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mmu_circPrkca_713
Basic information of circular RNA
PanCircBase ID:
mmu_circPrkca_713
mm39_Chr. Position ID:
chr11|107903452|108083038|-
Gene name:
Prkca
Transcript:
ENSMUST00000059595.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
8,7,6,5,4,3
Exon/intron offsets:
0,318,1598,41348,45135,179503
Genomic length:
179586
Exon/intron sizes in nt:
97,135,157,129,112,83
Flanking exon/introns:
chr11:107877211-107903452|chr11:108083038-108231471
Splice length:
713
Other database IDs:
circAtlas: mmu-Prkca_0030
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_79579
Human Ortholog IDs:
Mature spliced Sequence:
TTTGCTGTTTTGTGGTTCATAAGAGGTGCCATGAGTTCGTTACGTTCTCTTGTCCGGGTGCGGATAAGGGACCTGACACTGACGACCCCAGGAGCAAGCACAAGTTCAAAATCCACACATACGGAAGCCCTACCTTCTGTGATCACTGTGGGTCCCTGCTCTATGGACTTATCCACCAAGGGATGAAATGTGACACCTGCGACATGAATGTTCACAAGCAGTGTGTGATCAATGTCCCTAGCCTCTGCGGAATGGATCACACAGAGAAGAGGGGGCGGATTTATCTGAAGGCTGAGGTCACTGATGAAAAGCTCCACGTCACGGTACGAGATGCAAAAAATCTAATCCCTATGGATCCAAATGGGCTTTCGGATCCTTATGTGAAGCTGAAACTTATCCCTGACCCCAAGAATGAGAGCAAACAGAAAACCAAAACCATCCGCTCCACACTGAATCCTCAGTGGAATGAGTCCTTCACGTTCAAATTAAAACCTTCAGACAAAGACCGGCGACTGTCTGTAGAAATCTGGGACTGGGATCGGACGACTCGGAATGACTTCATGGGATCCCTTTCCTTTGGTGTCTCAGAGCTAATGAAGATGCCGGCCAGTGGATGGTATAAACTGCTCAACCAAGAAGAGGGCGAATACTACAATGTGCCCATTCCAGAAGGAGATGAAGAAGGCAACATGGAACTCAGGCAGAAGTTTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTCAACCAAGAAGAGGGC
60.25
GTCAGGTCCCTTATCCGCAC
60.18
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTCAACCAAGAAGAGGGC
60.25
GTGTCAGGTCCCTTATCCGC
60.18
168
PCR template sequence:
ATGGTATAAACTGCTCAACCAAGAAGAGGGCGAATACTACAATGTGCCCATTCCAGAAGGAGATGAAGAAGGCAACATGGAACTCAGGCAGAAGTTTGAGTTTGCTGTTTTGTGGTTCATAAGAGGTGCCATGAGTTCGTTACGTTCTCTTGTCCGGGTGCGGATAAGGGACCTGACACTGACGACCCCAGGAGCAAGCA
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-181a-5p(1), mmu-miR-298-5p(1), mmu-miR-181b-5p(1), mmu-miR-218-5p(1), mmu-miR-541-5p(1), mmu-miR-1187(1), mmu-miR-335-3p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCAGAAGTTTGAGTTTGCTGTTTTGT
siRNA sets
AGCAAACTCAAACTTCTGC, CAGCAAACTCAAACTTCTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPRKCA_713_ORF_1
0.8474
0.242233111
0.921571632
717
ORF sequence:
ATGAAATGTGACACCTGCGACATGAATGTTCACAAGCAGTGTGTGATCAATGTCCCTAGCCTCTGCGGAATGGATCACACAGAGAAGAGGGGGCGGATTTATCTGAAGGCTGAGGTCACTGATGAAAAGCTCCACGTCACGGTACGAGATGCAAAAAATCTAATCCCTATGGATCCAAATGGGCTTTCGGATCCTTATGTGAAGCTGAAACTTATCCCTGACCCCAAGAATGAGAGCAAACAGAAAACCAAAACCATCCGCTCCACACTGAATCCTCAGTGGAATGAGTCCTTCACGTTCAAATTAAAACCTTCAGACAAAGACCGGCGACTGTCTGTAGAAATCTGGGACTGGGATCGGACGACTCGGAATGACTTCATGGGATCCCTTTCCTTTGGTGTCTCAGAGCTAATGAAGATGCCGGCCAGTGGATGGTATAAACTGCTCAACCAAGAAGAGGGCGAATACTACAATGTGCCCATTCCAGAAGGAGATGAAGAAGGCAACATGGAACTCAGGCAGAAGTTTGAGTTTGCTGTTTTGTGGTTCATAAGAGGTGCCATGAGTTCGTTACGTTCTCTTGTCCGGGTGCGGATAAGGGACCTGACACTGACGACCCCAGGAGCAAGCACAAGTTCAAAATCCACACATACGGAAGCCCTACCTTCTGTGATCACTGTGGGTCCCTGCTCTATGGACTTATCCACCAAGGGATGA
Peptide sequence:
MKCDTCDMNVHKQCVINVPSLCGMDHTEKRGRIYLKAEVTDEKLHVTVRDAKNLIPMDPNGLSDPYVKLKLIPDPKNESKQKTKTIRSTLNPQWNESFTFKLKPSDKDRRLSVEIWDWDRTTRNDFMGSLSFGVSELMKMPASGWYKLLNQEEGEYYNVPIPEGDEEGNMELRQKFEFAVLWFIRGAMSSLRSLVRVRIRDLTLTTPGASTSSKSTHTEALPSVITVGPCSMDLSTKG
IRESfinder result
IRESfinder score
0.387193088
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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