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mmu_ciPikfyve_1301
Basic information of circular RNA
PanCircBase ID:
mmu_ciPikfyve_1301
mm39_Chr. Position ID:
chr1|65289445|65290746|+
Gene name:
Pikfyve
Transcript:
ENSMUST00000081154.14
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
21
Exon/intron offsets:
0
Genomic length:
1301
Exon/intron sizes in nt:
1301
Flanking exon/introns:
chr1:65289445-65290763
Splice length:
1301
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAGGATGCTTGTGTGCACTAGTGCACCTAGTAGTGGAATTCCAATAACATAAATAATGCCTGCTTTTAGTTATGATACATTGATGGTCACATGTGAATTGATAGAATATTTAAACTTATAAAGTAACCGTGAAGGGTTTTTGTTCATGAATAAATAATTGTACCTTAAGTAAGAATGAAAAAAATTCAGAGAGAGGAAAGAGAAATGTTTGTATTATAGAACTTACAAAGTTGATCCACAAAAGCTGGTTTTTGAAACCAAAAGTCTACATTTTGATTATAAGCATGTACAATTTAGGTAGGTTTCCCTTTGCATAGTGTTATAAAAGAGTCAGCCGTTTATCTTACTGTTTGTAGTTCTACCACTGAGTTATACTACCAGACCAACCTTTTGTCTCATTAGTGTGTTCTTCTTGTAAATGTCTTAAATAAATTTATAGAGACAAACACATTTTATAATGTTGTAATATTTCTAGTGATAGCCATAAAGACCTTACATGCCTGTTAGGTTTTTGTTGTTATGTTAAAAAATTATCTGTCAAAAGCAGCCTAAAGGAGAAAGGGTTATTTGGTTCATAGTTGAAGGATACAGTCCTTCATGGCAGGGAAAGTCACAGAAGCTAGAGCTTGAAGTAACTGATGATAGGAAGCCAGCATTCAGGGGAAAGCATTGAATGCATGCACGGATGCTGTGCTCAGCCTCACTCCCTTTCTCATTGTTGTTTGTTTTTGGTAATGCTGCTTCCATAATAAAATATTTATCTCCAACAAAAATTTTTTTCTTGAAGCTTGTGTAGTTCCAGGACAACTTTAAGCATGATTTTCTGAAAGTGTGTAGGGTTTTTTTCCCTTAGAAATTAATGGACTCCTTAGGTAATACTAAGGATACAGATTTTAACAAGCGTACATGCAAAGTCTCTAATTTTGGTTAGTTGTGTTACGTACAGTTAGGAGCTGTTTTCCATACTCAGTGACTAGAGGGCAGAAGAGCACTGTCTTTTTTTTTTCTCCCCAATGTTGATTGGGATTGAAACTGAAAGACAGTTTTACCTCTTCCTAATGCAAATCAGTTTTATTCCACTTATTTTACAGTTTGTGCATTCTCATTAAATAATTTTTTAAAGATACTAACGAAATAGGAGTGGAAACGATGCTATAGTGTGGCTAGTCTACACTTGTTTGACAGAATGAGGTAAAACCTGTTCCACAGCATCATTAGATATGTTTTTCTTTAGTACTTCATCATAAGCATATTTAATAATTAGAATATAGTCTTTGTGGTAATGTTGCCATATTTCTAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTTCCACAGCATCATTAGATATGT
56.88
TGGAATTCCACTACTAGGTGCAC
60.06
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTTCCACAGCATCATTAGATATGT
56.88
TGGAATTCCACTACTAGGTGCA
58.82
144
PCR template sequence:
GTTCCACAGCATCATTAGATATGTTTTTCTTTAGTACTTCATCATAAGCATATTTAATAATTAGAATATAGTCTTTGTGGTAATGTTGCCATATTTCTAAGTAGGATGCTTGTGTGCACTAGTGCACCTAGTAGTGGAATTCCAATAACATAAATAATGCCTGCTTTTAGTTATGATACATTGATGGTCACATGTGAATT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-miR-103-3p(2), mmu-miR-107-3p(2), mmu-miR-18a-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-411-3p(1), mmu-miR-382-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-300-3p(1), mmu-miR-369-3p(1), mmu-miR-335-3p(1), mmu-miR-3065-5p(1), mmu-miR-544-5p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCCATATTTCTAAGTAGGATGCTTGT
siRNA sets
ATCCTACTTAGAAATATGG, TCCTACTTAGAAATATGGC, CATCCTACTTAGAAATATG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.882510969
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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