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mmu_circArfgef2_583
Basic information of circular RNA
PanCircBase ID:
mmu_circArfgef2_583
mm39_Chr. Position ID:
chr2|166676390|166678377|+
Gene name:
Arfgef2
Transcript:
ENSMUST00000099078.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
4,5,6
Exon/intron offsets:
0,1142,1731
Genomic length:
1987
Exon/intron sizes in nt:
147,180,256
Flanking exon/introns:
chr2:166669585-166676390|chr2:166678377-166684604
Splice length:
583
Other database IDs:
circBase: mmu_circ_0009586, CIRCpedia: MMU_CIRCpedia_11616, circAtlas: mmu-Arfgef2_0011
Human Ortholog IDs:
Mature spliced Sequence:
AAACTCATCGCATATGGACACATCACTGGCAATGCCCCTGACAGTGGCGCTCCTGGGAAGCGGCTGATCGACAGGATCGTTGAAACCATTTGCAATTGTTTTCAGGGCCCTCAGACAGATGAAGGGGTTCAGCTACAAATCATTAAGGCTCTGCTGACTGCTGTGACATCCCCACACATTGAAATCCATGAGGGCACCATCCTGCAGACAGTGAGGACCTGCTACAATATCTATCTGGCCAGCAAAAACCTCATCAATCAAACCACCGCCAAGGCCACCCTTACCCAAATGCTGAATGTCATCTTCACCCGCATGGAAAACCAAGTGTTACAGGAGGCCAGAGAATTGGAAAAACCAATGCAGTCAAAACCTCAGTCCCCGGTGATCCAGGCCACAGCAGGCTCTCCCAAGTTCAGCCGCCTGAAGCAGAGCCAGGCCCAGAGCAAACCCACGACTCCTGAGAAAGCAGAGCTGCCCAATGGGGACCATGCCCAGAGTGGCCTAGGAAAAGTGAGCTTGGAAAATGGAGAAGCTCCCCGAGAGAGAGGCTCGCCAGTCTCTGGGAGAGCCGAGCCTTCGAGGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCAGAGTGGCCTAGGAAAA
59.01
GATCCTGTCGATCAGCCGC
60.66
171
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTGGCCTAGGAAAAGTGAGCT
60
GATCCTGTCGATCAGCCGC
60.66
165
PCR template sequence:
GACCATGCCCAGAGTGGCCTAGGAAAAGTGAGCTTGGAAAATGGAGAAGCTCCCCGAGAGAGAGGCTCGCCAGTCTCTGGGAGAGCCGAGCCTTCGAGGGAAACTCATCGCATATGGACACATCACTGGCAATGCCCCTGACAGTGGCGCTCCTGGGAAGCGGCTGATCGACAGGATCGTTGAAACCATTTGCAATTGTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-326-3p(2), mmu-miR-181a-5p(1), mmu-miR-181b-5p(1), mmu-miR-149-5p(1), mmu-miR-370-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-466a-5p(1), mmu-miR-129-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GAGCCTTCGAGGGAAACTCATCGCAT
siRNA sets
ATGCGATGAGTTTCCCTCG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARFGEF2_583_ORF_1
1.0849
0.365903235
0.946650128
642
ORF sequence:
ATGGAGAAGCTCCCCGAGAGAGAGGCTCGCCAGTCTCTGGGAGAGCCGAGCCTTCGAGGGAAACTCATCGCATATGGACACATCACTGGCAATGCCCCTGACAGTGGCGCTCCTGGGAAGCGGCTGATCGACAGGATCGTTGAAACCATTTGCAATTGTTTTCAGGGCCCTCAGACAGATGAAGGGGTTCAGCTACAAATCATTAAGGCTCTGCTGACTGCTGTGACATCCCCACACATTGAAATCCATGAGGGCACCATCCTGCAGACAGTGAGGACCTGCTACAATATCTATCTGGCCAGCAAAAACCTCATCAATCAAACCACCGCCAAGGCCACCCTTACCCAAATGCTGAATGTCATCTTCACCCGCATGGAAAACCAAGTGTTACAGGAGGCCAGAGAATTGGAAAAACCAATGCAGTCAAAACCTCAGTCCCCGGTGATCCAGGCCACAGCAGGCTCTCCCAAGTTCAGCCGCCTGAAGCAGAGCCAGGCCCAGAGCAAACCCACGACTCCTGAGAAAGCAGAGCTGCCCAATGGGGACCATGCCCAGAGTGGCCTAGGAAAAGTGAGCTTGGAAAATGGAGAAGCTCCCCGAGAGAGAGGCTCGCCAGTCTCTGGGAGAGCCGAGCCTTCGAGG
Peptide sequence:
MEKLPEREARQSLGEPSLRGKLIAYGHITGNAPDSGAPGKRLIDRIVETICNCFQGPQTDEGVQLQIIKALLTAVTSPHIEIHEGTILQTVRTCYNIYLASKNLINQTTAKATLTQMLNVIFTRMENQVLQEARELEKPMQSKPQSPVIQATAGSPKFSRLKQSQAQSKPTTPEKAELPNGDHAQSGLGKVSLENGEAPRERGSPVSGRAEPSR
IRESfinder result
IRESfinder score
0.42991454
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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