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mmu_circAfdn_280
Basic information of circular RNA
PanCircBase ID:
mmu_circAfdn_280
mm39_Chr. Position ID:
chr17|14042527|14043720|+
Gene name:
Afdn
Transcript:
ENSMUST00000170827.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
7,8
Exon/intron offsets:
0,1025
Genomic length:
1193
Exon/intron sizes in nt:
1,12,168
Flanking exon/introns:
chr17:14038540-14042527|chr17:14043720-14049190
Splice length:
280
Other database IDs:
circAtlas: mmu-Mllt4_0007
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_54359
Human Ortholog IDs:
Mature spliced Sequence:
GTTATGCTTCCTCCTGGAGCCCAGCATTCTGATGAGAGAGGTGCTAAGGAAATAATTCTTGACGATGATGAATGTCCTTTACAAATCTTCAGGGAATGGCCAAGTGACAAAGGGATTTTAGTCTTTCAGTTGAAGAGGAGACCACCGGACTACATCCCAAAGAAAATGAAGAAACATGTTGAAGGGAAGTCGTTGAAGGGGAAAGACAGAGCTGACGGGTCTGGCTACGGCTCCGCTCTTCCTCCCGAGAAGCTGCCCTACTTAGTAGAGCTAAGCCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGGAAGTCGTTGAAGGGGAA
59.6
GCACCTCTCTCATCAGAATGCT
60.16
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGAAGTCGTTGAAGGGGAA
59.6
AGCACCTCTCTCATCAGAATGC
60.16
142
PCR template sequence:
GAAGGGAAGTCGTTGAAGGGGAAAGACAGAGCTGACGGGTCTGGCTACGGCTCCGCTCTTCCTCCCGAGAAGCTGCCCTACTTAGTAGAGCTAAGCCCAGGTTATGCTTCCTCCTGGAGCCCAGCATTCTGATGAGAGAGGTGCTAAGGAAATAATTCTTGACGATGATGAATGTCCTTTACAAATCTTCAGGGAATGGC
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-181a-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-181b-5p(1), mmu-miR-27a-5p(1), mmu-miR-670-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GAGCTAAGCCCAGGTTATGCTTCCTC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAFDN_280_ORF_1
0.6369
0.119627967
0.205399847
309
ORF sequence:
ATGCTTCCTCCTGGAGCCCAGCATTCTGATGAGAGAGGTGCTAAGGAAATAATTCTTGACGATGATGAATGTCCTTTACAAATCTTCAGGGAATGGCCAAGTGACAAAGGGATTTTAGTCTTTCAGTTGAAGAGGAGACCACCGGACTACATCCCAAAGAAAATGAAGAAACATGTTGAAGGGAAGTCGTTGAAGGGGAAAGACAGAGCTGACGGGTCTGGCTACGGCTCCGCTCTTCCTCCCGAGAAGCTGCCCTACTTAGTAGAGCTAAGCCCAGGTTATGCTTCCTCCTGGAGCCCAGCATTCTGA
Peptide sequence:
MLPPGAQHSDERGAKEIILDDDECPLQIFREWPSDKGILVFQLKRRPPDYIPKKMKKHVEGKSLKGKDRADGSGYGSALPPEKLPYLVELSPGYASSWSPAF
IRESfinder result
IRESfinder score
0.428172543
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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