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mmu_circLnx1_304
Basic information of circular RNA
PanCircBase ID:
mmu_circLnx1_304
mm39_Chr. Position ID:
chr5|74768397|74771472|-
Gene name:
Lnx1
Transcript:
ENSMUST00000113531.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
9,8
Exon/intron offsets:
0,2940
Genomic length:
3075
Exon/intron sizes in nt:
1,69,135
Flanking exon/introns:
chr5:74766923-74768397|chr5:74771472-74780634
Splice length:
304
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GCCAGTGAAAGACGCGTCCATCTCGTCGTGTCCCGCCAGGTTCGACAGTCCAGCCCAGACATCTTTCAAGAAGCTGGCTGGATCAGCAATGGCCAGCAATCCCCAGGCCCAGGAGAGAGGAACACAGCTTCTAAGCCTGCAGCCACCTGTCATGAGAAGGTTGTAAGTGTCTGGAAAGACCCCAGCGAGTCTCTCGGCATGACCGTCGGAGGGGGAGCATCCCACAGGGAATGGGACTTGCCCATCTATGTCATCAGTGTTGAACCCGGCGGAGTCATAAGCAGAGACGGGAGAATAAAAACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CACAGGGAATGGGACTTGCC
60.97
GATGTCTGGGCTGGACTGTC
60.11
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCACAGGGAATGGGACTTGC
60.97
GATGTCTGGGCTGGACTGTC
60.11
146
PCR template sequence:
GTCGGAGGGGGAGCATCCCACAGGGAATGGGACTTGCCCATCTATGTCATCAGTGTTGAACCCGGCGGAGTCATAAGCAGAGACGGGAGAATAAAAACAGGCCAGTGAAAGACGCGTCCATCTCGTCGTGTCCCGCCAGGTTCGACAGTCCAGCCCAGACATCTTTCAAGAAGCTGGCTGGATCAGCAATGGCCAGCAAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-207(1), mmu-miR-490-3p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAATAAAAACAGGCCAGTGAAAGAC
siRNA sets
TTTCACTGGCCTGTTTTTA, ACTGGCCTGTTTTTATTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCLNX1_304_ORF_1
1.1723
-0.024116136
0.086812991
114
ORF sequence:
ATGACCGTCGGAGGGGGAGCATCCCACAGGGAATGGGACTTGCCCATCTATGTCATCAGTGTTGAACCCGGCGGAGTCATAAGCAGAGACGGGAGAATAAAAACAGGCCAGTGA
Peptide sequence:
MTVGGGASHREWDLPIYVISVEPGGVISRDGRIKTGQ
IRESfinder result
IRESfinder score
0.255360306
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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