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mmu_circSyn2_389
Basic information of circular RNA
PanCircBase ID:
mmu_circSyn2_389
mm39_Chr. Position ID:
chr6|115238615|115251217|+
Gene name:
Syn2
Transcript:
ENSMUST00000009538.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
8,9,10,11
Exon/intron offsets:
0,867,2177,12541
Genomic length:
12602
Exon/intron sizes in nt:
75,103,150,61
Flanking exon/introns:
chr6:115231693-115238615|chr6:115251217-115255061
Splice length:
389
Other database IDs:
circAtlas: mmu-Syn2_0012
Human Ortholog IDs:
Mature spliced Sequence:
GAGGACATCCATCTCAGGGAACTGGAAGACAAACACTGGCTCGGCGATGCTGGAGCAAATTGCCATGTCGGACCGGTACAAGCTCTGGGTAGATGCCTGCTCTGAAATGTTTGGTGGCCTGGACATCTGTGCAGTCAAAGCCGTGCATGGCAAAGATGGCAAAGACTACATTTTTGAGGTCATGGACTGCAGCATGCCATTGATTGGGGAACACCAAGTGGAGGACAGACAACTCATCACTGATCTAGTCATCAGCAAGATGAACCAGCTATTGTCCAGGACTCCTGCCCTGTCTCCACAGAGACCTTTAACCACCCAACAGCCACAGAGTGGAACACTTAAGGAACCGGACTCCAGCAAGACCCCTCCTCAGCGGCCACCTCCCCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TAACCACCCAACAGCCACAG
60.18
CCGACATGGCAATTTGCTCC
60.18
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TAACCACCCAACAGCCACAG
60.18
CGGTCCGACATGGCAATTTG
60.18
156
PCR template sequence:
CTGTCTCCACAGAGACCTTTAACCACCCAACAGCCACAGAGTGGAACACTTAAGGAACCGGACTCCAGCAAGACCCCTCCTCAGCGGCCACCTCCCCAAGGAGGACATCCATCTCAGGGAACTGGAAGACAAACACTGGCTCGGCGATGCTGGAGCAAATTGCCATGTCGGACCGGTACAAGCTCTGGGTAGATGCCTGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-199a-5p(1), mmu-miR-92a-3p(1), mmu-miR-709(1), mmu-miR-431-5p(1), mmu-miR-680(1), mmu-miR-670-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCACCTCCCCAAGGAGGACATCCATC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSYN2_389_ORF_1
0.6389
0.194344492
0.465177064
435
ORF sequence:
ATGCTGGAGCAAATTGCCATGTCGGACCGGTACAAGCTCTGGGTAGATGCCTGCTCTGAAATGTTTGGTGGCCTGGACATCTGTGCAGTCAAAGCCGTGCATGGCAAAGATGGCAAAGACTACATTTTTGAGGTCATGGACTGCAGCATGCCATTGATTGGGGAACACCAAGTGGAGGACAGACAACTCATCACTGATCTAGTCATCAGCAAGATGAACCAGCTATTGTCCAGGACTCCTGCCCTGTCTCCACAGAGACCTTTAACCACCCAACAGCCACAGAGTGGAACACTTAAGGAACCGGACTCCAGCAAGACCCCTCCTCAGCGGCCACCTCCCCAAGGAGGACATCCATCTCAGGGAACTGGAAGACAAACACTGGCTCGGCGATGCTGGAGCAAATTGCCATGTCGGACCGGTACAAGCTCTGGGTAG
Peptide sequence:
MLEQIAMSDRYKLWVDACSEMFGGLDICAVKAVHGKDGKDYIFEVMDCSMPLIGEHQVEDRQLITDLVISKMNQLLSRTPALSPQRPLTTQQPQSGTLKEPDSSKTPPQRPPPQGGHPSQGTGRQTLARRCWSKLPCRTGTSSG
IRESfinder result
IRESfinder score
0.297877659
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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