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mmu_circAgpat4_694
Basic information of circular RNA
PanCircBase ID:
mmu_circAgpat4_694
mm39_Chr. Position ID:
chr17|12429097|12435779|+
Gene name:
Agpat4
Transcript:
ENSMUST00000024594.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
4,5,6,7,8
Exon/intron offsets:
0,428,3244,5065,6483
Genomic length:
6682
Exon/intron sizes in nt:
1,62,15,41,03,76,199
Flanking exon/introns:
chr17:12417808-12429097|chr17:12435779-12437871
Splice length:
694
Other database IDs:
circAtlas: mmu-Agpat4_0003
Human Ortholog IDs:
Mature spliced Sequence:
AACTCCAAAGTCCTGGCCAAGAAAGAACTGGCTTATGTCCCAATCATTGGCTGGATGTGGTACTTCGTGGAAATGATCTTTTGCACACGCAAGTGGGAGCAAGATCGGCAGACGGTTGCCAAGAGCCTGCTGCACCTCCGGGACTACCCAGAGAAGTATCTGTTCCTGATCCACTGTGAGGGCACACGGTTCACAGAGAAGAAACACCAAATCAGCATGCAGGTGGCCCAAGCCAAGGGGCTGCCCAGCCTCAAACACCACCTGCTGCCGCGCACCAAAGGCTTTGCTATTACTGTGAAGTGCTTGCGAGATGTTGTCCCAGCTGTATATGACTGTACACTCAATTTCAGAAACAATGAAAACCCAACACTGCTGGGAGTCTTAAATGGAAAGAAATATCACGCTGACTGCTACGTTCGGAGGATCCCCATGGAGGACATTCCGGAGGATGAGGACAAGTGCTCTGCCTGGTTACACAAGCTCTACCAGGAGAAGGATGCCTTTCAGGAGGAATACTACAGGACAGGGGTCTTCCCAGAGACTCCCTGGGTTCCCCCACGGCGGCCCTGGTCTCTGGTCAACTGGTTGTTCTGGGCATCGCTGCTGCTCTACCCTTTCTTCCAGTTCCTAGTTAGCATGGTCAGCAGCGGTTCCTCGGTGACGCTGGCCAGCTTGGTCCTCATCTTCTGTATGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGCTGCTCTACCCTTTCT
59.75
CGAAGTACCACATCCAGCCA
59.75
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGCTGCTCTACCCTTTCT
59.75
ACGAAGTACCACATCCAGCC
59.75
163
PCR template sequence:
GCATCGCTGCTGCTCTACCCTTTCTTCCAGTTCCTAGTTAGCATGGTCAGCAGCGGTTCCTCGGTGACGCTGGCCAGCTTGGTCCTCATCTTCTGTATGGAACTCCAAAGTCCTGGCCAAGAAAGAACTGGCTTATGTCCCAATCATTGGCTGGATGTGGTACTTCGTGGAAATGATCTTTTGCACACGCAAGTGGGAGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(2), mmu-miR-669d-5p(2), mmu-miR-27a-3p(1), mmu-miR-7b-5p(1), mmu-miR-7a-5p(1), mmu-miR-339-5p(1), mmu-miR-214-3p(1), mmu-miR-128-3p(1), mmu-miR-503-5p(1), mmu-miR-499-5p(1), mmu-miR-207(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATCTTCTGTATGGAACTCCAAAGTCC
siRNA sets
ACTTTGGAGTTCCATACAG, CTTTGGAGTTCCATACAGA, TTTGGAGTTCCATACAGAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAGPAT4_694_ORF_1
0.9607
0.239541431
0.967721758
819
ORF sequence:
ATGTGGTACTTCGTGGAAATGATCTTTTGCACACGCAAGTGGGAGCAAGATCGGCAGACGGTTGCCAAGAGCCTGCTGCACCTCCGGGACTACCCAGAGAAGTATCTGTTCCTGATCCACTGTGAGGGCACACGGTTCACAGAGAAGAAACACCAAATCAGCATGCAGGTGGCCCAAGCCAAGGGGCTGCCCAGCCTCAAACACCACCTGCTGCCGCGCACCAAAGGCTTTGCTATTACTGTGAAGTGCTTGCGAGATGTTGTCCCAGCTGTATATGACTGTACACTCAATTTCAGAAACAATGAAAACCCAACACTGCTGGGAGTCTTAAATGGAAAGAAATATCACGCTGACTGCTACGTTCGGAGGATCCCCATGGAGGACATTCCGGAGGATGAGGACAAGTGCTCTGCCTGGTTACACAAGCTCTACCAGGAGAAGGATGCCTTTCAGGAGGAATACTACAGGACAGGGGTCTTCCCAGAGACTCCCTGGGTTCCCCCACGGCGGCCCTGGTCTCTGGTCAACTGGTTGTTCTGGGCATCGCTGCTGCTCTACCCTTTCTTCCAGTTCCTAGTTAGCATGGTCAGCAGCGGTTCCTCGGTGACGCTGGCCAGCTTGGTCCTCATCTTCTGTATGGAACTCCAAAGTCCTGGCCAAGAAAGAACTGGCTTATGTCCCAATCATTGGCTGGATGTGGTACTTCGTGGAAATGATCTTTTGCACACGCAAGTGGGAGCAAGATCGGCAGACGGTTGCCAAGAGCCTGCTGCACCTCCGGGACTACCCAGAGAAGTATCTGTTCCTGATCCACTGTGA
Peptide sequence:
MWYFVEMIFCTRKWEQDRQTVAKSLLHLRDYPEKYLFLIHCEGTRFTEKKHQISMQVAQAKGLPSLKHHLLPRTKGFAITVKCLRDVVPAVYDCTLNFRNNENPTLLGVLNGKKYHADCYVRRIPMEDIPEDEDKCSAWLHKLYQEKDAFQEEYYRTGVFPETPWVPPRRPWSLVNWLFWASLLLYPFFQFLVSMVSSGSSVTLASLVLIFCMELQSPGQERTGLCPNHWLDVVLRGNDLLHTQVGARSADGCQEPAAPPGLPREVSVPDPL
IRESfinder result
IRESfinder score
0.407317518
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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