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mmu_circSlk_364
Basic information of circular RNA
PanCircBase ID:
mmu_circSlk_364
mm39_Chr. Position ID:
chr19|47597343|47600490|+
Gene name:
Slk
Transcript:
ENSMUST00000026043.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
2,3,4
Exon/intron offsets:
0,2670,2997
Genomic length:
3147
Exon/intron sizes in nt:
1,65,49,150
Flanking exon/introns:
chr19:47568782-47597343|chr19:47600490-47603634
Splice length:
364
Other database IDs:
CIRCpedia: MMU_CIRCpedia_21128, circAtlas: mmu-Slk_0002
circBase: hsa_circ_0005321, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_325
Human Ortholog IDs:
Mature spliced Sequence:
GCCCAGAATAAAGAGACCAATGTTTTAGCTGCTGCAAAGGTGATTGACACCAAATCTGAAGAAGAGCTTGAAGATTATATGGTTGAGATTGACATATTAGCATCTTGTGATCACCCAAACATCGTCAAGCTTCTAGATGCCTTCTATTACGAGAACAACCTTTGGATCCTCATTGAATTCTGTGCAGGGGGAGCAGTGGATGCTGTGATGCTTGAACTTGAGAGACCATTAACTGAATCCCAAATCCAAGTAGTCTGCAAGCAGACATTAGAGGCATTGAATTACTTACATGACAATAAAATCATCCACCGAGATCTAAAAGCTGGCAATATTCTCTTTACCTTAGATGGAGACATTAAATTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGAGGCATTGAATTACTTACATGACA
58.89
TCAATCACCTTTGCAGCAGC
59.4
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGAGGCATTGAATTACTTACATGACA
58.89
CAATCACCTTTGCAGCAGCT
59.4
141
PCR template sequence:
ACATTAGAGGCATTGAATTACTTACATGACAATAAAATCATCCACCGAGATCTAAAAGCTGGCAATATTCTCTTTACCTTAGATGGAGACATTAAATTAGGCCCAGAATAAAGAGACCAATGTTTTAGCTGCTGCAAAGGTGATTGACACCAAATCTGAAGAAGAGCTTGAAGATTATATGGTTGAGATTGACATATTAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-541-5p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GACATTAAATTAGGCCCAGAATAAAG
siRNA sets
TTATTCTGGGCCTAATTTA, TATTCTGGGCCTAATTTAA, TCTGGGCCTAATTTAATGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSLK_364_ORF_1
1.0663
0.101687882
0.327793788
297
ORF sequence:
ATGGTTGAGATTGACATATTAGCATCTTGTGATCACCCAAACATCGTCAAGCTTCTAGATGCCTTCTATTACGAGAACAACCTTTGGATCCTCATTGAATTCTGTGCAGGGGGAGCAGTGGATGCTGTGATGCTTGAACTTGAGAGACCATTAACTGAATCCCAAATCCAAGTAGTCTGCAAGCAGACATTAGAGGCATTGAATTACTTACATGACAATAAAATCATCCACCGAGATCTAAAAGCTGGCAATATTCTCTTTACCTTAGATGGAGACATTAAATTAGGCCCAGAATAA
Peptide sequence:
MVEIDILASCDHPNIVKLLDAFYYENNLWILIEFCAGGAVDAVMLELERPLTESQIQVVCKQTLEALNYLHDNKIIHRDLKAGNILFTLDGDIKLGPE
IRESfinder result
IRESfinder score
0.753482688
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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