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mmu_circPkn2_301
Basic information of circular RNA
PanCircBase ID:
mmu_circPkn2_301
mm39_Chr. Position ID:
chr3|142559174|142559475|-
Gene name:
Pkn2
Transcript:
ENSMUST00000043812.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
1
Exon/intron indexes:
2
Exon/intron offsets:
0
Genomic length:
301
Exon/intron sizes in nt:
301
Flanking exon/introns:
chr3:142545123-142559174|chr3:142559475-142587371
Splice length:
301
Other database IDs:
CIRCpedia: MMU_CIRCpedia_37571, circAtlas: mmu-Pkn2_0003
circBase: hsa_circ_0000089, circAtlas: hsa-PKN2_0005, CIRCpedia: HSA_CIRCpedia_108853
Human Ortholog IDs:
Mature spliced Sequence:
GGAGATTCCCGGACTCTTCCATTTTCTGAGAATGTGAGTGCTGTTCAGAAATTAGACTTTTCAGATACAATGGTGCAACAGAAATTGGACGACATCAAGGATCGAATAAAGAGAGAAATAAGGAAAGAACTGAAAATCAAAGAAGGAGCTGAAAACCTGAGGAAAGTTACAACAGATAAGAAAAATTTGGCTTATGTAGACAACATTTTGAAAAAATCAAATAAAAAATTAGAAGAATTACATCACAAGCTACAAGAATTAAATGCACACATCGTTGTATCGGATCCAGAGGACTCCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AATGCACACATCGTTGTATCGG
59.65
CCTTGATGTCGTCCAATTTCTGT
59.25
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AATGCACACATCGTTGTATCGG
59.65
CCTTGATGTCGTCCAATTTCTGTT
59.78
140
PCR template sequence:
AACATTTTGAAAAAATCAAATAAAAAATTAGAAGAATTACATCACAAGCTACAAGAATTAAATGCACACATCGTTGTATCGGATCCAGAGGACTCCACAGGGAGATTCCCGGACTCTTCCATTTTCTGAGAATGTGAGTGCTGTTCAGAAATTAGACTTTTCAGATACAATGGTGCAACAGAAATTGGACGACATCAAGG
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-23b-3p(1), mmu-miR-23a-3p(1), mmu-miR-1187(1)
siRNAs for circular RNA silencing
Junction sequence
GAGGACTCCACAGGGAGATTCCCGGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPKN2_301_ORF_1
0.872
0.100523502
0.314695586
339
ORF sequence:
ATGCACACATCGTTGTATCGGATCCAGAGGACTCCACAGGGAGATTCCCGGACTCTTCCATTTTCTGAGAATGTGAGTGCTGTTCAGAAATTAGACTTTTCAGATACAATGGTGCAACAGAAATTGGACGACATCAAGGATCGAATAAAGAGAGAAATAAGGAAAGAACTGAAAATCAAAGAAGGAGCTGAAAACCTGAGGAAAGTTACAACAGATAAGAAAAATTTGGCTTATGTAGACAACATTTTGAAAAAATCAAATAAAAAATTAGAAGAATTACATCACAAGCTACAAGAATTAAATGCACACATCGTTGTATCGGATCCAGAGGACTCCACA
Peptide sequence:
MHTSLYRIQRTPQGDSRTLPFSENVSAVQKLDFSDTMVQQKLDDIKDRIKREIRKELKIKEGAENLRKVTTDKKNLAYVDNILKKSNKKLEELHHKLQELNAHIVVSDPEDST
IRESfinder result
IRESfinder score
0.589340482
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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