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mmu_circAbcc9_301
Basic information of circular RNA
PanCircBase ID:
mmu_circAbcc9_301
mm39_Chr. Position ID:
chr6|142540434|142544883|-
Gene name:
Abcc9
Transcript:
ENSMUST00000100827.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
39,38,37
Exon/intron offsets:
0,3399,4345
Genomic length:
4449
Exon/intron sizes in nt:
6,31,34,104
Flanking exon/introns:
chr6:142536229-142540434|chr6:142544883-142546633
Splice length:
301
Other database IDs:
circAtlas: mmu-Abcc9_0033
Human Ortholog IDs:
Mature spliced Sequence:
GTTTAACCTGGATCCTGAATGCAAGTGCACAGATGACAGGCTCTGGGAGGCTCTAGAAATTGCCCAGCTGAAGAATATGGTCAAATCTCTGCCCGGAGGCTTAGATGCCACTGTCACCGAAGGTGGTGAGAACTTCAGTGTTGGACAGAGACAGCTGTTCTGCCTGGCCAGGGCCTTTGTTCGGAAGAGCAGTATACTCATCATGGATGAAGCCACTGCTTCCATCGACATGGCCACGGAAAACATTTTGCAGAAAGTAGTCATGACAGCCTTTGCGGATCGCACGGTCGTAACCATAGCT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCATGACAGCCTTTGCGGAT
60.04
CCTCCGGGCAGAGATTTGAC
60.46
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATCGACATGGCCACGGAAAA
60.32
CTCCGGGCAGAGATTTGACC
60.46
176
PCR template sequence:
CATGGATGAAGCCACTGCTTCCATCGACATGGCCACGGAAAACATTTTGCAGAAAGTAGTCATGACAGCCTTTGCGGATCGCACGGTCGTAACCATAGCTGTTTAACCTGGATCCTGAATGCAAGTGCACAGATGACAGGCTCTGGGAGGCTCTAGAAATTGCCCAGCTGAAGAATATGGTCAAATCTCTGCCCGGAGGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-140-5p(1), mmu-miR-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CGTAACCATAGCTGTTTAACCTGGAT
siRNA sets
TTAAACAGCTATGGTTACG, CAGGTTAAACAGCTATGGT, GTTAAACAGCTATGGTTAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCABCC9_301_ORF_1
1.3249
0.290317825
0.515152379
231
ORF sequence:
ATGGTCAAATCTCTGCCCGGAGGCTTAGATGCCACTGTCACCGAAGGTGGTGAGAACTTCAGTGTTGGACAGAGACAGCTGTTCTGCCTGGCCAGGGCCTTTGTTCGGAAGAGCAGTATACTCATCATGGATGAAGCCACTGCTTCCATCGACATGGCCACGGAAAACATTTTGCAGAAAGTAGTCATGACAGCCTTTGCGGATCGCACGGTCGTAACCATAGCTGTTTAA
Peptide sequence:
MVKSLPGGLDATVTEGGENFSVGQRQLFCLARAFVRKSSILIMDEATASIDMATENILQKVVMTAFADRTVVTIAV
IRESfinder result
IRESfinder score
0.19814385
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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