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mmu_circSlk_549
Basic information of circular RNA
PanCircBase ID:
mmu_circSlk_549
mm39_Chr. Position ID:
chr19|47600013|47605042|+
Gene name:
Slk
Transcript:
ENSMUST00000026043.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
3,4,5,6,7
Exon/intron offsets:
0,327,3621,3831,4947
Genomic length:
5029
Exon/intron sizes in nt:
49,150,73,195,82
Flanking exon/introns:
chr19:47597508-47600013|chr19:47605042-47607629
Splice length:
549
Other database IDs:
circAtlas: mmu-Slk_0010
Human Ortholog IDs:
Mature spliced Sequence:
ATCCTCATTGAATTCTGTGCAGGGGGAGCAGTGGATGCTGTGATGCTTGAACTTGAGAGACCATTAACTGAATCCCAAATCCAAGTAGTCTGCAAGCAGACATTAGAGGCATTGAATTACTTACATGACAATAAAATCATCCACCGAGATCTAAAAGCTGGCAATATTCTCTTTACCTTAGATGGAGACATTAAATTAGCGGATTTTGGAGTATCAGCTAAAAATACCAGGACAATTCAAAGGAGGGATTCATTTATTGGCACACCATATTGGATGGCTCCTGAAGTAGTCATGTGTGAGACATCAAAGGACAGACCTTATGACTACAAAGCTGATGTTTGGTCCCTGGGTATTACTTTAATAGAAATGGCTGAGATAGAGCCACCTCATCATGAGTTAAATCCAATGCGCGTGCTGCTGAAAATTGCAAAATCTGAGCCCCCAACATTAGCACAGCCATCAAAATGGTCTTCAAATTTTAAGGACTTTCTAAGGAAATGCTTGGAAAAGAATGTGGATGCGCGGTGGACCACGTCTCAGCTGTTGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAAAGAATGTGGATGCGCGG
59.83
TCTGCTTGCAGACTACTTGGA
59.03
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAAAGAATGTGGATGCGCGG
59.83
CTGCTTGCAGACTACTTGGA
57.54
143
PCR template sequence:
AGCACAGCCATCAAAATGGTCTTCAAATTTTAAGGACTTTCTAAGGAAATGCTTGGAAAAGAATGTGGATGCGCGGTGGACCACGTCTCAGCTGTTGCAGATCCTCATTGAATTCTGTGCAGGGGGAGCAGTGGATGCTGTGATGCTTGAACTTGAGAGACCATTAACTGAATCCCAAATCCAAGTAGTCTGCAAGCAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-15b-5p(1), mmu-miR-24-3p(1), mmu-miR-433-3p(1), mmu-miR-541-5p(1), mmu-miR-377-3p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCAGCTGTTGCAGATCCTCATTGAAT
siRNA sets
AATGAGGATCTGCAACAGC, CAATGAGGATCTGCAACAG, ATGAGGATCTGCAACAGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSLK_549_ORF_1
0.8784
0.038531276
0.984368456
1056
ORF sequence:
ATGCTTGAACTTGAGAGACCATTAACTGAATCCCAAATCCAAGTAGTCTGCAAGCAGACATTAGAGGCATTGAATTACTTACATGACAATAAAATCATCCACCGAGATCTAAAAGCTGGCAATATTCTCTTTACCTTAGATGGAGACATTAAATTAGCGGATTTTGGAGTATCAGCTAAAAATACCAGGACAATTCAAAGGAGGGATTCATTTATTGGCACACCATATTGGATGGCTCCTGAAGTAGTCATGTGTGAGACATCAAAGGACAGACCTTATGACTACAAAGCTGATGTTTGGTCCCTGGGTATTACTTTAATAGAAATGGCTGAGATAGAGCCACCTCATCATGAGTTAAATCCAATGCGCGTGCTGCTGAAAATTGCAAAATCTGAGCCCCCAACATTAGCACAGCCATCAAAATGGTCTTCAAATTTTAAGGACTTTCTAAGGAAATGCTTGGAAAAGAATGTGGATGCGCGGTGGACCACGTCTCAGCTGTTGCAGATCCTCATTGAATTCTGTGCAGGGGGAGCAGTGGATGCTGTGATGCTTGAACTTGAGAGACCATTAACTGAATCCCAAATCCAAGTAGTCTGCAAGCAGACATTAGAGGCATTGAATTACTTACATGACAATAAAATCATCCACCGAGATCTAAAAGCTGGCAATATTCTCTTTACCTTAGATGGAGACATTAAATTAGCGGATTTTGGAGTATCAGCTAAAAATACCAGGACAATTCAAAGGAGGGATTCATTTATTGGCACACCATATTGGATGGCTCCTGAAGTAGTCATGTGTGAGACATCAAAGGACAGACCTTATGACTACAAAGCTGATGTTTGGTCCCTGGGTATTACTTTAATAGAAATGGCTGAGATAGAGCCACCTCATCATGAGTTAAATCCAATGCGCGTGCTGCTGAAAATTGCAAAATCTGAGCCCCCAACATTAGCACAGCCATCAAAATGGTCTTCAAATTTTAAGGACTTTCTAAGGAAATGCTTGGAAAAGAATGTGGATGCGCGGTGGACCACGTCTCAGCTGTTGCAG
Peptide sequence:
MLELERPLTESQIQVVCKQTLEALNYLHDNKIIHRDLKAGNILFTLDGDIKLADFGVSAKNTRTIQRRDSFIGTPYWMAPEVVMCETSKDRPYDYKADVWSLGITLIEMAEIEPPHHELNPMRVLLKIAKSEPPTLAQPSKWSSNFKDFLRKCLEKNVDARWTTSQLLQILIEFCAGGAVDAVMLELERPLTESQIQVVCKQTLEALNYLHDNKIIHRDLKAGNILFTLDGDIKLADFGVSAKNTRTIQRRDSFIGTPYWMAPEVVMCETSKDRPYDYKADVWSLGITLIEMAEIEPPHHELNPMRVLLKIAKSEPPTLAQPSKWSSNFKDFLRKCLEKNVDARWTTSQLLQ
IRESfinder result
IRESfinder score
0.61860286
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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