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mmu_circAff4_825
Basic information of circular RNA
PanCircBase ID:
mmu_circAff4_825
mm39_Chr. Position ID:
chr11|53263104|53266460|+
Gene name:
Aff4
Transcript:
ENSMUST00000060945.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,4
Exon/intron offsets:
0,3311
Genomic length:
3356
Exon/intron sizes in nt:
780,45
Flanking exon/introns:
chr11:53259613-53263104|chr11:53266460-53271412
Splice length:
825
Other database IDs:
circAtlas: mmu-Aff4_0003
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_375799
Human Ortholog IDs:
Mature spliced Sequence:
ACTAGCAAAGAAGATAAGTTATCAAGTCGGATTCAGAGCATGCTTGGAAACTACGATGAAATGAAGGATTACATAGGAGACAGATCGATACCAAAGCTTGTTGCAATTCCCAAGCCTGCAGTACCAACGACCACAGACGAGAAAGCAAACCCAAATTTTTTTGAGCAGAGACATGGAGGATCTCATCAGAGTAGCAAATGGACTCCTGTAGGCCCCGCCCCCAGCACCTCTCAGTCTCAGAAACGCTCCTCTGCCCTGCAGAGTGGACACAGCAGCCAACGGAGTGGTGCAGGAGGGAGTGGCGCCAGCAGCAGTGGCCAGAGGCATGACCGTGACTCCTACAGCAGTAGCAGGAAAAAAGGCCAGCACGGCTCAGAGCACTCCAAATCTCGATCCTCAAGCCCTGGAAAACCCCAGGCTGTTTCTTCATTAAGTTCTAGTCATTCCAGGTCTCATGGGAATGATCACCATAGCAAGGAACATCAGCGCTCCAAATCACCTCGGGACCCTGATGCCAACTGGGATTCTCCTTCCCGCGGACCTTTTTCAAGTGGGCAACATTCAAGTCAGTCTTTCCCACCTTCTTTGATGTCAAAATCTAGTTCAATGTTACAGAAACCCACTGCCTATGTACGGCCCATGGATGGACAGGAGTCTGTGGAACCAAAGCTGTCCTCTGAGCACTACAGCAGCCAGTCTCATGGTAATAGCATGACTGAGCTGAAGCCCAGCAGCAAAGCACATCTCACCAAGCTGAAAATTCCTTCCCGACCTTTGGATGCATCGGTTTCTGGTGATGTAAGCTGTGTAGATGAAATACTTAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGCAAAGCACATCTCACC
60.11
CCAAGCATGCTCTGAATCCG
59.34
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGCAGCAAAGCACATCTC
59.83
CCAAGCATGCTCTGAATCCG
59.34
145
PCR template sequence:
GCCCAGCAGCAAAGCACATCTCACCAAGCTGAAAATTCCTTCCCGACCTTTGGATGCATCGGTTTCTGGTGATGTAAGCTGTGTAGATGAAATACTTAAAACTAGCAAAGAAGATAAGTTATCAAGTCGGATTCAGAGCATGCTTGGAAACTACGATGAAATGAAGGATTACATAGGAGACAGATCGATACCAAAGCTTG
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(2), mmu-miR-205-5p(1), mmu-miR-298-5p(1), mmu-miR-216a-5p(1), mmu-miR-136-5p(1), mmu-miR-541-5p(1), mmu-miR-3470b(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
TGAAATACTTAAAACTAGCAAAGAAG
siRNA sets
TTCTTTGCTAGTTTTAAGT, CTTCTTTGCTAGTTTTAAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAFF4_825_ORF_1
0.8599
0.131719672
0.99979277
1611
ORF sequence:
ATGCTTGGAAACTACGATGAAATGAAGGATTACATAGGAGACAGATCGATACCAAAGCTTGTTGCAATTCCCAAGCCTGCAGTACCAACGACCACAGACGAGAAAGCAAACCCAAATTTTTTTGAGCAGAGACATGGAGGATCTCATCAGAGTAGCAAATGGACTCCTGTAGGCCCCGCCCCCAGCACCTCTCAGTCTCAGAAACGCTCCTCTGCCCTGCAGAGTGGACACAGCAGCCAACGGAGTGGTGCAGGAGGGAGTGGCGCCAGCAGCAGTGGCCAGAGGCATGACCGTGACTCCTACAGCAGTAGCAGGAAAAAAGGCCAGCACGGCTCAGAGCACTCCAAATCTCGATCCTCAAGCCCTGGAAAACCCCAGGCTGTTTCTTCATTAAGTTCTAGTCATTCCAGGTCTCATGGGAATGATCACCATAGCAAGGAACATCAGCGCTCCAAATCACCTCGGGACCCTGATGCCAACTGGGATTCTCCTTCCCGCGGACCTTTTTCAAGTGGGCAACATTCAAGTCAGTCTTTCCCACCTTCTTTGATGTCAAAATCTAGTTCAATGTTACAGAAACCCACTGCCTATGTACGGCCCATGGATGGACAGGAGTCTGTGGAACCAAAGCTGTCCTCTGAGCACTACAGCAGCCAGTCTCATGGTAATAGCATGACTGAGCTGAAGCCCAGCAGCAAAGCACATCTCACCAAGCTGAAAATTCCTTCCCGACCTTTGGATGCATCGGTTTCTGGTGATGTAAGCTGTGTAGATGAAATACTTAAAACTAGCAAAGAAGATAAGTTATCAAGTCGGATTCAGAGCATGCTTGGAAACTACGATGAAATGAAGGATTACATAGGAGACAGATCGATACCAAAGCTTGTTGCAATTCCCAAGCCTGCAGTACCAACGACCACAGACGAGAAAGCAAACCCAAATTTTTTTGAGCAGAGACATGGAGGATCTCATCAGAGTAGCAAATGGACTCCTGTAGGCCCCGCCCCCAGCACCTCTCAGTCTCAGAAACGCTCCTCTGCCCTGCAGAGTGGACACAGCAGCCAACGGAGTGGTGCAGGAGGGAGTGGCGCCAGCAGCAGTGGCCAGAGGCATGACCGTGACTCCTACAGCAGTAGCAGGAAAAAAGGCCAGCACGGCTCAGAGCACTCCAAATCTCGATCCTCAAGCCCTGGAAAACCCCAGGCTGTTTCTTCATTAAGTTCTAGTCATTCCAGGTCTCATGGGAATGATCACCATAGCAAGGAACATCAGCGCTCCAAATCACCTCGGGACCCTGATGCCAACTGGGATTCTCCTTCCCGCGGACCTTTTTCAAGTGGGCAACATTCAAGTCAGTCTTTCCCACCTTCTTTGATGTCAAAATCTAGTTCAATGTTACAGAAACCCACTGCCTATGTACGGCCCATGGATGGACAGGAGTCTGTGGAACCAAAGCTGTCCTCTGAGCACTACAGCAGCCAGTCTCATGGTAATAGCATGACTGAGCTGAAGCCCAGCAGCAAAGCACATCTCACCAAGCTGAAAATTCCTTCCCGACCTTTGGATGCATCGGTTTCTGGTGATGTAAGCTGTGTAGATGAAATACTTAAA
Peptide sequence:
MLGNYDEMKDYIGDRSIPKLVAIPKPAVPTTTDEKANPNFFEQRHGGSHQSSKWTPVGPAPSTSQSQKRSSALQSGHSSQRSGAGGSGASSSGQRHDRDSYSSSRKKGQHGSEHSKSRSSSPGKPQAVSSLSSSHSRSHGNDHHSKEHQRSKSPRDPDANWDSPSRGPFSSGQHSSQSFPPSLMSKSSSMLQKPTAYVRPMDGQESVEPKLSSEHYSSQSHGNSMTELKPSSKAHLTKLKIPSRPLDASVSGDVSCVDEILKTSKEDKLSSRIQSMLGNYDEMKDYIGDRSIPKLVAIPKPAVPTTTDEKANPNFFEQRHGGSHQSSKWTPVGPAPSTSQSQKRSSALQSGHSSQRSGAGGSGASSSGQRHDRDSYSSSRKKGQHGSEHSKSRSSSPGKPQAVSSLSSSHSRSHGNDHHSKEHQRSKSPRDPDANWDSPSRGPFSSGQHSSQSFPPSLMSKSSSMLQKPTAYVRPMDGQESVEPKLSSEHYSSQSHGNSMTELKPSSKAHLTKLKIPSRPLDASVSGDVSCVDEILK
IRESfinder result
IRESfinder score
0.510862548
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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