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mmu_circCaprin1_278
Basic information of circular RNA
PanCircBase ID:
mmu_circCaprin1_278
mm39_Chr. Position ID:
chr2|103606278|103608445|-
Gene name:
Caprin1
Transcript:
ENSMUST00000028607.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
9,8,7
Exon/intron offsets:
0,171,2029
Genomic length:
2167
Exon/intron sizes in nt:
87,53,138
Flanking exon/introns:
chr2:103606110-103606278|chr2:103608445-103609508
Splice length:
278
Other database IDs:
circBase: hsa_circ_0095750, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_4159
Human Ortholog IDs:
Mature spliced Sequence:
ATAAAGCTCTAAAGGAAATTGTTGAGCGTGTTTTCCAGTCAAACTACTTTGATAGCACTCACAATCATCAAAATGGGTTGTGTGAGGAGGAAGAGGCGGCTTCAGCGCCCACAGTGGAGGACCAGGTAGCTGAAGCTGAACCTGAGCCAGCGGAAGAATACACAGAGCAAAGTGAGGTTGAATCAACAGAGTATGTCAATAGGCAGTTCATGGCAGAAACACAGTTCAGCAGTGGTGAGAAGGAGCAAGTGGATGAGTGGACAGTTGAAACAGTTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGTGGTGAGAAGGAGCAA
60.25
GCCTCTTCCTCCTCACACAA
59.31
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGTGGTGAGAAGGAGCAA
60.25
CTTCCTCCTCACACAACCCA
59.24
143
PCR template sequence:
TGAATCAACAGAGTATGTCAATAGGCAGTTCATGGCAGAAACACAGTTCAGCAGTGGTGAGAAGGAGCAAGTGGATGAGTGGACAGTTGAAACAGTTGAGATAAAGCTCTAAAGGAAATTGTTGAGCGTGTTTTCCAGTCAAACTACTTTGATAGCACTCACAATCATCAAAATGGGTTGTGTGAGGAGGAAGAGGCGGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-24-3p(1), mmu-miR-149-5p(1), mmu-miR-22-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGAAACAGTTGAGATAAAGCTCTAAA
siRNA sets
TTTAGAGCTTTATCTCAAC, TAGAGCTTTATCTCAACTG, CTTTATCTCAACTGTTTCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCAPRIN1_278_ORF_1
1.0725
-0.218258675
0.029183998
90
ORF sequence:
ATGTCAATAGGCAGTTCATGGCAGAAACACAGTTCAGCAGTGGTGAGAAGGAGCAAGTGGATGAGTGGACAGTTGAAACAGTTGAGATAA
Peptide sequence:
MSIGSSWQKHSSAVVRRSKWMSGQLKQLR
IRESfinder result
IRESfinder score
0.399841219
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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