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mmu_circCdc27_362
Basic information of circular RNA
PanCircBase ID:
mmu_circCdc27_362
mm39_Chr. Position ID:
chr11|104406197|104408354|-
Gene name:
Cdc27
Transcript:
ENSMUST00000093923.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
14,13
Exon/intron offsets:
0,2004
Genomic length:
2157
Exon/intron sizes in nt:
2,09,153
Flanking exon/introns:
chr11:104403844-104406197|chr11:104408354-104411489
Splice length:
362
Other database IDs:
circAtlas: mmu-Cdc27_0013
circBase: hsa_circ_0044224, circAtlas: hsa-CDC27_0022, CIRCpedia: HSA_CIRCpedia_21121
Human Ortholog IDs:
Mature spliced Sequence:
GCTGAAAGAATATTCTCAGAGGTTAGAAGGATTGAGAGTTTCAGAGTTGAAGGAATGGAGATCTACTCTACAACACTCTGGCATCTTCAGAAAGACGTTGCTCTTTCAGTTCTTTCAAAAGATTTAACAGACATGGATAAGAATTCACCAGAGGCCTGGTGTGCTGCAGGGAATTGTTTCAGTCTACAACGAGAGCATGATATAGCAATTAAATTCTTCCAAAGAGCTATCCAGGTCGATCCAAATTACGCTTACGCCTATACTCTATTAGGACATGAGTTTGTGTTAACTGAAGAACTAGATAAAGCATTAGCATGTTTTCGAAATGCTATAAGAGTAAATCCCAGACATTACAATGCATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCATTAGCATGTTTTCGAAATGC
59.44
TCTGAAGATGCCAGAGTGTTGT
59.63
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCATTAGCATGTTTTCGAAATGC
58.19
TCTGAAGATGCCAGAGTGTTGT
59.63
147
PCR template sequence:
CTCTATTAGGACATGAGTTTGTGTTAACTGAAGAACTAGATAAAGCATTAGCATGTTTTCGAAATGCTATAAGAGTAAATCCCAGACATTACAATGCATGGCTGAAAGAATATTCTCAGAGGTTAGAAGGATTGAGAGTTTCAGAGTTGAAGGAATGGAGATCTACTCTACAACACTCTGGCATCTTCAGAAAGACGTTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-33-5p(1), mmu-miR-136-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTACAATGCATGGCTGAAAGAATAT
siRNA sets
ATATTCTTTCAGCCATGCA, ATTCTTTCAGCCATGCATT, TATTCTTTCAGCCATGCAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDC27_362_ORF_1
0.6921
-0.061514976
0.252485096
435
ORF sequence:
ATGGAGATCTACTCTACAACACTCTGGCATCTTCAGAAAGACGTTGCTCTTTCAGTTCTTTCAAAAGATTTAACAGACATGGATAAGAATTCACCAGAGGCCTGGTGTGCTGCAGGGAATTGTTTCAGTCTACAACGAGAGCATGATATAGCAATTAAATTCTTCCAAAGAGCTATCCAGGTCGATCCAAATTACGCTTACGCCTATACTCTATTAGGACATGAGTTTGTGTTAACTGAAGAACTAGATAAAGCATTAGCATGTTTTCGAAATGCTATAAGAGTAAATCCCAGACATTACAATGCATGGCTGAAAGAATATTCTCAGAGGTTAGAAGGATTGAGAGTTTCAGAGTTGAAGGAATGGAGATCTACTCTACAACACTCTGGCATCTTCAGAAAGACGTTGCTCTTTCAGTTCTTTCAAAAGATTTAA
Peptide sequence:
MEIYSTTLWHLQKDVALSVLSKDLTDMDKNSPEAWCAAGNCFSLQREHDIAIKFFQRAIQVDPNYAYAYTLLGHEFVLTEELDKALACFRNAIRVNPRHYNAWLKEYSQRLEGLRVSELKEWRSTLQHSGIFRKTLLFQFFQKI
IRESfinder result
IRESfinder score
0.806020647
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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