top of page
mmu_ciNdufs3_308
Basic information of circular RNA
PanCircBase ID:
mmu_ciNdufs3_308
mm39_Chr. Position ID:
chr2|90732882|90733190|-
Gene name:
Ndufs3
Transcript:
ENSMUST00000005647.4
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
3
Exon/intron offsets:
0
Genomic length:
308
Exon/intron sizes in nt:
308
Flanking exon/introns:
chr2:90732856-90733190
Splice length:
308
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAATATTCGTTGTCCTTGGGTCTGGGCCAGGAATTCACCATGGCACCTTAAGTCAGTAGTTCTCAACCTGTGGGTCGTGACCCTTCTGGGGTTGCTTATGACCATCAGAAAACACATATGTTTAGGTTATGATTCATAACTGGCAAAATTATAATCATGAAGTAGCAATAAAAATAATGTGGCTGGGGGTCACCACCACCTGAGGAAGTGTGTATTACAGGGTCACCGCATTAGAAAGGCTACAAACCACTGACTTAAGCCAAGTGATCCCTGCAGTGTGCTACGCCCTTAGTAGCTATGTCTTCTC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGTATTACAGGGTCACCGCA
60.07
ATGGTGAATTCCTGGCCCAG
60.03
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGTATTACAGGGTCACCGC
60.07
ATGGTGAATTCCTGGCCCAG
60.03
141
PCR template sequence:
GTGTGTATTACAGGGTCACCGCATTAGAAAGGCTACAAACCACTGACTTAAGCCAAGTGATCCCTGCAGTGTGCTACGCCCTTAGTAGCTATGTCTTCTCGTAATATTCGTTGTCCTTGGGTCTGGGCCAGGAATTCACCATGGCACCTTAAGTCAGTAGTTCTCAACCTGTGGGTCGTGACCCTTCTGGGGTTGCTTAT
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-140-5p(1), mmu-miR-10b-5p(1), mmu-miR-10a-5p(1), mmu-miR-1198-5p(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCTATGTCTTCTCGTAATATTCGTTG
siRNA sets
AACGAATATTACGAGAAGA, ACGAATATTACGAGAAGAC, ATATTACGAGAAGACATAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CINDUFS3_308_ORF_1
0.4692
-0.244223434
0.013372757
150
ORF sequence:
ATGTCTTCTCGTAATATTCGTTGTCCTTGGGTCTGGGCCAGGAATTCACCATGGCACCTTAAGTCAGTAGTTCTCAACCTGTGGGTCGTGACCCTTCTGGGGTTGCTTATGACCATCAGAAAACACATATGTTTAGGTTATGATTCATAA
Peptide sequence:
MSSRNIRCPWVWARNSPWHLKSVVLNLWVVTLLGLLMTIRKHICLGYDS
IRESfinder result
IRESfinder score
0.538326457
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page