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mmu_circPdcd11_995
Basic information of circular RNA
PanCircBase ID:
mmu_circPdcd11_995
mm39_Chr. Position ID:
chr19|47081220|47089609|+
Gene name:
Pdcd11
Transcript:
ENSMUST00000072141.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
2,3,4,5,6,7,8
Exon/intron offsets:
0,969,2426,4073,5339,5909,8281
Genomic length:
8389
Exon/intron sizes in nt:
11,91,32,16,81,62,12,40,00,000
Flanking exon/introns:
chr19:47079306-47081220|chr19:47089609-47091005
Splice length:
995
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CTGCAGAAGACCCCAACATGGCAAACCTGGAGGAAAGCTTCCCCCGAGGGGGGACACGGAAACTCCACAAATCAGAGAAGTCTTCCCAGCAGGTGGTTGAACAAGACAACTTATTTGATGTTTCCACAGAAGAAGGTCCCATTAAAAGGAAAAAGAGCCAGAAAGGGCCAGCAAAAACAAAAAAATTGAAAATTGAAAAGAGAAAATCCATCAAATCTATAAAAGAGAAGTTTGAAATTCTTAGTCTTGAGTCCCTATGTGAGGGGATGCGGATTTTGGGCTGTGTGAAGGAGGTGAGTGAGCTGGAGCTGGTGGTCAGCCTTCCCAACGGCCTCCAAGGGTTTGTGCAAGTGACCGAAGTCTGTGACGCCTACACTCAGAAGCTGAATGAGCAGGTGGCACAAGAAGAACCTCTGGAGGACCTGCTCCGCCTGCCTGAGCTCTTCTCCCCTGGAATGTTGGTGAGGTGTGTGGTGAGCAGCCTGGATGTCACAGAGAGTGGCAAGAAGAGCGTCAAGCTTTCTGTGAACCCCAAACGTGTCAACAAAGTGCTGAGTGCTGATGCCCTGAGGCCTGGCATGCTGCTGACAGGCACAGTGTCAAGCCTGGAAGACCATGGCTACCTAGTGGACATTGGCGTTGGTGGGACCAGAGCTTTTCTGTCACTTAAGAAGGCACAAGAGTACATCCGGCAGAAGAACAAAGGTGCTAAGTTCAAAGTCGGCCAGTACCTGACCTGTGTGGTTGAAGAGGTGAAAAGCAACGGAGGAGTTGTGAGTCTCTCTGTAGAGCACTCCGAGGTTTCCTCTGCCTTCGCAACTGAGGAGCAAAGCTGGAACCTGAATAACTTACTACCAGGGCTGCTGGTCAAAGCCCAGGTGCAGAAGGTAACTCAGTTTGGACTCCAGCTAAATTTCCTTACGTTCTTCAAGGGCCTGGTTGACTTCATGCATCTGGAGCCCAAGAAAATGGGATCTTATTCTTCAAATCAAACG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTTCAAGGGCCTGGTTGAC
59.89
TTGTGGAGTTTCCGTGTCCC
60.18
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTTCAAGGGCCTGGTTGACT
59.89
TTGTGGAGTTTCCGTGTCCC
60.18
140
PCR template sequence:
GTTTGGACTCCAGCTAAATTTCCTTACGTTCTTCAAGGGCCTGGTTGACTTCATGCATCTGGAGCCCAAGAAAATGGGATCTTATTCTTCAAATCAAACGCTGCAGAAGACCCCAACATGGCAAACCTGGAGGAAAGCTTCCCCCGAGGGGGGACACGGAAACTCCACAAATCAGAGAAGTCTTCCCAGCAGGTGGTTGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-7b-5p(1), mmu-miR-103-3p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-328-3p(1), mmu-miR-298-5p(1), mmu-miR-7a-5p(1), mmu-miR-324-5p(1), mmu-miR-149-5p(1), mmu-miR-382-5p(1), mmu-miR-370-3p(1), mmu-miR-107-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTCAAATCAAACGCTGCAGAAGACCC
siRNA sets
TTCTGCAGCGTTTGATTTG, TCTGCAGCGTTTGATTTGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDCD11_995_ORF_1
1.1107
0.222901361
0.997781484
1167
ORF sequence:
ATGGCAAACCTGGAGGAAAGCTTCCCCCGAGGGGGGACACGGAAACTCCACAAATCAGAGAAGTCTTCCCAGCAGGTGGTTGAACAAGACAACTTATTTGATGTTTCCACAGAAGAAGGTCCCATTAAAAGGAAAAAGAGCCAGAAAGGGCCAGCAAAAACAAAAAAATTGAAAATTGAAAAGAGAAAATCCATCAAATCTATAAAAGAGAAGTTTGAAATTCTTAGTCTTGAGTCCCTATGTGAGGGGATGCGGATTTTGGGCTGTGTGAAGGAGGTGAGTGAGCTGGAGCTGGTGGTCAGCCTTCCCAACGGCCTCCAAGGGTTTGTGCAAGTGACCGAAGTCTGTGACGCCTACACTCAGAAGCTGAATGAGCAGGTGGCACAAGAAGAACCTCTGGAGGACCTGCTCCGCCTGCCTGAGCTCTTCTCCCCTGGAATGTTGGTGAGGTGTGTGGTGAGCAGCCTGGATGTCACAGAGAGTGGCAAGAAGAGCGTCAAGCTTTCTGTGAACCCCAAACGTGTCAACAAAGTGCTGAGTGCTGATGCCCTGAGGCCTGGCATGCTGCTGACAGGCACAGTGTCAAGCCTGGAAGACCATGGCTACCTAGTGGACATTGGCGTTGGTGGGACCAGAGCTTTTCTGTCACTTAAGAAGGCACAAGAGTACATCCGGCAGAAGAACAAAGGTGCTAAGTTCAAAGTCGGCCAGTACCTGACCTGTGTGGTTGAAGAGGTGAAAAGCAACGGAGGAGTTGTGAGTCTCTCTGTAGAGCACTCCGAGGTTTCCTCTGCCTTCGCAACTGAGGAGCAAAGCTGGAACCTGAATAACTTACTACCAGGGCTGCTGGTCAAAGCCCAGGTGCAGAAGGTAACTCAGTTTGGACTCCAGCTAAATTTCCTTACGTTCTTCAAGGGCCTGGTTGACTTCATGCATCTGGAGCCCAAGAAAATGGGATCTTATTCTTCAAATCAAACGCTGCAGAAGACCCCAACATGGCAAACCTGGAGGAAAGCTTCCCCCGAGGGGGGACACGGAAACTCCACAAATCAGAGAAGTCTTCCCAGCAGGTGGTTGAACAAGACAACTTATTTGATGTTTCCACAGAAGAAGGTCCCATTAAAAGGAAAAAGAGCCAGAAAGGGCCAGCAAAAACAAAAAAATTGA
Peptide sequence:
MANLEESFPRGGTRKLHKSEKSSQQVVEQDNLFDVSTEEGPIKRKKSQKGPAKTKKLKIEKRKSIKSIKEKFEILSLESLCEGMRILGCVKEVSELELVVSLPNGLQGFVQVTEVCDAYTQKLNEQVAQEEPLEDLLRLPELFSPGMLVRCVVSSLDVTESGKKSVKLSVNPKRVNKVLSADALRPGMLLTGTVSSLEDHGYLVDIGVGGTRAFLSLKKAQEYIRQKNKGAKFKVGQYLTCVVEEVKSNGGVVSLSVEHSEVSSAFATEEQSWNLNNLLPGLLVKAQVQKVTQFGLQLNFLTFFKGLVDFMHLEPKKMGSYSSNQTLQKTPTWQTWRKASPEGGHGNSTNQRSLPSRWLNKTTYLMFPQKKVPLKGKRARKGQQKQKN
IRESfinder result
IRESfinder score
0.461578777
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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