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mmu_circArfgef2_804
Basic information of circular RNA
PanCircBase ID:
mmu_circArfgef2_804
mm39_Chr. Position ID:
chr2|166676390|166687521|+
Gene name:
Arfgef2
Transcript:
ENSMUST00000099078.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
4,5,6,7,8
Exon/intron offsets:
0,1142,1731,8214,10979
Genomic length:
11131
Exon/intron sizes in nt:
1,47,18,02,56,69,152
Flanking exon/introns:
chr2:166669585-166676390|chr2:166687521-166690786
Splice length:
804
Other database IDs:
circAtlas: mmu-Arfgef2_0037
circAtlas: hsa-ARFGEF2_0067, CIRCpedia: HSA_CIRCpedia_145585
Human Ortholog IDs:
Mature spliced Sequence:
AAACTCATCGCATATGGACACATCACTGGCAATGCCCCTGACAGTGGCGCTCCTGGGAAGCGGCTGATCGACAGGATCGTTGAAACCATTTGCAATTGTTTTCAGGGCCCTCAGACAGATGAAGGGGTTCAGCTACAAATCATTAAGGCTCTGCTGACTGCTGTGACATCCCCACACATTGAAATCCATGAGGGCACCATCCTGCAGACAGTGAGGACCTGCTACAATATCTATCTGGCCAGCAAAAACCTCATCAATCAAACCACCGCCAAGGCCACCCTTACCCAAATGCTGAATGTCATCTTCACCCGCATGGAAAACCAAGTGTTACAGGAGGCCAGAGAATTGGAAAAACCAATGCAGTCAAAACCTCAGTCCCCGGTGATCCAGGCCACAGCAGGCTCTCCCAAGTTCAGCCGCCTGAAGCAGAGCCAGGCCCAGAGCAAACCCACGACTCCTGAGAAAGCAGAGCTGCCCAATGGGGACCATGCCCAGAGTGGCCTAGGAAAAGTGAGCTTGGAAAATGGAGAAGCTCCCCGAGAGAGAGGCTCGCCAGTCTCTGGGAGAGCCGAGCCTTCGAGGGGCACTGACAGTGGAGCTCAGGAGGTGGTGAAGGACATCTTAGAGGACGTGGTCACGTCTGCTGTGAAAGAAGCAGCAGAAAAGCATGGTCTGCCGGAGCCCGACCGAGCCCTGGGTGCCCTAGAGTGCCAGGAATGCGCTGTTCCTCCTGGAGTTGATGAAAACTCACAGACCAACGGCATAGCAGACGACAGGCAGTCGCTATCCTCCGCAGATAATCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGCTGTTCCTCCTGGAGTTG
60.67
GATCCTGTCGATCAGCCGC
60.66
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGTTCCTCCTGGAGTTGA
59.31
GATCCTGTCGATCAGCCGC
60.66
162
PCR template sequence:
AGAGTGCCAGGAATGCGCTGTTCCTCCTGGAGTTGATGAAAACTCACAGACCAACGGCATAGCAGACGACAGGCAGTCGCTATCCTCCGCAGATAATCTGAAACTCATCGCATATGGACACATCACTGGCAATGCCCCTGACAGTGGCGCTCCTGGGAAGCGGCTGATCGACAGGATCGTTGAAACCATTTGCAATTGTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
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-335-3p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CGCAGATAATCTGAAACTCATCGCAT
siRNA sets
GAGTTTCAGATTATCTGCG,TGAGTTTCAGATTATCTGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARFGEF2_804_ORF_1
1.14
0.391158476
0.999652407
1320
ORF sequence:
ATGCTGAATGTCATCTTCACCCGCATGGAAAACCAAGTGTTACAGGAGGCCAGAGAATTGGAAAAACCAATGCAGTCAAAACCTCAGTCCCCGGTGATCCAGGCCACAGCAGGCTCTCCCAAGTTCAGCCGCCTGAAGCAGAGCCAGGCCCAGAGCAAACCCACGACTCCTGAGAAAGCAGAGCTGCCCAATGGGGACCATGCCCAGAGTGGCCTAGGAAAAGTGAGCTTGGAAAATGGAGAAGCTCCCCGAGAGAGAGGCTCGCCAGTCTCTGGGAGAGCCGAGCCTTCGAGGGGCACTGACAGTGGAGCTCAGGAGGTGGTGAAGGACATCTTAGAGGACGTGGTCACGTCTGCTGTGAAAGAAGCAGCAGAAAAGCATGGTCTGCCGGAGCCCGACCGAGCCCTGGGTGCCCTAGAGTGCCAGGAATGCGCTGTTCCTCCTGGAGTTGATGAAAACTCACAGACCAACGGCATAGCAGACGACAGGCAGTCGCTATCCTCCGCAGATAATCTGAAACTCATCGCATATGGACACATCACTGGCAATGCCCCTGACAGTGGCGCTCCTGGGAAGCGGCTGATCGACAGGATCGTTGAAACCATTTGCAATTGTTTTCAGGGCCCTCAGACAGATGAAGGGGTTCAGCTACAAATCATTAAGGCTCTGCTGACTGCTGTGACATCCCCACACATTGAAATCCATGAGGGCACCATCCTGCAGACAGTGAGGACCTGCTACAATATCTATCTGGCCAGCAAAAACCTCATCAATCAAACCACCGCCAAGGCCACCCTTACCCAAATGCTGAATGTCATCTTCACCCGCATGGAAAACCAAGTGTTACAGGAGGCCAGAGAATTGGAAAAACCAATGCAGTCAAAACCTCAGTCCCCGGTGATCCAGGCCACAGCAGGCTCTCCCAAGTTCAGCCGCCTGAAGCAGAGCCAGGCCCAGAGCAAACCCACGACTCCTGAGAAAGCAGAGCTGCCCAATGGGGACCATGCCCAGAGTGGCCTAGGAAAAGTGAGCTTGGAAAATGGAGAAGCTCCCCGAGAGAGAGGCTCGCCAGTCTCTGGGAGAGCCGAGCCTTCGAGGGGCACTGACAGTGGAGCTCAGGAGGTGGTGAAGGACATCTTAGAGGACGTGGTCACGTCTGCTGTGAAAGAAGCAGCAGAAAAGCATGGTCTGCCGGAGCCCGACCGAGCCCTGGGTGCCCTAGAGTGCCAGGAATGCGCTGTTCCTCCTGGAGTTGATGAAAACTCACAGACCAACGGCATAGCAGACGACAGGCAGTCGCTATCCTCCGCAGATAATCTG
Peptide sequence:
MLNVIFTRMENQVLQEARELEKPMQSKPQSPVIQATAGSPKFSRLKQSQAQSKPTTPEKAELPNGDHAQSGLGKVSLENGEAPRERGSPVSGRAEPSRGTDSGAQEVVKDILEDVVTSAVKEAAEKHGLPEPDRALGALECQECAVPPGVDENSQTNGIADDRQSLSSADNLKLIAYGHITGNAPDSGAPGKRLIDRIVETICNCFQGPQTDEGVQLQIIKALLTAVTSPHIEIHEGTILQTVRTCYNIYLASKNLINQTTAKATLTQMLNVIFTRMENQVLQEARELEKPMQSKPQSPVIQATAGSPKFSRLKQSQAQSKPTTPEKAELPNGDHAQSGLGKVSLENGEAPRERGSPVSGRAEPSRGTDSGAQEVVKDILEDVVTSAVKEAAEKHGLPEPDRALGALECQECAVPPGVDENSQTNGIADDRQSLSSADNL
IRESfinder result
IRESfinder score
0.409674809
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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