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mmu_ciApba1_1454
Basic information of circular RNA
PanCircBase ID:
mmu_ciApba1_1454
mm39_Chr. Position ID:
chr19|23912324|23913778|+
Gene name:
Apba1
Transcript:
ENSMUST00000025830.9
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
8
Exon/intron offsets:
0
Genomic length:
1454
Exon/intron sizes in nt:
1454
Flanking exon/introns:
chr19:23912324-23913781
Splice length:
1454
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGACTGGCTTCCCCATCCTTCCTCTGGGTTCCCCAACCTATCCTCCTGGATAGCCACTAAGTAGCAAGTTTATCAGAACACGAATCAGTCTGGCTCATCCTACATTAAACATATTTATTCAGTACATACTATGTATCAGGCACTGTTCTAGATCTGGAGATATAAGGCTGAATAAAGGTACAGGAGTTACACTTTGTGCAGGTTGGGGGGGATAGAAAATAGAGATAAGTTAACTTAATGAGACATGGAGAGTGCTGTACAGAAATATGAAATAAGATCAGTGCACAAAGGACAGGACTAGTTCACATAGGATCATGAGCATAGGTAACATTTAAACAGAGACTGGAATAGAATGAGACTAGGAAATAGCAGGCACAAAGGCCCAGAGGCAGGGGAGTGCTGAGTTTGCTTGGGAAGGAAGAGTGGCCATTCTGCCAGCAGGCTTTGAAAGAGGGAGCCCCAGATTTCGAGTCTAAGCAAGTCTTCATGGCACCAGAGTGTGCGCAGAGGAAATGTTGGGAGCTGTGCAGATCTCTCATGCTATCACAGTGAACTTAGTCACCCTGCTTCTCCTGGCACAGCGGCAGGAACATCACCCACAGACCCAGACCTCTTAACCACTGAGCCATCTCTCCAATTCCCTTTTCTCTACAAAATTACTTATGGCCATAAGTATAATAAAGGAAAAGAGATTAAGATAAAATCATGATACATTGTATAAATGCCAGGGCCAGCCATTTCAAAAAAAAAAAAATGTCATGAGATAGCCCTATATTTACACCTACTTACTTAAGTTTGGCTGTGAGAATAATATTGTATTTGATGTGACACTGTGGATAATTTCTACTTGACATTTTGAATTGGGGCCCAAGCAAGCATCCATGTCTATGAACACAAGCAGGATCTCTGTGCACCATGGTGCGTACAGACAGGAATGTGATCATTACCAATTCAGAGGCTGAGACCACAAATGATGTGGGTGGTTTTGAAAGACATGAAACTTACAAAATCTCAAAGGACCTTCACTTTGCATAATATTATTCTTAAAATGTACAGTATAGCCAGTGAATCTTTGTATTTGAATATAAACTAGAATCCAGTTGTGGACACAGTAATTAGAGTCAACTGTTACATATAATATAAATGTCCAGTGGGATGTGCAAAAATTGTACAGGATGTAGAGTGACATGTCATCATATATGACTGTCCTGCATATAGTAGGATGTCCTGTATCTCAGATTCCTGTCTACCACGTACCAATGACTCCCTTATGGGCACAGTCAAAACAAGAAACATACTGATTGTTTTTTCAAATAGTTCCTGGTAGGCTCTGGTACCCTGATGTAGACTGACTGACCTGCTATTTAGAAGCCTCAAGTGCCTCAAGGGATTGTCCAGGGTGGGTGTGCCAGGAGTTCCCCCACTCACCTCTATCTTCCCCTGTGCTGCTA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGCCTCAAGGGATTGTCCA
59.96
TGAGCCAGACTGATTCGTGT
59.03
174
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTCAAGGGATTGTCCAGGG
59.74
TGAGCCAGACTGATTCGTGT
59.03
171
PCR template sequence:
ACTGACCTGCTATTTAGAAGCCTCAAGTGCCTCAAGGGATTGTCCAGGGTGGGTGTGCCAGGAGTTCCCCCACTCACCTCTATCTTCCCCTGTGCTGCTAGTAAGACTGGCTTCCCCATCCTTCCTCTGGGTTCCCCAACCTATCCTCCTGGATAGCCACTAAGTAGCAAGTTTATCAGAACACGAATCAGTCTGGCTCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-296-5p(1), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-15b-5p(1), mmu-miR-222-3p(1), mmu-miR-203-3p(1), mmu-miR-324-5p(1), mmu-miR-326-3p(1), mmu-miR-24-3p(1), mmu-miR-411-3p(1), mmu-miR-190b-5p(1), mmu-miR-539-5p(1), mmu-miR-669d-5p(1), mmu-miR-344-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCCTGTGCTGCTAGTAAGACTGGCTT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.682860144
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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