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mmu_circRfx3_271
Basic information of circular RNA
PanCircBase ID:
mmu_circRfx3_271
mm39_Chr. Position ID:
chr19|27783587|27784308|-
Gene name:
Rfx3
Transcript:
ENSMUST00000165566.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
12,11
Exon/intron offsets:
0,605
Genomic length:
721
Exon/intron sizes in nt:
1,55,116
Flanking exon/introns:
chr19:27779879-27783587|chr19:27784308-27790977
Splice length:
271
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GCAATACTGGACGTTGTTGTGAATCTTCAGTTTAGCCTGATAGAAAAACTGTGGCAAACATTCTGGCGCTATTCCCCATCTACTCCAGCCGACGGCACTACCATCACGGAATCAAGCAATCTGAGTGAAATAGAAAGTCGACTTCCGAAAGCAAAGCTGATAACTCTGTGCAAACATGAGTCTATCCTGAAATGGATGTGTAACTGTGACCATGGGATGTACCAGGCTTTGGTGGAGATTCTCATCCCCGACGTCCTTAGACCCATTCCTA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GACCATGGGATGTACCAGGC
60.18
CGGCTGGAGTAGATGGGGAA
61.05
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GACCATGGGATGTACCAGGC
60.18
GGAGTAGATGGGGAATAGCGC
60.07
150
PCR template sequence:
AAACATGAGTCTATCCTGAAATGGATGTGTAACTGTGACCATGGGATGTACCAGGCTTTGGTGGAGATTCTCATCCCCGACGTCCTTAGACCCATTCCTAGCAATACTGGACGTTGTTGTGAATCTTCAGTTTAGCCTGATAGAAAAACTGTGGCAAACATTCTGGCGCTATTCCCCATCTACTCCAGCCGACGGCACTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-5101(1), mmu-miR-542-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGACCCATTCCTAGCAATACTGGACG
siRNA sets
TATTGCTAGGAATGGGTCT, CAGTATTGCTAGGAATGGG, AGTATTGCTAGGAATGGGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRFX3_271_ORF_1
0.6362
0.084955054
0.206856421
330
ORF sequence:
ATGGGATGTACCAGGCTTTGGTGGAGATTCTCATCCCCGACGTCCTTAGACCCATTCCTAGCAATACTGGACGTTGTTGTGAATCTTCAGTTTAGCCTGATAGAAAAACTGTGGCAAACATTCTGGCGCTATTCCCCATCTACTCCAGCCGACGGCACTACCATCACGGAATCAAGCAATCTGAGTGAAATAGAAAGTCGACTTCCGAAAGCAAAGCTGATAACTCTGTGCAAACATGAGTCTATCCTGAAATGGATGTGTAACTGTGACCATGGGATGTACCAGGCTTTGGTGGAGATTCTCATCCCCGACGTCCTTAGACCCATTCCT
Peptide sequence:
MGCTRLWWRFSSPTSLDPFLAILDVVVNLQFSLIEKLWQTFWRYSPSTPADGTTITESSNLSEIESRLPKAKLITLCKHESILKWMCNCDHGMYQALVEILIPDVLRPIP
IRESfinder result
IRESfinder score
0.509903517
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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