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mmu_circAkap13_478
Basic information of circular RNA
PanCircBase ID:
mmu_circAkap13_478
mm39_Chr. Position ID:
chr7|75334864|75347182|+
Gene name:
Akap13
Transcript:
ENSMUST00000166315.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
13,14,15,16
Exon/intron offsets:
0,2096,10507,12185
Genomic length:
12318
Exon/intron sizes in nt:
19,31,09,43,133
Flanking exon/introns:
chr7:75329621-75334864|chr7:75347182-75354112
Splice length:
478
Other database IDs:
CIRCpedia: MMU_CIRCpedia_215664, circAtlas: mmu-Akap13_0004
circAtlas: hsa-AKAP13_0003, CIRCpedia: HSA_CIRCpedia_15992
Human Ortholog IDs:
Mature spliced Sequence:
TTTCAGTCTGGAAGGCTTGACAGGAGGAGGTGTTGGAAATAAGCCATCCTCGTCTCTAGAAATGAGCTCTGCAAACTCCAGCGAGCTCAGAAACCCTTTCGGTGGTGAGGAACAGAGAAACTCTTTGATGTCACTTTCAGAAGAACATCTGGAGCCAGACCAGAGACAGCATCATAGGATGTTTGATCAGCAGACATGTTACAGGTCTAAACAACAGGGATTTAACTACTGTACATCAGCCATTTCTTCTCCATTGACAAAATCCATCTCATTAATGACAATCAGTCATCCTGGATTGGACAGTTCACGGCCCTTCCACAGTACCAGTGCCAACCTGACCGAGAGTATAACAGAAGAAAACTGTAACTTCCTGCCTCCAAGTCCCTCAAAAAAGAATTTTGAAGAAAAGAGTGGGACTAAGGTTAGTCGCACCTTCAGCTACATCAGGAATAAAATGTCCAGCAGCAAGAAGAGCAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGTTAGTCGCACCTTCAGCT
60.04
GTTTCTGAGCTCGCTGGAGT
60.04
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGTTAGTCGCACCTTCAGC
60.04
GTTTCTGAGCTCGCTGGAGT
60.04
153
PCR template sequence:
AAGTCCCTCAAAAAAGAATTTTGAAGAAAAGAGTGGGACTAAGGTTAGTCGCACCTTCAGCTACATCAGGAATAAAATGTCCAGCAGCAAGAAGAGCAAATTTCAGTCTGGAAGGCTTGACAGGAGGAGGTGTTGGAAATAAGCCATCCTCGTCTCTAGAAATGAGCTCTGCAAACTCCAGCGAGCTCAGAAACCCTTTC
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-let-7e-5p(1), mmu-miR-135a-5p(1), mmu-miR-18a-5p(1), mmu-let-7d-5p(1), mmu-miR-149-5p(1), mmu-miR-96-5p(1), mmu-miR-98-5p(1), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
CAAGAAGAGCAAATTTCAGTCTGGAA
siRNA sets
TTCCAGACTGAAATTTGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAKAP13_478_ORF_1
0.8829
0.038537833
0.461643832
459
ORF sequence:
ATGAGCTCTGCAAACTCCAGCGAGCTCAGAAACCCTTTCGGTGGTGAGGAACAGAGAAACTCTTTGATGTCACTTTCAGAAGAACATCTGGAGCCAGACCAGAGACAGCATCATAGGATGTTTGATCAGCAGACATGTTACAGGTCTAAACAACAGGGATTTAACTACTGTACATCAGCCATTTCTTCTCCATTGACAAAATCCATCTCATTAATGACAATCAGTCATCCTGGATTGGACAGTTCACGGCCCTTCCACAGTACCAGTGCCAACCTGACCGAGAGTATAACAGAAGAAAACTGTAACTTCCTGCCTCCAAGTCCCTCAAAAAAGAATTTTGAAGAAAAGAGTGGGACTAAGGTTAGTCGCACCTTCAGCTACATCAGGAATAAAATGTCCAGCAGCAAGAAGAGCAAATTTCAGTCTGGAAGGCTTGACAGGAGGAGGTGTTGGAAATAA
Peptide sequence:
MSSANSSELRNPFGGEEQRNSLMSLSEEHLEPDQRQHHRMFDQQTCYRSKQQGFNYCTSAISSPLTKSISLMTISHPGLDSSRPFHSTSANLTESITEENCNFLPPSPSKKNFEEKSGTKVSRTFSYIRNKMSSSKKSKFQSGRLDRRRCWK
IRESfinder result
IRESfinder score
0.636086609
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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