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mmu_circArl6_356
Basic information of circular RNA
PanCircBase ID:
mmu_circArl6_356
mm39_Chr. Position ID:
chr16|59441581|59444704|-
Gene name:
Arl6
Transcript:
ENSMUST00000023405.16
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,5,4,3
Exon/intron offsets:
0,1802,2659,3061
Genomic length:
3123
Exon/intron sizes in nt:
130,95,69,62
Flanking exon/introns:
chr16:59439213-59441581|chr16:59444704-59452673
Splice length:
356
Other database IDs:
CIRCpedia: MMU_CIRCpedia_24583, circAtlas: mmu-Arl6_0001
circAtlas: hsa-ARL6_0001, CIRCpedia: HSA_CIRCpedia_176548
Human Ortholog IDs:
Mature spliced Sequence:
GCTCAATCTCAAGATATAGTTCCAACCATAGGATTTAGCATAGAGAAATTCAAGTCCTCCAGTTTGTCTTTTACAGTGTTTGACATGTCAGGTCAAGGAAGGTACAGGAATCTCTGGGAACACTATTATAAAGATGGACAAGCCATTATTTTTGTCATTGATAGTAGTGATAAGTTAAGAATGGTTGTGGCCAAAGAAGAGCTTGATACCCTTCTGAATCACCCAGATATTAAGCACCGTCGAATTCCAATCTTGTTCTTTGCAAACAAAATGGACCTTAGAGACTCAGTGACCTCTGTGAAAGTGTCTCAGTTGCTGTGCTTAGAGAGCATTAAAGACAAGCCGTGGCATATTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTGTCTCAGTTGCTGTGCT
59.53
TGACCTGACATGTCAAACACTG
58.79
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTGTCTCAGTTGCTGTGCT
59.53
GACCTGACATGTCAAACACTGT
58.79
148
PCR template sequence:
TCTTTGCAAACAAAATGGACCTTAGAGACTCAGTGACCTCTGTGAAAGTGTCTCAGTTGCTGTGCTTAGAGAGCATTAAAGACAAGCCGTGGCATATTTGGCTCAATCTCAAGATATAGTTCCAACCATAGGATTTAGCATAGAGAAATTCAAGTCCTCCAGTTTGTCTTTTACAGTGTTTGACATGTCAGGTCAAGGAA
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-155-5p(1), mmu-miR-141-3p(1), mmu-miR-135a-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CGTGGCATATTTGGCTCAATCTCAAG
siRNA sets
AGATTGAGCCAAATATGCC, ATTGAGCCAAATATGCCAC, GATTGAGCCAAATATGCCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARL6_356_ORF_1
0.867
0.036777826
0.198271164
291
ORF sequence:
ATGTCAGGTCAAGGAAGGTACAGGAATCTCTGGGAACACTATTATAAAGATGGACAAGCCATTATTTTTGTCATTGATAGTAGTGATAAGTTAAGAATGGTTGTGGCCAAAGAAGAGCTTGATACCCTTCTGAATCACCCAGATATTAAGCACCGTCGAATTCCAATCTTGTTCTTTGCAAACAAAATGGACCTTAGAGACTCAGTGACCTCTGTGAAAGTGTCTCAGTTGCTGTGCTTAGAGAGCATTAAAGACAAGCCGTGGCATATTTGGCTCAATCTCAAGATATAG
Peptide sequence:
MSGQGRYRNLWEHYYKDGQAIIFVIDSSDKLRMVVAKEELDTLLNHPDIKHRRIPILFFANKMDLRDSVTSVKVSQLLCLESIKDKPWHIWLNLKI
IRESfinder result
IRESfinder score
0.832221953
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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