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mmu_circClock_314
Basic information of circular RNA
PanCircBase ID:
mmu_circClock_314
mm39_Chr. Position ID:
chr5|76414203|76451349|-
Gene name:
Clock
Transcript:
ENSMUST00000202651.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,4,3,2
Exon/intron offsets:
0,443,7602,37067
Genomic length:
37146
Exon/intron sizes in nt:
60,90,85,79
Flanking exon/introns:
chr5:76413786-76414203|chr5:76451349-76452501
Splice length:
314
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TGAAAGAAAAGCACAAGAAGAAACTTTTACAGGCGTTGTTGATTGGACTAGGGCAACGATTCCCAAAATCACCAGCAAGAGTTCTGATGGTCAGTCACACAGAAGACGGCCTTGCGTCTGTGGGTGTTGGAGACTCCATTCTAAAGATATAAAAAGTGAAAGAGGAGAAGTACAAATGTCTACCACAAGACGAAAACATAATGTGTTATGGTGTTTACCGTAAGCTGTAGTAAAATGAGCTCAATTGTTGACAGAGATGACAGTAGTATTTTTGATGGATTGGTGGAAGAAGATGACAAGGACAAAGCAAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGAGCTCAATTGTTGACAGAGA
57.66
GGGAATCGTTGCCCTAGTCC
60.18
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTCAATTGTTGACAGAGATGACA
59.55
GGGAATCGTTGCCCTAGTCC
60.18
140
PCR template sequence:
TTACCGTAAGCTGTAGTAAAATGAGCTCAATTGTTGACAGAGATGACAGTAGTATTTTTGATGGATTGGTGGAAGAAGATGACAAGGACAAAGCAAAAAGTGAAAGAAAAGCACAAGAAGAAACTTTTACAGGCGTTGTTGATTGGACTAGGGCAACGATTCCCAAAATCACCAGCAAGAGTTCTGATGGTCAGTCACAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
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-138-5p(1), mmu-miR-30b-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
ACAAAGCAAAAAGTGAAAGAAAAGCA
siRNA sets
TTTTCTTTCACTTTTTGCT,TTTCTTTCACTTTTTGCTT,CTTTTCTTTCACTTTTTGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCLOCK_314_ORF_1
0.9072
-0.089367718
0.174405411
330
ORF sequence:
ATGGTGTTTACCGTAAGCTGTAGTAAAATGAGCTCAATTGTTGACAGAGATGACAGTAGTATTTTTGATGGATTGGTGGAAGAAGATGACAAGGACAAAGCAAAAAGTGAAAGAAAAGCACAAGAAGAAACTTTTACAGGCGTTGTTGATTGGACTAGGGCAACGATTCCCAAAATCACCAGCAAGAGTTCTGATGGTCAGTCACACAGAAGACGGCCTTGCGTCTGTGGGTGTTGGAGACTCCATTCTAAAGATATAAAAAGTGAAAGAGGAGAAGTACAAATGTCTACCACAAGACGAAAACATAATGTGTTATGGTGTTTACCGTAA
Peptide sequence:
MVFTVSCSKMSSIVDRDDSSIFDGLVEEDDKDKAKSERKAQEETFTGVVDWTRATIPKITSKSSDGQSHRRRPCVCGCWRLHSKDIKSERGEVQMSTTRRKHNVLWCLP
IRESfinder result
IRESfinder score
0.344671786
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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