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mmu_circAgap3_274
Basic information of circular RNA
PanCircBase ID:
mmu_circAgap3_274
mm39_Chr. Position ID:
chr5|24692786|24698124|+
Gene name:
Agap3
Transcript:
ENSMUST00000024123.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
10,11
Exon/intron offsets:
0,5169
Genomic length:
5338
Exon/intron sizes in nt:
1,05,169
Flanking exon/introns:
chr5:24688431-24692786|chr5:24698124-24701730
Splice length:
274
Other database IDs:
CIRCpedia: MMU_CIRCpedia_14122, circAtlas: mmu-Agap3_0008
CIRCpedia: HSA_CIRCpedia_352111
Human Ortholog IDs:
Mature spliced Sequence:
GGGATCCTGCTGAAAAGAAGCGGCAAATCCTTGAACAAGGAGTGGAAGAAGAAGTATGTGACGCTGTGTGACAACGGGTTGCTTACTTACCACCCTAGCCTGCACGATTACATGCAAAACATCCACGGCAAAGAGATCGACCTCCTACGGACTACGGTGAAAGTGCCAGGGAAGCGTCTGCCCCGAGCCACACCCACTACAGCCCCAGGCACCAGTCCCCGTGCCAACGGGTTGGCAATGGAGCGGAGTAACACACAGCTGGGTGGGGCCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGAGCCACACCCACTACAG
60.08
AAGCAACCCGTTGTCACACA
60.68
175
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGAGCCACACCCACTACAG
60.08
GTTGTCACACAGCGTCACAT
59.06
166
PCR template sequence:
CGTCTGCCCCGAGCCACACCCACTACAGCCCCAGGCACCAGTCCCCGTGCCAACGGGTTGGCAATGGAGCGGAGTAACACACAGCTGGGTGGGGCCACAGGGGATCCTGCTGAAAAGAAGCGGCAAATCCTTGAACAAGGAGTGGAAGAAGAAGTATGTGACGCTGTGTGACAACGGGTTGCTTACTTACCACCCTAGCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-377-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGTGGGGCCACAGGGGATCCTGCTGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAGAP3_274_ORF_1
0.8441
0.429774951
0.440175652
234
ORF sequence:
ATGCAAAACATCCACGGCAAAGAGATCGACCTCCTACGGACTACGGTGAAAGTGCCAGGGAAGCGTCTGCCCCGAGCCACACCCACTACAGCCCCAGGCACCAGTCCCCGTGCCAACGGGTTGGCAATGGAGCGGAGTAACACACAGCTGGGTGGGGCCACAGGGGATCCTGCTGAAAAGAAGCGGCAAATCCTTGAACAAGGAGTGGAAGAAGAAGTATGTGACGCTGTGTGA
Peptide sequence:
MQNIHGKEIDLLRTTVKVPGKRLPRATPTTAPGTSPRANGLAMERSNTQLGGATGDPAEKKRQILEQGVEEEVCDAV
IRESfinder result
IRESfinder score
0.272234566
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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