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mmu_circPde4dip_606
Basic information of circular RNA
PanCircBase ID:
mmu_circPde4dip_606
mm39_Chr. Position ID:
chr3|97700054|97731641|-
Gene name:
Pde4dip
Transcript:
ENSMUST00000168438.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
8,7,6,5,4
Exon/intron offsets:
0,406,746,3993,31476
Genomic length:
31587
Exon/intron sizes in nt:
1,18,17,61,24,77,111
Flanking exon/introns:
chr3:97666246-97700054|chr3:97731641-97748949
Splice length:
606
Other database IDs:
circBase: mmu_circ_0010968, CIRCpedia: MMU_CIRCpedia_35645, circAtlas: mmu-Pde4dip_0007
Human Ortholog IDs:
Mature spliced Sequence:
CACCTCAATGACTTGAAGAAGGAGAACTTCAGCCTCAAGCTGCGCATCTACTTCCTGGAGGAGCGCATGCAACAGAAGTATGAAGTCAGCCGGGAGGATGTCTACAAGCGGAACATCGAGCTGAAGGTTGAAGTGGAGAGCCTGAAACGAGAACTCCAGGACAGGAAACAGCATCTAGATAAAACATGGGCCGATGCAGAGGATCTCAACAGCCAGAATGAGGCAGAGCTCCGGCGCCAGGTTGAAGAACGGCAGCAGGAGACAGAACACGTTTATGAGCTCCTAGGGAACAAGATCCAGCTGCTGCAGGAGGAACCCAGGCTAGCAAAGAATGAAGCCACAGAGATGGAGACTCTGGTGGAGGCAGAGAAGAGGTGCAATCTGGAGCTCTCAGAGAGGTGGACGAATGCTGCCAAGAACAGGGAAGATGCAGCAGGAGACCAGGAGAAGCCTGACCAATATTCTGAGGCACTGGCTCAGAGGGACAGGAGAATTGAAGAGCTGAGGCAGAGCTTGGCTGCTCAGGAGGGGCTTGTGGAACAGCTGTCTCAAGAGAAACGACAACTGTTACATCTGCTGGAGGAGCCAGCGAGCATGGAAGTGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGGAGGGGCTTGTGGAAC
60.3
CCTCCAGGAAGTAGATGCGC
60.25
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCAGGAGGGGCTTGTGGAA
60.46
CCTCCAGGAAGTAGATGCGC
60.25
146
PCR template sequence:
GCAGAGCTTGGCTGCTCAGGAGGGGCTTGTGGAACAGCTGTCTCAAGAGAAACGACAACTGTTACATCTGCTGGAGGAGCCAGCGAGCATGGAAGTGCAGCACCTCAATGACTTGAAGAAGGAGAACTTCAGCCTCAAGCTGCGCATCTACTTCCTGGAGGAGCGCATGCAACAGAAGTATGAAGTCAGCCGGGAGGATG
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-103-3p(1), mmu-miR-92a-3p(1), mmu-miR-25-3p(1), mmu-miR-370-3p(1), mmu-miR-107-3p(1), mmu-miR-129-5p(1), mmu-miR-207(1), mmu-miR-484(1)
siRNAs for circular RNA silencing
Junction sequence
CATGGAAGTGCAGCACCTCAATGACT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDE4DIP_606_ORF_1
1.2466
0.507964485
0.999385171
1146
ORF sequence:
ATGCAACAGAAGTATGAAGTCAGCCGGGAGGATGTCTACAAGCGGAACATCGAGCTGAAGGTTGAAGTGGAGAGCCTGAAACGAGAACTCCAGGACAGGAAACAGCATCTAGATAAAACATGGGCCGATGCAGAGGATCTCAACAGCCAGAATGAGGCAGAGCTCCGGCGCCAGGTTGAAGAACGGCAGCAGGAGACAGAACACGTTTATGAGCTCCTAGGGAACAAGATCCAGCTGCTGCAGGAGGAACCCAGGCTAGCAAAGAATGAAGCCACAGAGATGGAGACTCTGGTGGAGGCAGAGAAGAGGTGCAATCTGGAGCTCTCAGAGAGGTGGACGAATGCTGCCAAGAACAGGGAAGATGCAGCAGGAGACCAGGAGAAGCCTGACCAATATTCTGAGGCACTGGCTCAGAGGGACAGGAGAATTGAAGAGCTGAGGCAGAGCTTGGCTGCTCAGGAGGGGCTTGTGGAACAGCTGTCTCAAGAGAAACGACAACTGTTACATCTGCTGGAGGAGCCAGCGAGCATGGAAGTGCAGCACCTCAATGACTTGAAGAAGGAGAACTTCAGCCTCAAGCTGCGCATCTACTTCCTGGAGGAGCGCATGCAACAGAAGTATGAAGTCAGCCGGGAGGATGTCTACAAGCGGAACATCGAGCTGAAGGTTGAAGTGGAGAGCCTGAAACGAGAACTCCAGGACAGGAAACAGCATCTAGATAAAACATGGGCCGATGCAGAGGATCTCAACAGCCAGAATGAGGCAGAGCTCCGGCGCCAGGTTGAAGAACGGCAGCAGGAGACAGAACACGTTTATGAGCTCCTAGGGAACAAGATCCAGCTGCTGCAGGAGGAACCCAGGCTAGCAAAGAATGAAGCCACAGAGATGGAGACTCTGGTGGAGGCAGAGAAGAGGTGCAATCTGGAGCTCTCAGAGAGGTGGACGAATGCTGCCAAGAACAGGGAAGATGCAGCAGGAGACCAGGAGAAGCCTGACCAATATTCTGAGGCACTGGCTCAGAGGGACAGGAGAATTGAAGAGCTGAGGCAGAGCTTGGCTGCTCAGGAGGGGCTTGTGGAACAGCTGTCTCAAGAGAAACGACAACTGTTACATCTGCTGGAGGAGCCAGCGAGCATGGAAGTGCAG
Peptide sequence:
MQQKYEVSREDVYKRNIELKVEVESLKRELQDRKQHLDKTWADAEDLNSQNEAELRRQVEERQQETEHVYELLGNKIQLLQEEPRLAKNEATEMETLVEAEKRCNLELSERWTNAAKNREDAAGDQEKPDQYSEALAQRDRRIEELRQSLAAQEGLVEQLSQEKRQLLHLLEEPASMEVQHLNDLKKENFSLKLRIYFLEERMQQKYEVSREDVYKRNIELKVEVESLKRELQDRKQHLDKTWADAEDLNSQNEAELRRQVEERQQETEHVYELLGNKIQLLQEEPRLAKNEATEMETLVEAEKRCNLELSERWTNAAKNREDAAGDQEKPDQYSEALAQRDRRIEELRQSLAAQEGLVEQLSQEKRQLLHLLEEPASMEVQ
IRESfinder result
IRESfinder score
0.235105263
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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