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mmu_circClock_384
Basic information of circular RNA
PanCircBase ID:
mmu_circClock_384
mm39_Chr. Position ID:
chr5|76413637|76421890|-
Gene name:
Clock
Transcript:
ENSMUST00000202651.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,5,4,3
Exon/intron offsets:
0,566,1009,8168
Genomic length:
8253
Exon/intron sizes in nt:
149,60,90,85
Flanking exon/introns:
chr5:76410613-76413637|chr5:76421890-76451270
Splice length:
384
Other database IDs:
circBase: mmu_circ_0012787, CIRCpedia: MMU_CIRCpedia_29294, circAtlas: mmu-Clock_0020
circBase: hsa_circ_0126632, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_123916
Human Ortholog IDs:
Mature spliced Sequence:
AGTTCTGATGGTCAGTCACACAGAAGACGGCCTTGCGTCTGTGGGTGTTGGAGACTCCATTCTAAAGATATAAAAAGTGAAAGAGGAGAAGTACAAATGTCTACCACAAGACGAAAACATAATGTGTTATGGTGTTTACCGTAAGCTGTAGTAAAATGAGCTCAATTGTTGACAGAGATGACAGTAGTATTTTTGATGGATTGGTGGAAGAAGATGACAAGGACAAAGCAAAAAGAGTATCTAGAAACAAATCAGAAAAGAAACGTAGAGATCAGTTCAATGTCCTCATTAAGGAGCTGGGGTCTATGCTTCCTGGTAACGCGAGAAAGATGGACAAGTCTACTGTTCTACAGAAGAGCATTGATTTTTTGCGCAAACATAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGCTGGGGTCTATGCTTCC
59.89
GGAGTCTCCAACACCCACAG
59.96
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGAGCTGGGGTCTATGCTTC
59.89
GGAGTCTCCAACACCCACAG
59.96
150
PCR template sequence:
CTCATTAAGGAGCTGGGGTCTATGCTTCCTGGTAACGCGAGAAAGATGGACAAGTCTACTGTTCTACAGAAGAGCATTGATTTTTTGCGCAAACATAAAGAGTTCTGATGGTCAGTCACACAGAAGACGGCCTTGCGTCTGTGGGTGTTGGAGACTCCATTCTAAAGATATAAAAAGTGAAAGAGGAGAAGTACAAATGT
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
CGCAAACATAAAGAGTTCTGATGGTC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCLOCK_384_ORF_1
0.7532
-0.263990252
0.082656064
351
ORF sequence:
ATGACAGTAGTATTTTTGATGGATTGGTGGAAGAAGATGACAAGGACAAAGCAAAAAGAGTATCTAGAAACAAATCAGAAAAGAAACGTAGAGATCAGTTCAATGTCCTCATTAAGGAGCTGGGGTCTATGCTTCCTGGTAACGCGAGAAAGATGGACAAGTCTACTGTTCTACAGAAGAGCATTGATTTTTTGCGCAAACATAAAGAGTTCTGATGGTCAGTCACACAGAAGACGGCCTTGCGTCTGTGGGTGTTGGAGACTCCATTCTAAAGATATAAAAAGTGAAAGAGGAGAAGTACAAATGTCTACCACAAGACGAAAACATAATGTGTTATGGTGTTTACCGTAA
Peptide sequence:
MTVVFLMDWWKKMTRTKQKEYLETNQKRNVEISSMSSLRSWGLCFLVTRERWTSLLFYRRALIFCANIKSSDGQSHRRRPCVCGCWRLHSKDIKSERGEVQMSTTRRKHNVLWCLP
IRESfinder result
IRESfinder score
0.377578395
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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