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mmu_circAkap9_622
Basic information of circular RNA
PanCircBase ID:
mmu_circAkap9_622
mm39_Chr. Position ID:
chr5|4018579|4025710|+
Gene name:
Akap9
Transcript:
ENSMUST00000044492.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
8,9,10,11,12
Exon/intron offsets:
0,2084,3322,4176,7019
Genomic length:
7131
Exon/intron sizes in nt:
21,47,41,36,86,112
Flanking exon/introns:
chr5:4012457-4018579|chr5:4025710-4026127
Splice length:
622
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GATGATCTAAGGCTGCAGATGGAGGCCCAGCGCATATGCCTTTTTGTGGTTTACTCAACTCATGCGGATCAGGTTCGTGCACACATGGAAAAGGAGAGGGAGGAAGCTCTTTGCAGCCTTAAAGATGAGCTCATTTCCGCTCAACAGAAAAAGATCGACGAACTTCATAAAATGCACCAGTGCCAGCTCCAGAATTTTAAAATACAGGAGACAGGTGATGAGCCTTTACAGGTGCTCATTGAACGACTTCAACAGGCAGTGTCTGAGAAATGCTTTCACATTTCAAAGACCCTAAACAATGTTTTCGATGAATGCTATACTCCTTTAAAATGTGAAATGAATATAGAAGAGAAAGAGAATTCTGGTGTTTACACTTCTCAAAATCAAAGCCCAGAATTACAAGAGTATAGATACGAAGTTCAAGACTTTCAAGAGAGCATGCAAGTCCTTCTTGGTAAAGTGACGGAAGAATGCCGCAAACTCTCAGGACTGCAGACGCGCTTAGGCAAGATCCATGAACAACAGACAGATGGTGTGGCACTAGAGTTTGCTGAACAAAATGCGGCAGAAGAGGAAGCAGGTCTTCTGTCAGGTTGTTCTCAGAGTGCTTTACAGAGCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGACAGATGGTGTGGCACT
59.96
CGAACCTGATCCGCATGAGT
60.18
177
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGACAGATGGTGTGGCACT
59.96
ACGAACCTGATCCGCATGAG
60.18
178
PCR template sequence:
CAGACAGATGGTGTGGCACTAGAGTTTGCTGAACAAAATGCGGCAGAAGAGGAAGCAGGTCTTCTGTCAGGTTGTTCTCAGAGTGCTTTACAGAGCACAGGATGATCTAAGGCTGCAGATGGAGGCCCAGCGCATATGCCTTTTTGTGGTTTACTCAACTCATGCGGATCAGGTTCGTGCACACATGGAAAAGGAGAGGG
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-23b-3p(1), mmu-miR-141-3p(1), mmu-miR-30c-5p(1), mmu-miR-203-3p(1), mmu-miR-23a-3p(1), mmu-miR-96-5p(1), mmu-miR-1187(1), mmu-miR-3470b(1)
siRNAs for circular RNA silencing
Junction sequence
TTACAGAGCACAGGATGATCTAAGGC
siRNA sets
CTTAGATCATCCTGTGCTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAKAP9_622_ORF_1
1.2449
0.162266018
0.933535191
684
ORF sequence:
ATGCGGCAGAAGAGGAAGCAGGTCTTCTGTCAGGTTGTTCTCAGAGTGCTTTACAGAGCACAGGATGATCTAAGGCTGCAGATGGAGGCCCAGCGCATATGCCTTTTTGTGGTTTACTCAACTCATGCGGATCAGGTTCGTGCACACATGGAAAAGGAGAGGGAGGAAGCTCTTTGCAGCCTTAAAGATGAGCTCATTTCCGCTCAACAGAAAAAGATCGACGAACTTCATAAAATGCACCAGTGCCAGCTCCAGAATTTTAAAATACAGGAGACAGGTGATGAGCCTTTACAGGTGCTCATTGAACGACTTCAACAGGCAGTGTCTGAGAAATGCTTTCACATTTCAAAGACCCTAAACAATGTTTTCGATGAATGCTATACTCCTTTAAAATGTGAAATGAATATAGAAGAGAAAGAGAATTCTGGTGTTTACACTTCTCAAAATCAAAGCCCAGAATTACAAGAGTATAGATACGAAGTTCAAGACTTTCAAGAGAGCATGCAAGTCCTTCTTGGTAAAGTGACGGAAGAATGCCGCAAACTCTCAGGACTGCAGACGCGCTTAGGCAAGATCCATGAACAACAGACAGATGGTGTGGCACTAGAGTTTGCTGAACAAAATGCGGCAGAAGAGGAAGCAGGTCTTCTGTCAGGTTGTTCTCAGAGTGCTTTACAGAGCACA
Peptide sequence:
MRQKRKQVFCQVVLRVLYRAQDDLRLQMEAQRICLFVVYSTHADQVRAHMEKEREEALCSLKDELISAQQKKIDELHKMHQCQLQNFKIQETGDEPLQVLIERLQQAVSEKCFHISKTLNNVFDECYTPLKCEMNIEEKENSGVYTSQNQSPELQEYRYEVQDFQESMQVLLGKVTEECRKLSGLQTRLGKIHEQQTDGVALEFAEQNAAEEEAGLLSGCSQSALQST
IRESfinder result
IRESfinder score
0.535676071
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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