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mmu_circAgpat3_378
Basic information of circular RNA
PanCircBase ID:
mmu_circAgpat3_378
mm39_Chr. Position ID:
chr10|78109905|78118310|-
Gene name:
Agpat3
Transcript:
ENSMUST00000001240.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
9,8,7
Exon/intron offsets:
0,3938,8302
Genomic length:
8405
Exon/intron sizes in nt:
199,76,103
Flanking exon/introns:
chr10:78109609-78109905|chr10:78118310-78118928
Splice length:
378
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TTGCAGCTATCTATGACGTGACCCTGAACTTCAGAGGGAACAAGAACCCATCTCTACTGGGGATCCTGTATGGGAAGAAATATGAGGCAGACATGTGTGTGAGGAGGTTCCCCCTGGAAGACATCCCAGCAGATGAGACCAGCGCCGCCCAGTGGCTTCACAAGCTGTACCAGGAGAAGGATGCCCTGCAAGAGATGTACAAGCAGAAGGGTGTATTCCCAGGGGAGCAGTTCAAGCCTGCCCGAAGGCCGTGGACCCTCCTGAACTTCCTGTGCTGGGCCACCATCCTCCTCTCACCCCTCTTCAGCTTCGTCCTGGGTGTCTTTGCCAGTGGATCCCCGCTCCTCATCCTGACGTTCTTGGGGTTCGTGGGAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTCCTCTCACCCCTCTTCA
59.96
TCCCATACAGGATCCCCAGT
59.35
167
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTCTTCAGCTTCGTCCTGGG
60.11
TCCCATACAGGATCCCCAGT
59.35
154
PCR template sequence:
GCCACCATCCTCCTCTCACCCCTCTTCAGCTTCGTCCTGGGTGTCTTTGCCAGTGGATCCCCGCTCCTCATCCTGACGTTCTTGGGGTTCGTGGGAGCAGTTGCAGCTATCTATGACGTGACCCTGAACTTCAGAGGGAACAAGAACCCATCTCTACTGGGGATCCTGTATGGGAAGAAATATGAGGCAGACATGTGTGT
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-431-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-342-3p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
TTCGTGGGAGCAGTTGCAGCTATCTA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAGPAT3_378_ORF_1
1.2766
0.375454673
0.968712297
663
ORF sequence:
ATGTGTGTGAGGAGGTTCCCCCTGGAAGACATCCCAGCAGATGAGACCAGCGCCGCCCAGTGGCTTCACAAGCTGTACCAGGAGAAGGATGCCCTGCAAGAGATGTACAAGCAGAAGGGTGTATTCCCAGGGGAGCAGTTCAAGCCTGCCCGAAGGCCGTGGACCCTCCTGAACTTCCTGTGCTGGGCCACCATCCTCCTCTCACCCCTCTTCAGCTTCGTCCTGGGTGTCTTTGCCAGTGGATCCCCGCTCCTCATCCTGACGTTCTTGGGGTTCGTGGGAGCAGTTGCAGCTATCTATGACGTGACCCTGAACTTCAGAGGGAACAAGAACCCATCTCTACTGGGGATCCTGTATGGGAAGAAATATGAGGCAGACATGTGTGTGAGGAGGTTCCCCCTGGAAGACATCCCAGCAGATGAGACCAGCGCCGCCCAGTGGCTTCACAAGCTGTACCAGGAGAAGGATGCCCTGCAAGAGATGTACAAGCAGAAGGGTGTATTCCCAGGGGAGCAGTTCAAGCCTGCCCGAAGGCCGTGGACCCTCCTGAACTTCCTGTGCTGGGCCACCATCCTCCTCTCACCCCTCTTCAGCTTCGTCCTGGGTGTCTTTGCCAGTGGATCCCCGCTCCTCATCCTGACGTTCTTGGGGTTCGTGGGAGCA
Peptide sequence:
MCVRRFPLEDIPADETSAAQWLHKLYQEKDALQEMYKQKGVFPGEQFKPARRPWTLLNFLCWATILLSPLFSFVLGVFASGSPLLILTFLGFVGAVAAIYDVTLNFRGNKNPSLLGILYGKKYEADMCVRRFPLEDIPADETSAAQWLHKLYQEKDALQEMYKQKGVFPGEQFKPARRPWTLLNFLCWATILLSPLFSFVLGVFASGSPLLILTFLGFVGA
IRESfinder result
IRESfinder score
0.523968899
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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