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mmu_ciHerpud1_1236
Basic information of circular RNA
PanCircBase ID:
mmu_ciHerpud1_1236
mm39_Chr. Position ID:
chr8|95119152|95120388|+
Gene name:
Herpud1
Transcript:
ENSMUST00000161576.8
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
6
Exon/intron offsets:
0
Genomic length:
1236
Exon/intron sizes in nt:
1236
Flanking exon/introns:
chr8:95119152-95120423
Splice length:
1236
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGCACATGGGCTGTCTCTTTACTGAAAATGACACTATATTGTCACTTGAGTATAGATAGATTCTTTCAGTCTGTGACCCTTAAAGGAGGTGTGTTTACATTTTTGTCACTCTGGCACTTTTTGGTTCAAGGAGCACTAACACAGAATGCAGAAATCCTGTGTTAGCAAAAGAAAAATATTTTCATCATCTGGTCGGTGGATAAATGACCTGTCAGGCTCATGAAGTACAGTACAGAGCCACCCTGAAGCATAAGAGGCTGTATTTGTTTCCAGAAGGACAGAGTGTCCTTTATCAGGTCGTAGCTGCCTTTCAGGACAAAGTACAGACAGCGTCGTCACAGCTATGAAGGGCCAGTGACCCTTCGCACACTCTGTTTGCTCCAGCTGCCAGCTGGAGATAATTCTGCATCTTTCTCCGGGGGACATTTGGCAGTGTCAGAAGGATTTCCCAGCTAGAGGGCTGGTGTGTTTAAGTAGATGACAGGAAGAGATGCTTCAAAGTCTCCAGCAGTGTGCAGGAGAGCTCGCCTGGAGGACAGAGCCCCAGAAAGCTGGGCCTAGAAGGATAGGTCTCTGGTTAGAACGGAAAGAAGGAAGTTTTCCTGTAGAGTAAAATTGGGTTTTATCTTAGTTTTTCGAAATGTAAGAAGCACAAGCATTCTTAATATTTTGTCTTGAAAGTTGAATTTTGTAGATTTTTTTTCCAGTTAAAGCCTTTTATCAAACATTTCTATGTCTAGAATCAAATATTTCTATGACCAAATTAAGGTTGTTATCATATGATATATATATATATATAGAGAGAGAGAGAGAGATACACACATACACATATATATGATTACAGCAGCTTTATATATGATTATATCTCCCATCTCTTTTGGGTTTGGTTTGCTTTGATGCTGTGAGGCTGGAGTTGAACCCTAGGCCGCCCCGCTTCTCTCCAGGCAAGTGGGCACTTTCCACTAAGTTATAGCTTCAGCTTTTTCCTTTCTCTTTTTTTTTTTTTTTTTTTTTTTTTGAGGCAGGGTCTTGCTGAGTTGGTCAATAGCATTGACCTCACTCTGTAGCCAAGGCAGAATTGCTATTACTATTTACTGCCGGTGAATAAAACACACACCCCTGCTTTTAAGGACCAGAGGCCTAAGAGAATCTAGGGACTGGCAGACTGGCTGCACAGGTAGTATTGTGTAAGCTTTGGGGCCTTCAGATTCTTATGTGAATCCCACAGTGACT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGTAAGCTTTGGGGCCTT
59.81
CACACCTCCTTTAAGGGTCACA
59.89
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTGTGTAAGCTTTGGGGCCT
59.81
CACACCTCCTTTAAGGGTCACA
59.89
146
PCR template sequence:
CAGAGGCCTAAGAGAATCTAGGGACTGGCAGACTGGCTGCACAGGTAGTATTGTGTAAGCTTTGGGGCCTTCAGATTCTTATGTGAATCCCACAGTGACTGTAAGCACATGGGCTGTCTCTTTACTGAAAATGACACTATATTGTCACTTGAGTATAGATAGATTCTTTCAGTCTGTGACCCTTAAAGGAGGTGTGTTTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
17
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(2), mmu-miR-106a-5p(2), mmu-miR-20a-5p(2), mmu-miR-17-5p(2), mmu-miR-106b-5p(2), mmu-miR-30e-5p(1), mmu-miR-30a-5p(1), mmu-miR-30c-5p(1), mmu-miR-339-5p(1), mmu-miR-30b-5p(1), mmu-miR-297a-5p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1), mmu-miR-193b-3p(1), mmu-miR-574-5p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCCCACAGTGACTGTAAGCACATGGG
siRNA sets
NA
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
0.840291601
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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