCCTCAATGTAGAGATTATGTCATATCACTGGGAGTTGTCAAACCTCTTCTGTCCTTCATCAATCCCTCCATTCCCATCACCTTCCTTCGGAACGTCACATGGGTCATTGTCAATCTCTGCAGGAATAAAGACCCCCCACCGCCTATGGAGACAGTTCAGGAGATTTTGCCAGCTTTGTGTGTGCTCATCTACCATACGGACATAAAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTTGCCAGCTTTGTGTGTGC
60.46
AGCTTTCTTCTTGGGGAACA
56.95
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGCAGGAATAAAGACCCCC
59.44
TGTTCTTCCGGAGTTCAACTGT
59.83
141
PCR template sequence:
TGTCAATCTCTGCAGGAATAAAGACCCCCCACCGCCTATGGAGACAGTTCAGGAGATTTTGCCAGCTTTGTGTGTGCTCATCTACCATACGGACATAAATACGATGCGAAGACACAGAAATGAAGTGACAGTTGAACTCCGGAAGAACAAAAGAGACGAACACTTACTGAAAAAGAGAAATGTTCCCCAAGAAGAAAGCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-217-5p(1), mmu-miR-218-5p(1), mmu-miR-541-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TACGGACATAAATACGATGCGAAGAC
siRNA sets
TTCGCATCGTATTTATGTC,TCGCATCGTATTTATGTCC,CGCATCGTATTTATGTCCG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKPNA3_702_ORF_1
0.9815
0.011021452
0.998776063
1401
ORF sequence:
ATGCGAAGACACAGAAATGAAGTGACAGTTGAACTCCGGAAGAACAAAAGAGACGAACACTTACTGAAAAAGAGAAATGTTCCCCAAGAAGAAAGCTTAGAAGATTCAGATGTTGATGCTGATTTTAAAGCACAAAATGTAACACTAGAAGCTATATTACAGAATGCCACAAGTGATAATCCTGTAGTCCAGTTGAGTGCTGTGCAGGCAGCAAGGAAACTATTATCCAGTGACAGAAATCCACCAATTGATGACCTAATAAAATCTGGGATTTTACCAATTCTAGTCAAATGTCTAGAAAGAGATGATAATCCTTCATTACAGTTTGAAGCTGCTTGGGCACTAACTAATATAGCATCGGGAACTTCTGCACAGACTCAAGCTGTTGTACAGTCTAATGCAGTACCACTTTTTCTGCGACTCCTCCATTCCCCACATCAGAATGTTTGTGAACAAGCGGTGTGGGCTTTGGGAAACATTATAGGTGATGGTCCTCAATGTAGAGATTATGTCATATCACTGGGAGTTGTCAAACCTCTTCTGTCCTTCATCAATCCCTCCATTCCCATCACCTTCCTTCGGAACGTCACATGGGTCATTGTCAATCTCTGCAGGAATAAAGACCCCCCACCGCCTATGGAGACAGTTCAGGAGATTTTGCCAGCTTTGTGTGTGCTCATCTACCATACGGACATAAATACGATGCGAAGACACAGAAATGAAGTGACAGTTGAACTCCGGAAGAACAAAAGAGACGAACACTTACTGAAAAAGAGAAATGTTCCCCAAGAAGAAAGCTTAGAAGATTCAGATGTTGATGCTGATTTTAAAGCACAAAATGTAACACTAGAAGCTATATTACAGAATGCCACAAGTGATAATCCTGTAGTCCAGTTGAGTGCTGTGCAGGCAGCAAGGAAACTATTATCCAGTGACAGAAATCCACCAATTGATGACCTAATAAAATCTGGGATTTTACCAATTCTAGTCAAATGTCTAGAAAGAGATGATAATCCTTCATTACAGTTTGAAGCTGCTTGGGCACTAACTAATATAGCATCGGGAACTTCTGCACAGACTCAAGCTGTTGTACAGTCTAATGCAGTACCACTTTTTCTGCGACTCCTCCATTCCCCACATCAGAATGTTTGTGAACAAGCGGTGTGGGCTTTGGGAAACATTATAGGTGATGGTCCTCAATGTAGAGATTATGTCATATCACTGGGAGTTGTCAAACCTCTTCTGTCCTTCATCAATCCCTCCATTCCCATCACCTTCCTTCGGAACGTCACATGGGTCATTGTCAATCTCTGCAGGAATAAAGACCCCCCACCGCCTATGGAGACAGTTCAGGAGATTTTGCCAGCTTTGTGTGTGCTCATCTACCATACGGACATAAAT
Peptide sequence:
MRRHRNEVTVELRKNKRDEHLLKKRNVPQEESLEDSDVDADFKAQNVTLEAILQNATSDNPVVQLSAVQAARKLLSSDRNPPIDDLIKSGILPILVKCLERDDNPSLQFEAAWALTNIASGTSAQTQAVVQSNAVPLFLRLLHSPHQNVCEQAVWALGNIIGDGPQCRDYVISLGVVKPLLSFINPSIPITFLRNVTWVIVNLCRNKDPPPPMETVQEILPALCVLIYHTDINTMRRHRNEVTVELRKNKRDEHLLKKRNVPQEESLEDSDVDADFKAQNVTLEAILQNATSDNPVVQLSAVQAARKLLSSDRNPPIDDLIKSGILPILVKCLERDDNPSLQFEAAWALTNIASGTSAQTQAVVQSNAVPLFLRLLHSPHQNVCEQAVWALGNIIGDGPQCRDYVISLGVVKPLLSFINPSIPITFLRNVTWVIVNLCRNKDPPPPMETVQEILPALCVLIYHTDIN
IRESfinder result
IRESfinder score
0.537000973
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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