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mmu_ciPde4b_1346
Basic information of circular RNA
PanCircBase ID:
mmu_ciPde4b_1346
mm39_Chr. Position ID:
chr4|102453309|102454655|+
Gene name:
Pde4b
Transcript:
ENSMUST00000106911.8
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
10
Exon/intron offsets:
0
Genomic length:
1346
Exon/intron sizes in nt:
1346
Flanking exon/introns:
chr4:102453309-102454655
Splice length:
1346
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTATGAGCTGGGCACATGTGTGTGTAGCTCTCCACTACACACTCACACACACACACACACACACACAGACTCTCAGACATGCACATACACACACATATGCATACACCCACACACAGGGACACCCAGGGACACACACACACATACACACACACACACAGAGGTGCACACATGGACACACACACACACCATCCAACATTTATAAAAGAAGACGGATCACATATTCTTTTTCATTGAGTTTTATGATGCAGAAGCTGATGTAGCCTCTCTGTTAACTGCTGGAGCACCTAACCAAGGTCCTTCTATACAAAAAGACTGTTCCTTTGTCCTGAATATAGGCTCAGTCTCAGTAACGCAGAGTTCTTTGTGGACAGAACATCCTGCTGGGGAGGATGCAGAGAAAGCTGGCAGGCTGGGCTGCATTCGCCCAGAGGACAAAGATGGAAAGTATTCTGGGCACCAGGGAGAAAGTCTGCCCTGATAGGCAGGGCTAGGGATAACATGAAGAGCCTGTGACAATGCTGACCACTAAAGCCCAAACCCAGTAGCGGAGGAAGGGACTGAAAATGTTCTTTACTCCTGTAGGAGGCTGCACAGACACTGGCTGCTAAGTTTCTTGCAGCCTGGTCAAAGGATGAAGTGAGCTTCCTTGGAGGAAATCTTCTTCCATGAGGTCTTCTGAAAACTGCCATCAGAGAAAAGTGGACTAAACATTGAGCCAAGCCTCTGGCCAGCTATTCAAATTGAAATAAGTTACTCCCCTCAGCAGATAATCTTTGGAATAATACCACAGCAAATGTCTAAATGATGTTTCTTCCATGTCTGTGGGTGGTCCATAAACTCTAAGCTATTACCCATACCAGGCAGTCTTCATAACCTATTAATACTGAGTTAGGATTGAGTTCTACTCACTCCTCTGGCAGCTGAGCCCCCTTGATTTGACTTCAGGGATAATTAGCAAAGGCTGGAAAGTTTCCCCCAGCAGCTATCGCTGATAGAGCAAGGGAGAGACAGGGCAAAGGAGCAGAAGCCTGTGTGCAGTTGACCTGCCTTTGAAAGTAGCATCAGGTGAAGATGGGGTGTTGCCAAGTATAGGTCAGCAACTCAAGCTACAAACGCAAACATACTTGGGTGTTTCTCAACAAAAGAATGTGCAGAAACTTGTAGTTATCATGAAGAGGAGATACAGCCAGCCCACCATTCTCAGATTCTTATACGAACAGAACTCTAAACAAATGCATGAAAGAGTTGGTAGCTAATTTCTCCCAAATAAAATTTTATAAAATATTTTACACCATTAAAAAAAAAAAGCTTATTCTTAAATGTCTCTCATTTGGATTTGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGTTGGTAGCTAATTTCTCCCA
57.9
TGTGTGTGTGTGTGTGTGTG
59.13
167
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGTTGGTAGCTAATTTCTCCCA
57.9
TGTGTGTGTGTGTGTGTGTG
59.13
169
PCR template sequence:
GAGTTGGTAGCTAATTTCTCCCAAATAAAATTTTATAAAATATTTTACACCATTAAAAAAAAAAAGCTTATTCTTAAATGTCTCTCATTTGGATTTGCAGGTAAGTATGAGCTGGGCACATGTGTGTGTAGCTCTCCACTACACACTCACACACACACACACACACACACAGACTCTCAGACATGCACATACACACACAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
21
Interacting miRNAs (#binding sites)
mmu-miR-199a-5p(1), mmu-miR-103-3p(1), mmu-miR-221-3p(1), mmu-miR-217-5p(1), mmu-miR-222-3p(1), mmu-miR-339-5p(1), mmu-miR-24-3p(1), mmu-miR-22-3p(1), mmu-miR-182-5p(1), mmu-miR-192-5p(1), mmu-miR-215-5p(1), mmu-miR-297a-5p(1), mmu-miR-107-3p(1), mmu-miR-27a-5p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1), mmu-miR-539-5p(1), mmu-miR-669d-5p(1), mmu-miR-1904(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTGGATTTGCAGGTAAGTATGAGCT
siRNA sets
ATACTTACCTGCAAATCCA, CATACTTACCTGCAAATCC, TACTTACCTGCAAATCCAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIPDE4B_1346_ORF_1
0.3886
-0.407970866
0.017987804
312
ORF sequence:
ATGAAAGAGTTGGTAGCTAATTTCTCCCAAATAAAATTTTATAAAATATTTTACACCATTAAAAAAAAAAAGCTTATTCTTAAATGTCTCTCATTTGGATTTGCAGGTAAGTATGAGCTGGGCACATGTGTGTGTAGCTCTCCACTACACACTCACACACACACACACACACACACAGACTCTCAGACATGCACATACACACACATATGCATACACCCACACACAGGGACACCCAGGGACACACACACACATACACACACACACACAGAGGTGCACACATGGACACACACACACACCATCCAACATTTATAA
Peptide sequence:
MKELVANFSQIKFYKIFYTIKKKKLILKCLSFGFAGKYELGTCVCSSPLHTHTHTHTHTDSQTCTYTHICIHPHTGTPRDTHTHTHTHTEVHTWTHTHTIQHL
IRESfinder result
IRESfinder score
0.648268629
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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