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mmu_circSwt1_452_1
Basic information of circular RNA
PanCircBase ID:
mmu_circSwt1_452_1
mm39_Chr. Position ID:
chr1|151246329|151260255|-
Gene name:
Swt1
Transcript:
ENSMUST00000064771.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
19,18,17,16
Exon/intron offsets:
0,1729,8804,13738
Genomic length:
13926
Exon/intron sizes in nt:
6,56,71,32,188
Flanking exon/introns:
chr1:151244339-151246329|chr1:151260255-151264370
Splice length:
452
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTCAAGACAAAACTGAAGCCAAGTTCTTCAGAAAGCACAAGGAGTAAAGAGCAGGAAGACACTTCTTTGGTGAAGCTTCATAACCAAGATGTCAACGTTTTCCTGGATTCTAATCTTCCCCAGGCCACCAGGCATCAGGAAATCTGGTCTGTCCTGGAGAGTGTTTGGATGTCAATATATCAGAACAGCACAGATGTATTTCAAACACTGGACTCAAGTTCAACCCTGACAACTTCGAAAATAGCATCCTTTGAAGAAGCTTTTGTGTATCTTCAAAAGTTAATGGTGGCTGTGAAAGATATTCTTGAAGGAATTCAAAGGATTTTGGCTCCTAATAGTAATTACCAAGATGTTGAGACTCTCTATAACTTCCTAATCAAGTATGAGGTAAACAAAAATGTCAAATTCACTGCCCGGGAACTTTATGATTGTGTTTCTCAGACTGAGTACCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCAAATTCACTGCCCGGGAA
59.89
ACGTTGACATCTTGGTTATGAAGC
59.85
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATTCACTGCCCGGGAACTTT
59.89
ACGTTGACATCTTGGTTATGAAGC
59.85
146
PCR template sequence:
TTGAGACTCTCTATAACTTCCTAATCAAGTATGAGGTAAACAAAAATGTCAAATTCACTGCCCGGGAACTTTATGATTGTGTTTCTCAGACTGAGTACCGGTCAAGACAAAACTGAAGCCAAGTTCTTCAGAAAGCACAAGGAGTAAAGAGCAGGAAGACACTTCTTTGGTGAAGCTTCATAACCAAGATGTCAACGTTT
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-miR-199a-5p(1), mmu-miR-7b-5p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-382-5p(1), mmu-miR-34b-5p(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGACTGAGTACCGGTCAAGACAAAAC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSWT1_452_1_ORF_1
0.7717
0.017393693
0.168939956
300
ORF sequence:
ATGTCAATATATCAGAACAGCACAGATGTATTTCAAACACTGGACTCAAGTTCAACCCTGACAACTTCGAAAATAGCATCCTTTGAAGAAGCTTTTGTGTATCTTCAAAAGTTAATGGTGGCTGTGAAAGATATTCTTGAAGGAATTCAAAGGATTTTGGCTCCTAATAGTAATTACCAAGATGTTGAGACTCTCTATAACTTCCTAATCAAGTATGAGGTAAACAAAAATGTCAAATTCACTGCCCGGGAACTTTATGATTGTGTTTCTCAGACTGAGTACCGGTCAAGACAAAACTGA
Peptide sequence:
MSIYQNSTDVFQTLDSSSTLTTSKIASFEEAFVYLQKLMVAVKDILEGIQRILAPNSNYQDVETLYNFLIKYEVNKNVKFTARELYDCVSQTEYRSRQN
IRESfinder result
IRESfinder score
0.733303173
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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