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mmu_ciPkp2_976
Basic information of circular RNA
PanCircBase ID:
mmu_ciPkp2_976
mm39_Chr. Position ID:
chr16|16086571|16087547|+
Gene name:
Pkp2
Transcript:
ENSMUST00000039408.3
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
11
Exon/intron offsets:
0
Genomic length:
976
Exon/intron sizes in nt:
976
Flanking exon/introns:
chr16:16086571-16087548
Splice length:
976
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTCTCTTAGCACCTGCCCATCACGGTCTCTATTTTGCTGCCACCAGCACTATATAAACACTCTAGCTGCAGTTACTCTTTCCTGAGTCTGATGGGCAAGATAGCCACAAGTAGTATCACAGACCAGGGCTGCAGCTTCTCTAGTTTTTGGTGATTGAGCAAGGGAAGAACTGAGTGCCACATTAAATCTTTAAAAAGAAAAAATCTCAAGTGTCAAACAACTAATGTACAGATAACTGTTATGAATATCAAACCCTTGACATTAAAGAACTTTCTAGAACTCTGAATATAAGAGAGCTGTAATATAAAGAGTTTGCTTACTCTGAGTGACTCTGTCCCTAGGCACTAAAGTGCTGTAAGACGCTAAGCTGACTCTCCTCTCCCTTCCATTCTGAAGAAGCAGCTCAGGAAGGAGCCCACATTTTTGTTCATTATGGTTTTGCTTTCTGTGGTCTTGATTGCATGTCAGTGGACTACTGTGACACAGGAAATCCACTACAGTCTTCGGAAAAGAAAGTTCAGCCATGGTTTAGTAGTTAGAAAGTTAGTAAGTAAAGTCACAAAGAAACTGATCTCTAGCTAGAAATGGTAAGTTTAAGACACATTTAGAAAAGGAACGTAAAAAAACAGTGTCACTGTCAAATGTGATGGGGAAAAACTCCTACATTTAGTCTCAGAGGCAAGAACATTTTCAGTTGTTTTCTGTGTTGCAATCTGTAAATATATAACTATATAAATGTAAAGGGTCTATAAGTAATTAAAAGCTATAAATATATATAAATATCATGGATTTTTCCCTTGTAAATCATTTATTTATTAGCACTACCTTTGTGATTTAAAAAAAAAAAAAAAAGCATCTTGAAAAGTGACCTGTGGCCTTCAGTTCCTCTTTGTGTGGCAACTGTTGAAGCCAGGTGAAGGGAAGGCCAAAGCTGCACATGCTCACTGACCCAGAAACATCTCTGTCTTTTCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTTGAAGCCAGGTGAAGGGA
59.89
GCCCATCAGACTCAGGAAAGA
59.44
170
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGTGAAGGGAAGGCCAAAG
59.89
GCCCATCAGACTCAGGAAAGA
59.44
161
PCR template sequence:
TGGCCTTCAGTTCCTCTTTGTGTGGCAACTGTTGAAGCCAGGTGAAGGGAAGGCCAAAGCTGCACATGCTCACTGACCCAGAAACATCTCTGTCTTTTCAGTAAGTCTCTTAGCACCTGCCCATCACGGTCTCTATTTTGCTGCCACCAGCACTATATAAACACTCTAGCTGCAGTTACTCTTTCCTGAGTCTGATGGGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(1), mmu-miR-135a-5p(1), mmu-miR-23a-3p(1), mmu-miR-138-5p(1), mmu-miR-96-5p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-377-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTCTGTCTTTTCAGTAAGTCTCTTAG
siRNA sets
AAGAGACTTACTGAAAAGA, AGAGACTTACTGAAAAGAC, TAAGAGACTTACTGAAAAG
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
0.844146819
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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