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mmu_circOdf2_375
Basic information of circular RNA
PanCircBase ID:
mmu_circOdf2_375
mm39_Chr. Position ID:
chr2|29810786|29812383|+
Gene name:
Odf2
Transcript:
ENSMUST00000113757.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
15,16,17
Exon/intron offsets:
0,229,1438
Genomic length:
1597
Exon/intron sizes in nt:
11,11,05,159
Flanking exon/introns:
chr2:29807757-29810786|chr2:29812383-29813550
Splice length:
375
Other database IDs:
circAtlas: mmu-Odf2_0016
Human Ortholog IDs:
Mature spliced Sequence:
GCTAGCTTTGCCCCTATGGAGGACAAGCTCAACCAGGCTCACTTGGAGGTTCAGCAGCTGAAGGCGTCAGTGAAGAACTACGAGGGGATGATAGACAACTACAAGAGCCAGGTGATGAAAACAAGATTGGAGGCTGATGAAGTGGCTGCACAGCTAGAGCGCTGCGACAAAGAGAACAAGATGCTTAAAGACGAGATGAACAAAGAGATCGAGGCGGCCCGTCGGCAGTTCCAGTCACAGCTGGCTGACCTACAACAGCTGCCTGACATCCTCAAGATCACGGAGGCCAAGCTGGCTGAGTGCCAAGACCAGCTGCAGGGCTACGAGAGGAAGAACATCGACCTCACAGCCATCATTTCAGACCTGCGCAGCCGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGAGTGCCAAGACCAGCTG
60.95
TCAGCTGCTGAACCTCCAAG
59.96
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGAGTGCCAAGACCAGCTG
60.95
CTTCAGCTGCTGAACCTCCA
59.96
143
PCR template sequence:
GATCACGGAGGCCAAGCTGGCTGAGTGCCAAGACCAGCTGCAGGGCTACGAGAGGAAGAACATCGACCTCACAGCCATCATTTCAGACCTGCGCAGCCGGGCTAGCTTTGCCCCTATGGAGGACAAGCTCAACCAGGCTCACTTGGAGGTTCAGCAGCTGAAGGCGTCAGTGAAGAACTACGAGGGGATGATAGACAACT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-134-5p(1), mmu-miR-96-5p(1), mmu-miR-335-3p(1), mmu-miR-532-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CCTGCGCAGCCGGGCTAGCTTTGCCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCODF2_375_ORF_1
1.2486
0.667395242
0.993903879
735
ORF sequence:
ATGGAGGACAAGCTCAACCAGGCTCACTTGGAGGTTCAGCAGCTGAAGGCGTCAGTGAAGAACTACGAGGGGATGATAGACAACTACAAGAGCCAGGTGATGAAAACAAGATTGGAGGCTGATGAAGTGGCTGCACAGCTAGAGCGCTGCGACAAAGAGAACAAGATGCTTAAAGACGAGATGAACAAAGAGATCGAGGCGGCCCGTCGGCAGTTCCAGTCACAGCTGGCTGACCTACAACAGCTGCCTGACATCCTCAAGATCACGGAGGCCAAGCTGGCTGAGTGCCAAGACCAGCTGCAGGGCTACGAGAGGAAGAACATCGACCTCACAGCCATCATTTCAGACCTGCGCAGCCGGGCTAGCTTTGCCCCTATGGAGGACAAGCTCAACCAGGCTCACTTGGAGGTTCAGCAGCTGAAGGCGTCAGTGAAGAACTACGAGGGGATGATAGACAACTACAAGAGCCAGGTGATGAAAACAAGATTGGAGGCTGATGAAGTGGCTGCACAGCTAGAGCGCTGCGACAAAGAGAACAAGATGCTTAAAGACGAGATGAACAAAGAGATCGAGGCGGCCCGTCGGCAGTTCCAGTCACAGCTGGCTGACCTACAACAGCTGCCTGACATCCTCAAGATCACGGAGGCCAAGCTGGCTGAGTGCCAAGACCAGCTGCAGGGCTACGAGAGGAAGAACATCGACCTCACAGCCATCATTTCAGACCTGCGCAGCCGG
Peptide sequence:
MEDKLNQAHLEVQQLKASVKNYEGMIDNYKSQVMKTRLEADEVAAQLERCDKENKMLKDEMNKEIEAARRQFQSQLADLQQLPDILKITEAKLAECQDQLQGYERKNIDLTAIISDLRSRASFAPMEDKLNQAHLEVQQLKASVKNYEGMIDNYKSQVMKTRLEADEVAAQLERCDKENKMLKDEMNKEIEAARRQFQSQLADLQQLPDILKITEAKLAECQDQLQGYERKNIDLTAIISDLRSR
IRESfinder result
IRESfinder score
0.220355203
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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