top of page
mmu_circCdkal1_327
Basic information of circular RNA
PanCircBase ID:
mmu_circCdkal1_327
mm39_Chr. Position ID:
chr13|30030210|30038924|-
Gene name:
Cdkal1
Transcript:
ENSMUST00000140278.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
4,3,2
Exon/intron offsets:
0,3711,8670
Genomic length:
8714
Exon/intron sizes in nt:
113,170,44
Flanking exon/introns:
chr13:29961284-30030210|chr13:30038924-30039545
Splice length:
327
Other database IDs:
CIRCpedia: MMU_CIRCpedia_36257, circAtlas: mmu-Cdkal1_0011
circAtlas: hsa-CDKAL1_0018, CIRCpedia: HSA_CIRCpedia_99172
Human Ortholog IDs:
Mature spliced Sequence:
ATTCATCTTTCAAGAGGACTTGAGACCAATTTCAGAAAATCAAGATGCCTTCTGCGTCTTGTGATGTACTGCTGGATGACATAGAAGATATCATATCACAGGAAGATTCAAAGCCACAGGACAGACAGTTCTCAAGAAAGCATGTGTTTCCTAAAGTACGAAGGCGGAATACCCAAAAATATTTGCAAGAAGAGCCCAGGCCACCAAGTGACAGCACTATTCCAGGCATACAGAAAATTTGGATCCGAACATGGGGCTGCTCACATAATAATTCGGATGGAGAATACATGGCTGGACAGCTTGCTGCCTATGGCTATAAAATTACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACATGGGGCTGCTCACATAA
59.37
TCACAAGACGCAGAAGGCAT
59.96
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACATGGGGCTGCTCACATAA
59.37
ATCACAAGACGCAGAAGGCA
59.96
144
PCR template sequence:
ATACAGAAAATTTGGATCCGAACATGGGGCTGCTCACATAATAATTCGGATGGAGAATACATGGCTGGACAGCTTGCTGCCTATGGCTATAAAATTACAGATTCATCTTTCAAGAGGACTTGAGACCAATTTCAGAAAATCAAGATGCCTTCTGCGTCTTGTGATGTACTGCTGGATGACATAGAAGATATCATATCACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-146a-5p(1), mmu-miR-148b-3p(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TATAAAATTACAGATTCATCTTTCAA
siRNA sets
AAAGATGAATCTGTAATTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDKAL1_327_ORF_1
0.5833
0.063827017
0.153871918
306
ORF sequence:
ATGCCTTCTGCGTCTTGTGATGTACTGCTGGATGACATAGAAGATATCATATCACAGGAAGATTCAAAGCCACAGGACAGACAGTTCTCAAGAAAGCATGTGTTTCCTAAAGTACGAAGGCGGAATACCCAAAAATATTTGCAAGAAGAGCCCAGGCCACCAAGTGACAGCACTATTCCAGGCATACAGAAAATTTGGATCCGAACATGGGGCTGCTCACATAATAATTCGGATGGAGAATACATGGCTGGACAGCTTGCTGCCTATGGCTATAAAATTACAGATTCATCTTTCAAGAGGACTTGA
Peptide sequence:
MPSASCDVLLDDIEDIISQEDSKPQDRQFSRKHVFPKVRRRNTQKYLQEEPRPPSDSTIPGIQKIWIRTWGCSHNNSDGEYMAGQLAAYGYKITDSSFKRT
IRESfinder result
IRESfinder score
0.370100384
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page