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mmu_circPcgf5_514
Basic information of circular RNA
PanCircBase ID:
mmu_circPcgf5_514
mm39_Chr. Position ID:
chr19|36414554|36428023|+
Gene name:
Pcgf5
Transcript:
ENSMUST00000224679.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
4,5,6,7,8,9
Exon/intron offsets:
0,148,2844,5689,7833,13409
Genomic length:
13469
Exon/intron sizes in nt:
56,60,149,99,90,60
Flanking exon/introns:
chr19:36412066-36414554|chr19:36428023-36433020
Splice length:
514
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GCTGGATAACACGTTGGAGGAAATTATCTTTAAATTAGTGCCTGGACTACGAGAACAAGAACTTCAGCGTGAGTTGGAATTTTGGAAGAAAAACAAACCTCAAGAAAATGGGCAAGATGATATTTCGAAGGTTGACAAGTCTAAAGCAGATGAGGAAGGTGATGAAAACCAAGATGATAAGGACTATCATAGAAGTGACCCGCAAATTGCTATCTGTCTGGACTGTTTACGAAATAATGGGCAGTCAGGGGACAACGTAGTGAAGGGTCTCATGAAGAAATTTATTCGCTGTTCTACACGAGTTACTGTAGGAACTATTAAAAAGTTTCTAAGTTTAAAACTAAAACTTCCAAGTTCTTATGAGTTGGATGTGCTGTGCAATGGTGAAATTATGGGAAAGGATCATACTATGGAATTCATCTATATGACAAGATGGCGACTAAGAGGAGAAAATCTTTGCTGTCTGAACTGTTCAGCCTCGCAAGTCTGCTCTCAGGATGGCACTTTGTACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGACAAGATGGCGACTAAGAGG
59.83
TGTTCTCGTAGTCCAGGCAC
59.4
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GACAAGATGGCGACTAAGAGGA
59.57
TGTTCTCGTAGTCCAGGCAC
59.4
145
PCR template sequence:
ATTCATCTATATGACAAGATGGCGACTAAGAGGAGAAAATCTTTGCTGTCTGAACTGTTCAGCCTCGCAAGTCTGCTCTCAGGATGGCACTTTGTACCAGGCTGGATAACACGTTGGAGGAAATTATCTTTAAATTAGTGCCTGGACTACGAGAACAAGAACTTCAGCGTGAGTTGGAATTTTGGAAGAAAAACAAACCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
19
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-32-5p(1), mmu-miR-30e-5p(1), mmu-miR-106b-5p(1), mmu-miR-30a-5p(1), mmu-miR-30c-5p(1), mmu-miR-18a-5p(1), mmu-miR-101b-3p(1), mmu-miR-132-3p(1), mmu-miR-139-5p(1), mmu-miR-30d-5p(1), mmu-miR-30b-5p(1), mmu-miR-363-3p(1), mmu-miR-335-3p(1), mmu-miR-3087-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CACTTTGTACCAGGCTGGATAACACG
siRNA sets
TATCCAGCCTGGTACAAAG, TTATCCAGCCTGGTACAAA, ATCCAGCCTGGTACAAAGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPCGF5_514_ORF_1
0.8407
0.106975241
0.637722587
531
ORF sequence:
ATGGCACTTTGTACCAGGCTGGATAACACGTTGGAGGAAATTATCTTTAAATTAGTGCCTGGACTACGAGAACAAGAACTTCAGCGTGAGTTGGAATTTTGGAAGAAAAACAAACCTCAAGAAAATGGGCAAGATGATATTTCGAAGGTTGACAAGTCTAAAGCAGATGAGGAAGGTGATGAAAACCAAGATGATAAGGACTATCATAGAAGTGACCCGCAAATTGCTATCTGTCTGGACTGTTTACGAAATAATGGGCAGTCAGGGGACAACGTAGTGAAGGGTCTCATGAAGAAATTTATTCGCTGTTCTACACGAGTTACTGTAGGAACTATTAAAAAGTTTCTAAGTTTAAAACTAAAACTTCCAAGTTCTTATGAGTTGGATGTGCTGTGCAATGGTGAAATTATGGGAAAGGATCATACTATGGAATTCATCTATATGACAAGATGGCGACTAAGAGGAGAAAATCTTTGCTGTCTGAACTGTTCAGCCTCGCAAGTCTGCTCTCAGGATGGCACTTTGTACCAG
Peptide sequence:
MALCTRLDNTLEEIIFKLVPGLREQELQRELEFWKKNKPQENGQDDISKVDKSKADEEGDENQDDKDYHRSDPQIAICLDCLRNNGQSGDNVVKGLMKKFIRCSTRVTVGTIKKFLSLKLKLPSSYELDVLCNGEIMGKDHTMEFIYMTRWRLRGENLCCLNCSASQVCSQDGTLYQ
IRESfinder result
IRESfinder score
0.497628032
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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