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mmu_circPak2_499
Basic information of circular RNA
PanCircBase ID:
mmu_circPak2_499
mm39_Chr. Position ID:
chr16|31852604|31861995|-
Gene name:
Pak2
Transcript:
ENSMUST00000023467.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
10,9,8,7,6,5
Exon/intron offsets:
0,1108,3458,6012,7681,9359
Genomic length:
9391
Exon/intron sizes in nt:
113,49,64,133,108,32
Flanking exon/introns:
chr16:31850519-31852604|chr16:31861995-31862670
Splice length:
499
Other database IDs:
CIRCpedia: HSA_CIRCpedia_365287
Human Ortholog IDs:
Mature spliced Sequence:
AGAAAGATGGCTTCCCTTCTGGAACACCAGCACTGAACACCAAGGGGTCAGAGACATCAGCTGTAGTGACAGAGGAAGATGATGATGATGAAGACGCTGCTCCTCCCGTCATTGCCCCTCGGCCAGATCATACAAAATCAATTTACACACGGTCTGTCATCGACCCCATTCCTGCTCCAGTTGGTGATTCTAATGTTGACAGTGGTGCCAAGTCTTCAGACAAACAGAAAAAGAAAGCCAAGATGACCGATGAAGAGATTATGGAGAAATTAAGAACTATTGTGAGCATAGGGGACCCAAAGAAAAAATACACAAGATATGAAAAAATTGGGCAAGGGGCTTCTGGAACAGTTTTTACTGCCACTGATGTGGCCCTGGGGCAAGAGGTTGCTATCAAGCAGATTAATTTACAGAAACAACCAAAGAAGGAATTGATCATTAATGAAATTCTGGTGATGAAAGAGTTAAAGAATCCCAACATAGTTAACTTCTTGGACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACAGAAACAACCAAAGAAGGA
55.54
AGCTGATGTCTCTGACCCCT
59.96
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACAGAAACAACCAAAGAAGGA
55.54
CAGCTGATGTCTCTGACCCC
59.82
153
PCR template sequence:
AGATTAATTTACAGAAACAACCAAAGAAGGAATTGATCATTAATGAAATTCTGGTGATGAAAGAGTTAAAGAATCCCAACATAGTTAACTTCTTGGACAGAGAAAGATGGCTTCCCTTCTGGAACACCAGCACTGAACACCAAGGGGTCAGAGACATCAGCTGTAGTGACAGAGGAAGATGATGATGATGAAGACGCTGC
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-9-5p(1), mmu-miR-138-5p(1), mmu-miR-96-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTTCTTGGACAGAGAAAGATGGCTT
siRNA sets
AAGCCATCTTTCTCTGTCC, AGCCATCTTTCTCTGTCCA, CATCTTTCTCTGTCCAAGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPAK2_499_ORF_1
0.9972
0.065371058
0.332168777
339
ORF sequence:
ATGACCGATGAAGAGATTATGGAGAAATTAAGAACTATTGTGAGCATAGGGGACCCAAAGAAAAAATACACAAGATATGAAAAAATTGGGCAAGGGGCTTCTGGAACAGTTTTTACTGCCACTGATGTGGCCCTGGGGCAAGAGGTTGCTATCAAGCAGATTAATTTACAGAAACAACCAAAGAAGGAATTGATCATTAATGAAATTCTGGTGATGAAAGAGTTAAAGAATCCCAACATAGTTAACTTCTTGGACAGAGAAAGATGGCTTCCCTTCTGGAACACCAGCACTGAACACCAAGGGGTCAGAGACATCAGCTGTAGTGACAGAGGAAGATGA
Peptide sequence:
MTDEEIMEKLRTIVSIGDPKKKYTRYEKIGQGASGTVFTATDVALGQEVAIKQINLQKQPKKELIINEILVMKELKNPNIVNFLDRERWLPFWNTSTEHQGVRDISCSDRGR
IRESfinder result
IRESfinder score
0.525212809
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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