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mmu_circSmarca2_342
Basic information of circular RNA
PanCircBase ID:
mmu_circSmarca2_342
mm39_Chr. Position ID:
chr19|26654033|26656584|+
Gene name:
Smarca2
Transcript:
ENSMUST00000176769.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
15,16,17
Exon/intron offsets:
0,1682,2440
Genomic length:
2551
Exon/intron sizes in nt:
1,64,67,111
Flanking exon/introns:
chr19:26650246-26654033|chr19:26656584-26659270
Splice length:
342
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
CTCCAGGGCCTGGAATGGATGGTTTCCCTGTATAATAACAATCTGAACGGAATCTTAGCTGATGAAATGGGGCTAGGCAAGACCATCCAGACCATTGCACTCATCACGTATCTGATGGAGCACAAAAGGCTCAATGGTCCCTACCTCATCATCGTCCCCCTCTCGACTCTGTCTAACTGGACATATGAATTTGACAAATGGGCTCCTTCTGTGGTGAAAATTTCTTACAAGGGTACCCCTGCCATGCGACGCTCCCTCGTTCCCCAGCTACGGAGTGGCAAATTCAATGTCCTCCTGACTACTTACGAGTACATTATAAAAGACAAGCACATTCTTGCAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTTCCCCAGCTACGGAGTG
59.78
GGTCTTGCCTAGCCCCATTT
60.03
168
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTTCCCCAGCTACGGAGTG
59.78
CTGGATGGTCTTGCCTAGCC
60.18
174
PCR template sequence:
CATGCGACGCTCCCTCGTTCCCCAGCTACGGAGTGGCAAATTCAATGTCCTCCTGACTACTTACGAGTACATTATAAAAGACAAGCACATTCTTGCAAAGCTCCAGGGCCTGGAATGGATGGTTTCCCTGTATAATAACAATCTGAACGGAATCTTAGCTGATGAAATGGGGCTAGGCAAGACCATCCAGACCATTGCAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-let-7e-5p(1), mmu-miR-130a-3p(1), mmu-miR-431-5p(1), mmu-miR-130b-3p(1), mmu-miR-301b-3p(1), mmu-miR-218-5p(1), mmu-miR-301a-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CATTCTTGCAAAGCTCCAGGGCCTGG
siRNA sets
CAGGCCCTGGAGCTTTGCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMARCA2_342_ORF_1
1.2259
0.297865737
0.954547178
666
ORF sequence:
ATGGTTTCCCTGTATAATAACAATCTGAACGGAATCTTAGCTGATGAAATGGGGCTAGGCAAGACCATCCAGACCATTGCACTCATCACGTATCTGATGGAGCACAAAAGGCTCAATGGTCCCTACCTCATCATCGTCCCCCTCTCGACTCTGTCTAACTGGACATATGAATTTGACAAATGGGCTCCTTCTGTGGTGAAAATTTCTTACAAGGGTACCCCTGCCATGCGACGCTCCCTCGTTCCCCAGCTACGGAGTGGCAAATTCAATGTCCTCCTGACTACTTACGAGTACATTATAAAAGACAAGCACATTCTTGCAAAGCTCCAGGGCCTGGAATGGATGGTTTCCCTGTATAATAACAATCTGAACGGAATCTTAGCTGATGAAATGGGGCTAGGCAAGACCATCCAGACCATTGCACTCATCACGTATCTGATGGAGCACAAAAGGCTCAATGGTCCCTACCTCATCATCGTCCCCCTCTCGACTCTGTCTAACTGGACATATGAATTTGACAAATGGGCTCCTTCTGTGGTGAAAATTTCTTACAAGGGTACCCCTGCCATGCGACGCTCCCTCGTTCCCCAGCTACGGAGTGGCAAATTCAATGTCCTCCTGACTACTTACGAGTACATTATAAAAGACAAGCACATTCTTGCAAAG
Peptide sequence:
MVSLYNNNLNGILADEMGLGKTIQTIALITYLMEHKRLNGPYLIIVPLSTLSNWTYEFDKWAPSVVKISYKGTPAMRRSLVPQLRSGKFNVLLTTYEYIIKDKHILAKLQGLEWMVSLYNNNLNGILADEMGLGKTIQTIALITYLMEHKRLNGPYLIIVPLSTLSNWTYEFDKWAPSVVKISYKGTPAMRRSLVPQLRSGKFNVLLTTYEYIIKDKHILAK
IRESfinder result
IRESfinder score
0.565028106
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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