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mmu_circApc_646
Basic information of circular RNA
PanCircBase ID:
mmu_circApc_646
mm39_Chr. Position ID:
chr18|34433018|34443960|+
Gene name:
Apc
Transcript:
ENSMUST00000171187.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
9,10,11,12,13
Exon/intron offsets:
0,4617,5600,6297,10727
Genomic length:
10942
Exon/intron sizes in nt:
96,14,07,81,17,215
Flanking exon/introns:
chr18:34431854-34433018|chr18:34443960-34445057
Splice length:
646
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_123628
Human Ortholog IDs:
Mature spliced Sequence:
TGCCAGCTCCTGTTGAGCATCAGATCTGTCCTGCTGTGTGTGTTCTAATGAAGCTTTCATTTGATGAAGAGCATAGGCATGCAATGAATGAACTTGGGGGACTGCAGGCCATTGCAGAGTTATTGCAGGTGGACTGTGAGATGTATGGGCTTACTAATGACCACTACAGTGTTACTTTAAGACGGTATGCTGGAATGGCTTTGACAAACTTGACCTTTGGAGATGTTGCCAACAAGGCTACGCTGTGTTCTATGAAAGGCTGCATGAGAGCACTTGTGGCCCAGTTAAAATCTGAGAGTGAAGACTTACAGCAGGTTATTGCAAGTGTTTTGAGGAATTTGTCTTGGCGAGCAGATGTAAATAGCAAAAAGACGTTGAGAGAAGTTGGAAGTGTGAAAGCATTGATGGAATGTGCTTTGGAAGTTAAAAAGGAATCAACCCTCAAAAGCGTTTTGAGTGCCTTATGGAACCTGTCTGCACACTGCACTGAGAATAAGGCTGACATCTGTGCTGTGGATGGAGCACTGGCATTTCTGGTTGGCACCCTCACTTACCGGAGCCAGACAAATACTTTAGCCATTATTGAAAGTGGAGGTGGGATATTACGGAATGTGTCCAGCTTGATAGCTACAAACGAAGACCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CACTTACCGGAGCCAGACAA
59.68
AACACACACAGCAGGACAGA
59.46
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CACTTACCGGAGCCAGACAA
59.68
AGAACACACACAGCAGGACA
59.46
145
PCR template sequence:
TCACTTACCGGAGCCAGACAAATACTTTAGCCATTATTGAAAGTGGAGGTGGGATATTACGGAATGTGTCCAGCTTGATAGCTACAAACGAAGACCACAGTGCCAGCTCCTGTTGAGCATCAGATCTGTCCTGCTGTGTGTGTTCTAATGAAGCTTTCATTTGATGAAGAGCATAGGCATGCAATGAATGAACTTGGGGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-93-5p(1), mmu-miR-181b-5p(1), mmu-miR-214-3p(1), mmu-miR-149-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACGAAGACCACAGTGCCAGCTCCTGT
siRNA sets
CAGGAGCTGGCACTGTGGT, AGGAGCTGGCACTGTGGTC, CTGGCACTGTGGTCTTCGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAPC_646_ORF_1
0.8371
0.084082608
0.743683937
615
ORF sequence:
ATGAAGCTTTCATTTGATGAAGAGCATAGGCATGCAATGAATGAACTTGGGGGACTGCAGGCCATTGCAGAGTTATTGCAGGTGGACTGTGAGATGTATGGGCTTACTAATGACCACTACAGTGTTACTTTAAGACGGTATGCTGGAATGGCTTTGACAAACTTGACCTTTGGAGATGTTGCCAACAAGGCTACGCTGTGTTCTATGAAAGGCTGCATGAGAGCACTTGTGGCCCAGTTAAAATCTGAGAGTGAAGACTTACAGCAGGTTATTGCAAGTGTTTTGAGGAATTTGTCTTGGCGAGCAGATGTAAATAGCAAAAAGACGTTGAGAGAAGTTGGAAGTGTGAAAGCATTGATGGAATGTGCTTTGGAAGTTAAAAAGGAATCAACCCTCAAAAGCGTTTTGAGTGCCTTATGGAACCTGTCTGCACACTGCACTGAGAATAAGGCTGACATCTGTGCTGTGGATGGAGCACTGGCATTTCTGGTTGGCACCCTCACTTACCGGAGCCAGACAAATACTTTAGCCATTATTGAAAGTGGAGGTGGGATATTACGGAATGTGTCCAGCTTGATAGCTACAAACGAAGACCACAGTGCCAGCTCCTGTTGA
Peptide sequence:
MKLSFDEEHRHAMNELGGLQAIAELLQVDCEMYGLTNDHYSVTLRRYAGMALTNLTFGDVANKATLCSMKGCMRALVAQLKSESEDLQQVIASVLRNLSWRADVNSKKTLREVGSVKALMECALEVKKESTLKSVLSALWNLSAHCTENKADICAVDGALAFLVGTLTYRSQTNTLAIIESGGGILRNVSSLIATNEDHSASSC
IRESfinder result
IRESfinder score
0.575869216
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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