top of page
mmu_circAftph_307
Basic information of circular RNA
PanCircBase ID:
mmu_circAftph_307
mm39_Chr. Position ID:
chr11|20653710|20659746|-
Gene name:
Aftph
Transcript:
ENSMUST00000146722.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
5,4,3
Exon/intron offsets:
0,4970,5909
Genomic length:
6036
Exon/intron sizes in nt:
123,57,127
Flanking exon/introns:
chr11:20648373-20653710|chr11:20659746-20662163
Splice length:
307
Other database IDs:
circBase: mmu_circ_0000240, CIRCpedia: MMU_CIRCpedia_13029, circAtlas: mmu-Aftph_0012
circBase: hsa_circ_0054963, circAtlas: hsa-AFTPH_0010, CIRCpedia: HSA_CIRCpedia_42056
Human Ortholog IDs:
Mature spliced Sequence:
TGAGTTGAGGGGTGTATGGACCGAACTGCAGGACATCCATGATGCACATGGTTTGCGGTACCAGTGGGGTGGCTCACATAGCAACAAGAAGCTTTTGTGCTCCTTGGGAATAGACACTCGAAACATTCTATTCACTGGCAATAAGAAGCAACCTGTTATAGTGCCCATGTATGCAGCAGGATTGGGAATGTTAGAGCCCACCAAGGAACCATTAAAACCACTATCTGCTGCAGAAAAAATTGCTTCTATTGGTCAGACAACCGTTATGACACCAGAAATAAACACGTGTACATCTGATCCATTCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTTCTATTGGTCAGACAACCG
59.33
CTATGTGAGCCACCCCACTG
60.11
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCACTATCTGCTGCAGAAA
56.84
CTATGTGAGCCACCCCACTG
60.11
172
PCR template sequence:
ACCATTAAAACCACTATCTGCTGCAGAAAAAATTGCTTCTATTGGTCAGACAACCGTTATGACACCAGAAATAAACACGTGTACATCTGATCCATTCCAGTGAGTTGAGGGGTGTATGGACCGAACTGCAGGACATCCATGATGCACATGGTTTGCGGTACCAGTGGGGTGGCTCACATAGCAACAAGAAGCTTTTGTGC
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-140-5p(1), mmu-miR-15a-5p(1), mmu-miR-15b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGATCCATTCCAGTGAGTTGAGGGGT
siRNA sets
CAACTCACTGGAATGGATC, CTCAACTCACTGGAATGGA, CCTCAACTCACTGGAATGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAFTPH_307_ORF_1
0.9434
-0.085954534
0.056500064
144
ORF sequence:
ATGTATGCAGCAGGATTGGGAATGTTAGAGCCCACCAAGGAACCATTAAAACCACTATCTGCTGCAGAAAAAATTGCTTCTATTGGTCAGACAACCGTTATGACACCAGAAATAAACACGTGTACATCTGATCCATTCCAGTGA
Peptide sequence:
MYAAGLGMLEPTKEPLKPLSAAEKIASIGQTTVMTPEINTCTSDPFQ
IRESfinder result
IRESfinder score
0.576908097
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page