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mmu_circPde3b_1096
Basic information of circular RNA
PanCircBase ID:
mmu_circPde3b_1096
mm39_Chr. Position ID:
chr7|114105421|114126215|+
Gene name:
Pde3b
Transcript:
ENSMUST00000032909.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
5,6,7,8,9,10,11,12
Exon/intron offsets:
0,1908,2652,12094,13325,15477,17146,20594
Genomic length:
20794
Exon/intron sizes in nt:
10,72,11,74,14,01,38,10,00,00,000
Flanking exon/introns:
chr7:114097286-114105421|chr7:114126215-114129894
Splice length:
1096
Other database IDs:
CIRCpedia: MMU_CIRCpedia_214668, circAtlas: mmu-Pde3b_0003
circBase: hsa_circ_0095422, circAtlas: hsa-PDE3B_0002, CIRCpedia: HSA_CIRCpedia_114333
Human Ortholog IDs:
Mature spliced Sequence:
TCATGGATGCCACCTAAATGGGCCTTTTAGTTCAAATCTTTTTACAATTCCAAAGCAGAGGTCATCGTCTGTGTCACTGACGCACCATGCAGGTCTGAGAAGAGCTGGTGCTTTGCCCAGCCACAGTCTTCTGAATTCTTCAAGCCATGTACCAGTGTCTGCTGGCTCTCTAACTAATCGATCACCCATAGGATTTCCTGATACCACTGATTTTCTTACTAAGCCAAATATTATTTTACATAGATCACTGGGCAGTGTATCAAGTGCAGCAGATTTCCATCAGTACCTTAGGAACTCTGACAGCAATCTGTGTAGCAGCTGTGGACACCAAATACTCAAATATGTTTCAACATGTGAACCCGATGGTACAGACCACCCCAGTGAAAAATCAGGTGAAGAAGACAGCAGTGTTTTCTCAAAAGAACCATTGAACATTGTGGAAACCCAAGAAGAAGAGACCATGAAGAAAGCCTGCAGGGAGTTATTTTTGGAAGGTGATAGTCACCTGATGGAAGAGGCACAGCAACCAAATATCGATCAGGAAGTGTCACTGGATCCAATGTTAGTAGAAGATTATGATTCATTAATAGAAAAGATGAACAACTGGAATTTTCAGATTTTTGAGCTTGTAGAAAAGATGGGAGAAAAATCAGGAAGGATTCTCAGTCAGGTTATGTATACTTTATTTCAAGATACTGGTTTATTGGAAACATTTAAAATTCCCACTCAAGAATTTATGAATTATTTTCGTGCCTTAGAAAATGGCTACCGGGACATTCCATATCACAATCGTGTGCATGCCACAGATGTCCTACATGCTGTTTGGTATTTGACAACCCGACCAATTCCTGGCTTACCTCAGATCCATAATAACCATGAAACGGAAACCAAAGCAGATTCAGATGGTAGACTTGGTTCTGGACAGATTGCTTACATTTCTTCGAAGAGTTGCTGTATTCCAGATATGAGTTATGGCTGCCTATCTTCAAACATCCCTGCATTAGAATTGATGGCTTTGTATGTGGCAGCTGCCATGCACGATTACGATCACCCAGGAAGAACAAATGCGTTTCTAGTGGCTACAAATGCACCTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCTGCCATGCACGATTAC
59.97
ACACAGACGATGACCTCTGC
59.76
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCTTTGTATGTGGCAGCTG
59.83
ACACAGACGATGACCTCTGC
59.76
159
PCR template sequence:
TGCATTAGAATTGATGGCTTTGTATGTGGCAGCTGCCATGCACGATTACGATCACCCAGGAAGAACAAATGCGTTTCTAGTGGCTACAAATGCACCTCAGTCATGGATGCCACCTAAATGGGCCTTTTAGTTCAAATCTTTTTACAATTCCAAAGCAGAGGTCATCGTCTGTGTCACTGACGCACCATGCAGGTCTGAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
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-22-3p(1), mmu-miR-324-3p(1), mmu-miR-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAATGCACCTCAGTCATGGATGCCAC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDE3B_1096_ORF_1
0.8612
-0.009040509
0.986056444
1107
ORF sequence:
ATGCACCTCAGTCATGGATGCCACCTAAATGGGCCTTTTAGTTCAAATCTTTTTACAATTCCAAAGCAGAGGTCATCGTCTGTGTCACTGACGCACCATGCAGGTCTGAGAAGAGCTGGTGCTTTGCCCAGCCACAGTCTTCTGAATTCTTCAAGCCATGTACCAGTGTCTGCTGGCTCTCTAACTAATCGATCACCCATAGGATTTCCTGATACCACTGATTTTCTTACTAAGCCAAATATTATTTTACATAGATCACTGGGCAGTGTATCAAGTGCAGCAGATTTCCATCAGTACCTTAGGAACTCTGACAGCAATCTGTGTAGCAGCTGTGGACACCAAATACTCAAATATGTTTCAACATGTGAACCCGATGGTACAGACCACCCCAGTGAAAAATCAGGTGAAGAAGACAGCAGTGTTTTCTCAAAAGAACCATTGAACATTGTGGAAACCCAAGAAGAAGAGACCATGAAGAAAGCCTGCAGGGAGTTATTTTTGGAAGGTGATAGTCACCTGATGGAAGAGGCACAGCAACCAAATATCGATCAGGAAGTGTCACTGGATCCAATGTTAGTAGAAGATTATGATTCATTAATAGAAAAGATGAACAACTGGAATTTTCAGATTTTTGAGCTTGTAGAAAAGATGGGAGAAAAATCAGGAAGGATTCTCAGTCAGGTTATGTATACTTTATTTCAAGATACTGGTTTATTGGAAACATTTAAAATTCCCACTCAAGAATTTATGAATTATTTTCGTGCCTTAGAAAATGGCTACCGGGACATTCCATATCACAATCGTGTGCATGCCACAGATGTCCTACATGCTGTTTGGTATTTGACAACCCGACCAATTCCTGGCTTACCTCAGATCCATAATAACCATGAAACGGAAACCAAAGCAGATTCAGATGGTAGACTTGGTTCTGGACAGATTGCTTACATTTCTTCGAAGAGTTGCTGTATTCCAGATATGAGTTATGGCTGCCTATCTTCAAACATCCCTGCATTAGAATTGATGGCTTTGTATGTGGCAGCTGCCATGCACGATTACGATCACCCAGGAAGAACAAATGCGTTTCTAGTGGCTACAAATGCACCTCAG
Peptide sequence:
MHLSHGCHLNGPFSSNLFTIPKQRSSSVSLTHHAGLRRAGALPSHSLLNSSSHVPVSAGSLTNRSPIGFPDTTDFLTKPNIILHRSLGSVSSAADFHQYLRNSDSNLCSSCGHQILKYVSTCEPDGTDHPSEKSGEEDSSVFSKEPLNIVETQEEETMKKACRELFLEGDSHLMEEAQQPNIDQEVSLDPMLVEDYDSLIEKMNNWNFQIFELVEKMGEKSGRILSQVMYTLFQDTGLLETFKIPTQEFMNYFRALENGYRDIPYHNRVHATDVLHAVWYLTTRPIPGLPQIHNNHETETKADSDGRLGSGQIAYISSKSCCIPDMSYGCLSSNIPALELMALYVAAAMHDYDHPGRTNAFLVATNAPQ
IRESfinder result
IRESfinder score
0.722679829
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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