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mmu_circMsl1_379
Basic information of circular RNA
PanCircBase ID:
mmu_circMsl1_379
mm39_Chr. Position ID:
chr11|98693093|98695745|+
Gene name:
Msl1
Transcript:
ENSMUST00000037915.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
4,5,6,7,8
Exon/intron offsets:
0,514,1635,2034,2579
Genomic length:
2652
Exon/intron sizes in nt:
48,65,68,125,73
Flanking exon/introns:
chr11:98691208-98693093|chr11:98695745-98696167
Splice length:
379
Other database IDs:
circBase: hsa_circ_0106809, circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GGTGTCTGATGCCATCAAGTGTTGCAGGAGAAACTTCAGTCTTGGCTGTTCCTTCTTGGAGGGACCACTCAGTAGAGCCTCTAAGGGACCCAAATCCTTCAGACATTTTGGAGAACCTGGATGACAGTGTATTTTCAAAGAGGCATGCAAAACTGGAGCTAGACGAGAAGAGGAGAAAACGATGGGATATTCAGAGGATCAGGGAACAAAGAATTTTACAGCGACTGCAGCTCAGAATGTATAAAAAGAAAGGAATTCAGGAATCTGAGCCTGAGGTTACCTCATTTTTCCCTGAGCCAGATGATGTTGAAAGTTTGCTGATTACCCCCTTCTTGCCTGTTGTAGCATTTGGACGGCCATTGCCAAAATTAGCTCCACA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCCCTTCTTGCCTGTTGTA
59.6
TTGGGTCCCTTAGAGGCTCT
59.58
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TACCCCCTTCTTGCCTGTTG
59.6
TTGGGTCCCTTAGAGGCTCT
59.58
150
PCR template sequence:
CCTCATTTTTCCCTGAGCCAGATGATGTTGAAAGTTTGCTGATTACCCCCTTCTTGCCTGTTGTAGCATTTGGACGGCCATTGCCAAAATTAGCTCCACAGGTGTCTGATGCCATCAAGTGTTGCAGGAGAAACTTCAGTCTTGGCTGTTCCTTCTTGGAGGGACCACTCAGTAGAGCCTCTAAGGGACCCAAATCCTTC
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-31-5p(1), mmu-miR-182-5p(1), mmu-miR-484(1)
siRNAs for circular RNA silencing
Junction sequence
AATTAGCTCCACAGGTGTCTGATGCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMSL1_379_ORF_1
0.5798
0.017741122
0.368647065
495
ORF sequence:
ATGCCATCAAGTGTTGCAGGAGAAACTTCAGTCTTGGCTGTTCCTTCTTGGAGGGACCACTCAGTAGAGCCTCTAAGGGACCCAAATCCTTCAGACATTTTGGAGAACCTGGATGACAGTGTATTTTCAAAGAGGCATGCAAAACTGGAGCTAGACGAGAAGAGGAGAAAACGATGGGATATTCAGAGGATCAGGGAACAAAGAATTTTACAGCGACTGCAGCTCAGAATGTATAAAAAGAAAGGAATTCAGGAATCTGAGCCTGAGGTTACCTCATTTTTCCCTGAGCCAGATGATGTTGAAAGTTTGCTGATTACCCCCTTCTTGCCTGTTGTAGCATTTGGACGGCCATTGCCAAAATTAGCTCCACAGGTGTCTGATGCCATCAAGTGTTGCAGGAGAAACTTCAGTCTTGGCTGTTCCTTCTTGGAGGGACCACTCAGTAGAGCCTCTAAGGGACCCAAATCCTTCAGACATTTTGGAGAACCTGGATGA
Peptide sequence:
MPSSVAGETSVLAVPSWRDHSVEPLRDPNPSDILENLDDSVFSKRHAKLELDEKRRKRWDIQRIREQRILQRLQLRMYKKKGIQESEPEVTSFFPEPDDVESLLITPFLPVVAFGRPLPKLAPQVSDAIKCCRRNFSLGCSFLEGPLSRASKGPKSFRHFGEPG
IRESfinder result
IRESfinder score
0.568931544
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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