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mmu_ciPak2_1541
Basic information of circular RNA
PanCircBase ID:
mmu_ciPak2_1541
mm39_Chr. Position ID:
chr16|31860422|31861963|-
Gene name:
Pak2
Transcript:
ENSMUST00000023467.9
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
5
Exon/intron offsets:
0
Genomic length:
1541
Exon/intron sizes in nt:
1541
Flanking exon/introns:
chr16:31860393-31861963
Splice length:
1541
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTTAATAATTTATTATAATTTGCATTCTGATTTAGGTTGCTGTCTTAGTCAGGGTTTCTATTCCTGCACAAACATCATGACCAAGAAGCAAGTTGGGGAGGAAAGGGTTTATTTGGCTTACACTTCCATACTGCTGTTCATCACCAAAGGAATTCAGGACTGGAACTCAAGCAGGTCAGGAAGCAGGAGCTGATGCAGAGGCCATGGAGGAATGTTCTTTACTGGCTTGCTCAGCCTGCTTTCTTATAGAACCAAGACTACCAGCCCTGAGATGGTCCCACCCACAAGGGGCCTTTCCCCCTTGATCACTAATTGAGAAAATGCCTTACAGTTGTATCTCATGGAGGCATTTCCTCAACTGAAGCTCCTTTCTCTGTGATAACTCCAGCTGTGTGAAGTTGACACAAAACTAGCCAGTACAGTTGCCTAGAACAAGTCTATTTTAATTTGCTTGGTAAATATATAAAAACAAGGGTCTGGAGTGATTACTCCGCAGTTAAGGGCGCTGGCTGCTCTTCCAAAGGTCCTGAGTTCAGTTCTCAGCAATGACGTGGTGGCTCACAATCATCTGTAATGGGATCTGTTGCCCTCTACTGGTGTGTCTGAGTATAGCAACAATGTACTCATACATAAAATAAATACATCTTTAAATAGTTAAATGTGGTAGCCATCGCTTCCTGCCTTTTGGCTAAGATCAAGTGTAAATGTGGTAGCCATGTCTCCAACCCCAACTCTCAAGAGGCCAAGGTTGTGTAATCACTGTGAATTTGAAGGACTGGGTGACTAGCAAGACCGTATCTTAAAAAACCAAAAATAAAGTAAAATTAGCCATCAGATAAATACCTCTTTGTTTTTTCTTTCTTTCTTTCTTTCTTTTTTTAAAGTTAGCCATTTGTTTAATTGAAGAAACCATATTAAGTAAATAGGATTTGCTTGTTGGGCAGTTTAATCTTTATAATGGCTTCCAGTGCAATTTAATTACTCTTCCACTGTTTCCAGATTGAACCTGAATATGGTGAACTGGATGGCATAGTCTCTCCTCCCATAACCCCTACCAGTACCGTTCTGAGTGTGGTAAATTGTGTCACATTCTAAATAGTTTAAAAAACAAAACAAAACTTGTCAGCTCCTTTTCTTGCTTTGTTAACTGGTGAAGCTGGATCTCTTAAATTCCTCAAAATGAGGTTTATGTCTACAGAGTCCAGAGAACCTTCAGTTTGGTCTTAAGAAGATTGCTTACTTAACAGAGCACCGTGTGTGCTTATGTAAAGGGCAGGAATAGTGCCCCAGTGTACTCGGGAGCTCTGAACGTAGCTCAGTGGTAGAGCAGTCACACCATACACAGACCTCAGGATCAGTCATTAGCAGAGTCCCCTCCCACTGAAATGATACTCACCGTATATATTCATTTACTTTTTAATTGGTTGTATTGGAACCAGTGAAGTTTGGTAGTTTTTATATTAGCTATTGAAGAAATAAGCTTTTAAGACTGTTTTTATAGGGGAGCCCCATGTTAACCTTTGATGTTATTGGTTTA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGACTGTTTTTATAGGGGAGCCC
59.8
CCAACTTGCTTCTTGGTCATGA
59.11
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGACTGTTTTTATAGGGGAGCCC
59.8
TCTTGGTCATGATGTTTGTGCA
58.78
141
PCR template sequence:
AGTGAAGTTTGGTAGTTTTTATATTAGCTATTGAAGAAATAAGCTTTTAAGACTGTTTTTATAGGGGAGCCCCATGTTAACCTTTGATGTTATTGGTTTAGTAAGTTAATAATTTATTATAATTTGCATTCTGATTTAGGTTGCTGTCTTAGTCAGGGTTTCTATTCCTGCACAAACATCATGACCAAGAAGCAAGTTGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
16
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-134-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-146a-5p(1), mmu-miR-132-3p(1), mmu-miR-128-3p(1), mmu-miR-433-5p(1), mmu-miR-431-5p(1), mmu-miR-363-3p(1), mmu-miR-340-5p(1), mmu-miR-466a-5p(1), mmu-miR-466p-5p(1), mmu-miR-344d-3p(1), mmu-miR-146b-5p(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGTTATTGGTTTAGTAAGTTAATAAT
siRNA sets
TATTAACTTACTAAACCAA, ACTTACTAAACCAATAACA, ATTAACTTACTAAACCAAT
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
0.873704464
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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