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mmu_circCux1_418
Basic information of circular RNA
PanCircBase ID:
mmu_circCux1_418
mm39_Chr. Position ID:
chr5|136392112|136421247|-
Gene name:
Cux1
Transcript:
ENSMUST00000176216.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
7,6,5,4
Exon/intron offsets:
0,6859,10063,29056
Genomic length:
29135
Exon/intron sizes in nt:
77,124,138,79
Flanking exon/introns:
chr5:136388922-136392112|chr5:136421247-136436833
Splice length:
418
Other database IDs:
circAtlas: mmu-Cux1_0005
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_163114
Human Ortholog IDs:
Mature spliced Sequence:
ATTGATGCACTGAGTAAAAGAAGCAAAGAAGCAGAGGCAGCCTTCTTGACTGTGTACAAGAGACTAATTGATGTTCCAGATCCGGTACCAGCCCTGGACGTCGGGCAACAGCTGGAAATAAAAGTGCAGCGTCTACACGACATTGAAACAGAGAACCAGAAACTTAGGGAAACACTAGAAGAGTACAACAAGGAGTTTGCTGAAGTGAAAAATCAAGAGGTTACGATAAAAGCACTTAAGGAGAAAATCCGAGAATACGAGCAGACCCTGAAGAGTCAGGCCGAGACCATTGCTCTGGAGAAAGAGCAGAAGCTACAAAATGATTTTGCAGAGAAGGAGAGAAAGCTGCAAGAGACACAGATGTCCACCACCTCAAAACTGGAGGAAGCTGAGCACAAACTCCAGACTCTGCAAACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CACAGATGTCCACCACCTCA
59.31
GCTGGTACCGGATCTGGAAC
60.18
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACACAGATGTCCACCACCTC
59.31
GCTGGTACCGGATCTGGAAC
60.18
156
PCR template sequence:
AATGATTTTGCAGAGAAGGAGAGAAAGCTGCAAGAGACACAGATGTCCACCACCTCAAAACTGGAGGAAGCTGAGCACAAACTCCAGACTCTGCAAACAGATTGATGCACTGAGTAAAAGAAGCAAAGAAGCAGAGGCAGCCTTCTTGACTGTGTACAAGAGACTAATTGATGTTCCAGATCCGGTACCAGCCCTGGACG
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-148b-3p(1), mmu-miR-467b-5p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
ACTCTGCAAACAGATTGATGCACTGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCUX1_418_ORF_1
1.0589
0.283745997
0.830652251
516
ORF sequence:
ATGATTTTGCAGAGAAGGAGAGAAAGCTGCAAGAGACACAGATGTCCACCACCTCAAAACTGGAGGAAGCTGAGCACAAACTCCAGACTCTGCAAACAGATTGATGCACTGAGTAAAAGAAGCAAAGAAGCAGAGGCAGCCTTCTTGACTGTGTACAAGAGACTAATTGATGTTCCAGATCCGGTACCAGCCCTGGACGTCGGGCAACAGCTGGAAATAAAAGTGCAGCGTCTACACGACATTGAAACAGAGAACCAGAAACTTAGGGAAACACTAGAAGAGTACAACAAGGAGTTTGCTGAAGTGAAAAATCAAGAGGTTACGATAAAAGCACTTAAGGAGAAAATCCGAGAATACGAGCAGACCCTGAAGAGTCAGGCCGAGACCATTGCTCTGGAGAAAGAGCAGAAGCTACAAAATGATTTTGCAGAGAAGGAGAGAAAGCTGCAAGAGACACAGATGTCCACCACCTCAAAACTGGAGGAAGCTGAGCACAAACTCCAGACTCTGCAAACA
Peptide sequence:
MILQRRRESCKRHRCPPPQNWRKLSTNSRLCKQIDALSKRSKEAEAAFLTVYKRLIDVPDPVPALDVGQQLEIKVQRLHDIETENQKLRETLEEYNKEFAEVKNQEVTIKALKEKIREYEQTLKSQAETIALEKEQKLQNDFAEKERKLQETQMSTTSKLEEAEHKLQTLQT
IRESfinder result
IRESfinder score
0.412450846
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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