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mmu_circTop1_335
Basic information of circular RNA
PanCircBase ID:
mmu_circTop1_335
mm39_Chr. Position ID:
chr2|160526367|160535722|+
Gene name:
Top1
Transcript:
ENSMUST00000109468.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,6,7,8
Exon/intron offsets:
0,3200,5829,9248
Genomic length:
9355
Exon/intron sizes in nt:
56,96,76,107
Flanking exon/introns:
chr2:160524694-160526367|chr2:160535722-160540043
Splice length:
335
Other database IDs:
CIRCpedia: HSA_CIRCpedia_367517
Human Ortholog IDs:
Mature spliced Sequence:
ATTAGAGCTGCTGGGGATGCAAAAATAAAGAAGGAAAAGGAAAATGGCTTCTCTAGTCCGCCACGAATTAAAGATGAACCTGAGGATGATGGCTATTTTGCTCCTCCAAAAGAGGATATTAAGCCATTGAAGAGGCTTCGAGATGAAGATGATGCTGATTATAAACCTAAGAAAATTAAGACAGAAGATATCAAGAAGGAGAAGAAAAGAAAATCAGAAGAGGAAGAGGATGGTAAACTTAAAAAGCCCAAGAATAAAGATAAAGATAAAAAAGTTGCTGAGCCAGATAATAAGAAAAAGAAGCCGAAAAAGGAAGAGGAACAGAAGTGGAAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAAAAGTTGCTGAGCCAGAT
55.83
AGCCATCATCCTCAGGTTCA
58.41
161
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAAAAGTTGCTGAGCCAGAT
55.83
GCCATCATCCTCAGGTTCATCT
59.89
160
PCR template sequence:
AACTTAAAAAGCCCAAGAATAAAGATAAAGATAAAAAAGTTGCTGAGCCAGATAATAAGAAAAAGAAGCCGAAAAAGGAAGAGGAACAGAAGTGGAAATGATTAGAGCTGCTGGGGATGCAAAAATAAAGAAGGAAAAGGAAAATGGCTTCTCTAGTCCGCCACGAATTAAAGATGAACCTGAGGATGATGGCTATTTTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(1), mmu-miR-324-5p(1), mmu-miR-149-5p(1), mmu-miR-129-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAAGTGGAAATGATTAGAGCTGCTG
siRNA sets
AGCAGCTCTAATCATTTCC, CAGCTCTAATCATTTCCAC, TCTAATCATTTCCACTTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTOP1_335_ORF_1
1.1901
0.388316842
0.724467614
336
ORF sequence:
ATGATTAGAGCTGCTGGGGATGCAAAAATAAAGAAGGAAAAGGAAAATGGCTTCTCTAGTCCGCCACGAATTAAAGATGAACCTGAGGATGATGGCTATTTTGCTCCTCCAAAAGAGGATATTAAGCCATTGAAGAGGCTTCGAGATGAAGATGATGCTGATTATAAACCTAAGAAAATTAAGACAGAAGATATCAAGAAGGAGAAGAAAAGAAAATCAGAAGAGGAAGAGGATGGTAAACTTAAAAAGCCCAAGAATAAAGATAAAGATAAAAAAGTTGCTGAGCCAGATAATAAGAAAAAGAAGCCGAAAAAGGAAGAGGAACAGAAGTGGAAA
Peptide sequence:
MIRAAGDAKIKKEKENGFSSPPRIKDEPEDDGYFAPPKEDIKPLKRLRDEDDADYKPKKIKTEDIKKEKKRKSEEEEDGKLKKPKNKDKDKKVAEPDNKKKKPKKEEEQKWK
IRESfinder result
IRESfinder score
0.218911601
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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