top of page
mmu_circAff1_1153
Basic information of circular RNA
PanCircBase ID:
mmu_circAff1_1153
mm39_Chr. Position ID:
chr5|103976213|103982325|+
Gene name:
Aff1
Transcript:
ENSMUST00000054979.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
10,11
Exon/intron offsets:
0,5122
Genomic length:
6112
Exon/intron sizes in nt:
1,63,990
Flanking exon/introns:
chr5:103974046-103976213|chr5:103982325-103988921
Splice length:
1153
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CGCTCCGCAGACACTTCCCGAGCCCGTGGCCTCAGCACATTCCAGTAGTGGGGAGTCAGAGAGCAGCGAGTCAGACAGTTCCTCAGACTCTGAGAGTGAGAGCAGCTCCAGCGACAGCGAGGAGGAGGAAGAGAACGAGCCCCTGGAGACCCGGGCTCCCGAGCCCGAGCCTCCGACGACAAACAAATGGCAGCTGGACAACTGGTTGACCAAAGTCAACCAACCCTCAGTGCCCCTGGATGGCCGGGGGAGCACAGAGTCTCCACAATGGCGCCAGGAAAGTAAGGGTGTCGCTGAGGGCAGCAGTGACCAGCAGCATCCTGATTCCAAAGACCCTCTCCCAAAGAGCTCCAGCAAGACTCTCCGGGGTCCCTCTGAGGGGCCCCAGCCTGGGAAGAGGGGCTGTCCGAAATCCCCCGCTCAACAGGAACCCCCACCTCGGCAAACCGTGGGCAGCAAACAACCCAGGAAACCCGCCAAGGGCTCCGGCCAGGCAGAGCCCCAGGCCAGCTCGCAGGCAGAGAGTGAAGTAGGACCCCTTCCCTACGGCTCAAAGGAGCAGACTTCCAAAGACAGACCCAAGGTGAAGACGAAAGGCAGGCCGCGTGCCGTGGGCAGTCGGGAGCCTAAGCCAGAGGTCCCTGCGCCCACGCCTCAGGCAGCCGTGCCCAGACCGAAGCCGCCTGTGCCCACCCCCAGTGAGAAGAGGAAGCACAAGAGCTCCACGGCCCCCTCCAAGGCGCCCTCAGCCCCCCAGCCTCCGAAGGACAGTGCTGGGGACAGGAACCCAGAACACTCTGCTCTTGTCTCCTTGACTCAGAGCCAGGGTCCATCCCACAGCAGCAGGGGCAGCAGTGGCAGCGTCAGGACTAGTGGCTGCCGACAGGCTGTGATTGCCCAAGGGGACGGCTGTAAAGACAAGCTCCTGTTGCCTTTGAGAGACACCAAATTGCTCTCGCCGCTCAGGGACTCCCCACCACCGACAAGCTTGGTGGTGAAGATAACCCTAGACCTCCTCACGAGGATTCCCCAGCCTCTGGGGAAGGGGAGCCGCCCCAGGAAAGCAGAAGACAAGCAGCTGTCAGCAGGGAAGAAGCAGGACTCGGAGACCAAGAGCTGTGACAGCTCCAGCAGAGTGACCAAGAAGAGAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCAGCAGGGAAGAAGCAG
59.96
AACTGTCTGACTCGCTGCTC
60.04
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCAGCAGGGAAGAAGCAG
59.96
GAACTGTCTGACTCGCTGCT
60.04
155
PCR template sequence:
CCCCAGGAAAGCAGAAGACAAGCAGCTGTCAGCAGGGAAGAAGCAGGACTCGGAGACCAAGAGCTGTGACAGCTCCAGCAGAGTGACCAAGAAGAGAAAGCGCTCCGCAGACACTTCCCGAGCCCGTGGCCTCAGCACATTCCAGTAGTGGGGAGTCAGAGAGCAGCGAGTCAGACAGTTCCTCAGACTCTGAGAGTGAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-149-5p(1), mmu-miR-431-5p(1), mmu-miR-22-3p(1), mmu-miR-218-5p(1), mmu-miR-370-3p(1), mmu-miR-673-5p(1), mmu-miR-5101(1), mmu-miR-670-5p(1), mmu-miR-1904(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CAAGAAGAGAAAGCGCTCCGCAGACA
siRNA sets
TGTCTGCGGAGCGCTTTCT,GTCTGCGGAGCGCTTTCTC,TCTGCGGAGCGCTTTCTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.39552633
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page