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mmu_circPrkce_1180
Basic information of circular RNA
PanCircBase ID:
mmu_circPrkce_1180
mm39_Chr. Position ID:
chr17|86781744|86866733|+
Gene name:
Prkce
Transcript:
ENSMUST00000097275.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
3,4,5,6,7,8,9,10,11
Exon/intron offsets:
0,1198,2489,7803,13843,16434,18904,21621,84834
Genomic length:
84989
Exon/intron sizes in nt:
160,35,86,130,143,97,200,174,155
Flanking exon/introns:
chr17:86661046-86781744|chr17:86866733-86927319
Splice length:
1180
Other database IDs:
CIRCpedia: MMU_CIRCpedia_32458, circAtlas: mmu-Prkce_0002
circAtlas: hsa-PRKCE_0002, CIRCpedia: HSA_CIRCpedia_69566
Human Ortholog IDs:
Mature spliced Sequence:
CCCCTAAAGACAATGAAGAACGAGTGTTCAGGGAGCGTATGCGGCCAAGGAAGCGGCAAGGGGCTGTCAGGCGCAGGGTCCACCAGGTCAATGGCCACAAGTTCATGGCCACCTACTTGCGGCAACCCACCTACTGCTCCCACTGCAGAGATTTCATCTGGGGTGTCATAGGAAAACAGGGATATCAATGTCAAGTTTGCACTTGCGTTGTCCACAAGCGATGTCATGAGCTCATTATTACAAAGTGCGCTGGGCTGAAGAAACAGGAAACCCCTGACGAGGTGGGCTCCCAACGGTTCAGCGTCAACATGCCCCACAAGTTCGGGATCCACAACTACAAGGTCCCCACGTTCTGTGACCACTGTGGGTCCCTGCTCTGGGGCCTCTTGCGGCAGGGCTTGCAGTGTAAAGTCTGCAAAATGAATGTTCACCGGCGATGTGAGACCAATGTGGCTCCCAACTGTGGGGTAGACGCCAGAGGAATTGCCAAAGTGCTGGCTGACCTTGGTGTTACTCCAGACAAAATCACCAACAGTGGCCAAAGGAGGAAAAAGCTCGCTGCTGGTGCTGAGTCCCCACAGCCGGCTTCTGGAAACTCCCCATCTGAAGACGACCGATCCAAGTCAGCGCCCACCTCCCCTTGTGACCAGGAACTAAAAGAACTTGAAAACAACATTCGGAAGGCCTTGTCATTTGACAACCGAGGAGAGGAGCACCGAGCGTCGTCGGCCACCGATGGCCAGCTGGCAAGCCCCGGAGAGAACGGGGAAGTCCGGCCAGGCCAGGCCAAGCGCTTGGGGCTGGATGAGTTCAACTTCATCAAGGTGTTGGGCAAAGGCAGCTTTGGCAAGGTCATGTTGGCGGAACTCAAAGGCAAAGATGAAGTCTACGCTGTGAAGGTCTTGAAGAAGGACGTTATCCTACAAGACGATGATGTGGACTGCACAATGACAGAGAAGAGGATTTTGGCTCTGGCTCGGAAACACCCTTATCTAACCCAACTCTATTGCTGCTTCCAGACCAAGGACCGCCTCTTCTTCGTCATGGAATATGTAAATGGTGGAGACCTCATGTTCCAGATTCAGCGGTCCCGAAAATTTGATGAGCCTCGTTCTCGGTTCTATGCCGCAGAGGTCACATCAGCCCTCATGTTTCTCCACCAGCACGGAGTGATCTACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TATGCCGCAGAGGTCACATC
59.9
CATTGACCTGGTGGACCCTG
60.32
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTATGCCGCAGAGGTCACAT
59.89
CATTGACCTGGTGGACCCTG
60.32
153
PCR template sequence:
TTCAGCGGTCCCGAAAATTTGATGAGCCTCGTTCTCGGTTCTATGCCGCAGAGGTCACATCAGCCCTCATGTTTCTCCACCAGCACGGAGTGATCTACAGCCCCTAAAGACAATGAAGAACGAGTGTTCAGGGAGCGTATGCGGCCAAGGAAGCGGCAAGGGGCTGTCAGGCGCAGGGTCCACCAGGTCAATGGCCACAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
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-138-5p(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
GAGTGATCTACAGCCCCTAAAGACAA
siRNA sets
TTAGGGGCTGTAGATCACT, CTTTAGGGGCTGTAGATCA, TTTAGGGGCTGTAGATCAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPRKCE_1180_ORF_1
1.047
0.353884309
0.998319894
1149
ORF sequence:
ATGCGGCCAAGGAAGCGGCAAGGGGCTGTCAGGCGCAGGGTCCACCAGGTCAATGGCCACAAGTTCATGGCCACCTACTTGCGGCAACCCACCTACTGCTCCCACTGCAGAGATTTCATCTGGGGTGTCATAGGAAAACAGGGATATCAATGTCAAGTTTGCACTTGCGTTGTCCACAAGCGATGTCATGAGCTCATTATTACAAAGTGCGCTGGGCTGAAGAAACAGGAAACCCCTGACGAGGTGGGCTCCCAACGGTTCAGCGTCAACATGCCCCACAAGTTCGGGATCCACAACTACAAGGTCCCCACGTTCTGTGACCACTGTGGGTCCCTGCTCTGGGGCCTCTTGCGGCAGGGCTTGCAGTGTAAAGTCTGCAAAATGAATGTTCACCGGCGATGTGAGACCAATGTGGCTCCCAACTGTGGGGTAGACGCCAGAGGAATTGCCAAAGTGCTGGCTGACCTTGGTGTTACTCCAGACAAAATCACCAACAGTGGCCAAAGGAGGAAAAAGCTCGCTGCTGGTGCTGAGTCCCCACAGCCGGCTTCTGGAAACTCCCCATCTGAAGACGACCGATCCAAGTCAGCGCCCACCTCCCCTTGTGACCAGGAACTAAAAGAACTTGAAAACAACATTCGGAAGGCCTTGTCATTTGACAACCGAGGAGAGGAGCACCGAGCGTCGTCGGCCACCGATGGCCAGCTGGCAAGCCCCGGAGAGAACGGGGAAGTCCGGCCAGGCCAGGCCAAGCGCTTGGGGCTGGATGAGTTCAACTTCATCAAGGTGTTGGGCAAAGGCAGCTTTGGCAAGGTCATGTTGGCGGAACTCAAAGGCAAAGATGAAGTCTACGCTGTGAAGGTCTTGAAGAAGGACGTTATCCTACAAGACGATGATGTGGACTGCACAATGACAGAGAAGAGGATTTTGGCTCTGGCTCGGAAACACCCTTATCTAACCCAACTCTATTGCTGCTTCCAGACCAAGGACCGCCTCTTCTTCGTCATGGAATATGTAAATGGTGGAGACCTCATGTTCCAGATTCAGCGGTCCCGAAAATTTGATGAGCCTCGTTCTCGGTTCTATGCCGCAGAGGTCACATCAGCCCTCATGTTTCTCCACCAGCACGGAGTGATCTACAGCCCCTAA
Peptide sequence:
MRPRKRQGAVRRRVHQVNGHKFMATYLRQPTYCSHCRDFIWGVIGKQGYQCQVCTCVVHKRCHELIITKCAGLKKQETPDEVGSQRFSVNMPHKFGIHNYKVPTFCDHCGSLLWGLLRQGLQCKVCKMNVHRRCETNVAPNCGVDARGIAKVLADLGVTPDKITNSGQRRKKLAAGAESPQPASGNSPSEDDRSKSAPTSPCDQELKELENNIRKALSFDNRGEEHRASSATDGQLASPGENGEVRPGQAKRLGLDEFNFIKVLGKGSFGKVMLAELKGKDEVYAVKVLKKDVILQDDDVDCTMTEKRILALARKHPYLTQLYCCFQTKDRLFFVMEYVNGGDLMFQIQRSRKFDEPRSRFYAAEVTSALMFLHQHGVIYSP
IRESfinder result
IRESfinder score
0.229624461
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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