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mmu_circPlekhh2_420
Basic information of circular RNA
PanCircBase ID:
mmu_circPlekhh2_420
mm39_Chr. Position ID:
chr17|84884585|84893904|+
Gene name:
Plekhh2
Transcript:
ENSMUST00000047206.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
15,16,17
Exon/intron offsets:
0,6307,9139
Genomic length:
9319
Exon/intron sizes in nt:
1,59,81,180
Flanking exon/introns:
chr17:84883231-84884585|chr17:84893904-84896812
Splice length:
420
Other database IDs:
CIRCpedia: MMU_CIRCpedia_219623, circAtlas: mmu-Plekhh2_0001
circBase: hsa_circ_0054324, circAtlas: hsa-PLEKHH2_0053, CIRCpedia: HSA_CIRCpedia_41372
Human Ortholog IDs:
Mature spliced Sequence:
CTGGCCACAGAGAAGCACACATACTATCTGACGGCGGATTCTCCCAATATACTGGAAGAATGGATCAAAGTGTTACAGAGCGTTCTGCGAGTACAAGCTGCGAACCCTCTTTGCCTGCAGCCTGAGGGCAAACCCGCAGTAAAGGGCTTGCTCACCAAGGTGAAGCATGGCTACTCTAAGAGGGTCTGGTGCATGCTTGTTGGAAAGGTCTTGTATTATTTCCGCAATCAAGAGGATAAGTTCCCTCTAGGTCAGCTCAAACTCTGGGAGGCTAAGGTGGAAGAGGTGGACAGGTCCTGTGACTCCGACGAGGACTATGAGACCCGGGGGTGCTATCTGCTGTCCACTCACTACACCATCATTGTCCACCCCAAAGACCAGGGCCCTACTTACCTGCTCATCGGATCTAAGCACGAGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CACCATCATTGTCCACCCCA
59.96
TTGTACTCGCAGAACGCTCT
59.4
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACACCATCATTGTCCACCCC
59.96
TTGTACTCGCAGAACGCTCT
59.4
164
PCR template sequence:
GACCCGGGGGTGCTATCTGCTGTCCACTCACTACACCATCATTGTCCACCCCAAAGACCAGGGCCCTACTTACCTGCTCATCGGATCTAAGCACGAGAAGCTGGCCACAGAGAAGCACACATACTATCTGACGGCGGATTCTCCCAATATACTGGAAGAATGGATCAAAGTGTTACAGAGCGTTCTGCGAGTACAAGCTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-1187(1), mmu-miR-369-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TAAGCACGAGAAGCTGGCCACAGAGA
siRNA sets
TCTCTGTGGCCAGCTTCTC,TGTGGCCAGCTTCTCGTGC,TCTGTGGCCAGCTTCTCGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPLEKHH2_420_ORF_1
1.0288
0.375125283
0.945851037
648
ORF sequence:
ATGCTTGTTGGAAAGGTCTTGTATTATTTCCGCAATCAAGAGGATAAGTTCCCTCTAGGTCAGCTCAAACTCTGGGAGGCTAAGGTGGAAGAGGTGGACAGGTCCTGTGACTCCGACGAGGACTATGAGACCCGGGGGTGCTATCTGCTGTCCACTCACTACACCATCATTGTCCACCCCAAAGACCAGGGCCCTACTTACCTGCTCATCGGATCTAAGCACGAGAAGCTGGCCACAGAGAAGCACACATACTATCTGACGGCGGATTCTCCCAATATACTGGAAGAATGGATCAAAGTGTTACAGAGCGTTCTGCGAGTACAAGCTGCGAACCCTCTTTGCCTGCAGCCTGAGGGCAAACCCGCAGTAAAGGGCTTGCTCACCAAGGTGAAGCATGGCTACTCTAAGAGGGTCTGGTGCATGCTTGTTGGAAAGGTCTTGTATTATTTCCGCAATCAAGAGGATAAGTTCCCTCTAGGTCAGCTCAAACTCTGGGAGGCTAAGGTGGAAGAGGTGGACAGGTCCTGTGACTCCGACGAGGACTATGAGACCCGGGGGTGCTATCTGCTGTCCACTCACTACACCATCATTGTCCACCCCAAAGACCAGGGCCCTACTTACCTGCTCATCGGATCTAAGCACGAGAAG
Peptide sequence:
MLVGKVLYYFRNQEDKFPLGQLKLWEAKVEEVDRSCDSDEDYETRGCYLLSTHYTIIVHPKDQGPTYLLIGSKHEKLATEKHTYYLTADSPNILEEWIKVLQSVLRVQAANPLCLQPEGKPAVKGLLTKVKHGYSKRVWCMLVGKVLYYFRNQEDKFPLGQLKLWEAKVEEVDRSCDSDEDYETRGCYLLSTHYTIIVHPKDQGPTYLLIGSKHEK
IRESfinder result
IRESfinder score
0.406099065
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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