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mmu_circPde3b_1300
Basic information of circular RNA
PanCircBase ID:
mmu_circPde3b_1300
mm39_Chr. Position ID:
chr7|114105421|114130098|+
Gene name:
Pde3b
Transcript:
ENSMUST00000032909.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
5,6,7,8,9,10,11,12,13
Exon/intron offsets:
0,1908,2652,12094,13325,15477,17146,20594,24473
Genomic length:
24677
Exon/intron sizes in nt:
1,07,21,17,41,40,13,81,00,00,00,00,000
Flanking exon/introns:
chr7:114097286-114105421|chr7:114130098-114131481
Splice length:
1300
Other database IDs:
circAtlas: mmu-Pde3b_0034
Human Ortholog IDs:
Mature spliced Sequence:
TCATGGATGCCACCTAAATGGGCCTTTTAGTTCAAATCTTTTTACAATTCCAAAGCAGAGGTCATCGTCTGTGTCACTGACGCACCATGCAGGTCTGAGAAGAGCTGGTGCTTTGCCCAGCCACAGTCTTCTGAATTCTTCAAGCCATGTACCAGTGTCTGCTGGCTCTCTAACTAATCGATCACCCATAGGATTTCCTGATACCACTGATTTTCTTACTAAGCCAAATATTATTTTACATAGATCACTGGGCAGTGTATCAAGTGCAGCAGATTTCCATCAGTACCTTAGGAACTCTGACAGCAATCTGTGTAGCAGCTGTGGACACCAAATACTCAAATATGTTTCAACATGTGAACCCGATGGTACAGACCACCCCAGTGAAAAATCAGGTGAAGAAGACAGCAGTGTTTTCTCAAAAGAACCATTGAACATTGTGGAAACCCAAGAAGAAGAGACCATGAAGAAAGCCTGCAGGGAGTTATTTTTGGAAGGTGATAGTCACCTGATGGAAGAGGCACAGCAACCAAATATCGATCAGGAAGTGTCACTGGATCCAATGTTAGTAGAAGATTATGATTCATTAATAGAAAAGATGAACAACTGGAATTTTCAGATTTTTGAGCTTGTAGAAAAGATGGGAGAAAAATCAGGAAGGATTCTCAGTCAGGTTATGTATACTTTATTTCAAGATACTGGTTTATTGGAAACATTTAAAATTCCCACTCAAGAATTTATGAATTATTTTCGTGCCTTAGAAAATGGCTACCGGGACATTCCATATCACAATCGTGTGCATGCCACAGATGTCCTACATGCTGTTTGGTATTTGACAACCCGACCAATTCCTGGCTTACCTCAGATCCATAATAACCATGAAACGGAAACCAAAGCAGATTCAGATGGTAGACTTGGTTCTGGACAGATTGCTTACATTTCTTCGAAGAGTTGCTGTATTCCAGATATGAGTTATGGCTGCCTATCTTCAAACATCCCTGCATTAGAATTGATGGCTTTGTATGTGGCAGCTGCCATGCACGATTACGATCACCCAGGAAGAACAAATGCGTTTCTAGTGGCTACAAATGCACCTCAGGCAGTTTTATACAATGACAGATCTGTTCTAGAGAATCATCATGCTGCATCAGCTTGGAATCTGTATCTTTCTCGCCCAGAGTACAACTTCCTCCTTAACCTTGATCACATGGAATTCAAGCGGTTTCGATTTTTAGTTATAGAAGCAATCCTTGCTACAGATCTCAAAAAACATTTTGATTTCCTTGCAGAATTCAATGCCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAATTCAAGCGGTTTCGA
58.11
ACACAGACGATGACCTCTGC
59.76
169
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACATGGAATTCAAGCGGTTTCG
60.1
ACACAGACGATGACCTCTGC
59.76
172
PCR template sequence:
TCACATGGAATTCAAGCGGTTTCGATTTTTAGTTATAGAAGCAATCCTTGCTACAGATCTCAAAAAACATTTTGATTTCCTTGCAGAATTCAATGCCAAGTCATGGATGCCACCTAAATGGGCCTTTTAGTTCAAATCTTTTTACAATTCCAAAGCAGAGGTCATCGTCTGTGTCACTGACGCACCATGCAGGTCTGAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-124-3p(1), mmu-miR-9-5p(1), mmu-miR-1a-3p(1), mmu-miR-206-3p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-351-5p(1), mmu-miR-22-3p(1), mmu-miR-324-3p(1), mmu-miR-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTCAATGCCAAGTCATGGATGCCAC
siRNA sets
ATCCATGACTTGGCATTGA, TGGCATCCATGACTTGGCA, CATCCATGACTTGGCATTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDE3B_1300_ORF_1
0.9356
-0.004058219
0.997152267
1308
ORF sequence:
ATGCCAAGTCATGGATGCCACCTAAATGGGCCTTTTAGTTCAAATCTTTTTACAATTCCAAAGCAGAGGTCATCGTCTGTGTCACTGACGCACCATGCAGGTCTGAGAAGAGCTGGTGCTTTGCCCAGCCACAGTCTTCTGAATTCTTCAAGCCATGTACCAGTGTCTGCTGGCTCTCTAACTAATCGATCACCCATAGGATTTCCTGATACCACTGATTTTCTTACTAAGCCAAATATTATTTTACATAGATCACTGGGCAGTGTATCAAGTGCAGCAGATTTCCATCAGTACCTTAGGAACTCTGACAGCAATCTGTGTAGCAGCTGTGGACACCAAATACTCAAATATGTTTCAACATGTGAACCCGATGGTACAGACCACCCCAGTGAAAAATCAGGTGAAGAAGACAGCAGTGTTTTCTCAAAAGAACCATTGAACATTGTGGAAACCCAAGAAGAAGAGACCATGAAGAAAGCCTGCAGGGAGTTATTTTTGGAAGGTGATAGTCACCTGATGGAAGAGGCACAGCAACCAAATATCGATCAGGAAGTGTCACTGGATCCAATGTTAGTAGAAGATTATGATTCATTAATAGAAAAGATGAACAACTGGAATTTTCAGATTTTTGAGCTTGTAGAAAAGATGGGAGAAAAATCAGGAAGGATTCTCAGTCAGGTTATGTATACTTTATTTCAAGATACTGGTTTATTGGAAACATTTAAAATTCCCACTCAAGAATTTATGAATTATTTTCGTGCCTTAGAAAATGGCTACCGGGACATTCCATATCACAATCGTGTGCATGCCACAGATGTCCTACATGCTGTTTGGTATTTGACAACCCGACCAATTCCTGGCTTACCTCAGATCCATAATAACCATGAAACGGAAACCAAAGCAGATTCAGATGGTAGACTTGGTTCTGGACAGATTGCTTACATTTCTTCGAAGAGTTGCTGTATTCCAGATATGAGTTATGGCTGCCTATCTTCAAACATCCCTGCATTAGAATTGATGGCTTTGTATGTGGCAGCTGCCATGCACGATTACGATCACCCAGGAAGAACAAATGCGTTTCTAGTGGCTACAAATGCACCTCAGGCAGTTTTATACAATGACAGATCTGTTCTAGAGAATCATCATGCTGCATCAGCTTGGAATCTGTATCTTTCTCGCCCAGAGTACAACTTCCTCCTTAACCTTGATCACATGGAATTCAAGCGGTTTCGATTTTTAGTTATAGAAGCAATCCTTGCTACAGATCTCAAAAAACATTTTGATTTCCTTGCAGAATTCAATGCCAAG
Peptide sequence:
MPSHGCHLNGPFSSNLFTIPKQRSSSVSLTHHAGLRRAGALPSHSLLNSSSHVPVSAGSLTNRSPIGFPDTTDFLTKPNIILHRSLGSVSSAADFHQYLRNSDSNLCSSCGHQILKYVSTCEPDGTDHPSEKSGEEDSSVFSKEPLNIVETQEEETMKKACRELFLEGDSHLMEEAQQPNIDQEVSLDPMLVEDYDSLIEKMNNWNFQIFELVEKMGEKSGRILSQVMYTLFQDTGLLETFKIPTQEFMNYFRALENGYRDIPYHNRVHATDVLHAVWYLTTRPIPGLPQIHNNHETETKADSDGRLGSGQIAYISSKSCCIPDMSYGCLSSNIPALELMALYVAAAMHDYDHPGRTNAFLVATNAPQAVLYNDRSVLENHHAASAWNLYLSRPEYNFLLNLDHMEFKRFRFLVIEAILATDLKKHFDFLAEFNAK
IRESfinder result
IRESfinder score
0.745372489
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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