top of page
mmu_circNdufs1_291
Basic information of circular RNA
PanCircBase ID:
mmu_circNdufs1_291
mm39_Chr. Position ID:
chr1|63190709|63192063|-
Gene name:
Ndufs1
Transcript:
ENSMUST00000027111.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
14,13
Exon/intron offsets:
0,1224
Genomic length:
1354
Exon/intron sizes in nt:
1,61,130
Flanking exon/introns:
chr1:63189270-63190709|chr1:63192063-63195362
Splice length:
291
Other database IDs:
circAtlas: mmu-Ndufs1_0022
CIRCpedia: HSA_CIRCpedia_174585
Human Ortholog IDs:
Mature spliced Sequence:
CTGGCTTCATAATGACTTAAAAGTGGCCCTCATCGGTAGTCCAGTGGACCTCACTTACAGATACGACCATCTAGGAGACTCTCCTAAAATTCTGCAAGACATTGCTTCAGGGAGGCATTCATTCTGCGAGGTCTTAAAGGATGCTAAAAAACCAATGGTGGTTTTAGGCAGTTCTGCACTCCAGAGAGATGATGGAGCAGCAATTCTTGTAGCTGTGTCCAACATGGTACAAAAGATTCGAGTGACAACCGGTGTTGCTGCAGAGTGGAAAGTTATGAATATTCTGCATAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATTCGAGTGACAACCGGTGT
59.61
GGAGAGTCTCCTAGATGGTCGT
60.16
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAGCAGCAATTCTTGTAGC
58.91
CACTGGACTACCGATGAGGG
59.25
145
PCR template sequence:
ATGGAGCAGCAATTCTTGTAGCTGTGTCCAACATGGTACAAAAGATTCGAGTGACAACCGGTGTTGCTGCAGAGTGGAAAGTTATGAATATTCTGCATAGCTGGCTTCATAATGACTTAAAAGTGGCCCTCATCGGTAGTCCAGTGGACCTCACTTACAGATACGACCATCTAGGAGACTCTCCTAAAATTCTGCAAGAC
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-431-5p(1), mmu-miR-3470b(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATATTCTGCATAGCTGGCTTCATAAT
siRNA sets
ATTATGAAGCCAGCTATGC, TATGAAGCCAGCTATGCAG, TTATGAAGCCAGCTATGCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNDUFS1_291_ORF_1
0.9966
0.113035275
0.533178171
426
ORF sequence:
ATGGTGGTTTTAGGCAGTTCTGCACTCCAGAGAGATGATGGAGCAGCAATTCTTGTAGCTGTGTCCAACATGGTACAAAAGATTCGAGTGACAACCGGTGTTGCTGCAGAGTGGAAAGTTATGAATATTCTGCATAGCTGGCTTCATAATGACTTAAAAGTGGCCCTCATCGGTAGTCCAGTGGACCTCACTTACAGATACGACCATCTAGGAGACTCTCCTAAAATTCTGCAAGACATTGCTTCAGGGAGGCATTCATTCTGCGAGGTCTTAAAGGATGCTAAAAAACCAATGGTGGTTTTAGGCAGTTCTGCACTCCAGAGAGATGATGGAGCAGCAATTCTTGTAGCTGTGTCCAACATGGTACAAAAGATTCGAGTGACAACCGGTGTTGCTGCAGAGTGGAAAGTTATGAATATTCTGCAT
Peptide sequence:
MVVLGSSALQRDDGAAILVAVSNMVQKIRVTTGVAAEWKVMNILHSWLHNDLKVALIGSPVDLTYRYDHLGDSPKILQDIASGRHSFCEVLKDAKKPMVVLGSSALQRDDGAAILVAVSNMVQKIRVTTGVAAEWKVMNILH
IRESfinder result
IRESfinder score
0.540349578
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page