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mmu_circAbca8b_424
Basic information of circular RNA
PanCircBase ID:
mmu_circAbca8b_424
mm39_Chr. Position ID:
chr11|109828532|109831729|-
Gene name:
Abca8b
Transcript:
ENSMUST00000020948.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
34,33,32,31
Exon/intron offsets:
0,186,732,3105
Genomic length:
3197
Exon/intron sizes in nt:
95,76,161,92
Flanking exon/introns:
chr11:109827642-109828532|chr11:109831729-109832371
Splice length:
424
Other database IDs:
circAtlas: mmu-Abca8b_0021
Human Ortholog IDs:
Mature spliced Sequence:
GTGAGATTCTAGGATTGTTGGGACACAATGGAGCTGGCAAAAGTACATCTCTTAAAATGATAAGTGGAGACACAAAAGTCACAGCTGGGCAGGTGTTACTGAAAGGGAGCAGAGAAGGGGACACCCCGGGGTTCCTGGGGTACTGTCCTCAGGAGAATGCTCTGTGGCCCAACCTCACTGTGAAGGAGCACCTGGAGATATTTGCTGCAGTGAGGGGCTTGCGCAAAAGTCACGCTGCAGTCGCCATCACAAGGTTGGCAGATGCGCTCAAGCTGCAGGACCAGCTGAAGTCTCCTGTGAAGACGCTGTCAGAGGGAGTGAAGAGAAAGCTGTGCTTCGTGCTGAGCATCCTGGGGAACCCATCTATATTGCTTCTAGATGAGCCGTCCACTGGGCTGGATCCTGAGGGGCAGCAGCAAATATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTAGATGAGCCGTCCACTGG
59.61
GCCCAGCTGTGACTTTTGTG
59.97
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTAGATGAGCCGTCCACTGG
59.61
CTGCCCAGCTGTGACTTTTG
59.69
142
PCR template sequence:
GAAAGCTGTGCTTCGTGCTGAGCATCCTGGGGAACCCATCTATATTGCTTCTAGATGAGCCGTCCACTGGGCTGGATCCTGAGGGGCAGCAGCAAATATGGTGAGATTCTAGGATTGTTGGGACACAATGGAGCTGGCAAAAGTACATCTCTTAAAATGATAAGTGGAGACACAAAAGTCACAGCTGGGCAGGTGTTACT
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-101a-3p(1), mmu-miR-136-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGCAGCAAATATGGTGAGATTCTAGG
siRNA sets
AATCTCACCATATTTGCTG, AGAATCTCACCATATTTGC, TCTCACCATATTTGCTGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCABCA8B_424_ORF_1
1.0521
0.235900202
0.737947634
468
ORF sequence:
ATGAGCCGTCCACTGGGCTGGATCCTGAGGGGCAGCAGCAAATATGGTGAGATTCTAGGATTGTTGGGACACAATGGAGCTGGCAAAAGTACATCTCTTAAAATGATAAGTGGAGACACAAAAGTCACAGCTGGGCAGGTGTTACTGAAAGGGAGCAGAGAAGGGGACACCCCGGGGTTCCTGGGGTACTGTCCTCAGGAGAATGCTCTGTGGCCCAACCTCACTGTGAAGGAGCACCTGGAGATATTTGCTGCAGTGAGGGGCTTGCGCAAAAGTCACGCTGCAGTCGCCATCACAAGGTTGGCAGATGCGCTCAAGCTGCAGGACCAGCTGAAGTCTCCTGTGAAGACGCTGTCAGAGGGAGTGAAGAGAAAGCTGTGCTTCGTGCTGAGCATCCTGGGGAACCCATCTATATTGCTTCTAGATGAGCCGTCCACTGGGCTGGATCCTGAGGGGCAGCAGCAAATA
Peptide sequence:
MSRPLGWILRGSSKYGEILGLLGHNGAGKSTSLKMISGDTKVTAGQVLLKGSREGDTPGFLGYCPQENALWPNLTVKEHLEIFAAVRGLRKSHAAVAITRLADALKLQDQLKSPVKTLSEGVKRKLCFVLSILGNPSILLLDEPSTGLDPEGQQQI
IRESfinder result
IRESfinder score
0.505192962
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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