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mmu_circPappa2_1323
Basic information of circular RNA
PanCircBase ID:
mmu_circPappa2_1323
mm39_Chr. Position ID:
chr1|158589099|158642442|-
Gene name:
Pappa2
Transcript:
ENSMUST00000159861.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
19,18,17,16,15,14,13,12
Exon/intron offsets:
0,1539,3398,20651,22367,26060,52810,53207
Genomic length:
53343
Exon/intron sizes in nt:
1,10,13,61,69,21,41,78,00,00,00,000
Flanking exon/introns:
chr1:158578171-158589099|chr1:158642442-158660278
Splice length:
1323
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GTGTGTTTCAATAGGCCAGGGGTTGCAGTGGCAATTTACATTTTCTTGGCATCGGATGGCGTGACCCCTGGGGAGCATCAGCAGGCAACAGTGACCCTTTACCTGATTGATGTCAGTGGAAGCAACCACTCTCTTGGAACCTATGGACTGTCGTGTCAACAAAATCCACTGGTTATCAATGTGAGCCATCATGTGAATGTCTACCCCCAACATACCTCCTCCATGCTGCTGAATTTTTCATCCCCACTGGTGGGCATCTCAGCAGTGGCTCTAAGGACATCCTCCCAGACCAGTTCTTCAGCTCCCAGTAACTGCATCCCAGAGCAAAATTATGAGGGAAAGAGCTGTGCTCAACGACCTTGTGGAGAACAGGGAAGATGTGCGCCATTGCTACTCGATCATACGGACATGGTGAATTGTACCTCCAGTAGCCCAGGTCACATGGAGTGCGCTATCACTTGTCAAAGGGGGTATGTCCTTCAGACCAGCAGTGGGCAGTACCTGAGGAACATGCAGAAAGAGATTCTCCTTACTTGTTCCTCTGGCCACTGGGACAAGGATGTGATCTGCAAGCGTCTTGACTGTGGTGTCCCAGACTCCTCCTTGGTGAATTATGCAAACTTCTCCTGCTTGGAGGGTACAGACTTTCTGAAACAATGTTCCATCTCGTGTGTCCCACCGGCTAAGCTCCAAGGACTGAACCCATGGCTGACATGTCTTGAAGATGGACTCTGGTCTCTCCCTGAAGTCTACTGCAAGTTGGAATGTGAAGCTCCTCCAGTTATTCCCAATGCCAATCTGCTCCTGCCACATTTCCTGGAAGGCAACCATGATGTGGGCACCATCTGCAAATATGAGTGCAAACCAGGCTACTATGTGAAGGAGACTTCAGGAAGTCAAGGCAAGAACAAGTTCCTGAAGATCCAGTGCCTGGATGATGGAAGCTGGGAACAAGGGAGCTGCGTCCCCGTGGTTTGTGAGCCTCCTCCTCCGGTGTTTGAAGGCATGTACGAATGTACTGATGGCTTCAAGCTGGACAGCCAGTGTGTGCTCAACTGTAACCAGGAAACGGAAGGGATTCCCATCCTCTGCACTAAAGAGGGGTTGTGGACCCAGGAATTCAAGTTGTGTGAAAACCTGCAAGGAGAATGCCCACCACCCACCTCAGAGCTGAATTCTGTGGAGTACAAGTGTGGACAGGGATATGGGATCGGTGCAGTGTGCTCCCCATCATGTGTAATCCCCCCTAGTGACCCTGTGATACTACCAGAGAATGTGACTACTGACACTTTGGAGCACTGGATGGAACCTGTCAAAGTCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCCCTAGTGACCCTGTGAT
60.33
GTCACTGTTGCCTGCTGATG
59.48
176
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCCCCTAGTGACCCTGTGAT
60.33
GGTCACTGTTGCCTGCTGAT
60.61
177
PCR template sequence:
CTCCCCATCATGTGTAATCCCCCCTAGTGACCCTGTGATACTACCAGAGAATGTGACTACTGACACTTTGGAGCACTGGATGGAACCTGTCAAAGTCCAGGTGTGTTTCAATAGGCCAGGGGTTGCAGTGGCAATTTACATTTTCTTGGCATCGGATGGCGTGACCCCTGGGGAGCATCAGCAGGCAACAGTGACCCTTT
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(2), mmu-miR-23a-3p(2), mmu-miR-103-3p(1), mmu-miR-298-5p(1), mmu-miR-185-5p(1), mmu-miR-339-5p(1), mmu-miR-181b-5p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-107-3p(1), mmu-miR-377-3p(1), mmu-miR-532-5p(1), mmu-miR-697(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGTCAAAGTCCAGGTGTGTTTCAATA
siRNA sets
TATTGAAACACACCTGGAC, AAACACACCTGGACTTTGA, ATTGAAACACACCTGGACT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPAPPA2_1323_ORF_1
0.6493
0.177934345
0.999999264
2424
ORF sequence:
ATGCTGCTGAATTTTTCATCCCCACTGGTGGGCATCTCAGCAGTGGCTCTAAGGACATCCTCCCAGACCAGTTCTTCAGCTCCCAGTAACTGCATCCCAGAGCAAAATTATGAGGGAAAGAGCTGTGCTCAACGACCTTGTGGAGAACAGGGAAGATGTGCGCCATTGCTACTCGATCATACGGACATGGTGAATTGTACCTCCAGTAGCCCAGGTCACATGGAGTGCGCTATCACTTGTCAAAGGGGGTATGTCCTTCAGACCAGCAGTGGGCAGTACCTGAGGAACATGCAGAAAGAGATTCTCCTTACTTGTTCCTCTGGCCACTGGGACAAGGATGTGATCTGCAAGCGTCTTGACTGTGGTGTCCCAGACTCCTCCTTGGTGAATTATGCAAACTTCTCCTGCTTGGAGGGTACAGACTTTCTGAAACAATGTTCCATCTCGTGTGTCCCACCGGCTAAGCTCCAAGGACTGAACCCATGGCTGACATGTCTTGAAGATGGACTCTGGTCTCTCCCTGAAGTCTACTGCAAGTTGGAATGTGAAGCTCCTCCAGTTATTCCCAATGCCAATCTGCTCCTGCCACATTTCCTGGAAGGCAACCATGATGTGGGCACCATCTGCAAATATGAGTGCAAACCAGGCTACTATGTGAAGGAGACTTCAGGAAGTCAAGGCAAGAACAAGTTCCTGAAGATCCAGTGCCTGGATGATGGAAGCTGGGAACAAGGGAGCTGCGTCCCCGTGGTTTGTGAGCCTCCTCCTCCGGTGTTTGAAGGCATGTACGAATGTACTGATGGCTTCAAGCTGGACAGCCAGTGTGTGCTCAACTGTAACCAGGAAACGGAAGGGATTCCCATCCTCTGCACTAAAGAGGGGTTGTGGACCCAGGAATTCAAGTTGTGTGAAAACCTGCAAGGAGAATGCCCACCACCCACCTCAGAGCTGAATTCTGTGGAGTACAAGTGTGGACAGGGATATGGGATCGGTGCAGTGTGCTCCCCATCATGTGTAATCCCCCCTAGTGACCCTGTGATACTACCAGAGAATGTGACTACTGACACTTTGGAGCACTGGATGGAACCTGTCAAAGTCCAGGTGTGTTTCAATAGGCCAGGGGTTGCAGTGGCAATTTACATTTTCTTGGCATCGGATGGCGTGACCCCTGGGGAGCATCAGCAGGCAACAGTGACCCTTTACCTGATTGATGTCAGTGGAAGCAACCACTCTCTTGGAACCTATGGACTGTCGTGTCAACAAAATCCACTGGTTATCAATGTGAGCCATCATGTGAATGTCTACCCCCAACATACCTCCTCCATGCTGCTGAATTTTTCATCCCCACTGGTGGGCATCTCAGCAGTGGCTCTAAGGACATCCTCCCAGACCAGTTCTTCAGCTCCCAGTAACTGCATCCCAGAGCAAAATTATGAGGGAAAGAGCTGTGCTCAACGACCTTGTGGAGAACAGGGAAGATGTGCGCCATTGCTACTCGATCATACGGACATGGTGAATTGTACCTCCAGTAGCCCAGGTCACATGGAGTGCGCTATCACTTGTCAAAGGGGGTATGTCCTTCAGACCAGCAGTGGGCAGTACCTGAGGAACATGCAGAAAGAGATTCTCCTTACTTGTTCCTCTGGCCACTGGGACAAGGATGTGATCTGCAAGCGTCTTGACTGTGGTGTCCCAGACTCCTCCTTGGTGAATTATGCAAACTTCTCCTGCTTGGAGGGTACAGACTTTCTGAAACAATGTTCCATCTCGTGTGTCCCACCGGCTAAGCTCCAAGGACTGAACCCATGGCTGACATGTCTTGAAGATGGACTCTGGTCTCTCCCTGAAGTCTACTGCAAGTTGGAATGTGAAGCTCCTCCAGTTATTCCCAATGCCAATCTGCTCCTGCCACATTTCCTGGAAGGCAACCATGATGTGGGCACCATCTGCAAATATGAGTGCAAACCAGGCTACTATGTGAAGGAGACTTCAGGAAGTCAAGGCAAGAACAAGTTCCTGAAGATCCAGTGCCTGGATGATGGAAGCTGGGAACAAGGGAGCTGCGTCCCCGTGGTTTGTGAGCCTCCTCCTCCGGTGTTTGAAGGCATGTACGAATGTACTGATGGCTTCAAGCTGGACAGCCAGTGTGTGCTCAACTGTAACCAGGAAACGGAAGGGATTCCCATCCTCTGCACTAAAGAGGGGTTGTGGACCCAGGAATTCAAGTTGTGTGAAAACCTGCAAGGAGAATGCCCACCACCCACCTCAGAGCTGAATTCTGTGGAGTACAAGTGTGGACAGGGATATGGGATCGGTGCAGTGTGCTCCCCATCATGTGTAATCCCCCCTAGTGACCCTGTGATACTACCAGAGAATGTGACTACTGACACTTTGGAGCACTGGATGGAACCTGTCAAAGTCCAG
Peptide sequence:
MLLNFSSPLVGISAVALRTSSQTSSSAPSNCIPEQNYEGKSCAQRPCGEQGRCAPLLLDHTDMVNCTSSSPGHMECAITCQRGYVLQTSSGQYLRNMQKEILLTCSSGHWDKDVICKRLDCGVPDSSLVNYANFSCLEGTDFLKQCSISCVPPAKLQGLNPWLTCLEDGLWSLPEVYCKLECEAPPVIPNANLLLPHFLEGNHDVGTICKYECKPGYYVKETSGSQGKNKFLKIQCLDDGSWEQGSCVPVVCEPPPPVFEGMYECTDGFKLDSQCVLNCNQETEGIPILCTKEGLWTQEFKLCENLQGECPPPTSELNSVEYKCGQGYGIGAVCSPSCVIPPSDPVILPENVTTDTLEHWMEPVKVQVCFNRPGVAVAIYIFLASDGVTPGEHQQATVTLYLIDVSGSNHSLGTYGLSCQQNPLVINVSHHVNVYPQHTSSMLLNFSSPLVGISAVALRTSSQTSSSAPSNCIPEQNYEGKSCAQRPCGEQGRCAPLLLDHTDMVNCTSSSPGHMECAITCQRGYVLQTSSGQYLRNMQKEILLTCSSGHWDKDVICKRLDCGVPDSSLVNYANFSCLEGTDFLKQCSISCVPPAKLQGLNPWLTCLEDGLWSLPEVYCKLECEAPPVIPNANLLLPHFLEGNHDVGTICKYECKPGYYVKETSGSQGKNKFLKIQCLDDGSWEQGSCVPVVCEPPPPVFEGMYECTDGFKLDSQCVLNCNQETEGIPILCTKEGLWTQEFKLCENLQGECPPPTSELNSVEYKCGQGYGIGAVCSPSCVIPPSDPVILPENVTTDTLEHWMEPVKVQ
IRESfinder result
IRESfinder score
0.476467527
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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