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mmu_circAkap9_540
Basic information of circular RNA
PanCircBase ID:
mmu_circAkap9_540
mm39_Chr. Position ID:
chr5|4055409|4064079|+
Gene name:
Akap9
Transcript:
ENSMUST00000044492.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
19,20,21
Exon/intron offsets:
0,2934,8440
Genomic length:
8670
Exon/intron sizes in nt:
10,42,06,230
Flanking exon/introns:
chr5:4054943-4055409|chr5:4064079-4078373
Splice length:
540
Other database IDs:
circAtlas: hsa-AKAP9_0085
Human Ortholog IDs:
Mature spliced Sequence:
GATGGACATGACGATCAGGAAGTTGAGGAACAGACGTTAAAAGACAAGACATTGGAGAGAAGCCCTGAAGATGCTCTTCTCGATAGAAACCTGTCCAATGAAAGGTACGCTCTCAAAAAAGCTAATAATAGACTTCTGAAGATCTTGTTAGAGGTTGTCAAGACAACATCAGCTGCTGAAGAAACAATTGGCCGCCATGTTCTTGGGATTCTGGACCGATCTAGTAAAGGTCAGACAGCTAGCAGCCTGCTTTGGAGGTCAGAAGCAGACGCATCCGCCACGACTTGTGCACCAGAAGATTGTGCAAGAGCTATGGATGAGTCCATACCCTCCTATCCTGGAACTGCCATAGCAACACATGACAGCATTTGGTCCAAAGTCACAGAGGAAGGAGCAGAGCTGTCACAGCGGCTCGTGAGGAGTGGTTTTGCTGGGCCTGTAATAGATCCTGAAAATGAAGAACTTATGCTGAACATCAGCTCTCGACTACAAGCAGCTGTTGAAAAACTCCTAGAAGCCATAAGTGAAACCAACACTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCAGCTCTCGACTACAAGCAG
59.53
AGCATCTTCAGGGCTTCTCTC
59.51
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCAGCTCTCGACTACAAGCAG
59.53
GAGCATCTTCAGGGCTTCTCT
59.51
141
PCR template sequence:
AATAGATCCTGAAAATGAAGAACTTATGCTGAACATCAGCTCTCGACTACAAGCAGCTGTTGAAAAACTCCTAGAAGCCATAAGTGAAACCAACACTCAGGATGGACATGACGATCAGGAAGTTGAGGAACAGACGTTAAAAGACAAGACATTGGAGAGAAGCCCTGAAGATGCTCTTCTCGATAGAAACCTGTCCAATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-29b-2-5p(1), mmu-miR-1198-5p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AACCAACACTCAGGATGGACATGACG
siRNA sets
TCATGTCCATCCTGAGTGT, GTCATGTCCATCCTGAGTG, ATGTCCATCCTGAGTGTTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAKAP9_540_ORF_1
1.0415
0.18174401
0.950436931
768
ORF sequence:
ATGGATGAGTCCATACCCTCCTATCCTGGAACTGCCATAGCAACACATGACAGCATTTGGTCCAAAGTCACAGAGGAAGGAGCAGAGCTGTCACAGCGGCTCGTGAGGAGTGGTTTTGCTGGGCCTGTAATAGATCCTGAAAATGAAGAACTTATGCTGAACATCAGCTCTCGACTACAAGCAGCTGTTGAAAAACTCCTAGAAGCCATAAGTGAAACCAACACTCAGGATGGACATGACGATCAGGAAGTTGAGGAACAGACGTTAAAAGACAAGACATTGGAGAGAAGCCCTGAAGATGCTCTTCTCGATAGAAACCTGTCCAATGAAAGGTACGCTCTCAAAAAAGCTAATAATAGACTTCTGAAGATCTTGTTAGAGGTTGTCAAGACAACATCAGCTGCTGAAGAAACAATTGGCCGCCATGTTCTTGGGATTCTGGACCGATCTAGTAAAGGTCAGACAGCTAGCAGCCTGCTTTGGAGGTCAGAAGCAGACGCATCCGCCACGACTTGTGCACCAGAAGATTGTGCAAGAGCTATGGATGAGTCCATACCCTCCTATCCTGGAACTGCCATAGCAACACATGACAGCATTTGGTCCAAAGTCACAGAGGAAGGAGCAGAGCTGTCACAGCGGCTCGTGAGGAGTGGTTTTGCTGGGCCTGTAATAGATCCTGAAAATGAAGAACTTATGCTGAACATCAGCTCTCGACTACAAGCAGCTGTTGAAAAACTCCTAGAAGCCATAAGTGAAACCAACACTCAG
Peptide sequence:
MDESIPSYPGTAIATHDSIWSKVTEEGAELSQRLVRSGFAGPVIDPENEELMLNISSRLQAAVEKLLEAISETNTQDGHDDQEVEEQTLKDKTLERSPEDALLDRNLSNERYALKKANNRLLKILLEVVKTTSAAEETIGRHVLGILDRSSKGQTASSLLWRSEADASATTCAPEDCARAMDESIPSYPGTAIATHDSIWSKVTEEGAELSQRLVRSGFAGPVIDPENEELMLNISSRLQAAVEKLLEAISETNTQ
IRESfinder result
IRESfinder score
0.402605678
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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