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mmu_circAp3b1_399
Basic information of circular RNA
PanCircBase ID:
mmu_circAp3b1_399
mm39_Chr. Position ID:
chr13|94531226|94545351|+
Gene name:
Ap3b1
Transcript:
ENSMUST00000022196.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
3,4,5,6
Exon/intron offsets:
0,8619,9228,14058
Genomic length:
14125
Exon/intron sizes in nt:
75,96,161,67
Flanking exon/introns:
chr13:94527375-94531226|chr13:94545351-94554468
Splice length:
399
Other database IDs:
circBase: mmu_circ_0004898, CIRCpedia: MMU_CIRCpedia_34802, circAtlas: mmu-Ap3b1_0023
circAtlas: hsa-AP3B1_0042, CIRCpedia: HSA_CIRCpedia_363322
Human Ortholog IDs:
Mature spliced Sequence:
ATGATTGCGAAGGGGAAAAATGCCTCGGAACTCTTCCCTGCTGTTGTGAAGAATGTGGCCAGTAAAAACATCGAGATCAAGAAGTTGGTGTACGTTTACCTTGTCCGATATGCTGAAGAACAGCAGGACCTGGCTCTTCTGTCCATAAGCACTTTCCAGCGAGCTTTGAAGGACCCGAATCAACTAATCCGTGCAAGTGCCTTGAGAGTTTTGTCAAGTATTAGAGTGCCAATTATCGTGCCTGTCATGATGCTGGCTATTAAGGAGGCTTCAGCTGACCTGTCGCCATATGTTAGGAAGAATGCAGCCCATGCTATTCAGAAGCTGTACAGTCTTGACCCCGAGCAGAAGGAGATGTTAATTGAAGTCATTGAGAAGCTTCTGAAAGACAAGAGCACG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCCCATGCTATTCAGAAGCTG
59.39
TCACAACAGCAGGGAAGAGT
58.87
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTACAGTCTTGACCCCGAGC
60.11
CTCGATGTTTTTACTGGCCACA
59.19
148
PCR template sequence:
GAATGCAGCCCATGCTATTCAGAAGCTGTACAGTCTTGACCCCGAGCAGAAGGAGATGTTAATTGAAGTCATTGAGAAGCTTCTGAAAGACAAGAGCACGATGATTGCGAAGGGGAAAAATGCCTCGGAACTCTTCCCTGCTGTTGTGAAGAATGTGGCCAGTAAAAACATCGAGATCAAGAAGTTGGTGTACGTTTACC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-106b-5p(1), mmu-miR-96-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGACAAGAGCACGATGATTGCGAAGG
siRNA sets
AATCATCGTGCTCTTGTCT, CTTCGCAATCATCGTGCTC, TTCGCAATCATCGTGCTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAP3B1_399_ORF_1
1.1712
0.346104759
0.983535587
798
ORF sequence:
ATGATTGCGAAGGGGAAAAATGCCTCGGAACTCTTCCCTGCTGTTGTGAAGAATGTGGCCAGTAAAAACATCGAGATCAAGAAGTTGGTGTACGTTTACCTTGTCCGATATGCTGAAGAACAGCAGGACCTGGCTCTTCTGTCCATAAGCACTTTCCAGCGAGCTTTGAAGGACCCGAATCAACTAATCCGTGCAAGTGCCTTGAGAGTTTTGTCAAGTATTAGAGTGCCAATTATCGTGCCTGTCATGATGCTGGCTATTAAGGAGGCTTCAGCTGACCTGTCGCCATATGTTAGGAAGAATGCAGCCCATGCTATTCAGAAGCTGTACAGTCTTGACCCCGAGCAGAAGGAGATGTTAATTGAAGTCATTGAGAAGCTTCTGAAAGACAAGAGCACGATGATTGCGAAGGGGAAAAATGCCTCGGAACTCTTCCCTGCTGTTGTGAAGAATGTGGCCAGTAAAAACATCGAGATCAAGAAGTTGGTGTACGTTTACCTTGTCCGATATGCTGAAGAACAGCAGGACCTGGCTCTTCTGTCCATAAGCACTTTCCAGCGAGCTTTGAAGGACCCGAATCAACTAATCCGTGCAAGTGCCTTGAGAGTTTTGTCAAGTATTAGAGTGCCAATTATCGTGCCTGTCATGATGCTGGCTATTAAGGAGGCTTCAGCTGACCTGTCGCCATATGTTAGGAAGAATGCAGCCCATGCTATTCAGAAGCTGTACAGTCTTGACCCCGAGCAGAAGGAGATGTTAATTGAAGTCATTGAGAAGCTTCTGAAAGACAAGAGCACG
Peptide sequence:
MIAKGKNASELFPAVVKNVASKNIEIKKLVYVYLVRYAEEQQDLALLSISTFQRALKDPNQLIRASALRVLSSIRVPIIVPVMMLAIKEASADLSPYVRKNAAHAIQKLYSLDPEQKEMLIEVIEKLLKDKSTMIAKGKNASELFPAVVKNVASKNIEIKKLVYVYLVRYAEEQQDLALLSISTFQRALKDPNQLIRASALRVLSSIRVPIIVPVMMLAIKEASADLSPYVRKNAAHAIQKLYSLDPEQKEMLIEVIEKLLKDKST
IRESfinder result
IRESfinder score
0.527941703
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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