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mmu_ciHerc2_1340
Basic information of circular RNA
PanCircBase ID:
mmu_ciHerc2_1340
mm39_Chr. Position ID:
chr7|55818764|55820104|+
Gene name:
Herc2
Transcript:
ENSMUST00000076226.13
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
53
Exon/intron offsets:
0
Genomic length:
1340
Exon/intron sizes in nt:
1340
Flanking exon/introns:
chr7:55818764-55820133
Splice length:
1340
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAATGTTTGGTGGGATGTGTCAGGAAATACTCTGATTTGGAAGGTGGATCGTAGACCTTTGCAGTGAACTGAGGAACCTGCAGCTTTCCTAATACTCTCTCAAAATTCACTTTATATTTCAGTTCATAAATAATTTTCAAGTTACAGAGTAGTATGTTGTGTATTGCTAGATTTTAAACAGAATGAACAACAAATTTTATTAAATGGCCAATTGATAAAAGGTTCACTGTTTTTTGTTATATTTTTATATATGAAGTATTAGTTCTTATTATACTTCTGGCTAGAAATTTTTCTAACTTACAGATAAGTTTTAGGGATTACACTAAAACTGTGTGTGCTGACAGGGCAGATATGAGACAGGATGGAGAAGGTGGGGGCATTATCTTATTCTAACTATAGTATTTCTGTGACTTAGTATAAAATGACTGTCTCTAGCCAGAAGTCTATAAATATATTATATATGGGGCTTAGAGTGAGATCTTACTCTAATTAGGTCGTGATAAGGAGAGATGTGTTCCGGTAAATATTTAAAGGGTTGCTCTCTGCTCCTGGTGGGTAAGCACATGGCTCTGCACCTGCCCAAGACCTCTGAATTCACGAATGTAAGGCATGCAACCTTTACATTTAATCTGCCTTAAGTAGCTCAGTGGTTGAGCTCCATACAACCTCCCCACAGCTAGCATCCCCTCCCTCTGGTATTCCTGAGTTAACATTTTCTAAATCTATATCTTATCTTTGCTGCCTTGTTTCCTTCTGGGCAGCCCTCCCATGGGACTGCACCTTTGCACCTACATTTCGACTGTCTCACCCTCCTGCTCCTTCACAGTGTAGTCCATCCAATGCTCCTTTCATGAAGGAACCCCTTCTTCCCTCTTCTGTGTTTCTTGATGGGAAATCCTAAAAGTCCTACCTCTGTCCCCTGCCCAGCCATTGGCCATTGACTCTTTATTGACCAGTCCAAAAAAAAAAAAAAAACCCCAAAAAACAAAACAAAAAGAACAGTGTTGGCAGGGACCCACAGCAGACATGTGAATTCCCATGTAAGCATAAATCAATTTCCCTACAGAGATGTTCTTGTTTTTCCAGAGTAAGGTTAAATTTTTATGTTACATTTTGTATTTAAAAAAAATCTTATAGGTTCACACTTCCACAATACTGTCTTATTTTACTTTAATTTAAAATATGGGTTTGTGTGTGTGTATGTGTGTTTGTACCGTGTGGATTCAGGTCATCAGGTTTAGCAGCAAATACCTTTATCTTCTACGAGTTCTAGTGATAACCATCTTAGTAGATAAATATAACTTAAATTTTGGTTACTAAGAATGTTTTGTTTTTGTTT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACGAGTTCTAGTGATAACCATCT
56.56
AGCTGCAGGTTCCTCAGTTC
59.96
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACGAGTTCTAGTGATAACCATCT
56.56
AGGAAAGCTGCAGGTTCCTC
59.96
168
PCR template sequence:
AGCAGCAAATACCTTTATCTTCTACGAGTTCTAGTGATAACCATCTTAGTAGATAAATATAACTTAAATTTTGGTTACTAAGAATGTTTTGTTTTTGTTTGTAATGTTTGGTGGGATGTGTCAGGAAATACTCTGATTTGGAAGGTGGATCGTAGACCTTTGCAGTGAACTGAGGAACCTGCAGCTTTCCTAATACTCTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-let-7e-5p(1), mmu-let-7c-5p(1), mmu-miR-18a-5p(1), mmu-miR-433-5p(1), mmu-miR-218-5p(1), mmu-miR-342-5p(1), mmu-miR-466d-3p(1), mmu-miR-98-5p(1), mmu-miR-410-3p(1), mmu-miR-466b-3p(1), mmu-miR-376a-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTGTTTTTGTTTGTAATGTTTGGTG
siRNA sets
AAACATTACAAACAAAAAC, AACATTACAAACAAAAACA
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
0.892661207
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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