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mmu_circArntl2_413
Basic information of circular RNA
PanCircBase ID:
mmu_circArntl2_413
mm39_Chr. Position ID:
chr6|146722101|146724193|+
Gene name:
Arntl2
Transcript:
ENSMUST00000129788.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
7,8,9
Exon/intron offsets:
0,1306,1985
Genomic length:
2092
Exon/intron sizes in nt:
6,52,41,107
Flanking exon/introns:
chr6:146720432-146722101|chr6:146724193-146724591
Splice length:
413
Other database IDs:
circAtlas: mmu-Arntl2_0009
Human Ortholog IDs:
Mature spliced Sequence:
AATGAAGAGCTGTACCGTCCCTGTCAAAGAAGAGCAGCCATGCTCGTCCTGCTCAAAGAAGAAAGACCATAGAAAATTCCACACCGTCCATTGCACTGGATACTTGAGAAGCTGGCCTCTGAATGTTGTTGGCATGGAGAAAGAGTCGGGTGGTGGGAAGGACAGCGGTCCTCTTACCTGCCTTGTGGCTATGGGACGGTTGCATCCATACATTGTCCCTCAAAAGAGTGGCAAGATCAACGTGAGACCGGCTGAGTTCATAACTCGCTTCGCAATGAACGGGAAATTCGTCTATGTTGACCAAAGGGCAACGGCAATTTTAGGATACCTGCCTCAGGAACTTTTGGGAACTTCATGTTATGAATATTTTCATCAGGATGACCACAGTAGTTTGACTGACAAGCACAAAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCCTCAGGAACTTTTGGGA
59.15
TGCAATGGACGGTGTGGAAT
60.25
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCCTCAGGAACTTTTGGGA
59.15
TTCTTTGAGCAGGACGAGCA
59.61
144
PCR template sequence:
GCAATTTTAGGATACCTGCCTCAGGAACTTTTGGGAACTTCATGTTATGAATATTTTCATCAGGATGACCACAGTAGTTTGACTGACAAGCACAAAGCAGAATGAAGAGCTGTACCGTCCCTGTCAAAGAAGAGCAGCCATGCTCGTCCTGCTCAAAGAAGAAAGACCATAGAAAATTCCACACCGTCCATTGCACTGGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-26a-5p(1), mmu-miR-130a-3p(1), mmu-miR-26b-5p(1), mmu-miR-130b-3p(1), mmu-miR-301b-3p(1), mmu-miR-218-5p(1), mmu-miR-301a-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AAGCACAAAGCAGAATGAAGAGCTGT
siRNA sets
TCTTCATTCTGCTTTGTGC, CTCTTCATTCTGCTTTGTG, TTCATTCTGCTTTGTGCTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARNTL2_413_ORF_1
0.6713
0.094918689
0.3505139
417
ORF sequence:
ATGAAGAGCTGTACCGTCCCTGTCAAAGAAGAGCAGCCATGCTCGTCCTGCTCAAAGAAGAAAGACCATAGAAAATTCCACACCGTCCATTGCACTGGATACTTGAGAAGCTGGCCTCTGAATGTTGTTGGCATGGAGAAAGAGTCGGGTGGTGGGAAGGACAGCGGTCCTCTTACCTGCCTTGTGGCTATGGGACGGTTGCATCCATACATTGTCCCTCAAAAGAGTGGCAAGATCAACGTGAGACCGGCTGAGTTCATAACTCGCTTCGCAATGAACGGGAAATTCGTCTATGTTGACCAAAGGGCAACGGCAATTTTAGGATACCTGCCTCAGGAACTTTTGGGAACTTCATGTTATGAATATTTTCATCAGGATGACCACAGTAGTTTGACTGACAAGCACAAAGCAGAATGA
Peptide sequence:
MKSCTVPVKEEQPCSSCSKKKDHRKFHTVHCTGYLRSWPLNVVGMEKESGGGKDSGPLTCLVAMGRLHPYIVPQKSGKINVRPAEFITRFAMNGKFVYVDQRATAILGYLPQELLGTSCYEYFHQDDHSSLTDKHKAE
IRESfinder result
IRESfinder score
0.524703672
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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