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mmu_circCdc27_481
Basic information of circular RNA
PanCircBase ID:
mmu_circCdc27_481
mm39_Chr. Position ID:
chr11|104411489|104413648|-
Gene name:
Cdc27
Transcript:
ENSMUST00000093923.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
12,11,10
Exon/intron offsets:
0,717,2059
Genomic length:
2159
Exon/intron sizes in nt:
17,32,08,100
Flanking exon/introns:
chr11:104408354-104411489|chr11:104413648-104416876
Splice length:
481
Other database IDs:
circAtlas: mmu-Cdc27_0002
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
TACAACACCTCAGGTATTGAGCCCCACTATCACATCTCCCCCAAACGCATTGCCTCGGAGAAGTTCCCGCCTTTTCACTAGTGACAGTTCTACAACCAAGGAGAATAGCAAAAAGTTAAAAATGAAGTTTCCACCTAAAATCCCTAACAGAAAAACAAAAAGTAAAACTAATAAAGGAGGACTAACTCAGCCCAGCATAAACGATAGTCTGGAAATTACAAAACTGGACTCCTCTATCATTTCAGAAGGGAAAATAACCACAGTCACACCTCAGATCCAGGCATTTAACCTACAAAAGGCAGCAGCAGAAGGTTTGATGAGCCTTCTTCGTGAAATGGGAAAAGGTTATTTAGCTTTGTGTTCATACAACTGCAAAGAAGCTATCAATATTTTGAGCCATCTACCTTCTCATCACTACAGTACTGGTTGGGTCCTATGCCAGATTGGACGGGCTTATTTTGAACTTTCAGAATACATGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGGTTGGGTCCTATGCCAG
60.11
GTCACTAGTGAAAAGGCGGGA
60
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGGTTGGGTCCTATGCCAG
60.11
TGTCACTAGTGAAAAGGCGGG
60.27
145
PCR template sequence:
TATCAATATTTTGAGCCATCTACCTTCTCATCACTACAGTACTGGTTGGGTCCTATGCCAGATTGGACGGGCTTATTTTGAACTTTCAGAATACATGCAGTACAACACCTCAGGTATTGAGCCCCACTATCACATCTCCCCCAAACGCATTGCCTCGGAGAAGTTCCCGCCTTTTCACTAGTGACAGTTCTACAACCAAG
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-9-5p(1), mmu-miR-203-3p(1), mmu-miR-541-5p(1), mmu-miR-383-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAATACATGCAGTACAACACCTCAG
siRNA sets
GTTGTACTGCATGTATTCT, TGTTGTACTGCATGTATTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDC27_481_ORF_1
0.6257
0.022111588
0.303805133
441
ORF sequence:
ATGAAGTTTCCACCTAAAATCCCTAACAGAAAAACAAAAAGTAAAACTAATAAAGGAGGACTAACTCAGCCCAGCATAAACGATAGTCTGGAAATTACAAAACTGGACTCCTCTATCATTTCAGAAGGGAAAATAACCACAGTCACACCTCAGATCCAGGCATTTAACCTACAAAAGGCAGCAGCAGAAGGTTTGATGAGCCTTCTTCGTGAAATGGGAAAAGGTTATTTAGCTTTGTGTTCATACAACTGCAAAGAAGCTATCAATATTTTGAGCCATCTACCTTCTCATCACTACAGTACTGGTTGGGTCCTATGCCAGATTGGACGGGCTTATTTTGAACTTTCAGAATACATGCAGTACAACACCTCAGGTATTGAGCCCCACTATCACATCTCCCCCAAACGCATTGCCTCGGAGAAGTTCCCGCCTTTTCACTAG
Peptide sequence:
MKFPPKIPNRKTKSKTNKGGLTQPSINDSLEITKLDSSIISEGKITTVTPQIQAFNLQKAAAEGLMSLLREMGKGYLALCSYNCKEAINILSHLPSHHYSTGWVLCQIGRAYFELSEYMQYNTSGIEPHYHISPKRIASEKFPPFH
IRESfinder result
IRESfinder score
0.770906094
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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