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mmu_circSin3a_362
Basic information of circular RNA
PanCircBase ID:
mmu_circSin3a_362
mm39_Chr. Position ID:
chr9|57024665|57026471|+
Gene name:
Sin3a
Transcript:
ENSMUST00000167715.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
18,19,20
Exon/intron offsets:
0,688,1711
Genomic length:
1806
Exon/intron sizes in nt:
174,93,95
Flanking exon/introns:
chr9:57020999-57024665|chr9:57026471-57032452
Splice length:
362
Other database IDs:
circBase: mmu_circ_0015712, CIRCpedia: MMU_CIRCpedia_23755, circAtlas: mmu-Sin3a_0004
circAtlas: hsa-SIN3A_0049, CIRCpedia: HSA_CIRCpedia_162433
Human Ortholog IDs:
Mature spliced Sequence:
CTACAGCACATCGTCAGCGACGAGGTCTGTGTGCAGGTTACTGATCTTTACTTGGCAGAAAACAATAACGGAGCCACGGGAGGCCAGCTCAACAGTCAGACTTCAAGGAGCCTTCTGGAGTCAGCATACCAGCGGAAGGCAGAGCAGCTTATGTCAGATGAGAACTGCTTCAAGCTAATGTTCATTCAAAGTCAAGGTCAAGTTCAGCTGACTGTTGAGCTCCTGGACACAGAAGAGGAGAACTCAGATGACCCCGTGGAAGCAGAGCGTTGGTCAGACTACGTGGAGCGATATATGAGTTCTGATACTACTTCTCCTGAACTTCGAGAACATCTGGCACAGAAACCAGTATTTCTCCCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCGTTGGTCAGACTACGTG
60.04
CCCGTGGCTCCGTTATTGTT
60.68
177
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCGTTGGTCAGACTACGTG
60.04
CTCCCGTGGCTCCGTTATTG
60.81
179
PCR template sequence:
CAGAGCGTTGGTCAGACTACGTGGAGCGATATATGAGTTCTGATACTACTTCTCCTGAACTTCGAGAACATCTGGCACAGAAACCAGTATTTCTCCCAAGCTACAGCACATCGTCAGCGACGAGGTCTGTGTGCAGGTTACTGATCTTTACTTGGCAGAAAACAATAACGGAGCCACGGGAGGCCAGCTCAACAGTCAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-29b-1-5p(1), mmu-miR-539-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TATTTCTCCCAAGCTACAGCACATCG
siRNA sets
GATGTGCTGTAGCTTGGGA,ATGTGCTGTAGCTTGGGAG,TGTGCTGTAGCTTGGGAGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSIN3A_362_ORF_1
0.4841
0.127541713
0.264248722
390
ORF sequence:
ATGTCAGATGAGAACTGCTTCAAGCTAATGTTCATTCAAAGTCAAGGTCAAGTTCAGCTGACTGTTGAGCTCCTGGACACAGAAGAGGAGAACTCAGATGACCCCGTGGAAGCAGAGCGTTGGTCAGACTACGTGGAGCGATATATGAGTTCTGATACTACTTCTCCTGAACTTCGAGAACATCTGGCACAGAAACCAGTATTTCTCCCAAGCTACAGCACATCGTCAGCGACGAGGTCTGTGTGCAGGTTACTGATCTTTACTTGGCAGAAAACAATAACGGAGCCACGGGAGGCCAGCTCAACAGTCAGACTTCAAGGAGCCTTCTGGAGTCAGCATACCAGCGGAAGGCAGAGCAGCTTATGTCAGATGAGAACTGCTTCAAGCTAA
Peptide sequence:
MSDENCFKLMFIQSQGQVQLTVELLDTEEENSDDPVEAERWSDYVERYMSSDTTSPELREHLAQKPVFLPSYSTSSATRSVCRLLIFTWQKTITEPREASSTVRLQGAFWSQHTSGRQSSLCQMRTASS
IRESfinder result
IRESfinder score
0.540063691
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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