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mmu_circAbcd3_225
Basic information of circular RNA
PanCircBase ID:
mmu_circAbcd3_225
mm39_Chr. Position ID:
chr3|121585382|121590134|-
Gene name:
Abcd3
Transcript:
ENSMUST00000197383.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
4,3,2
Exon/intron offsets:
0,1070,4715
Genomic length:
4752
Exon/intron sizes in nt:
89,99,37
Flanking exon/introns:
chr3:121579720-121585382|chr3:121590134-121608657
Splice length:
225
Other database IDs:
CIRCpedia: MMU_CIRCpedia_37558, circAtlas: mmu-Abcd3_0001
circAtlas: hsa-ABCD3_0001, CIRCpedia: HSA_CIRCpedia_154226
Human Ortholog IDs:
Mature spliced Sequence:
TAAGAAAAGTGGAAAACCGCCATTACAGAATAATGAGAAAGAAGGAAAGAAAGAGCGAGCTGTGGTGGACAAAGTGTTTTTATCAAGGCTCTCACAGATCCTAAAAATTATGGTTCCTAGAACATTTTGTAAAGAGACAGGCTACTTGTTACTTATTGCGGTTATGCTGGTATCTCGAACATACTGTGATGTTTGGATGATTCAGAATGGGACGCTCATTGAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCGGTTATGCTGGTATCTCGA
60
ACACTTTGTCCACCACAGCT
59.74
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCGGTTATGCTGGTATCTCG
60.27
ACACTTTGTCCACCACAGCT
59.74
146
PCR template sequence:
TTTGTAAAGAGACAGGCTACTTGTTACTTATTGCGGTTATGCTGGTATCTCGAACATACTGTGATGTTTGGATGATTCAGAATGGGACGCTCATTGAGAGTAAGAAAAGTGGAAAACCGCCATTACAGAATAATGAGAAAGAAGGAAAGAAAGAGCGAGCTGTGGTGGACAAAGTGTTTTTATCAAGGCTCTCACAGATC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CGCTCATTGAGAGTAAGAAAAGTGGA
siRNA sets
CTTTTCTTACTCTCAATGA, TTTTCTTACTCTCAATGAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCABCD3_225_ORF_1
0.9517
0.045206779
0.298877645
339
ORF sequence:
ATGGTTCCTAGAACATTTTGTAAAGAGACAGGCTACTTGTTACTTATTGCGGTTATGCTGGTATCTCGAACATACTGTGATGTTTGGATGATTCAGAATGGGACGCTCATTGAGAGTAAGAAAAGTGGAAAACCGCCATTACAGAATAATGAGAAAGAAGGAAAGAAAGAGCGAGCTGTGGTGGACAAAGTGTTTTTATCAAGGCTCTCACAGATCCTAAAAATTATGGTTCCTAGAACATTTTGTAAAGAGACAGGCTACTTGTTACTTATTGCGGTTATGCTGGTATCTCGAACATACTGTGATGTTTGGATGATTCAGAATGGGACGCTCATTGAG
Peptide sequence:
MVPRTFCKETGYLLLIAVMLVSRTYCDVWMIQNGTLIESKKSGKPPLQNNEKEGKKERAVVDKVFLSRLSQILKIMVPRTFCKETGYLLLIAVMLVSRTYCDVWMIQNGTLIE
IRESfinder result
IRESfinder score
0.56037001
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
RPF, cORF, m6A
mmu_circAbcd3_001
Evidence
Peptide sequence:
MVPRTFCKETGYLLLIAVMLVSRTYCDVWMIQNGTLIESKKSGKPPLQNNEKEGKKERAVVDKVFLSRLSQILKIMVPRTFCKETGYLLLIAVMLVSRTYCDVWMIQNGTLIESKKSGKPPLQNNEKEGKKERAVVDKVFLSRLSQILKI
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