top of page
mmu_circAbca3_672
Basic information of circular RNA
PanCircBase ID:
mmu_circAbca3_672
mm39_Chr. Position ID:
chr17|24593217|24596833|+
Gene name:
Abca3
Transcript:
ENSMUST00000133816.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
7,8,9,10
Exon/intron offsets:
0,2120,2421,3442
Genomic length:
3616
Exon/intron sizes in nt:
2,60,11,71,21,174
Flanking exon/introns:
chr17:24585907-24593217|chr17:24596833-24600872
Splice length:
672
Other database IDs:
CIRCpedia: MMU_CIRCpedia_227778, circAtlas: mmu-Abca3_0004
Human Ortholog IDs:
Mature spliced Sequence:
GATACATTCGGGAAGGCTTCCTGGCCATGCAACATGCTGTAGACAAAGCCATCATGCGTTACCATGCCAACACCTCTGCACAGCAGCTGTTCCAGAAGCTCATGGTGATCACCAAAAGGTTCCCGTTCCCACCATACATCTCAGATCCATTCCTCATTGCCATCCAGTACCAGCTTCCTCTGCTGCTCATGCTGAGTTTCACCTACACCTCCCTCACCATCATCCGGGCTGTGGTGCAGGAGAAGGAGAAAAAACTAAAGGAGTACATGCGCATGATGGGGCTTAACAGCTGGCTACACTGGAGCGCTTGGTTCCTCATGTTCTTCCTATTCTTCCTCATCGTGGTCTCCTTCATGACCCTCCTGTTCTGTGTCAAAGTGAAGAAGGACATAGCAGTCCTTTCCAACAGCGACCCCTCCCTGGTCCTGGCGTTCCTGCTGTGTTTTGCAATCTCCTCCATTTCCTTCAGCTTCATGGTCAGCACCTTCTTCAGTAAAGCCAACATAGCAGCAGCCGTGGGTGGCTTCCTGTACTTCTTCACCTATACCCCCTACTTTTTCGTGGCTCCTCGGTACAACTGGATGACACTGAGTCAAAAGCTCTTGTCCTGTCTCCTATCTAATGTTGCCATGGCAATGGGAGCCCAGCTCATAGGAAAATTCGAAGCCAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCTCTTGTCCTGTCTCCT
57.98
GGCATGGTAACGCATGATGG
59.69
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCTCTTGTCCTGTCTCCT
57.98
GCATGGTAACGCATGATGGC
60.32
143
PCR template sequence:
TACAACTGGATGACACTGAGTCAAAAGCTCTTGTCCTGTCTCCTATCTAATGTTGCCATGGCAATGGGAGCCCAGCTCATAGGAAAATTCGAAGCCAAAGGATACATTCGGGAAGGCTTCCTGGCCATGCAACATGCTGTAGACAAAGCCATCATGCGTTACCATGCCAACACCTCTGCACAGCAGCTGTTCCAGAAGCT
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-199a-5p(1), mmu-miR-135a-5p(1), mmu-miR-298-5p(1), mmu-miR-214-3p(1), mmu-miR-483-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
TTCGAAGCCAAAGGATACATTCGGGA
siRNA sets
AATGTATCCTTTGGCTTCG,ATGTATCCTTTGGCTTCGA,GAATGTATCCTTTGGCTTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCABCA3_672_ORF_1
1.2609
0.363290268
0.999684032
1317
ORF sequence:
ATGCAACATGCTGTAGACAAAGCCATCATGCGTTACCATGCCAACACCTCTGCACAGCAGCTGTTCCAGAAGCTCATGGTGATCACCAAAAGGTTCCCGTTCCCACCATACATCTCAGATCCATTCCTCATTGCCATCCAGTACCAGCTTCCTCTGCTGCTCATGCTGAGTTTCACCTACACCTCCCTCACCATCATCCGGGCTGTGGTGCAGGAGAAGGAGAAAAAACTAAAGGAGTACATGCGCATGATGGGGCTTAACAGCTGGCTACACTGGAGCGCTTGGTTCCTCATGTTCTTCCTATTCTTCCTCATCGTGGTCTCCTTCATGACCCTCCTGTTCTGTGTCAAAGTGAAGAAGGACATAGCAGTCCTTTCCAACAGCGACCCCTCCCTGGTCCTGGCGTTCCTGCTGTGTTTTGCAATCTCCTCCATTTCCTTCAGCTTCATGGTCAGCACCTTCTTCAGTAAAGCCAACATAGCAGCAGCCGTGGGTGGCTTCCTGTACTTCTTCACCTATACCCCCTACTTTTTCGTGGCTCCTCGGTACAACTGGATGACACTGAGTCAAAAGCTCTTGTCCTGTCTCCTATCTAATGTTGCCATGGCAATGGGAGCCCAGCTCATAGGAAAATTCGAAGCCAAAGGATACATTCGGGAAGGCTTCCTGGCCATGCAACATGCTGTAGACAAAGCCATCATGCGTTACCATGCCAACACCTCTGCACAGCAGCTGTTCCAGAAGCTCATGGTGATCACCAAAAGGTTCCCGTTCCCACCATACATCTCAGATCCATTCCTCATTGCCATCCAGTACCAGCTTCCTCTGCTGCTCATGCTGAGTTTCACCTACACCTCCCTCACCATCATCCGGGCTGTGGTGCAGGAGAAGGAGAAAAAACTAAAGGAGTACATGCGCATGATGGGGCTTAACAGCTGGCTACACTGGAGCGCTTGGTTCCTCATGTTCTTCCTATTCTTCCTCATCGTGGTCTCCTTCATGACCCTCCTGTTCTGTGTCAAAGTGAAGAAGGACATAGCAGTCCTTTCCAACAGCGACCCCTCCCTGGTCCTGGCGTTCCTGCTGTGTTTTGCAATCTCCTCCATTTCCTTCAGCTTCATGGTCAGCACCTTCTTCAGTAAAGCCAACATAGCAGCAGCCGTGGGTGGCTTCCTGTACTTCTTCACCTATACCCCCTACTTTTTCGTGGCTCCTCGGTACAACTGGATGACACTGAGTCAAAAGCTCTTGTCCTGTCTCCTATCTAATGTTGCCATGGCAATGGGAGCCCAGCTCATAGGAAAATTCGAAGCCAAA
Peptide sequence:
MQHAVDKAIMRYHANTSAQQLFQKLMVITKRFPFPPYISDPFLIAIQYQLPLLLMLSFTYTSLTIIRAVVQEKEKKLKEYMRMMGLNSWLHWSAWFLMFFLFFLIVVSFMTLLFCVKVKKDIAVLSNSDPSLVLAFLLCFAISSISFSFMVSTFFSKANIAAAVGGFLYFFTYTPYFFVAPRYNWMTLSQKLLSCLLSNVAMAMGAQLIGKFEAKGYIREGFLAMQHAVDKAIMRYHANTSAQQLFQKLMVITKRFPFPPYISDPFLIAIQYQLPLLLMLSFTYTSLTIIRAVVQEKEKKLKEYMRMMGLNSWLHWSAWFLMFFLFFLIVVSFMTLLFCVKVKKDIAVLSNSDPSLVLAFLLCFAISSISFSFMVSTFFSKANIAAAVGGFLYFFTYTPYFFVAPRYNWMTLSQKLLSCLLSNVAMAMGAQLIGKFEAK
IRESfinder result
IRESfinder score
0.597533792
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page