top of page
mmu_circAtpaf1_418
Basic information of circular RNA
PanCircBase ID:
mmu_circAtpaf1_418
mm39_Chr. Position ID:
chr4|115645458|115655258|+
Gene name:
Atpaf1
Transcript:
ENSMUST00000176047.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
2,3,4,5,6,7
Exon/intron offsets:
0,2319,2961,7142,8493,9704
Genomic length:
9800
Exon/intron sizes in nt:
109,51,63,51,48,96
Flanking exon/introns:
chr4:115642501-115645458|chr4:115655258-115657514
Splice length:
418
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTCTGACCCAGCGGCCTTTGAGTCCCGCCTGGAGAAGCGCAGTGAGTTCCGAAAGCAGCCAGTGGGGCACTCCAAACAAAGTGATTTTATCAAGTGTATGGAGCAGAAGACAGATGCCTTGGGGAAACAGCCTGTGAGCAAAGGATTCACTAAGGACAAGACTCTCAGTTCAGTCTTCAACGTTGAGATGGTGAAAGACAAAACTGCGGAGGAAATAAAACAGATTTGGCAGCAGTATTTTTCAGCAAAAGACACAGTCTACGCAGTTATTCCTAAAGAGAAGTTTGATTTGATCTGGAACAGGGCTCAGTCCTGCCCAACATTTCTTTGTGCACTACCAAGAAGGGATGGTTATGAGTTCTTTGTAGGACAATGGACAGGTACAGAGCTCCACTTCACTGCACTTATAAATATTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCACTACCAAGAAGGGATGG
59.72
ACTTTGTTTGGAGTGCCCCA
60.03
170
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGCACTACCAAGAAGGGA
58.57
ACTTTGTTTGGAGTGCCCCA
60.03
172
PCR template sequence:
AACATTTCTTTGTGCACTACCAAGAAGGGATGGTTATGAGTTCTTTGTAGGACAATGGACAGGTACAGAGCTCCACTTCACTGCACTTATAAATATTCAGGTCTGACCCAGCGGCCTTTGAGTCCCGCCTGGAGAAGCGCAGTGAGTTCCGAAAGCAGCCAGTGGGGCACTCCAAACAAAGTGATTTTATCAAGTGTATG
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-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-200c-3p(1), mmu-miR-207(1), mmu-miR-3087-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
TATAAATATTCAGGTCTGACCCAGCG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATPAF1_418_ORF_1
0.9262
0.063082618
0.284428313
327
ORF sequence:
ATGGAGCAGAAGACAGATGCCTTGGGGAAACAGCCTGTGAGCAAAGGATTCACTAAGGACAAGACTCTCAGTTCAGTCTTCAACGTTGAGATGGTGAAAGACAAAACTGCGGAGGAAATAAAACAGATTTGGCAGCAGTATTTTTCAGCAAAAGACACAGTCTACGCAGTTATTCCTAAAGAGAAGTTTGATTTGATCTGGAACAGGGCTCAGTCCTGCCCAACATTTCTTTGTGCACTACCAAGAAGGGATGGTTATGAGTTCTTTGTAGGACAATGGACAGGTACAGAGCTCCACTTCACTGCACTTATAAATATTCAGGTCTGA
Peptide sequence:
MEQKTDALGKQPVSKGFTKDKTLSSVFNVEMVKDKTAEEIKQIWQQYFSAKDTVYAVIPKEKFDLIWNRAQSCPTFLCALPRRDGYEFFVGQWTGTELHFTALINIQV
IRESfinder result
IRESfinder score
0.685708162
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page