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mmu_ciHerc1_877
Basic information of circular RNA
PanCircBase ID:
mmu_ciHerc1_877
mm39_Chr. Position ID:
chr9|66369202|66370079|+
Gene name:
Herc1
Transcript:
ENSMUST00000042824.13
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
44
Exon/intron offsets:
0
Genomic length:
877
Exon/intron sizes in nt:
877
Flanking exon/introns:
chr9:66369202-66370110
Splice length:
877
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGTGTGTGACTGCAGCGGGGGCTGCTCTGACTTATTTTCCTGCCCTCCTGTTCATACAGCTTACTAACAGCAGCCTTGCCTAGAGTTGAAGGAGTCTTTCATCTCATCCTGAGGTTTGGGGATTTAATGATTGAGCATTGCGTTGATACCCACAAACTGATAAGAAAGTCTATCTTGTTGCTTTCTCTGTGTAATTTATTGCTTCTCTCCCCAGACTAGATGACTAGAGCCATATTGTGGCAATACTTCATTGTGATGTTGAAGAGAAATTTCAAAACTTGACATTAGGCCCTAGTACATTGCTGGGTTGTATAACATGATTGCTTTAATCACATTCCTGTCTGAGTGCATGCTCTTGTCCTTCATAGTTTCTATTTAGTCAGTGTAAGGCTCATGTGGGAACCAGTGCCTACCCAGATCTTATAACACCCCTCGTCCAGGGATAGAGTTCATGTAGGTTTATGTGTATATTAGTTATTTAGCATTACATTTTTATAGGGAAAACTTTAAAGCTCATAGATGTGAACTTTTATCTACTTGATTAGGTTAATAACATAAATGAAACATAATGGCATCTTAGAAATTCAGAAAATAGGTCTTATAGCCAGGTAAAAAGTGTTTTCACTAGAGAATTTTTTTTAATGGTTTAAGATAAATTTAAATTAGTGAATTCCTTTTTTATTTCCAGCAGAATAATCTTAATTTATAAGTTAAGCAAATAGAAGAAAAGCAAAGCACACTTTCAGATTGTGTGGTCTGAATTCTGACTTGAAAGAAAATTATGTAGCACTAATGAGCACCATTGAATTATTGTAGGATATTAAAAAAAGTAGCTAGTTTTATATCACAAATAATCTACCTCTTACCCTAAGTTGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCACTAATGAGCACCATTGA
57.65
TGAACAGGAGGGCAGGAAAA
59.15
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCACTAATGAGCACCATTGA
57.65
TGTATGAACAGGAGGGCAGG
59.09
150
PCR template sequence:
AAATTATGTAGCACTAATGAGCACCATTGAATTATTGTAGGATATTAAAAAAAGTAGCTAGTTTTATATCACAAATAATCTACCTCTTACCCTAAGTTGAGTGTGTGTGACTGCAGCGGGGGCTGCTCTGACTTATTTTCCTGCCCTCCTGTTCATACAGCTTACTAACAGCAGCCTTGCCTAGAGTTGAAGGAGTCTTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-155-5p(1), mmu-let-7a-5p(1), mmu-miR-1a-3p(1), mmu-miR-206-3p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-221-3p(1), mmu-let-7c-5p(1), mmu-miR-143-3p(1), mmu-miR-185-5p(1), mmu-miR-362-5p(1), mmu-miR-98-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-188-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TACCCTAAGTTGAGTGTGTGTGACTG
siRNA sets
ACACACACTCAACTTAGGG, CACACACACTCAACTTAGG
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
0.931310867
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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