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mmu_circHerc1_286
Basic information of circular RNA
PanCircBase ID:
mmu_circHerc1_286
mm39_Chr. Position ID:
chr9|66307049|66307461|+
Gene name:
Herc1
Transcript:
ENSMUST00000042824.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
15,16
Exon/intron offsets:
0,279
Genomic length:
412
Exon/intron sizes in nt:
1,53,133
Flanking exon/introns:
chr9:66306761-66307049|chr9:66307461-66309805
Splice length:
286
Other database IDs:
circAtlas: hsa-HERC1_0026, CIRCpedia: HSA_CIRCpedia_144262
Human Ortholog IDs:
Mature spliced Sequence:
GATCAAGCATTTGGAGAGCTGGAAAAGAATAGTGATAAATATCTTCTTGGAACATCATCTTCAGAGAACAGTCAGCCTGCTCATCTTCATGAACTACTGTGTTCATTACAGAAACAACTGCTTGCTTTTTGCCACATTAATAATGTTACTGAGAACTCAAGCAGTGTGGCATTGCTTCATAAACATCTTCAGCTTTTGCTGCCTCATGCCACAGATATTTATTCACGTTCCGCAAATTTGCTTAAAGAAAGTCCTTGGAATGGCAGTGTTGGAGAAAAATTGAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGCCTCATGCCACAGATA
60.18
TGAAGATGAGCAGGCTGACT
58.73
178
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGCCTCATGCCACAGATA
60.18
ATGAAGATGAGCAGGCTGACT
59.16
179
PCR template sequence:
CTTCAGCTTTTGCTGCCTCATGCCACAGATATTTATTCACGTTCCGCAAATTTGCTTAAAGAAAGTCCTTGGAATGGCAGTGTTGGAGAAAAATTGAGAGGATCAAGCATTTGGAGAGCTGGAAAAGAATAGTGATAAATATCTTCTTGGAACATCATCTTCAGAGAACAGTCAGCCTGCTCATCTTCATGAACTACTGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-1a-3p(1), mmu-miR-709(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-324-3p(1), mmu-miR-802-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GAAAAATTGAGAGGATCAAGCATTTG
siRNA sets
CAAATGCTTGATCCTCTCA, AAATGCTTGATCCTCTCAA, AATGCTTGATCCTCTCAAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.840385801
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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