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mmu_circRfx3_1040
Basic information of circular RNA
PanCircBase ID:
mmu_circRfx3_1040
mm39_Chr. Position ID:
chr19|27792884|27900666|-
Gene name:
Rfx3
Transcript:
ENSMUST00000165566.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
9,8,7,6,5,4,3,2
Exon/intron offsets:
0,10548,15126,21922,34226,52028,85294,107723
Genomic length:
107782
Exon/intron sizes in nt:
122,120,182,75,259,98,125,59
Flanking exon/introns:
chr19:27791090-27792884|chr19:27900666-27960253
Splice length:
1040
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AGATTTTTATCAGAGGAATGTAGACTGGAATCTGCAATGGTTCTCAAAATCCCAAAGTGAGACCATCATGCAGACTTCAGAGACGGGTTCAGACACAGGTTCGACAGTGACTCTGCAGACGTCTGTGGCTAGCCAAGCAGCAGTGCCTACACAGGTGGTACAGCAAGTGCCAGTGCAGCAGCAGGTGCAGCAGGTACAGACAGTTCAGCAGGTCCAACATGTCTACCCAGCTCAGGTGCAGTATGTGGAAGGAAGTGATACTGTCTATACCAATGGAGCAATCCGAACAACAACTTATCCCTACACAGAAACACAGATGTACAGCCAAAACACTGGAGGAAATTACTTTGATACTCAAGGAAGTTCTGCCCAGGTGACAACTGTGGTGTCCTCCCACAGTATGGTGGGTACTGGTGGGATTCAGATGGGCGTCACAGGAGGACAACTCATCAGCAGCTCGGGAGGAACCTATTTGATCGGCAATTCAATGGAGAACTCTGGTCACTCAGTGACACACACAACTCGGGCCTCCCCAGCAACAATTGAAATGGCGATTGAGACGCTGCAAAAGTCTGACGGTCTGTCCACTCACAGAAGCTCTCTTCTCAACAGCCATCTGCAATGGCTGCTGGACAATTATGAGACAGCGGAGGGAGTGAGCCTGCCGAGGAGCACGCTGTACAACCACTACCTTCGACACTGCCAGGAGCACAAGCTGGACCCGGTCAATGCCGCCTCTTTCGGAAAACTAATAAGGTCCATTTTTATGGGGCTACGAACTAGGAGATTAGGCACTAGAGGAAACTCCAAATACCATTACTATGGGATTCGTGTGAAGCCAGATTCTCCTCTTAACCGTCTACAAGAAGATATGCAGTACATGGCTATGAGGCAGCAGCCCATGCAACAGAAGCAAAGGTACAAGCCTATGCAGAAAGTGGATGGGGTTGCAGATGGTTTCACAGGAAGTGGCCAACAGACAGGCACATCTGTTGAGCAAACTGTAATTGCCCAAAGTCAACATCATCAACAGTTTTTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACAGGCACATCTGTTGAGCA
59.89
CCTGTGTCTGAACCCGTCTC
60.04
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGAAGTGGCCAACAGACAG
59.89
CCTGTGTCTGAACCCGTCTC
60.04
176
PCR template sequence:
GATGGGGTTGCAGATGGTTTCACAGGAAGTGGCCAACAGACAGGCACATCTGTTGAGCAAACTGTAATTGCCCAAAGTCAACATCATCAACAGTTTTTAGAGATTTTTATCAGAGGAATGTAGACTGGAATCTGCAATGGTTCTCAAAATCCCAAAGTGAGACCATCATGCAGACTTCAGAGACGGGTTCAGACACAGGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
18
Interacting miRNAs (#binding sites)
mmu-miR-136-5p(2), mmu-miR-370-3p(2), mmu-miR-29b-2-5p(2), mmu-miR-140-5p(1), mmu-miR-134-5p(1), mmu-let-7a-5p(1), mmu-miR-199a-5p(1), mmu-miR-375-3p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-let-7c-5p(1), mmu-let-7d-5p(1), mmu-miR-382-5p(1), mmu-miR-34b-5p(1), mmu-miR-98-5p(1), mmu-miR-484(1)
siRNAs for circular RNA silencing
Junction sequence
CAACAGTTTTTAGAGATTTTTATCAG
siRNA sets
ATAAAAATCTCTAAAAACT, TAAAAATCTCTAAAAACTG, AAAATCTCTAAAAACTGTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRFX3_1040_ORF_1
0.911
0.191746302
0.987554024
996
ORF sequence:
ATGCAGACTTCAGAGACGGGTTCAGACACAGGTTCGACAGTGACTCTGCAGACGTCTGTGGCTAGCCAAGCAGCAGTGCCTACACAGGTGGTACAGCAAGTGCCAGTGCAGCAGCAGGTGCAGCAGGTACAGACAGTTCAGCAGGTCCAACATGTCTACCCAGCTCAGGTGCAGTATGTGGAAGGAAGTGATACTGTCTATACCAATGGAGCAATCCGAACAACAACTTATCCCTACACAGAAACACAGATGTACAGCCAAAACACTGGAGGAAATTACTTTGATACTCAAGGAAGTTCTGCCCAGGTGACAACTGTGGTGTCCTCCCACAGTATGGTGGGTACTGGTGGGATTCAGATGGGCGTCACAGGAGGACAACTCATCAGCAGCTCGGGAGGAACCTATTTGATCGGCAATTCAATGGAGAACTCTGGTCACTCAGTGACACACACAACTCGGGCCTCCCCAGCAACAATTGAAATGGCGATTGAGACGCTGCAAAAGTCTGACGGTCTGTCCACTCACAGAAGCTCTCTTCTCAACAGCCATCTGCAATGGCTGCTGGACAATTATGAGACAGCGGAGGGAGTGAGCCTGCCGAGGAGCACGCTGTACAACCACTACCTTCGACACTGCCAGGAGCACAAGCTGGACCCGGTCAATGCCGCCTCTTTCGGAAAACTAATAAGGTCCATTTTTATGGGGCTACGAACTAGGAGATTAGGCACTAGAGGAAACTCCAAATACCATTACTATGGGATTCGTGTGAAGCCAGATTCTCCTCTTAACCGTCTACAAGAAGATATGCAGTACATGGCTATGAGGCAGCAGCCCATGCAACAGAAGCAAAGGTACAAGCCTATGCAGAAAGTGGATGGGGTTGCAGATGGTTTCACAGGAAGTGGCCAACAGACAGGCACATCTGTTGAGCAAACTGTAATTGCCCAAAGTCAACATCATCAACAGTTTTTAGAGATTTTTATCAGAGGAATGTAG
Peptide sequence:
MQTSETGSDTGSTVTLQTSVASQAAVPTQVVQQVPVQQQVQQVQTVQQVQHVYPAQVQYVEGSDTVYTNGAIRTTTYPYTETQMYSQNTGGNYFDTQGSSAQVTTVVSSHSMVGTGGIQMGVTGGQLISSSGGTYLIGNSMENSGHSVTHTTRASPATIEMAIETLQKSDGLSTHRSSLLNSHLQWLLDNYETAEGVSLPRSTLYNHYLRHCQEHKLDPVNAASFGKLIRSIFMGLRTRRLGTRGNSKYHYYGIRVKPDSPLNRLQEDMQYMAMRQQPMQQKQRYKPMQKVDGVADGFTGSGQQTGTSVEQTVIAQSQHHQQFLEIFIRGM
IRESfinder result
IRESfinder score
0.51183956
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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