top of page
mmu_circPrkaa1_839
Basic information of circular RNA
PanCircBase ID:
mmu_circPrkaa1_839
mm39_Chr. Position ID:
chr15|5203688|5206686|+
Gene name:
Prkaa1
Transcript:
ENSMUST00000051186.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
6,7,8
Exon/intron offsets:
0,2278,2871
Genomic length:
2998
Exon/intron sizes in nt:
225,487,127
Flanking exon/introns:
chr15:5199497-5203688|chr15:5206686-5208168
Splice length:
839
Other database IDs:
circBase: mmu_circ_0005694, CIRCpedia: MMU_CIRCpedia_22177, circAtlas: mmu-Prkaa1_0005
circAtlas: hsa-PRKAA1_0008, CIRCpedia: HSA_CIRCpedia_100981
Human Ortholog IDs:
Mature spliced Sequence:
ATTGTACGCAGGCCCCGAGGTGGACATCTGGAGCAGCGGGGTCATTCTCTATGCTTTGCTGTGTGGAACCCTCCCTTTTGATGATGACCATGTGCCAACTCTTTTTAAGAAGATATGTGATGGGATCTTTTATACCCCTCAGTACTTAAACCCTTCAGTAATCAGCCTTTTGAAACATATGCTGCAGGTGGATCCCATGAAGAGGGCCGCAATAAAAGATATCAGGGAACACGAGTGGTTTAAACAGGACCTTCCGAAGTATCTCTTTCCTGAGGACCCATCTTATAGTTCAACCATGATCGATGACGAAGCCTTGAAAGAAGTGTGTGAGAAGTTCGAGTGTTCGGAGGAGGAGGTCCTCAGCTGCCTGTACAACAGAAACCACCAGGACCCACTAGCCGTCGCCTACCACCTCATCATAGACAACAGGAGAATAATGAATGAAGCCAAAGATTTCTACCTAGCAACCAGCCCACCTGACTCTTTCCTGGACGACCACCATTTAACTCGGCCTCACCCTGAAAGAGTACCGTTCTTGGTTGCCGAAACACCACGGGCCCGGCACACCCTGGATGAATTAAACCCACAGAAATCCAAACACCAAGGTGTACGGAAGGCAAAATGGCATTTGGGAATTCGAAGTCAAAGCCGACCCAATGATATCATGGCAGAAGTTTGTAGAGCAATCAAGCAGTTGGATTATGAATGGAAGGTTGTAAACCCCTATTATTTGCGTGTACGAAGGAAGAATCCTGTGACAAGCACATTTTCCAAAATGAGTCTACAGCTATACCAAGTGGATAGTAGGACTTACTTGTTGGATTTCCGTAGTATTGATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGAAGAATCCTGTGACAAGCAC
59.51
ATAGAGAATGACCCCGCTGC
59.61
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGAAGAATCCTGTGACAAGCAC
59.51
GCATAGAGAATGACCCCGCT
59.61
150
PCR template sequence:
CGAAGGAAGAATCCTGTGACAAGCACATTTTCCAAAATGAGTCTACAGCTATACCAAGTGGATAGTAGGACTTACTTGTTGGATTTCCGTAGTATTGATGATTGTACGCAGGCCCCGAGGTGGACATCTGGAGCAGCGGGGTCATTCTCTATGCTTTGCTGTGTGGAACCCTCCCTTTTGATGATGACCATGTGCCAACT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-103-3p(1), mmu-miR-96-5p(1), mmu-miR-107-3p(1), mmu-miR-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CGTAGTATTGATGATTGTACGCAGGC
siRNA sets
TACAATCATCAATACTACG, GTACAATCATCAATACTAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPRKAA1_839_ORF_1
0.7249
0.115282024
0.915465085
810
ORF sequence:
ATGCTGCAGGTGGATCCCATGAAGAGGGCCGCAATAAAAGATATCAGGGAACACGAGTGGTTTAAACAGGACCTTCCGAAGTATCTCTTTCCTGAGGACCCATCTTATAGTTCAACCATGATCGATGACGAAGCCTTGAAAGAAGTGTGTGAGAAGTTCGAGTGTTCGGAGGAGGAGGTCCTCAGCTGCCTGTACAACAGAAACCACCAGGACCCACTAGCCGTCGCCTACCACCTCATCATAGACAACAGGAGAATAATGAATGAAGCCAAAGATTTCTACCTAGCAACCAGCCCACCTGACTCTTTCCTGGACGACCACCATTTAACTCGGCCTCACCCTGAAAGAGTACCGTTCTTGGTTGCCGAAACACCACGGGCCCGGCACACCCTGGATGAATTAAACCCACAGAAATCCAAACACCAAGGTGTACGGAAGGCAAAATGGCATTTGGGAATTCGAAGTCAAAGCCGACCCAATGATATCATGGCAGAAGTTTGTAGAGCAATCAAGCAGTTGGATTATGAATGGAAGGTTGTAAACCCCTATTATTTGCGTGTACGAAGGAAGAATCCTGTGACAAGCACATTTTCCAAAATGAGTCTACAGCTATACCAAGTGGATAGTAGGACTTACTTGTTGGATTTCCGTAGTATTGATGATTGTACGCAGGCCCCGAGGTGGACATCTGGAGCAGCGGGGTCATTCTCTATGCTTTGCTGTGTGGAACCCTCCCTTTTGATGATGACCATGTGCCAACTCTTTTTAAGAAGATATGTGATGGGATCTTTTATACCCCTCAGTACTTAA
Peptide sequence:
MLQVDPMKRAAIKDIREHEWFKQDLPKYLFPEDPSYSSTMIDDEALKEVCEKFECSEEEVLSCLYNRNHQDPLAVAYHLIIDNRRIMNEAKDFYLATSPPDSFLDDHHLTRPHPERVPFLVAETPRARHTLDELNPQKSKHQGVRKAKWHLGIRSQSRPNDIMAEVCRAIKQLDYEWKVVNPYYLRVRRKNPVTSTFSKMSLQLYQVDSRTYLLDFRSIDDCTQAPRWTSGAAGSFSMLCCVEPSLLMMTMCQLFLRRYVMGSFIPLST
IRESfinder result
IRESfinder score
0.575899322
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page