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mmu_ciSlk_1282
Basic information of circular RNA
PanCircBase ID:
mmu_ciSlk_1282
mm39_Chr. Position ID:
chr19|47609391|47610673|+
Gene name:
Slk
Transcript:
ENSMUST00000026043.12
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
9
Exon/intron offsets:
0
Genomic length:
1282
Exon/intron sizes in nt:
1282
Flanking exon/introns:
chr19:47609391-47610674
Splice length:
1282
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGAGTGTGTCTGGGGCCTTGTTCGGTTTTGCTTTGTTATTTTGGCTTTGTTATTTGAATTTCTAGTTCATTGCTACCTTAAAACACTATTATATCAATGTAATACTAACCCTATTAACTCTTTTGGGGTCATAAGGCAATCAAAAAGAATTGGAGAGAAATATTCTGGGAATAACCTTCAGATTTTTTGGTAGAGCCTGTTCATTTTTGCAAATGACGTAAACAGGACAAGACAGTTTGTTGTTTTCATTTAGTTTCTCTTGCACATGTCTGAGTACAATTTTAGCAAGTTTAGTAAGGCTCCAAAGGGTCAGGATATGTAGCAAAAGAGAGGTTTTTTTTTTTTTAATGCATTGTATTTATTACTTTGAATGTTTATGGGTGTGTGTGCATATGTGCCATAAAGAGCATCTCCAGGCCAGGGGATAACTTAGGGGAGCCGGCTCTCTTCCACTGGAACTACTTCTGTGGGAACTAAGGGATGCTAATTATATATCCCTTGCTGTAGAAGCTGGAGAAATGTGAAATTTATAGGTTAAGGAAGGTTTTGTGTGTGCACACACACACGTGCATACGTACATTTAAAGCATGTCCGTGATAGAGGAATGCGGGGCTGCTGCTGCTGCCGCAGTCAGATTTGGAGGGGAACGTGAGTGAGGCCCTAGATCTGGAGGATGGAGAAGTGAGATGTGGCTGGAAGGTGCCCAAGGCAAACCTGAATTTTGACACAATTTCAGTTTCGTGCCTTTTCTCCACTTCCTGTTTTGGGACTCCTCTTCTCTCTCTTTCAGTTCCCTCCTTTCCCCTCTTTCCCTTTCTCTTCCCCTTCTCCTTGCACAGTTTTTTCTTTCATTCCCTCCCTATGCTTCTTGTCTCTTTCCAGAGTCTTGTATGGAGCCCTCCAACCTCTCGTCAAACTCCTGAGTGCTGGGCTTGGCTCTCCACACCCCCACCCCAGTAAACAAAGTAATTGTCTCCCTGTAGGGGTGAGAGCCACTCAGTGAAAGATGAAGAGGTTAATGTGTCAGAGTCACCATGCAGTGTCTAACAGCCCTGCACTTGACCAGAAGGCTCACTCTCACTTAGAGTTTGTTCTTTGTCATCTGCAAAGTTGAATGTGAGCTCTCAATTTAGGAATAAGGTGATAAAGCTGTTGTACAGATATTCCTACTGCTTTCTATGTGCAGCTCATAGCTGGCAAGACATCTTCAGTTTTAAAGAGGAAAATATCTTTCATGGGTGATATTTACACAAAACCTAACCCAAAATGAAATCTCATTCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTCATAGCTGGCAAGACATC
59.13
GCCAAAATAACAAAGCAAAACCGA
59.73
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTCATAGCTGGCAAGACATC
59.13
AGCCAAAATAACAAAGCAAAACCG
59.73
143
PCR template sequence:
TGCAGCTCATAGCTGGCAAGACATCTTCAGTTTTAAAGAGGAAAATATCTTTCATGGGTGATATTTACACAAAACCTAACCCAAAATGAAATCTCATTCAGTGAGTGTGTCTGGGGCCTTGTTCGGTTTTGCTTTGTTATTTTGGCTTTGTTATTTGAATTTCTAGTTCATTGCTACCTTAAAACACTATTATATCAATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
20
Interacting miRNAs (#binding sites)
mmu-miR-181a-5p(2), mmu-miR-181d-5p(2), mmu-miR-124-3p(1), mmu-miR-221-3p(1), mmu-miR-217-5p(1), mmu-miR-222-3p(1), mmu-miR-324-5p(1), mmu-miR-185-5p(1), mmu-miR-181b-5p(1), mmu-miR-431-5p(1), mmu-miR-483-5p(1), mmu-miR-192-5p(1), mmu-miR-215-5p(1), mmu-miR-297a-5p(1), mmu-miR-384-3p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1), mmu-miR-188-3p(1), mmu-miR-3065-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GAAATCTCATTCAGTGAGTGTGTCTG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.86635275
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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