top of page
mmu_circAbca9_584
Basic information of circular RNA
PanCircBase ID:
mmu_circAbca9_584
mm39_Chr. Position ID:
chr11|110001112|110007976|-
Gene name:
Abca9
Transcript:
ENSMUST00000044850.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
32,31,30,29,28
Exon/intron offsets:
0,2905,3937,5157,6772
Genomic length:
6864
Exon/intron sizes in nt:
161,92,118,121,92
Flanking exon/introns:
chr11:109999722-110001112|chr11:110007976-110008906
Splice length:
584
Other database IDs:
circAtlas: mmu-Abca9_0015
Human Ortholog IDs:
Mature spliced Sequence:
CCTTACCTTCACTTTCTTCTTTTCTTTTTCATTCTGCGATGTCTGGAAAGATACCTCAGGAAGAAGTCACTGAGAGTGGACCCTGTGTTCAGAATTTCTCCGAGAAGTTGTCCTGCTGTTCCGAACCCAGAAGAGCCCGGAGAAGAGGATGAAGATGTTCAGATGGAAAGAGTGAGAACAACGGGCGCCATGGCTACCCTACAGACTGATGAGAAACCAGTCATCATTGCAAGCTGTCTGCGGAAGGAATATATAGGCAGAACGAAAAGGTGCTTTTCCAAAATGAAGAAAAAGATCGCCACGAGGAACATCTCCTTCTGTGTTAAAAAAGGTGAAGTCCTAGGGCTCTTAGGACACAATGGAGCTGGCAAAAGTACAACAATTAGCATGATAACAGGAGACACAATACCAACCGCAGGTCAGGTGTTTTTGAAAGGGAGCGGTGGGGGTGCTGCCCTCGGATTCTTGGGGTACTGCCCTCAGGAGAACGTGCTGTGGCCCAACCTGACAGTGAAGGAACACCTGGAGTTGTATGCTGCTGTGAAGGGGCTGAAGAAAAAGGATGCTGTGGTCACCATCACACG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTATGCTGCTGTGAAGGGG
60.04
ACACAGGGTCCACTCTCAGT
60.11
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTATGCTGCTGTGAAGGGG
60.04
CACAGGGTCCACTCTCAGTG
59.68
142
PCR template sequence:
AGAACGTGCTGTGGCCCAACCTGACAGTGAAGGAACACCTGGAGTTGTATGCTGCTGTGAAGGGGCTGAAGAAAAAGGATGCTGTGGTCACCATCACACGCCTTACCTTCACTTTCTTCTTTTCTTTTTCATTCTGCGATGTCTGGAAAGATACCTCAGGAAGAAGTCACTGAGAGTGGACCCTGTGTTCAGAATTTCTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-136-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
TCACCATCACACGCCTTACCTTCACT
siRNA sets
AAGGTAAGGCGTGTGATGG, AGTGAAGGTAAGGCGTGTG, AGGTAAGGCGTGTGATGGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCABCA9_584_ORF_1
0.9066
0.116793952
0.614231508
495
ORF sequence:
ATGGAAAGAGTGAGAACAACGGGCGCCATGGCTACCCTACAGACTGATGAGAAACCAGTCATCATTGCAAGCTGTCTGCGGAAGGAATATATAGGCAGAACGAAAAGGTGCTTTTCCAAAATGAAGAAAAAGATCGCCACGAGGAACATCTCCTTCTGTGTTAAAAAAGGTGAAGTCCTAGGGCTCTTAGGACACAATGGAGCTGGCAAAAGTACAACAATTAGCATGATAACAGGAGACACAATACCAACCGCAGGTCAGGTGTTTTTGAAAGGGAGCGGTGGGGGTGCTGCCCTCGGATTCTTGGGGTACTGCCCTCAGGAGAACGTGCTGTGGCCCAACCTGACAGTGAAGGAACACCTGGAGTTGTATGCTGCTGTGAAGGGGCTGAAGAAAAAGGATGCTGTGGTCACCATCACACGCCTTACCTTCACTTTCTTCTTTTCTTTTTCATTCTGCGATGTCTGGAAAGATACCTCAGGAAGAAGTCACTGA
Peptide sequence:
MERVRTTGAMATLQTDEKPVIIASCLRKEYIGRTKRCFSKMKKKIATRNISFCVKKGEVLGLLGHNGAGKSTTISMITGDTIPTAGQVFLKGSGGGAALGFLGYCPQENVLWPNLTVKEHLELYAAVKGLKKKDAVVTITRLTFTFFFSFSFCDVWKDTSGRSH
IRESfinder result
IRESfinder score
0.402425568
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page