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mmu_circArhgef9_495
Basic information of circular RNA
PanCircBase ID:
mmu_circArhgef9_495
mm39_Chr. Position ID:
chrX|94114778|94125316|-
Gene name:
Arhgef9
Transcript:
ENSMUST00000113876.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
7,6,5
Exon/intron offsets:
0,6266,10305
Genomic length:
10538
Exon/intron sizes in nt:
13,21,30,233
Flanking exon/introns:
chrX:94102666-94114778|chrX:94125316-94144562
Splice length:
495
Other database IDs:
circBase: mmu_circ_0016418, CIRCpedia: MMU_CIRCpedia_35018, circAtlas: mmu-Arhgef9_0005
circBase: hsa_circ_0090868, circAtlas: hsa-ARHGEF9_0005, CIRCpedia: HSA_CIRCpedia_66129
Human Ortholog IDs:
Mature spliced Sequence:
CAAGATGGATTCTGGATATACTCTGAATATTGTAACAACCACCTGGATGCCTGCATGGAACTCTCCAAGCTGATGAAGGACAGCCGCTATCAACACTTCTTTGAGGCCTGCCGCCTCTTGCAGCAGATGATCGACATTGCTATTGATGGTTTTCTTTTGACTCCAGTACAGAAGATCTGCAAATATCCCTTACAATTGGCCGAGCTCCTAAAGTATACTGCCCAAGATCACAGTGATTACAGATACGTTGCAGCTGCTTTGGCTGTCATGAGAAATGTGACTCAGCAGATCAATGAACGCAAGCGACGTCTGGAGAATATTGACAAGATTGCGCAATGGCAGGCCTCTGTCCTAGACTGGGAGGGAGAGGACATCTTAGACAGGAGCTCGGAGCTGATCTACACTGGAGAGATGGCCTGGATCTACCAGCCCTATGGCCGCAACCAGCAGAGAGTCTTCTTCCTGTTTGACCACCAGATGGTCCTCTGCAAGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGGAGAGATGGCCTGGAT
60.03
AGAGTTCCATGCAGGCATCC
60.11
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGGAGAGATGGCCTGGAT
60.03
GGAGAGTTCCATGCAGGCAT
60.11
159
PCR template sequence:
GATCTACACTGGAGAGATGGCCTGGATCTACCAGCCCTATGGCCGCAACCAGCAGAGAGTCTTCTTCCTGTTTGACCACCAGATGGTCCTCTGCAAGAAGCAAGATGGATTCTGGATATACTCTGAATATTGTAACAACCACCTGGATGCCTGCATGGAACTCTCCAAGCTGATGAAGGACAGCCGCTATCAACACTTCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-199a-5p(1), mmu-miR-298-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CCTCTGCAAGAAGCAAGATGGATTCT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARHGEF9_495_ORF_1
1.1599
0.376517629
0.994429301
936
ORF sequence:
ATGGAACTCTCCAAGCTGATGAAGGACAGCCGCTATCAACACTTCTTTGAGGCCTGCCGCCTCTTGCAGCAGATGATCGACATTGCTATTGATGGTTTTCTTTTGACTCCAGTACAGAAGATCTGCAAATATCCCTTACAATTGGCCGAGCTCCTAAAGTATACTGCCCAAGATCACAGTGATTACAGATACGTTGCAGCTGCTTTGGCTGTCATGAGAAATGTGACTCAGCAGATCAATGAACGCAAGCGACGTCTGGAGAATATTGACAAGATTGCGCAATGGCAGGCCTCTGTCCTAGACTGGGAGGGAGAGGACATCTTAGACAGGAGCTCGGAGCTGATCTACACTGGAGAGATGGCCTGGATCTACCAGCCCTATGGCCGCAACCAGCAGAGAGTCTTCTTCCTGTTTGACCACCAGATGGTCCTCTGCAAGAAGCAAGATGGATTCTGGATATACTCTGAATATTGTAACAACCACCTGGATGCCTGCATGGAACTCTCCAAGCTGATGAAGGACAGCCGCTATCAACACTTCTTTGAGGCCTGCCGCCTCTTGCAGCAGATGATCGACATTGCTATTGATGGTTTTCTTTTGACTCCAGTACAGAAGATCTGCAAATATCCCTTACAATTGGCCGAGCTCCTAAAGTATACTGCCCAAGATCACAGTGATTACAGATACGTTGCAGCTGCTTTGGCTGTCATGAGAAATGTGACTCAGCAGATCAATGAACGCAAGCGACGTCTGGAGAATATTGACAAGATTGCGCAATGGCAGGCCTCTGTCCTAGACTGGGAGGGAGAGGACATCTTAGACAGGAGCTCGGAGCTGATCTACACTGGAGAGATGGCCTGGATCTACCAGCCCTATGGCCGCAACCAGCAGAGAGTCTTCTTCCTGTTTGACCACCAGATGGTCCTCTGCAAGAAG
Peptide sequence:
MELSKLMKDSRYQHFFEACRLLQQMIDIAIDGFLLTPVQKICKYPLQLAELLKYTAQDHSDYRYVAAALAVMRNVTQQINERKRRLENIDKIAQWQASVLDWEGEDILDRSSELIYTGEMAWIYQPYGRNQQRVFFLFDHQMVLCKKQDGFWIYSEYCNNHLDACMELSKLMKDSRYQHFFEACRLLQQMIDIAIDGFLLTPVQKICKYPLQLAELLKYTAQDHSDYRYVAAALAVMRNVTQQINERKRRLENIDKIAQWQASVLDWEGEDILDRSSELIYTGEMAWIYQPYGRNQQRVFFLFDHQMVLCKK
IRESfinder result
IRESfinder score
0.476983324
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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