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mmu_circAfdn_985
Basic information of circular RNA
PanCircBase ID:
mmu_circAfdn_985
mm39_Chr. Position ID:
chr17|14038382|14055618|+
Gene name:
Afdn
Transcript:
ENSMUST00000170827.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
6,7,8,9,10,11,12
Exon/intron offsets:
0,4145,5170,10808,11749,14247,17117
Genomic length:
17236
Exon/intron sizes in nt:
15,81,12,16,89,52,63,70,000
Flanking exon/introns:
chr17:14030832-14038382|chr17:14055618-14066533
Splice length:
985
Other database IDs:
CIRCpedia: MMU_CIRCpedia_8644, circAtlas: mmu-Mllt4_0048
Human Ortholog IDs:
Mature spliced Sequence:
GTGGAACACTGAGGATATATGCAGATAGTTTAAAACCAAATATTCCATACAAGACAATCCTGCTGTCTACTACCGATACCGCAGACTTTGCTGTAGCCGAATCTTTGGAGAAGTATGGTCTGGAAAAAGAGAATCCCAAGGACTACTGTATTGCCCGGGTTATGCTTCCTCCTGGAGCCCAGCATTCTGATGAGAGAGGTGCTAAGGAAATAATTCTTGACGATGATGAATGTCCTTTACAAATCTTCAGGGAATGGCCAAGTGACAAAGGGATTTTAGTCTTTCAGTTGAAGAGGAGACCACCGGACTACATCCCAAAGAAAATGAAGAAACATGTTGAAGGGAAGTCGTTGAAGGGGAAAGACAGAGCTGACGGGTCTGGCTACGGCTCCGCTCTTCCTCCCGAGAAGCTGCCCTACTTAGTAGAGCTAAGCCCAGATGGCTCTGACTCCAGAGACAAGCCAAAGTTATACCGCCTTCAATTAAGTGTGACTGAAGTTGGGACAGAGAAATTTGATGACAATTCTATCCAGCTGTTTGGCCCCGGAATTCAGCCCCATCACTGTGATCTCACCAACATGGATGGAGTGGTCACTGTGACACCCAGAAGTATGGATGCAGAGACCTACGTGGATGGTCAGCGCATCTCAGAGACCACAATGCTGCAGAGTGGCATGAGACTGCAGTTTGGCACCTCGCATGTGTTTAAGTTTGTGGACCCCATCCAGGACCACGTTCTTTCCAAGAGATCTGTGGATGGAGGCCTGATGGTCAAGGGCCCAAGACATAAACCTGGAGCTGTTCAGGAGACAACCTTTGAATTGGGAGGAGATGTCCACAGTGGGACAGCATTGCCGGCAAGCAGGAGCACTACTAGACTGGACAGTGACAGGGTGTCCTCTGCCTCTAGCACAGCTGAGCGAGGGATGGTGAAGCCGATGATCCGACTGGACCAGGAGCAGGAATATCGACGACGAGAAAACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGATGATCCGACTGGACCAG
59.97
GCAAAGTCTGCGGTATCGGT
60.74
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGAAGCCGATGATCCGACTG
59.9
GCAAAGTCTGCGGTATCGGT
60.74
146
PCR template sequence:
GTGACAGGGTGTCCTCTGCCTCTAGCACAGCTGAGCGAGGGATGGTGAAGCCGATGATCCGACTGGACCAGGAGCAGGAATATCGACGACGAGAAAACAGGTGGAACACTGAGGATATATGCAGATAGTTTAAAACCAAATATTCCATACAAGACAATCCTGCTGTCTACTACCGATACCGCAGACTTTGCTGTAGCCGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
17
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(2), mmu-miR-27a-3p(2), mmu-miR-181a-5p(1), mmu-miR-103-3p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-298-5p(1), mmu-miR-709(1), mmu-miR-181b-5p(1), mmu-miR-128-3p(1), mmu-miR-136-5p(1), mmu-miR-107-3p(1), mmu-miR-27a-5p(1), mmu-miR-452-3p(1), mmu-miR-3470b(1), mmu-miR-670-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GACGAGAAAACAGGTGGAACACTGAG
siRNA sets
TGTTCCACCTGTTTTCTCG, AGTGTTCCACCTGTTTTCT, GTTCCACCTGTTTTCTCGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAFDN_985_ORF_1
0.9093
0.25760952
0.973490197
852
ORF sequence:
ATGCTTCCTCCTGGAGCCCAGCATTCTGATGAGAGAGGTGCTAAGGAAATAATTCTTGACGATGATGAATGTCCTTTACAAATCTTCAGGGAATGGCCAAGTGACAAAGGGATTTTAGTCTTTCAGTTGAAGAGGAGACCACCGGACTACATCCCAAAGAAAATGAAGAAACATGTTGAAGGGAAGTCGTTGAAGGGGAAAGACAGAGCTGACGGGTCTGGCTACGGCTCCGCTCTTCCTCCCGAGAAGCTGCCCTACTTAGTAGAGCTAAGCCCAGATGGCTCTGACTCCAGAGACAAGCCAAAGTTATACCGCCTTCAATTAAGTGTGACTGAAGTTGGGACAGAGAAATTTGATGACAATTCTATCCAGCTGTTTGGCCCCGGAATTCAGCCCCATCACTGTGATCTCACCAACATGGATGGAGTGGTCACTGTGACACCCAGAAGTATGGATGCAGAGACCTACGTGGATGGTCAGCGCATCTCAGAGACCACAATGCTGCAGAGTGGCATGAGACTGCAGTTTGGCACCTCGCATGTGTTTAAGTTTGTGGACCCCATCCAGGACCACGTTCTTTCCAAGAGATCTGTGGATGGAGGCCTGATGGTCAAGGGCCCAAGACATAAACCTGGAGCTGTTCAGGAGACAACCTTTGAATTGGGAGGAGATGTCCACAGTGGGACAGCATTGCCGGCAAGCAGGAGCACTACTAGACTGGACAGTGACAGGGTGTCCTCTGCCTCTAGCACAGCTGAGCGAGGGATGGTGAAGCCGATGATCCGACTGGACCAGGAGCAGGAATATCGACGACGAGAAAACAGGTGGAACACTGAGGATATATGCAGATAG
Peptide sequence:
MLPPGAQHSDERGAKEIILDDDECPLQIFREWPSDKGILVFQLKRRPPDYIPKKMKKHVEGKSLKGKDRADGSGYGSALPPEKLPYLVELSPDGSDSRDKPKLYRLQLSVTEVGTEKFDDNSIQLFGPGIQPHHCDLTNMDGVVTVTPRSMDAETYVDGQRISETTMLQSGMRLQFGTSHVFKFVDPIQDHVLSKRSVDGGLMVKGPRHKPGAVQETTFELGGDVHSGTALPASRSTTRLDSDRVSSASSTAERGMVKPMIRLDQEQEYRRRENRWNTEDICR
IRESfinder result
IRESfinder score
0.477680472
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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