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mmu_circRad23b_751
Basic information of circular RNA
PanCircBase ID:
mmu_circRad23b_751
mm39_Chr. Position ID:
chr4|55366776|55382615|+
Gene name:
Rad23b
Transcript:
ENSMUST00000030134.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
2,3,4,5,6,7
Exon/intron offsets:
0,1268,3427,11457,14212,15703
Genomic length:
15839
Exon/intron sizes in nt:
82,80,26,95,61,28,136
Flanking exon/introns:
chr4:55350427-55366776|chr4:55382615-55383586
Splice length:
751
Other database IDs:
circBase: hsa_circ_0087856, circAtlas: hsa-RAD23B_0036
Human Ortholog IDs:
Mature spliced Sequence:
GTAAAGGCATTGAAAGAGAAGATTGAATCTGAAAAGGGGAAAGATGCCTTTCCGGTAGCAGGTCAGAAGTTAATTTATGCAGGCAAAATCCTCAGTGATGATACTGCTCTCAAAGAATATAAAATTGATGAGAAAAACTTTGTGGTGGTTATGGTGACAAAACCCAAAGCAGTGACCACAGCAGTGCCAGCTACAACCCAGCCATCAAGTACTCCCAGCCCCACTGCAGTCAGTTCTTCCCCAGCAGTGGCTGCGGCCCAGGCTCCAGCTCCCACCCCTGCTCTGCCTCCCACTTCCACTCCTGCCTCCACTGCTCCAGCCTCCACTACAGCCTCTTCTGAACCCGCACCTGCTGGTGCCACTCAGCCTGAGAAACCTGCAGAAAAGCCAGCCCAGACACCAGTGCTTACTAGCCCAGCACCAGCTGACAGTACACCAGGAGATTCTTCCCGGTCAAATCTTTTTGAAGATGCAACAAGTGCCCTTGTGACAGGTCAGTCTTATGAGAATATGGTAACTGAGATCATGTCAATGGGCTATGAACGAGAACAAGTAATTGCAGCCCTGAGAGCCAGCTTCAACAACCCTGACAGAGCTGTGGAATATCTTCTAATGGGAATCCCTGGAGATAGAGAAAGTCAGGCTGTGGTTGACCCTCCTCCTCAGGCTGTGAGTACTGGAACTCCTCAGTCTCCAGCAGTAGCTGCAGCTGCAGCAACCACGACAGCAACTACAACAACCACTTCTGGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTCCTCAGTCTCCAGCAGT
59.89
ACTTCTGACCTGCTACCGGA
60.25
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTCCTCAGTCTCCAGCAGT
59.89
AACTTCTGACCTGCTACCGG
59.39
141
PCR template sequence:
GACCCTCCTCCTCAGGCTGTGAGTACTGGAACTCCTCAGTCTCCAGCAGTAGCTGCAGCTGCAGCAACCACGACAGCAACTACAACAACCACTTCTGGAGGTAAAGGCATTGAAAGAGAAGATTGAATCTGAAAAGGGGAAAGATGCCTTTCCGGTAGCAGGTCAGAAGTTAATTTATGCAGGCAAAATCCTCAGTGATG
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-146a-5p(1), mmu-miR-709(1), mmu-miR-138-5p(1), mmu-miR-149-5p(1), mmu-miR-370-3p(1), mmu-miR-541-5p(1), mmu-miR-705(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACCACTTCTGGAGGTAAAGGCATTGA
siRNA sets
TCAATGCCTTTACCTCCAG, AATGCCTTTACCTCCAGAA, CCTTTACCTCCAGAAGTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAD23B_751_ORF_1
1.288
0.15993053
0.908508065
627
ORF sequence:
ATGGTGACAAAACCCAAAGCAGTGACCACAGCAGTGCCAGCTACAACCCAGCCATCAAGTACTCCCAGCCCCACTGCAGTCAGTTCTTCCCCAGCAGTGGCTGCGGCCCAGGCTCCAGCTCCCACCCCTGCTCTGCCTCCCACTTCCACTCCTGCCTCCACTGCTCCAGCCTCCACTACAGCCTCTTCTGAACCCGCACCTGCTGGTGCCACTCAGCCTGAGAAACCTGCAGAAAAGCCAGCCCAGACACCAGTGCTTACTAGCCCAGCACCAGCTGACAGTACACCAGGAGATTCTTCCCGGTCAAATCTTTTTGAAGATGCAACAAGTGCCCTTGTGACAGGTCAGTCTTATGAGAATATGGTAACTGAGATCATGTCAATGGGCTATGAACGAGAACAAGTAATTGCAGCCCTGAGAGCCAGCTTCAACAACCCTGACAGAGCTGTGGAATATCTTCTAATGGGAATCCCTGGAGATAGAGAAAGTCAGGCTGTGGTTGACCCTCCTCCTCAGGCTGTGAGTACTGGAACTCCTCAGTCTCCAGCAGTAGCTGCAGCTGCAGCAACCACGACAGCAACTACAACAACCACTTCTGGAGGTAAAGGCATTGAAAGAGAAGATTGA
Peptide sequence:
MVTKPKAVTTAVPATTQPSSTPSPTAVSSSPAVAAAQAPAPTPALPPTSTPASTAPASTTASSEPAPAGATQPEKPAEKPAQTPVLTSPAPADSTPGDSSRSNLFEDATSALVTGQSYENMVTEIMSMGYEREQVIAALRASFNNPDRAVEYLLMGIPGDRESQAVVDPPPQAVSTGTPQSPAVAAAAATTTATTTTTSGGKGIERED
IRESfinder result
IRESfinder score
0.582448944
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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