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mmu_circSwt1_469
Basic information of circular RNA
PanCircBase ID:
mmu_circSwt1_469
mm39_Chr. Position ID:
chr1|151255133|151264519|-
Gene name:
Swt1
Transcript:
ENSMUST00000064771.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
17,16,15
Exon/intron offsets:
0,4934,9237
Genomic length:
9386
Exon/intron sizes in nt:
13,21,88,149
Flanking exon/introns:
chr1:151248125-151255133|chr1:151264519-151267186
Splice length:
469
Other database IDs:
circAtlas: mmu-Swt1_0013
circBase: hsa_circ_0004689, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_29192
Human Ortholog IDs:
Mature spliced Sequence:
CAAATAAGGCAGTGGATTTTACAACAGTGAAATTCTTGCTTCAGGATTCTAAAAGTTTGTTACATGCCTTCAGTACAAGGTCAAATTATGATGGAGTTCTTCCCCAGACCTTTGCTCAAGTAAACAAACTACTGCAAGTACTCGCAGAGGTCAAGACAAAACTGAAGCCAAGTTCTTCAGAAAGCACAAGGAGTAAAGAGCAGGAAGACACTTCTTTGGTGAAGCTTCATAACCAAGATGTCAACGTTTTCCTGGATTCTAATCTTCCCCAGGCCACCAGGCATCAGGAAATCTGGTCTGTCCTGGAGAGTGTTTGGATGTCAATATATCAGAACAGCACAGATGTATTTCAAACACTGGACTCAAGTTCAACCCTGACAACTTCGAAAATAGCATCCTTTGAAGAAGCTTTTGTGTATCTTCAAAAGTTAATGGTGGCTGTGAAAGATATTCTTGAAGGAATTCAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCTGACAACTTCGAAAATAGCA
59.25
TGACCTTGTACTGAAGGCATGT
59.63
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCCTGACAACTTCGAAAATAGC
57.66
TGACCTTGTACTGAAGGCATGT
59.63
180
PCR template sequence:
CAACCCTGACAACTTCGAAAATAGCATCCTTTGAAGAAGCTTTTGTGTATCTTCAAAAGTTAATGGTGGCTGTGAAAGATATTCTTGAAGGAATTCAAAGCAAATAAGGCAGTGGATTTTACAACAGTGAAATTCTTGCTTCAGGATTCTAAAAGTTTGTTACATGCCTTCAGTACAAGGTCAAATTATGATGGAGTTCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-199a-5p(1), mmu-miR-7b-5p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-382-5p(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AAGGAATTCAAAGCAAATAAGGCAGT
siRNA sets
TATTTGCTTTGAATTCCTT, TTATTTGCTTTGAATTCCT, CTTATTTGCTTTGAATTCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSWT1_469_ORF_1
0.8303
-0.084544028
0.051210192
159
ORF sequence:
ATGTCAATATATCAGAACAGCACAGATGTATTTCAAACACTGGACTCAAGTTCAACCCTGACAACTTCGAAAATAGCATCCTTTGAAGAAGCTTTTGTGTATCTTCAAAAGTTAATGGTGGCTGTGAAAGATATTCTTGAAGGAATTCAAAGCAAATAA
Peptide sequence:
MSIYQNSTDVFQTLDSSSTLTTSKIASFEEAFVYLQKLMVAVKDILEGIQSK
IRESfinder result
IRESfinder score
0.682553954
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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