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mmu_circTop1_578
Basic information of circular RNA
PanCircBase ID:
mmu_circTop1_578
mm39_Chr. Position ID:
chr2|160544621|160547241|+
Gene name:
Top1
Transcript:
ENSMUST00000109468.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
10,11,12,13
Exon/intron offsets:
0,870,2081,2475
Genomic length:
2620
Exon/intron sizes in nt:
1,22,12,31,88,145
Flanking exon/introns:
chr2:160540159-160544621|chr2:160547241-160554564
Splice length:
578
Other database IDs:
circAtlas: mmu-Top1_0006
circBase: hsa_circ_0115216, circAtlas: hsa-TOP1_0005, CIRCpedia: HSA_CIRCpedia_34216
Human Ortholog IDs:
Mature spliced Sequence:
GTAAAGTTATGAAGCTGAGTCCTAAAGCAGAAGAAGTAGCTACATTCTTTGCAAAAATGCTTGACCACGAATATACTACTAAGGAAATATTCAGGAAAAATTTCTTTAAAGATTGGAGAAAGGAAATGACTAATGACGAAAAAAATACGATTACCAACCTAAGCAAATGCGACTTTACACAGATGAGCCAGTATTTCAAAGCGCAGTCAGAAGCTCGGAAACAGATGAGCAAGGAAGAAAAATTGAAAATCAAAGAAGAAAATGAAAAGTTATTGAAAGAATACGGCTTTTGTGTAATGGATAATCATAGAGAGCGGATTGCCAACTTCAAGATAGAGCCTCCGGGGCTTTTCCGAGGCCGAGGGAACCACCCCAAGATGGGTATGCTGAAGAGAAGGATCATGCCTGAGGACATCATCATCAACTGTAGCAAAGACGCAAAGGTTCCTTCTCCCCCTCCTGGACATAAATGGAAGGAAGTCCGACATGATAACAAGGTTACTTGGCTGGTCTCCTGGACAGAGAATATCCAAGGTTCTATCAAATATATCATGCTGAATCCCAGTTCACGAATCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TACTTGGCTGGTCTCCTGGA
59.88
TCGTGGTCAAGCATTTTTGCA
59.59
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TACTTGGCTGGTCTCCTGGA
59.88
CGTGGTCAAGCATTTTTGCA
58.15
148
PCR template sequence:
AGTCCGACATGATAACAAGGTTACTTGGCTGGTCTCCTGGACAGAGAATATCCAAGGTTCTATCAAATATATCATGCTGAATCCCAGTTCACGAATCAAGGTAAAGTTATGAAGCTGAGTCCTAAAGCAGAAGAAGTAGCTACATTCTTTGCAAAAATGCTTGACCACGAATATACTACTAAGGAAATATTCAGGAAAAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-139-5p(1), mmu-miR-190b-5p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTCACGAATCAAGGTAAAGTTATGAA
siRNA sets
TAACTTTACCTTGATTCGT,ATAACTTTACCTTGATTCG,AACTTTACCTTGATTCGTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTOP1_578_ORF_1
0.8841
0.182891394
0.789453044
582
ORF sequence:
ATGAAGCTGAGTCCTAAAGCAGAAGAAGTAGCTACATTCTTTGCAAAAATGCTTGACCACGAATATACTACTAAGGAAATATTCAGGAAAAATTTCTTTAAAGATTGGAGAAAGGAAATGACTAATGACGAAAAAAATACGATTACCAACCTAAGCAAATGCGACTTTACACAGATGAGCCAGTATTTCAAAGCGCAGTCAGAAGCTCGGAAACAGATGAGCAAGGAAGAAAAATTGAAAATCAAAGAAGAAAATGAAAAGTTATTGAAAGAATACGGCTTTTGTGTAATGGATAATCATAGAGAGCGGATTGCCAACTTCAAGATAGAGCCTCCGGGGCTTTTCCGAGGCCGAGGGAACCACCCCAAGATGGGTATGCTGAAGAGAAGGATCATGCCTGAGGACATCATCATCAACTGTAGCAAAGACGCAAAGGTTCCTTCTCCCCCTCCTGGACATAAATGGAAGGAAGTCCGACATGATAACAAGGTTACTTGGCTGGTCTCCTGGACAGAGAATATCCAAGGTTCTATCAAATATATCATGCTGAATCCCAGTTCACGAATCAAGGTAAAGTTATGA
Peptide sequence:
MKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNDEKNTITNLSKCDFTQMSQYFKAQSEARKQMSKEEKLKIKEENEKLLKEYGFCVMDNHRERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKVKL
IRESfinder result
IRESfinder score
0.455283688
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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