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mmu_circAp3b1_1274
Basic information of circular RNA
PanCircBase ID:
mmu_circAp3b1_1274
mm39_Chr. Position ID:
chr13|94608183|94668574|+
Gene name:
Ap3b1
Transcript:
ENSMUST00000022196.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
16,17,18,19,20,21,22,23,24
Exon/intron offsets:
0,1123,5290,8051,11537,21993,30242,56489,60306
Genomic length:
60391
Exon/intron sizes in nt:
187,131,163,148,148,73,107,232,85
Flanking exon/introns:
chr13:94599080-94608183|chr13:94668574-94679286
Splice length:
1274
Other database IDs:
CIRCpedia: MMU_CIRCpedia_34854, circAtlas: mmu-Ap3b1_0009
circAtlas: hsa-AP3B1_0010
Human Ortholog IDs:
Mature spliced Sequence:
ACAAAATTGCTTACCCAGTACATATTAAATCTCGGCAAGTATGATCAAAACTACGACATCAGAGACCGCACACGATTTATTAGGCAGCTTATTGTTCCGAACGAGAAGAGTGGAGCCTTAAGTAAATATGCCAAAAAAATCTTCCTAGCACCGAAGCCTGCGCCACTGCTCGAGTCTCCCTTTAAAGATAGGGATCGCTTCCAGCTTGGCACCTTATCTCATACTCTCAACATTAAAGCGTCCGGGTACCTGGAATTATCTAATTGGCCAGAGGTGGCGCCTGACCCATCGGTTCGCAATGTAGAAGTAATAGAGTCAGCAAAAGAATGGACCCCACTTGGGAAAACAAAGAAAGAAAAACCCATGAAGAAATTTTACTCTGAATCTGAGGAGGAGGAGGACGAGGACGAGGATGAGGACGAGGAGGAGGAAGAAAAGGAAGATGAGGATGAGAACCCCTCTGATAGCAGCAGTGACAGTGAGAGCGGGTCCGGAAGTGAGAGTGGAGACACAGGCACCGAGGACAGCAGTGAGGACTCGTCCAGTGGACAAGACAGCGAGACCGGAAGCCAGGCAGAAGCGGAACGCCAGAAGGTGGCCAAGAGGAACTCCAAAACCAAGAGGAAAAGTGATTCAGAAAATAGGGAGAAGAAAAATGAAAACTCAAAAGCTTCTGAATCGTCCAGTGAGGAGTCCAGTTCCATGGAAGACAGTTCTTCCGAGTCAGAGTCAGAGTCAGGCTCTGACAGTGAGCCTGCGCCCAGAAACGTGGCTCCGGCAAAAGAAAGAAAACCCCAGCAAGAAAGACATCCTCCCTCCAAAGATGTTTTCCTTCTAGATCTGGACGACTTTAACCCAGTATCCACCCCAGTTGCCCTTCCTACACCAGCCCTTTCTCCAAGCTTGATAGCTGATCTTGAAGGTCTAAACTTGTCAACTTCTTCATCAGTCATCAACGTCAGTACGCCTGTCTTCGTGCCAACAAAAACACATGAGCTGCTTCACCGAATGCATGGGAAAGGACTGGCCGCCCACTACTGCTTCCCAAGACAGCCCTGCATCTTCAGTGACAAGATGGTCTCTGTACAGATCACCCTGACTAATACTTCTGATCGAAAAATAGAAAACATCCACATAGGGGGGAAAGGGCTTCCTGTGGGCATGCAGATGCATGCCTTTCATCCAATAGACTCTCTGGAGCCTAAGGGGTCCGTGACTGTCTCAGTGGGTATTGACTTTTGTGATTCTACACAGACGGCCAGTTTCCAATTGTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTCTCTGGAGCCTAAGGGG
60.03
ATCGTGTGCGGTCTCTGATG
60.18
161
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTCCGTGACTGTCTCAGTGG
60.04
ATCGTGTGCGGTCTCTGATG
60.18
142
PCR template sequence:
CCTTTCATCCAATAGACTCTCTGGAGCCTAAGGGGTCCGTGACTGTCTCAGTGGGTATTGACTTTTGTGATTCTACACAGACGGCCAGTTTCCAATTGTGACAAAATTGCTTACCCAGTACATATTAAATCTCGGCAAGTATGATCAAAACTACGACATCAGAGACCGCACACGATTTATTAGGCAGCTTATTGTTCCGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-146a-5p(1), mmu-miR-138-5p(1), mmu-miR-136-5p(1), mmu-miR-22-3p(1), mmu-miR-96-5p(1), mmu-miR-383-5p(1), mmu-miR-1198-5p(1), mmu-miR-207(1), mmu-miR-335-3p(1), mmu-miR-350-3p(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GTTTCCAATTGTGACAAAATTGCTTA
siRNA sets
ATTTTGTCACAATTGGAAA,AATTTTGTCACAATTGGAA,TAAGCAATTTTGTCACAAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAP3B1_1274_ORF_1
1.0056
0.303905143
0.987765925
912
ORF sequence:
ATGAAGAAATTTTACTCTGAATCTGAGGAGGAGGAGGACGAGGACGAGGATGAGGACGAGGAGGAGGAAGAAAAGGAAGATGAGGATGAGAACCCCTCTGATAGCAGCAGTGACAGTGAGAGCGGGTCCGGAAGTGAGAGTGGAGACACAGGCACCGAGGACAGCAGTGAGGACTCGTCCAGTGGACAAGACAGCGAGACCGGAAGCCAGGCAGAAGCGGAACGCCAGAAGGTGGCCAAGAGGAACTCCAAAACCAAGAGGAAAAGTGATTCAGAAAATAGGGAGAAGAAAAATGAAAACTCAAAAGCTTCTGAATCGTCCAGTGAGGAGTCCAGTTCCATGGAAGACAGTTCTTCCGAGTCAGAGTCAGAGTCAGGCTCTGACAGTGAGCCTGCGCCCAGAAACGTGGCTCCGGCAAAAGAAAGAAAACCCCAGCAAGAAAGACATCCTCCCTCCAAAGATGTTTTCCTTCTAGATCTGGACGACTTTAACCCAGTATCCACCCCAGTTGCCCTTCCTACACCAGCCCTTTCTCCAAGCTTGATAGCTGATCTTGAAGGTCTAAACTTGTCAACTTCTTCATCAGTCATCAACGTCAGTACGCCTGTCTTCGTGCCAACAAAAACACATGAGCTGCTTCACCGAATGCATGGGAAAGGACTGGCCGCCCACTACTGCTTCCCAAGACAGCCCTGCATCTTCAGTGACAAGATGGTCTCTGTACAGATCACCCTGACTAATACTTCTGATCGAAAAATAGAAAACATCCACATAGGGGGGAAAGGGCTTCCTGTGGGCATGCAGATGCATGCCTTTCATCCAATAGACTCTCTGGAGCCTAAGGGGTCCGTGACTGTCTCAGTGGGTATTGACTTTTGTGATTCTACACAGACGGCCAGTTTCCAATTGTGA
Peptide sequence:
MKKFYSESEEEEDEDEDEDEEEEEKEDEDENPSDSSSDSESGSGSESGDTGTEDSSEDSSSGQDSETGSQAEAERQKVAKRNSKTKRKSDSENREKKNENSKASESSSEESSSMEDSSSESESESGSDSEPAPRNVAPAKERKPQQERHPPSKDVFLLDLDDFNPVSTPVALPTPALSPSLIADLEGLNLSTSSSVINVSTPVFVPTKTHELLHRMHGKGLAAHYCFPRQPCIFSDKMVSVQITLTNTSDRKIENIHIGGKGLPVGMQMHAFHPIDSLEPKGSVTVSVGIDFCDSTQTASFQL
IRESfinder result
IRESfinder score
0.549032642
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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