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mmu_circMrpl39_308
Basic information of circular RNA
PanCircBase ID:
mmu_circMrpl39_308
mm39_Chr. Position ID:
chr16|84527306|84529369|-
Gene name:
Mrpl39
Transcript:
ENSMUST00000116584.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
5,4,3
Exon/intron offsets:
0,409,1923
Genomic length:
2063
Exon/intron sizes in nt:
6,81,00,140
Flanking exon/introns:
chr16:84524484-84527306|chr16:84529369-84531294
Splice length:
308
Other database IDs:
circAtlas: mmu-Mrpl39_0010
Human Ortholog IDs:
Mature spliced Sequence:
ATCTGAGTGAGTGGTACTGCAGTAAGTCCATCCTGGCTCTTGTGGACGGACAACCGTGGGACATGTATAAGCCTCTGACCAAGTCTTGTGAGATCAAATTTCTTACTTTCAAAGACCCTGACCCAAAAGAAGTGAATAAGGCGTATTGGCGTTCTTGTGCCATGATGCTGGGCTGTGTAATCGAAAGGGCATTCAAAGATGACTATGTGGTCAGCCTGGTCAGAGCACCGGAAGTTCCTGTGATTGCTGGGGCCTTCTGCTATGATGTCACTTTGGATAAGAGACTGGATGAGTGGATGCCAACAAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTTCCTGTGATTGCTGGGG
59.96
TACATGTCCCACGGTTGTCC
59.68
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTCAGAGCACCGGAAGTTCC
60.67
TACATGTCCCACGGTTGTCC
59.68
157
PCR template sequence:
GGTCAGCCTGGTCAGAGCACCGGAAGTTCCTGTGATTGCTGGGGCCTTCTGCTATGATGTCACTTTGGATAAGAGACTGGATGAGTGGATGCCAACAAAAATCTGAGTGAGTGGTACTGCAGTAAGTCCATCCTGGCTCTTGTGGACGGACAACCGTGGGACATGTATAAGCCTCTGACCAAGTCTTGTGAGATCAAATT
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-452-3p(1), mmu-miR-540-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GATGCCAACAAAAATCTGAGTGAGTG
siRNA sets
CACTCAGATTTTTGTTGGC, ACTCAGATTTTTGTTGGCA, TCACTCAGATTTTTGTTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMRPL39_308_ORF_1
0.9849
0.180095403
0.295023208
252
ORF sequence:
ATGTATAAGCCTCTGACCAAGTCTTGTGAGATCAAATTTCTTACTTTCAAAGACCCTGACCCAAAAGAAGTGAATAAGGCGTATTGGCGTTCTTGTGCCATGATGCTGGGCTGTGTAATCGAAAGGGCATTCAAAGATGACTATGTGGTCAGCCTGGTCAGAGCACCGGAAGTTCCTGTGATTGCTGGGGCCTTCTGCTATGATGTCACTTTGGATAAGAGACTGGATGAGTGGATGCCAACAAAAATCTGA
Peptide sequence:
MYKPLTKSCEIKFLTFKDPDPKEVNKAYWRSCAMMLGCVIERAFKDDYVVSLVRAPEVPVIAGAFCYDVTLDKRLDEWMPTKI
IRESfinder result
IRESfinder score
0.366847414
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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