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mmu_circClock_235
Basic information of circular RNA
PanCircBase ID:
mmu_circClock_235
mm39_Chr. Position ID:
chr5|76414203|76421890|-
Gene name:
Clock
Transcript:
ENSMUST00000202651.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
5,4,3
Exon/intron offsets:
0,443,7602
Genomic length:
7687
Exon/intron sizes in nt:
60,90,85
Flanking exon/introns:
chr5:76413786-76414203|chr5:76421890-76451270
Splice length:
235
Other database IDs:
CIRCpedia: MMU_CIRCpedia_29295, circAtlas: mmu-Clock_0005
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
AGTTCTGATGGTCAGTCACACAGAAGACGGCCTTGCGTCTGTGGGTGTTGGAGACTCCATTCTAAAGATATAAAAAGTGAAAGAGGAGAAGTACAAATGTCTACCACAAGACGAAAACATAATGTGTTATGGTGTTTACCGTAAGCTGTAGTAAAATGAGCTCAATTGTTGACAGAGATGACAGTAGTATTTTTGATGGATTGGTGGAAGAAGATGACAAGGACAAAGCAAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCGTAAGCTGTAGTAAAATGAGC
59.13
GGAGTCTCCAACACCCACAG
59.96
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCGTAAGCTGTAGTAAAATGAGCT
58.89
GGAGTCTCCAACACCCACAG
59.96
155
PCR template sequence:
TTACCGTAAGCTGTAGTAAAATGAGCTCAATTGTTGACAGAGATGACAGTAGTATTTTTGATGGATTGGTGGAAGAAGATGACAAGGACAAAGCAAAAAGAGTTCTGATGGTCAGTCACACAGAAGACGGCCTTGCGTCTGTGGGTGTTGGAGACTCCATTCTAAAGATATAAAAAGTGAAAGAGGAGAAGTACAAATGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-134-5p(1), mmu-miR-30e-5p(1), mmu-miR-30a-5p(1), mmu-miR-30c-5p(1), mmu-miR-30b-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
ACAAAGCAAAAAGAGTTCTGATGGTC
siRNA sets
CCATCAGAACTCTTTTTGC, CATCAGAACTCTTTTTGCT, AGAACTCTTTTTGCTTTGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCLOCK_235_ORF_1
1.1052
0.102925429
0.185569489
180
ORF sequence:
ATGGTGTTTACCGTAAGCTGTAGTAAAATGAGCTCAATTGTTGACAGAGATGACAGTAGTATTTTTGATGGATTGGTGGAAGAAGATGACAAGGACAAAGCAAAAAGAGTTCTGATGGTCAGTCACACAGAAGACGGCCTTGCGTCTGTGGGTGTTGGAGACTCCATTCTAAAGATATAA
Peptide sequence:
MVFTVSCSKMSSIVDRDDSSIFDGLVEEDDKDKAKRVLMVSHTEDGLASVGVGDSILKI
IRESfinder result
IRESfinder score
0.283901489
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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