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mmu_circPrkce_1025
Basic information of circular RNA
PanCircBase ID:
mmu_circPrkce_1025
mm39_Chr. Position ID:
chr17|86781744|86803539|+
Gene name:
Prkce
Transcript:
ENSMUST00000097275.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
3,4,5,6,7,8,9,10
Exon/intron offsets:
0,1198,2489,7803,13843,16434,18904,21621
Genomic length:
21795
Exon/intron sizes in nt:
160,35,86,130,143,97,200,174
Flanking exon/introns:
chr17:86661046-86781744|chr17:86803539-86866578
Splice length:
1025
Other database IDs:
circBase: mmu_circ_0007079, CIRCpedia: MMU_CIRCpedia_32457, circAtlas: mmu-Prkce_0004
circBase: hsa_circ_0120157, circAtlas: hsa-PRKCE_0004, CIRCpedia: HSA_CIRCpedia_41494
Human Ortholog IDs:
Mature spliced Sequence:
CCCCTAAAGACAATGAAGAACGAGTGTTCAGGGAGCGTATGCGGCCAAGGAAGCGGCAAGGGGCTGTCAGGCGCAGGGTCCACCAGGTCAATGGCCACAAGTTCATGGCCACCTACTTGCGGCAACCCACCTACTGCTCCCACTGCAGAGATTTCATCTGGGGTGTCATAGGAAAACAGGGATATCAATGTCAAGTTTGCACTTGCGTTGTCCACAAGCGATGTCATGAGCTCATTATTACAAAGTGCGCTGGGCTGAAGAAACAGGAAACCCCTGACGAGGTGGGCTCCCAACGGTTCAGCGTCAACATGCCCCACAAGTTCGGGATCCACAACTACAAGGTCCCCACGTTCTGTGACCACTGTGGGTCCCTGCTCTGGGGCCTCTTGCGGCAGGGCTTGCAGTGTAAAGTCTGCAAAATGAATGTTCACCGGCGATGTGAGACCAATGTGGCTCCCAACTGTGGGGTAGACGCCAGAGGAATTGCCAAAGTGCTGGCTGACCTTGGTGTTACTCCAGACAAAATCACCAACAGTGGCCAAAGGAGGAAAAAGCTCGCTGCTGGTGCTGAGTCCCCACAGCCGGCTTCTGGAAACTCCCCATCTGAAGACGACCGATCCAAGTCAGCGCCCACCTCCCCTTGTGACCAGGAACTAAAAGAACTTGAAAACAACATTCGGAAGGCCTTGTCATTTGACAACCGAGGAGAGGAGCACCGAGCGTCGTCGGCCACCGATGGCCAGCTGGCAAGCCCCGGAGAGAACGGGGAAGTCCGGCCAGGCCAGGCCAAGCGCTTGGGGCTGGATGAGTTCAACTTCATCAAGGTGTTGGGCAAAGGCAGCTTTGGCAAGGTCATGTTGGCGGAACTCAAAGGCAAAGATGAAGTCTACGCTGTGAAGGTCTTGAAGAAGGACGTTATCCTACAAGACGATGATGTGGACTGCACAATGACAGAGAAGAGGATTTTGGCTCTGGCTCGGAAACACCCTTATCTAACCCAACTCTATTGCTGCTTCCAGACCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATTTTGGCTCTGGCTCGGAA
59.96
CATTGACCTGGTGGACCCTG
60.32
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACGATGATGTGGACTGCACA
59.68
GCATACGCTCCCTGAACACT
60.11
140
PCR template sequence:
AGACGATGATGTGGACTGCACAATGACAGAGAAGAGGATTTTGGCTCTGGCTCGGAAACACCCTTATCTAACCCAACTCTATTGCTGCTTCCAGACCAAGCCCCTAAAGACAATGAAGAACGAGTGTTCAGGGAGCGTATGCGGCCAAGGAAGCGGCAAGGGGCTGTCAGGCGCAGGGTCCACCAGGTCAATGGCCACAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(1), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-181b-5p(1), mmu-miR-24-3p(1), mmu-miR-301b-3p(1), mmu-miR-705(1), mmu-miR-29b-2-5p(1), mmu-miR-300-3p(1), mmu-miR-670-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTTCCAGACCAAGCCCCTAAAGACAA
siRNA sets
TTTAGGGGCTTGGTCTGGA, CTTTAGGGGCTTGGTCTGG, TCTTTAGGGGCTTGGTCTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPRKCE_1025_ORF_1
0.8419
0.301563874
0.997168358
1158
ORF sequence:
ATGCGGCCAAGGAAGCGGCAAGGGGCTGTCAGGCGCAGGGTCCACCAGGTCAATGGCCACAAGTTCATGGCCACCTACTTGCGGCAACCCACCTACTGCTCCCACTGCAGAGATTTCATCTGGGGTGTCATAGGAAAACAGGGATATCAATGTCAAGTTTGCACTTGCGTTGTCCACAAGCGATGTCATGAGCTCATTATTACAAAGTGCGCTGGGCTGAAGAAACAGGAAACCCCTGACGAGGTGGGCTCCCAACGGTTCAGCGTCAACATGCCCCACAAGTTCGGGATCCACAACTACAAGGTCCCCACGTTCTGTGACCACTGTGGGTCCCTGCTCTGGGGCCTCTTGCGGCAGGGCTTGCAGTGTAAAGTCTGCAAAATGAATGTTCACCGGCGATGTGAGACCAATGTGGCTCCCAACTGTGGGGTAGACGCCAGAGGAATTGCCAAAGTGCTGGCTGACCTTGGTGTTACTCCAGACAAAATCACCAACAGTGGCCAAAGGAGGAAAAAGCTCGCTGCTGGTGCTGAGTCCCCACAGCCGGCTTCTGGAAACTCCCCATCTGAAGACGACCGATCCAAGTCAGCGCCCACCTCCCCTTGTGACCAGGAACTAAAAGAACTTGAAAACAACATTCGGAAGGCCTTGTCATTTGACAACCGAGGAGAGGAGCACCGAGCGTCGTCGGCCACCGATGGCCAGCTGGCAAGCCCCGGAGAGAACGGGGAAGTCCGGCCAGGCCAGGCCAAGCGCTTGGGGCTGGATGAGTTCAACTTCATCAAGGTGTTGGGCAAAGGCAGCTTTGGCAAGGTCATGTTGGCGGAACTCAAAGGCAAAGATGAAGTCTACGCTGTGAAGGTCTTGAAGAAGGACGTTATCCTACAAGACGATGATGTGGACTGCACAATGACAGAGAAGAGGATTTTGGCTCTGGCTCGGAAACACCCTTATCTAACCCAACTCTATTGCTGCTTCCAGACCAAGCCCCTAAAGACAATGAAGAACGAGTGTTCAGGGAGCGTATGCGGCCAAGGAAGCGGCAAGGGGCTGTCAGGCGCAGGGTCCACCAGGTCAATGGCCACAAGTTCATGGCCACCTACTTGCGGCAACCCACCTACTGCTCCCACTGCAGAGATTTCATCTGGGGTGTCATAG
Peptide sequence:
MRPRKRQGAVRRRVHQVNGHKFMATYLRQPTYCSHCRDFIWGVIGKQGYQCQVCTCVVHKRCHELIITKCAGLKKQETPDEVGSQRFSVNMPHKFGIHNYKVPTFCDHCGSLLWGLLRQGLQCKVCKMNVHRRCETNVAPNCGVDARGIAKVLADLGVTPDKITNSGQRRKKLAAGAESPQPASGNSPSEDDRSKSAPTSPCDQELKELENNIRKALSFDNRGEEHRASSATDGQLASPGENGEVRPGQAKRLGLDEFNFIKVLGKGSFGKVMLAELKGKDEVYAVKVLKKDVILQDDDVDCTMTEKRILALARKHPYLTQLYCCFQTKPLKTMKNECSGSVCGQGSGKGLSGAGSTRSMATSSWPPTCGNPPTAPTAEISSGVS
IRESfinder result
IRESfinder score
0.205915756
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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