top of page
mmu_circCux1_221
Basic information of circular RNA
PanCircBase ID:
mmu_circCux1_221
mm39_Chr. Position ID:
chr5|136361477|136388922|-
Gene name:
Cux1
Transcript:
ENSMUST00000176216.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
10,9,8
Exon/intron offsets:
0,7465,27378
Genomic length:
27445
Exon/intron sizes in nt:
105,49,67
Flanking exon/introns:
chr5:136355792-136361477|chr5:136388922-136392112
Splice length:
221
Other database IDs:
circBase: mmu_circ_0012214, CIRCpedia: MMU_CIRCpedia_8397, circAtlas: mmu-Cux1_0026
Human Ortholog IDs:
Mature spliced Sequence:
CCCTGGAAAAAACTCGAACAGAATTATTTGACCTGAAAACCAAATATGATGAAGAAACTACTGCAAAGGCCGATGAGATCGAGATGATCATGACCGACCTTGAACGAGCCAACCAGAGGGCAGAGGTGGCACAGAGAGAAGCAGAGACTTTAAGGGAACAGCTCTCATCGGCCAACCACTCTCTCCAACTGGCCTCGCAGATCCAGAAGGCTCCAGATGTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGGCACAGAGAGAAGCAGA
59.68
ATCTCATCGGCCTTTGCAGT
59.75
175
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGGTGGCACAGAGAGAAGC
60.39
ATCTCATCGGCCTTTGCAGT
59.75
178
PCR template sequence:
AGAGGTGGCACAGAGAGAAGCAGAGACTTTAAGGGAACAGCTCTCATCGGCCAACCACTCTCTCCAACTGGCCTCGCAGATCCAGAAGGCTCCAGATGTGCCCTGGAAAAAACTCGAACAGAATTATTTGACCTGAAAACCAAATATGATGAAGAAACTACTGCAAAGGCCGATGAGATCGAGATGATCATGACCGACCT
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-433-3p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGCTCCAGATGTGCCCTGGAAAAAAC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCUX1_221_ORF_1
0.9734
0.237108469
0.228252023
174
ORF sequence:
ATGATCATGACCGACCTTGAACGAGCCAACCAGAGGGCAGAGGTGGCACAGAGAGAAGCAGAGACTTTAAGGGAACAGCTCTCATCGGCCAACCACTCTCTCCAACTGGCCTCGCAGATCCAGAAGGCTCCAGATGTGCCCTGGAAAAAACTCGAACAGAATTATTTGACCTGA
Peptide sequence:
MIMTDLERANQRAEVAQREAETLREQLSSANHSLQLASQIQKAPDVPWKKLEQNYLT
IRESfinder result
IRESfinder score
0.452613309
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page