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mmu_circSmarca2_195
Basic information of circular RNA
PanCircBase ID:
mmu_circSmarca2_195
mm39_Chr. Position ID:
chr19|26668744|26669667|+
Gene name:
Smarca2
Transcript:
ENSMUST00000176769.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
20,21
Exon/intron offsets:
0,836
Genomic length:
923
Exon/intron sizes in nt:
108,87
Flanking exon/introns:
chr19:26661322-26668744|chr19:26669667-26673575
Splice length:
195
Other database IDs:
CIRCpedia: MMU_CIRCpedia_14825, circAtlas: mmu-Smarca2_0021
circBase: hsa_circ_0138480, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_140598
Human Ortholog IDs:
Mature spliced Sequence:
GTTGAGTATGTGATCAAGTGTGACATGTCAGCTCTGCAGAAGATTCTGTACCGTCACATGCAAGCCAAGGGGATCCTCCTCACGGACGGGTCTGAGAAAGATAAGAAGGGGAAAGGAGGTGCCAAGACACTTATGAACACCATCATGCAGCTGAGAAAAATATGCAACCACCCATATATGTTTCAGCACATTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGAAAGGAGGTGCCAAGACA
59.89
TTGGCTTGCATGTGACGGTA
60.25
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGAAAGGAGGTGCCAAGACA
59.89
TGCAGAGCTGACATGTCACA
59.61
124
PCR template sequence:
AGATAAGAAGGGGAAAGGAGGTGCCAAGACACTTATGAACACCATCATGCAGCTGAGAAAAATATGCAACCACCCATATATGTTTCAGCACATTGAGGTTGAGTATGTGATCAAGTGTGACATGTCAGCTCTGCAGAAGATTCTGTACCGTCACATGCAAGCCAAGGGGATCCTCCTCACGGACGGGTCTGAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-494-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCAGCACATTGAGGTTGAGTATGTGA
siRNA sets
ACTCAACCTCAATGTGCTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMARCA2_195_ORF_1
1.2874
0.339769978
0.76354816
366
ORF sequence:
ATGTCAGCTCTGCAGAAGATTCTGTACCGTCACATGCAAGCCAAGGGGATCCTCCTCACGGACGGGTCTGAGAAAGATAAGAAGGGGAAAGGAGGTGCCAAGACACTTATGAACACCATCATGCAGCTGAGAAAAATATGCAACCACCCATATATGTTTCAGCACATTGAGGTTGAGTATGTGATCAAGTGTGACATGTCAGCTCTGCAGAAGATTCTGTACCGTCACATGCAAGCCAAGGGGATCCTCCTCACGGACGGGTCTGAGAAAGATAAGAAGGGGAAAGGAGGTGCCAAGACACTTATGAACACCATCATGCAGCTGAGAAAAATATGCAACCACCCATATATGTTTCAGCACATTGAG
Peptide sequence:
MSALQKILYRHMQAKGILLTDGSEKDKKGKGGAKTLMNTIMQLRKICNHPYMFQHIEVEYVIKCDMSALQKILYRHMQAKGILLTDGSEKDKKGKGGAKTLMNTIMQLRKICNHPYMFQHIE
IRESfinder result
IRESfinder score
0.397344389
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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