top of page
mmu_circApc_550
Basic information of circular RNA
PanCircBase ID:
mmu_circApc_550
mm39_Chr. Position ID:
chr18|34437635|34443960|+
Gene name:
Apc
Transcript:
ENSMUST00000171187.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
10,11,12,13
Exon/intron offsets:
0,983,1680,6110
Genomic length:
6325
Exon/intron sizes in nt:
140,78,117,215
Flanking exon/introns:
chr18:34433114-34437635|chr18:34443960-34445057
Splice length:
550
Other database IDs:
circBase: hsa_circ_0073604
Human Ortholog IDs:
Mature spliced Sequence:
GGGGACTGCAGGCCATTGCAGAGTTATTGCAGGTGGACTGTGAGATGTATGGGCTTACTAATGACCACTACAGTGTTACTTTAAGACGGTATGCTGGAATGGCTTTGACAAACTTGACCTTTGGAGATGTTGCCAACAAGGCTACGCTGTGTTCTATGAAAGGCTGCATGAGAGCACTTGTGGCCCAGTTAAAATCTGAGAGTGAAGACTTACAGCAGGTTATTGCAAGTGTTTTGAGGAATTTGTCTTGGCGAGCAGATGTAAATAGCAAAAAGACGTTGAGAGAAGTTGGAAGTGTGAAAGCATTGATGGAATGTGCTTTGGAAGTTAAAAAGGAATCAACCCTCAAAAGCGTTTTGAGTGCCTTATGGAACCTGTCTGCACACTGCACTGAGAATAAGGCTGACATCTGTGCTGTGGATGGAGCACTGGCATTTCTGGTTGGCACCCTCACTTACCGGAGCCAGACAAATACTTTAGCCATTATTGAAAGTGGAGGTGGGATATTACGGAATGTGTCCAGCTTGATAGCTACAAACGAAGACCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CACTTACCGGAGCCAGACAA
59.68
CATCTCACAGTCCACCTGCA
59.68
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CACTTACCGGAGCCAGACAA
59.68
ACATCTCACAGTCCACCTGC
59.68
147
PCR template sequence:
TCACTTACCGGAGCCAGACAAATACTTTAGCCATTATTGAAAGTGGAGGTGGGATATTACGGAATGTGTCCAGCTTGATAGCTACAAACGAAGACCACAGGGGGACTGCAGGCCATTGCAGAGTTATTGCAGGTGGACTGTGAGATGTATGGGCTTACTAATGACCACTACAGTGTTACTTTAAGACGGTATGCTGGAAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-93-5p(1), mmu-miR-149-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACGAAGACCACAGGGGGACTGCAGGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAPC_550_ORF_1
0.8772
0.034718007
0.614474639
549
ORF sequence:
ATGTATGGGCTTACTAATGACCACTACAGTGTTACTTTAAGACGGTATGCTGGAATGGCTTTGACAAACTTGACCTTTGGAGATGTTGCCAACAAGGCTACGCTGTGTTCTATGAAAGGCTGCATGAGAGCACTTGTGGCCCAGTTAAAATCTGAGAGTGAAGACTTACAGCAGGTTATTGCAAGTGTTTTGAGGAATTTGTCTTGGCGAGCAGATGTAAATAGCAAAAAGACGTTGAGAGAAGTTGGAAGTGTGAAAGCATTGATGGAATGTGCTTTGGAAGTTAAAAAGGAATCAACCCTCAAAAGCGTTTTGAGTGCCTTATGGAACCTGTCTGCACACTGCACTGAGAATAAGGCTGACATCTGTGCTGTGGATGGAGCACTGGCATTTCTGGTTGGCACCCTCACTTACCGGAGCCAGACAAATACTTTAGCCATTATTGAAAGTGGAGGTGGGATATTACGGAATGTGTCCAGCTTGATAGCTACAAACGAAGACCACAGGGGGACTGCAGGCCATTGCAGAGTTATTGCAGGTGGACTGTGA
Peptide sequence:
MYGLTNDHYSVTLRRYAGMALTNLTFGDVANKATLCSMKGCMRALVAQLKSESEDLQQVIASVLRNLSWRADVNSKKTLREVGSVKALMECALEVKKESTLKSVLSALWNLSAHCTENKADICAVDGALAFLVGTLTYRSQTNTLAIIESGGGILRNVSSLIATNEDHRGTAGHCRVIAGGL
IRESfinder result
IRESfinder score
0.557112646
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page