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mmu_circCerkl_657
Basic information of circular RNA
PanCircBase ID:
mmu_circCerkl_657
mm39_Chr. Position ID:
chr2|79173560|79223529|-
Gene name:
Cerkl
Transcript:
ENSMUST00000143974.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,11705,18107,25463,49726
Genomic length:
49969
Exon/intron sizes in nt:
75,14,36,41,32,243
Flanking exon/introns:
chr2:79172824-79173560|chr2:79223529-79259045
Splice length:
657
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGGCACCAGGCATGATCTGCTGAGCAAAGAAGAGTCCCTAGAACTTGAAGACATCTTCTCAGTGAAGCTGAAGCGGCGTTGCTGGGCCAAGCATCCAGGCAGAGACACACTGCTGGGCATAACGCTTTTCATCTGCTTGAAGGAGCAACGGAACAAACTAAAGGACTCCACGCTGGATCTTATTAACTTCAGTGAAGACCACTGTGACATATGGTTTAGACAGTTCAAGAAAATCTTGGATGGTTTCACAAGCAGGCCCAAGGCTCTCAAGATCCTCCTCAACCCCCAGAGTCACAGAAAGGAGTCTGTCCACGTCTATTACGAGAAGGTGGAGCCTCTGCTGAAGCTTGCGGGCATAGAGACTGATGTGACAATAACAGAATATGAAGGGCATGCCCTGTCTCTGCTTGACGAATGTGAACTCCGAGGATTTGATGGTGTTGTCTGTGTTGGTGGAGATGGATCTGCGAGTGAGGCCGCCCGCGCTTTGCTCCTCAGAGCTCAGAAGAACGCGGGAGTGGAGATGGACTGCATCCCGACTCTCGTTGGAGCAGAGCTTCCTCTTGGCTTCATTCCAGCAGGATCTACTAACGCACTGGCACATTCTCTCTTTGGAACTCCTCACGTGGTGACTGCAACCATGCATATTATACTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AACGCACTGGCACATTCTCT
60.25
CAACGCCGCTTCAGCTTC
59.83
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AACGCACTGGCACATTCTCT
60.25
AACGCCGCTTCAGCTTCA
60.28
148
PCR template sequence:
CTTCCTCTTGGCTTCATTCCAGCAGGATCTACTAACGCACTGGCACATTCTCTCTTTGGAACTCCTCACGTGGTGACTGCAACCATGCATATTATACTAGGTGGCACCAGGCATGATCTGCTGAGCAAAGAAGAGTCCCTAGAACTTGAAGACATCTTCTCAGTGAAGCTGAAGCGGCGTTGCTGGGCCAAGCATCCAGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-298-5p(1), mmu-miR-23a-3p(1), mmu-miR-127-5p(1), mmu-miR-370-3p(1), mmu-miR-541-5p(1), mmu-miR-452-3p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CATATTATACTAGGTGGCACCAGGCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCERKL_657_ORF_1
1.0753
0.208223028
0.963415853
789
ORF sequence:
ATGGACTGCATCCCGACTCTCGTTGGAGCAGAGCTTCCTCTTGGCTTCATTCCAGCAGGATCTACTAACGCACTGGCACATTCTCTCTTTGGAACTCCTCACGTGGTGACTGCAACCATGCATATTATACTAGGTGGCACCAGGCATGATCTGCTGAGCAAAGAAGAGTCCCTAGAACTTGAAGACATCTTCTCAGTGAAGCTGAAGCGGCGTTGCTGGGCCAAGCATCCAGGCAGAGACACACTGCTGGGCATAACGCTTTTCATCTGCTTGAAGGAGCAACGGAACAAACTAAAGGACTCCACGCTGGATCTTATTAACTTCAGTGAAGACCACTGTGACATATGGTTTAGACAGTTCAAGAAAATCTTGGATGGTTTCACAAGCAGGCCCAAGGCTCTCAAGATCCTCCTCAACCCCCAGAGTCACAGAAAGGAGTCTGTCCACGTCTATTACGAGAAGGTGGAGCCTCTGCTGAAGCTTGCGGGCATAGAGACTGATGTGACAATAACAGAATATGAAGGGCATGCCCTGTCTCTGCTTGACGAATGTGAACTCCGAGGATTTGATGGTGTTGTCTGTGTTGGTGGAGATGGATCTGCGAGTGAGGCCGCCCGCGCTTTGCTCCTCAGAGCTCAGAAGAACGCGGGAGTGGAGATGGACTGCATCCCGACTCTCGTTGGAGCAGAGCTTCCTCTTGGCTTCATTCCAGCAGGATCTACTAACGCACTGGCACATTCTCTCTTTGGAACTCCTCACGTGGTGACTGCAACCATGCATATTATACTA
Peptide sequence:
MDCIPTLVGAELPLGFIPAGSTNALAHSLFGTPHVVTATMHIILGGTRHDLLSKEESLELEDIFSVKLKRRCWAKHPGRDTLLGITLFICLKEQRNKLKDSTLDLINFSEDHCDIWFRQFKKILDGFTSRPKALKILLNPQSHRKESVHVYYEKVEPLLKLAGIETDVTITEYEGHALSLLDECELRGFDGVVCVGGDGSASEAARALLLRAQKNAGVEMDCIPTLVGAELPLGFIPAGSTNALAHSLFGTPHVVTATMHIIL
IRESfinder result
IRESfinder score
0.524692124
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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