top of page
mmu_circAtxn2l_469
Basic information of circular RNA
PanCircBase ID:
mmu_circAtxn2l_469
mm39_Chr. Position ID:
chr7|126096664|126098413|-
Gene name:
Atxn2l
Transcript:
ENSMUST00000040202.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
9,8,7
Exon/intron offsets:
0,612,1657
Genomic length:
1749
Exon/intron sizes in nt:
176,201,92
Flanking exon/introns:
chr7:126096536-126096664|chr7:126098413-126099300
Splice length:
469
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TCTAATGGATGGGATCCCAATGAGATGTTCAAATTTAATGAGGAGAACTATGGAGTGAAGACCACCTATGACAGCAGTCTATCTTCTTACACGGTTCCCTTAGAAAAGGACAACTCTGAAGAGTTTCGGCAGCGGGAGCTTCGAGCGGCCCAGTTGGCTCGAGAGATTGAGTCTAGTCCCCAGTACCGCCTACGGATTGCTATGGAAAATGACGATGGGAGAACAGAGGAGGAGAAGCACAGTGCTGTTCAGCGGCAGGGGTCTGGGCGGGAGAGCCCCAGCTTGGTATCCAGGGAGGGGAAGTATATCCCCCTGCCTCAGCGAGTTCGAGAAGGTCCCCGGGGAGGAGTTCGATGCAGCAGTTCTCGAGGAGGGCGCCCTGGCCTTAGCTCTTTGCCACCTCGTGGCCCTCACCATCTTGACAACAGCAGTCCTGGCCCTGGGTCTGAGGCACGTGGTATCAATGGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TAGCTCTTTGCCACCTCGTG
60.04
GACTGCTGTCATAGGTGGTCT
59.17
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TAGCTCTTTGCCACCTCGTG
60.04
AGACTGCTGTCATAGGTGGTC
59.17
163
PCR template sequence:
GGAGGGCGCCCTGGCCTTAGCTCTTTGCCACCTCGTGGCCCTCACCATCTTGACAACAGCAGTCCTGGCCCTGGGTCTGAGGCACGTGGTATCAATGGAGTCTAATGGATGGGATCCCAATGAGATGTTCAAATTTAATGAGGAGAACTATGGAGTGAAGACCACCTATGACAGCAGTCTATCTTCTTACACGGTTCCCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-let-7e-5p(1), mmu-miR-146a-5p(1), mmu-miR-207(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGTATCAATGGAGTCTAATGGATGGG
siRNA sets
ATCCATTAGACTCCATTGA,CATTAGACTCCATTGATAC,CATCCATTAGACTCCATTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATXN2L_469_ORF_1
0.8269
0.300151451
0.940507419
729
ORF sequence:
ATGACGATGGGAGAACAGAGGAGGAGAAGCACAGTGCTGTTCAGCGGCAGGGGTCTGGGCGGGAGAGCCCCAGCTTGGTATCCAGGGAGGGGAAGTATATCCCCCTGCCTCAGCGAGTTCGAGAAGGTCCCCGGGGAGGAGTTCGATGCAGCAGTTCTCGAGGAGGGCGCCCTGGCCTTAGCTCTTTGCCACCTCGTGGCCCTCACCATCTTGACAACAGCAGTCCTGGCCCTGGGTCTGAGGCACGTGGTATCAATGGAGTCTAATGGATGGGATCCCAATGAGATGTTCAAATTTAATGAGGAGAACTATGGAGTGAAGACCACCTATGACAGCAGTCTATCTTCTTACACGGTTCCCTTAGAAAAGGACAACTCTGAAGAGTTTCGGCAGCGGGAGCTTCGAGCGGCCCAGTTGGCTCGAGAGATTGAGTCTAGTCCCCAGTACCGCCTACGGATTGCTATGGAAAATGACGATGGGAGAACAGAGGAGGAGAAGCACAGTGCTGTTCAGCGGCAGGGGTCTGGGCGGGAGAGCCCCAGCTTGGTATCCAGGGAGGGGAAGTATATCCCCCTGCCTCAGCGAGTTCGAGAAGGTCCCCGGGGAGGAGTTCGATGCAGCAGTTCTCGAGGAGGGCGCCCTGGCCTTAGCTCTTTGCCACCTCGTGGCCCTCACCATCTTGACAACAGCAGTCCTGGCCCTGGGTCTGAGGCACGTGGTATCAATGGA
Peptide sequence:
MTMGEQRRRSTVLFSGRGLGGRAPAWYPGRGSISPCLSEFEKVPGEEFDAAVLEEGALALALCHLVALTILTTAVLALGLRHVVSMESNGWDPNEMFKFNEENYGVKTTYDSSLSSYTVPLEKDNSEEFRQRELRAAQLAREIESSPQYRLRIAMENDDGRTEEEKHSAVQRQGSGRESPSLVSREGKYIPLPQRVREGPRGGVRCSSSRGGRPGLSSLPPRGPHHLDNSSPGPGSEARGING
IRESfinder result
IRESfinder score
0.47923174
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page