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mmu_ciHerc3_421
Basic information of circular RNA
PanCircBase ID:
mmu_ciHerc3_421
mm39_Chr. Position ID:
chr6|58808917|58809338|+
Gene name:
Herc3
Transcript:
ENSMUST00000122981.2
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
1
Exon/intron offsets:
0
Genomic length:
421
Exon/intron sizes in nt:
421
Flanking exon/introns:
chr6:58808917-58809386
Splice length:
421
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGTGTGGACTGAAGGGCTGGACCTGGGGAGACTCGCTCGTGCTGCTGCCGGGAGCGTGTGCAGCTCGGGGCCCCAGGGGAGGAATGCTTGAACTTTGCTGTTCCTGGCTGTTTTCTTTTAGAGTTCACACCTGCCCCACTAGGAAGTGCCTTAAATTTTACCTAAGGCGTCGAAGGTTTTACTGGGATTTGTCTCATCCGGGGTGCTTTGGGGGAGGACGATTCAAGTGATATCTTCCATTTTTTATGTGCCTTCTGTCTCTTTCCACAAATAGGAAGCTATTTCTAGAACCTTTCATTTGATAATTTGATAAAGTGAACTGATTTTTAGCTTTAGATTGGAAAGACAGGAAAGAGAAGTAAAAAGGATTAGCATTTTAAAATGCAGCCAGAGCGATGTGGTACTTTCAGAGGCAAATGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAAATGCAGCCAGAGCGATG
59.55
CAAAGTTCAAGCATTCCTCCCC
59.77
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAAATGCAGCCAGAGCGATG
59.55
GCAAAGTTCAAGCATTCCTCCC
60.35
141
PCR template sequence:
TGATTTTTAGCTTTAGATTGGAAAGACAGGAAAGAGAAGTAAAAAGGATTAGCATTTTAAAATGCAGCCAGAGCGATGTGGTACTTTCAGAGGCAAATGAGTGTGTGGACTGAAGGGCTGGACCTGGGGAGACTCGCTCGTGCTGCTGCCGGGAGCGTGTGCAGCTCGGGGCCCCAGGGGAGGAATGCTTGAACTTTGCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-124-3p(1), mmu-miR-16-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CAGAGGCAAATGAGTGTGTGGACTGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIHERC3_421_ORF_3
0.646
-0.025729308
0.034811491
117
ORF sequence:
ATGTGGTACTTTCAGAGGCAAATGAGTGTGTGGACTGAAGGGCTGGACCTGGGGAGACTCGCTCGTGCTGCTGCCGGGAGCGTGTGCAGCTCGGGGCCCCAGGGGAGGAATGCTTGA
Peptide sequence:
MWYFQRQMSVWTEGLDLGRLARAAAGSVCSSGPQGRNA
IRESfinder result
IRESfinder score
0.866909091
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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