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mmu_ciPfdn2_999
Basic information of circular RNA
PanCircBase ID:
mmu_ciPfdn2_999
mm39_Chr. Position ID:
chr1|171184396|171185395|+
Gene name:
Pfdn2
Transcript:
ENSMUST00000135941.8
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
3
Exon/intron offsets:
0
Genomic length:
999
Exon/intron sizes in nt:
999
Flanking exon/introns:
chr1:171184396-171185417
Splice length:
999
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGAGCAAGAATTCCTCTATAGGCGTTTGGGCAGCCAAGAGGTTAAATGTAGGTGACTAGGGATTTAGGGAATTCATGTTGATGGTAGCATGCAGCCTGTTAGCTATCTACTGTGCCCTTTATACTATTACAAAGTTGAAGTCCAACTCCTTAAGTGAGGAGTTGTTGGCTGTGTGCCCTTTCCATGGGCTCTTTGATGTGGTTGAGTGGGGAGGGAATGGGTAGAGCAGTGTTTCTCACAATATAGTCTGTGGATCCCTGAGTCAGAATCTCCTGAAGAACTTGTTTAGCAGTGTTGGGCATCAGACCCAGGGCCTCATGCGCAGTAGGCTAAATACTCTTCTCATTGAGCTACACCTCCAGCCAAGGACCAGTTTAAAATGCAGCTTCTTAAGAGCTCTCGATCCACGGAACCAGACCCTTAAAGAAACCATAAGTGACCTTTTAAAGGGAGAAAGAATCCTGACTGGGGTGGCATACATTGATGTTTAACTTGCTGAGATGATGAGGCAGAGGAATCGGATTTGAAGCCTGCTTGGGCTAACTAAAAATCAATCACTTAAAAAAAAAATGAATGTGACCTAAGAGAAGAAACCATAGCATGACAAATGCTCTTTTAAGAGCAAGCAACCCACCCTCCCTGGGCAGGGACTGAGGGTGGAAAGTTGCTGGAGAGGGGACAGTAATTGTCTTAAGTGATGTAGCTGCTGGTGAGCCACTAGTGCTCCTGTGGGTATCTCCATCCATTCCCACAAGGGTGCTCCAGGTTAGACTCATGGGCCACAAAACAAAACAGAGAAATACGATTATGAGATGGGATGGGTTGGTGGCAAGTGGATGAGAGTGGGCTGTTTGATCATATGCTTTTATAACATTATCAAAGAATAATGAAAATAAGTAGCTCAGATGGTTCCCCTTTATAAGCCACTGTGTTCTTGTCTCACTGCCTCCAACTGTAGCACAGTCCGGGGCAGAGGAGGGAGACCTGCACTCCTTCTC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGCCTCCAACTGTAGCACA
59.96
AGGCTGCATGCTACCATCAA
59.74
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CACTGCCTCCAACTGTAGCA
59.96
AGGCTGCATGCTACCATCAA
59.74
156
PCR template sequence:
AGCTCAGATGGTTCCCCTTTATAAGCCACTGTGTTCTTGTCTCACTGCCTCCAACTGTAGCACAGTCCGGGGCAGAGGAGGGAGACCTGCACTCCTTCTCGTGAGCAAGAATTCCTCTATAGGCGTTTGGGCAGCCAAGAGGTTAAATGTAGGTGACTAGGGATTTAGGGAATTCATGTTGATGGTAGCATGCAGCCTGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-709(1), mmu-miR-181b-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-335-3p(1), mmu-miR-490-3p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGCACTCCTTCTCGTGAGCAAGAATT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIPFDN2_999_ORF_3
0.6757
-0.184049135
0.024562729
153
ORF sequence:
ATGGTTCCCCTTTATAAGCCACTGTGTTCTTGTCTCACTGCCTCCAACTGTAGCACAGTCCGGGGCAGAGGAGGGAGACCTGCACTCCTTCTCGTGAGCAAGAATTCCTCTATAGGCGTTTGGGCAGCCAAGAGGTTAAATGTAGGTGACTAG
Peptide sequence:
MVPLYKPLCSCLTASNCSTVRGRGGRPALLLVSKNSSIGVWAAKRLNVGD
IRESfinder result
IRESfinder score
0.705432412
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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