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mmu_circAfdn_603
Basic information of circular RNA
PanCircBase ID:
mmu_circAfdn_603
mm39_Chr. Position ID:
chr17|14052629|14069515|+
Gene name:
Afdn
Transcript:
ENSMUST00000170827.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
11,12,13,14,15
Exon/intron offsets:
0,2870,13904,14066,16740
Genomic length:
16886
Exon/intron sizes in nt:
70,11,96,22,06,146
Flanking exon/introns:
chr17:14050394-14052629|chr17:14069515-14069829
Splice length:
603
Other database IDs:
circAtlas: mmu-Mllt4_0095
Human Ortholog IDs:
Mature spliced Sequence:
AGCTGTTCAGGAGACAACCTTTGAATTGGGAGGAGATGTCCACAGTGGGACAGCATTGCCGGCAAGCAGGAGCACTACTAGACTGGACAGTGACAGGGTGTCCTCTGCCTCTAGCACAGCTGAGCGAGGGATGGTGAAGCCGATGATCCGACTGGACCAGGAGCAGGAATATCGACGACGAGAAAACAGGACTCAGGATGCTACTGGGCCTGAACTGATACTGCCTGCCAGCATTGAATTCAGGGAAAGCTCTGAAGACTCTTTTTTATCTGCCATTATAAACTATACCAATAGTTCTACAGTTCATTTTAAGTTGTCACCTACATATGTGTTATACATGGCATGCCGGTATGTATTGTCCAGCCAGCACAGGCCCGACATCAGTCCTACAGAGCGTACACATAAGGCCATTGCTGTTGTCAACAAGATGGTGAGCATGATGGAAGGGGTCATCCAGAAACAGAAGAACATTGCAGGAGCACTTGCTTTTTGGATGGCAAATGCATCTGAGCTTCTCAACTTCATCAAGCAGGACCGAGACCTTAGTCGGATCACGCTGGATGCCCAGGATGTCCTAGCACACTTGGTTCAGATGGCATTTAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGATGCCCAGGATGTCCTA
60.03
CACCCTGTCACTGTCCAGTC
59.97
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GATGCCCAGGATGTCCTAGC
59.96
CACCCTGTCACTGTCCAGTC
59.97
144
PCR template sequence:
CATCTGAGCTTCTCAACTTCATCAAGCAGGACCGAGACCTTAGTCGGATCACGCTGGATGCCCAGGATGTCCTAGCACACTTGGTTCAGATGGCATTTAAAGCTGTTCAGGAGACAACCTTTGAATTGGGAGGAGATGTCCACAGTGGGACAGCATTGCCGGCAAGCAGGAGCACTACTAGACTGGACAGTGACAGGGTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-697(2), mmu-miR-298-5p(1), mmu-miR-709(1), mmu-miR-466d-3p(1), mmu-miR-484(1), mmu-miR-1199-5p(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGATGGCATTTAAAGCTGTTCAGGAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAFDN_603_ORF_1
1.0982
0.252323792
0.996138929
1074
ORF sequence:
ATGGTGAAGCCGATGATCCGACTGGACCAGGAGCAGGAATATCGACGACGAGAAAACAGGACTCAGGATGCTACTGGGCCTGAACTGATACTGCCTGCCAGCATTGAATTCAGGGAAAGCTCTGAAGACTCTTTTTTATCTGCCATTATAAACTATACCAATAGTTCTACAGTTCATTTTAAGTTGTCACCTACATATGTGTTATACATGGCATGCCGGTATGTATTGTCCAGCCAGCACAGGCCCGACATCAGTCCTACAGAGCGTACACATAAGGCCATTGCTGTTGTCAACAAGATGGTGAGCATGATGGAAGGGGTCATCCAGAAACAGAAGAACATTGCAGGAGCACTTGCTTTTTGGATGGCAAATGCATCTGAGCTTCTCAACTTCATCAAGCAGGACCGAGACCTTAGTCGGATCACGCTGGATGCCCAGGATGTCCTAGCACACTTGGTTCAGATGGCATTTAAAGCTGTTCAGGAGACAACCTTTGAATTGGGAGGAGATGTCCACAGTGGGACAGCATTGCCGGCAAGCAGGAGCACTACTAGACTGGACAGTGACAGGGTGTCCTCTGCCTCTAGCACAGCTGAGCGAGGGATGGTGAAGCCGATGATCCGACTGGACCAGGAGCAGGAATATCGACGACGAGAAAACAGGACTCAGGATGCTACTGGGCCTGAACTGATACTGCCTGCCAGCATTGAATTCAGGGAAAGCTCTGAAGACTCTTTTTTATCTGCCATTATAAACTATACCAATAGTTCTACAGTTCATTTTAAGTTGTCACCTACATATGTGTTATACATGGCATGCCGGTATGTATTGTCCAGCCAGCACAGGCCCGACATCAGTCCTACAGAGCGTACACATAAGGCCATTGCTGTTGTCAACAAGATGGTGAGCATGATGGAAGGGGTCATCCAGAAACAGAAGAACATTGCAGGAGCACTTGCTTTTTGGATGGCAAATGCATCTGAGCTTCTCAACTTCATCAAGCAGGACCGAGACCTTAGTCGGATCACGCTGGATGCCCAGGATGTCCTAGCACACTTGGTTCAGATGGCATTT
Peptide sequence:
MVKPMIRLDQEQEYRRRENRTQDATGPELILPASIEFRESSEDSFLSAIINYTNSSTVHFKLSPTYVLYMACRYVLSSQHRPDISPTERTHKAIAVVNKMVSMMEGVIQKQKNIAGALAFWMANASELLNFIKQDRDLSRITLDAQDVLAHLVQMAFKAVQETTFELGGDVHSGTALPASRSTTRLDSDRVSSASSTAERGMVKPMIRLDQEQEYRRRENRTQDATGPELILPASIEFRESSEDSFLSAIINYTNSSTVHFKLSPTYVLYMACRYVLSSQHRPDISPTERTHKAIAVVNKMVSMMEGVIQKQKNIAGALAFWMANASELLNFIKQDRDLSRITLDAQDVLAHLVQMAF
IRESfinder result
IRESfinder score
0.369003683
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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