top of page
mmu_circPrdx1_254
Basic information of circular RNA
PanCircBase ID:
mmu_circPrdx1_254
mm39_Chr. Position ID:
chr4|116550079|116551044|+
Gene name:
Prdx1
Transcript:
ENSMUST00000135573.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
4,5
Exon/intron offsets:
0,834
Genomic length:
965
Exon/intron sizes in nt:
1,23,131
Flanking exon/introns:
chr4:116549126-116550079|chr4:116551044-116556367
Splice length:
254
Other database IDs:
CIRCpedia: MMU_CIRCpedia_221906
Human Ortholog IDs:
Mature spliced Sequence:
GATTAACACACCCAAGAAACAAGGAGGATTGGGACCCATGAACATTCCCTTAATATCAGATCCCAAGCGCACCATTGCTCAGGATTATGGAGTCTTAAAGGCTGATGAAGGTATCTCTTTCAGGGGCCTTTTTATTATTGATGATAAAGGTATCCTTCGACAGATAACAATAAACGATCTTCCCGTTGGCCGCTCTGTGGATGAGATTATACGACTAGTCCAGGCCTTCCAGTTCACTGACAAACATGGTGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCCGCTCTGTGGATGAGATT
60.18
AATGGTGCGCTTGGGATCTG
61.03
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCCGCTCTGTGGATGAGATT
60.18
CAATGGTGCGCTTGGGATCT
61.03
143
PCR template sequence:
CTTCGACAGATAACAATAAACGATCTTCCCGTTGGCCGCTCTGTGGATGAGATTATACGACTAGTCCAGGCCTTCCAGTTCACTGACAAACATGGTGAAGGATTAACACACCCAAGAAACAAGGAGGATTGGGACCCATGAACATTCCCTTAATATCAGATCCCAAGCGCACCATTGCTCAGGATTATGGAGTCTTAAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
NA
Interacting miRNAs (#binding sites)
NA
siRNAs for circular RNA silencing
Junction sequence
AAACATGGTGAAGGATTAACACACCC
siRNA sets
TGTTAATCCTTCACCATGT, TTAATCCTTCACCATGTTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPRDX1_254_ORF_1
1.0178
0.158077067
0.29856796
258
ORF sequence:
ATGAACATTCCCTTAATATCAGATCCCAAGCGCACCATTGCTCAGGATTATGGAGTCTTAAAGGCTGATGAAGGTATCTCTTTCAGGGGCCTTTTTATTATTGATGATAAAGGTATCCTTCGACAGATAACAATAAACGATCTTCCCGTTGGCCGCTCTGTGGATGAGATTATACGACTAGTCCAGGCCTTCCAGTTCACTGACAAACATGGTGAAGGATTAACACACCCAAGAAACAAGGAGGATTGGGACCCATGA
Peptide sequence:
MNIPLISDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEIIRLVQAFQFTDKHGEGLTHPRNKEDWDP
IRESfinder result
IRESfinder score
0.74390386
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page