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mmu_circSil1_383
Basic information of circular RNA
PanCircBase ID:
mmu_circSil1_383
mm39_Chr. Position ID:
chr18|35474150|35551248|-
Gene name:
Sil1
Transcript:
ENSMUST00000237896.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
4,3,2
Exon/intron offsets:
0,62228,76959
Genomic length:
77098
Exon/intron sizes in nt:
100,144,139
Flanking exon/introns:
chr18:35458528-35474150|chr18:35551248-35631843
Splice length:
383
Other database IDs:
CIRCpedia: MMU_CIRCpedia_39371, circAtlas: mmu-Sil1_0009
circBase: hsa_circ_0074179
Human Ortholog IDs:
Mature spliced Sequence:
AATAATTTTGCACTCACCAACCCAGAGAAGAGCATCCACCAGGAATCAGATACAAAGGAGACCAGGGAAGAGGAGGAGCTAGACACCGAGATCCTGGAGGTGTTCCACCCAACTCAAGAGTGGCAGACCCTTCAACCAGTGCCTTGCTCTTTCACGAAGCAGGTGTTTGCTGCTTTTCTTGAGTGCAGAAGCTACGTGTGCTCTTCTTAAGACTGATGTGGCCATCTCTGTCACACTAATAACAGGGTGTGTAGAAGAACACCATTATTAGCGTTGGGAGAATGCTGGACATCAACGCCAACACATACACATCTCAGGACCTCAAGAGTGCGCTGGCCAAATTCAAGGAGGGGACCGAGATGGAGAATTCAAAGGATGAACTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGCCAAATTCAAGGAGGGGA
59.96
TCTCGGTGTCTAGCTCCTCC
60.11
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTCAGGACCTCAAGAGTGCG
60.11
CGGTGTCTAGCTCCTCCTCT
60.11
159
PCR template sequence:
GCTGGACATCAACGCCAACACATACACATCTCAGGACCTCAAGAGTGCGCTGGCCAAATTCAAGGAGGGGACCGAGATGGAGAATTCAAAGGATGAACTGAATAATTTTGCACTCACCAACCCAGAGAAGAGCATCCACCAGGAATCAGATACAAAGGAGACCAGGGAAGAGGAGGAGCTAGACACCGAGATCCTGGAGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-124-3p(1), mmu-miR-15a-5p(1), mmu-miR-150-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-130a-3p(1), mmu-miR-149-5p(1), mmu-miR-301b-3p(1), mmu-miR-297a-5p(1), mmu-miR-301a-3p(1), mmu-miR-1187(1)
siRNAs for circular RNA silencing
Junction sequence
AAAGGATGAACTGAATAATTTTGCAC
siRNA sets
AAATTATTCAGTTCATCCT, AATTATTCAGTTCATCCTT, AAAATTATTCAGTTCATCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSIL1_383_ORF_1
0.993
0.385779943
0.602135584
312
ORF sequence:
ATGCTGGACATCAACGCCAACACATACACATCTCAGGACCTCAAGAGTGCGCTGGCCAAATTCAAGGAGGGGACCGAGATGGAGAATTCAAAGGATGAACTGAATAATTTTGCACTCACCAACCCAGAGAAGAGCATCCACCAGGAATCAGATACAAAGGAGACCAGGGAAGAGGAGGAGCTAGACACCGAGATCCTGGAGGTGTTCCACCCAACTCAAGAGTGGCAGACCCTTCAACCAGTGCCTTGCTCTTTCACGAAGCAGGTGTTTGCTGCTTTTCTTGAGTGCAGAAGCTACGTGTGCTCTTCTTAA
Peptide sequence:
MLDINANTYTSQDLKSALAKFKEGTEMENSKDELNNFALTNPEKSIHQESDTKETREEEELDTEILEVFHPTQEWQTLQPVPCSFTKQVFAAFLECRSYVCSS
IRESfinder result
IRESfinder score
0.618973421
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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