top of page
mmu_ciClk3_1919
Basic information of circular RNA
PanCircBase ID:
mmu_ciClk3_1919
mm39_Chr. Position ID:
chr9|57666187|57668106|-
Gene name:
Clk3
Transcript:
ENSMUST00000065330.8
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
3
Exon/intron offsets:
0
Genomic length:
1919
Exon/intron sizes in nt:
1919
Flanking exon/introns:
chr9:57666006-57668106
Splice length:
1919
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGAGTGGTGGCCAGAGTGTGCTAATAGGGGCCTAAAGGCCTCACCTCTTTCTCGCTTCTCTCAGGCTAGCTGGTCTGGGTGAGTACTGGCAACCCTGTGTACATACACCATTGTGGGTACACACATGAGGTGTGTGTGTGCGTGTGTGCTGTCTGGTATAGGACTGAGCAAGGATGGTATGCCTTCCATTTTCTGGCCCCTTGCCAGTGGCAACTATAAGGGCTCTGGCTCCGGCGTTGGCTGATTTCCAGCCTGTCTATATCTTTCCACTGTTCCATACACAGGCTACATGGTACACATGATTGGGACACACTTCTCAGGGCTGGTACTAAGATTGTTGTTTGTGGTTTGGGGCTATATGGCCTGGTCTTCTTCACATCAGGTCTGTCCCCATCGGGCCCACCCCATAGCTAAGTGCTTTGATGAGTGTGGATTTGACCTTCTCTGCAGCCTCATCTCCACAGTCCTCCTCTCCCAGAGGACCAGAGTCTGTTATTACCCAATAAAAAGGGGACACTTTACCAGTTAATTTTATTTTTCTTTTTTAAATGCTGGGAGTCCAACCCAGGGCCCATACATACGAGGCAGATACTCTACCACTGAACTGTATCACACCCCATTCCCTACACCTCCTCTTTGTTTTTGAAAGTCTTATGTATTCCAACCTAGCCTAAAACTCATGATCCTTTTCCCTCTACTTCCTGAGTGCTGGGCACCACCGCCTGGCTTCCTAGGCTTTTCTTTTTTTGATATGGGTCTTGAATTTCTGTGTTTACTTTTCCAAGTTGCTGGTCTGTAAGAGCACATCACTTTGCCCTGTCAGTCAGCTCAGGTTGGAAGCTTCTCATCAGACCTCCAGCCAGGCTCTCTTCTACCTTGTTCCTTTGTAGGTGTGCTACTTACGGTAAGGAGAGGCAGCTGTCTGCGTGGTGAGATCCCAGGCCTCACCTTGTTGCAGGCCACTTAAAGACCAGAGCTTGGCCAGCATTCTAGGGTGGTGTGTGGAACAGACCAAGAGCCCACACTGTATTCAATCCCATGGAAAAGGAAGGTCACTCGTGTTTACAAGGCTATGTGCTGTCTTCTCTTCTTCCTGTTTGTTCTCCCCGTGTTGTCCTCCTGCTGGCCAAGCGGCCTCTTAGTAGTGGTGGGTTTGGTGAAGGTATCTTCTCTACCCAGCGCTTGACCTGAGTGGTGTGAGCTGAAGGTTGACTTGCCGGTGAATCAATCATGGCTTGTGGCCTCACACAGTGCCGTATGCTGCCACTGGGTGGCAGTGCAAGTCTGGTGCTCTGCTTATTTTTGGTGCCCTCTGTCGTCGTGGGCTGGGTCTGGCTTAGGAGTGGCACAAGTCCTAAGGCCAGGTCAGGAGCTGGCTTGGGGCCTGAAGGTCGGCCAGCCCAAAGGATCTCAGCCAGGCTCATTTCCTGCTGGAGTTTGGTGGCAGGAGGGCTGCTGGCAGAAGTCTGTTTCTGGTAGTTGGTTAAGTCTGGCCAAGGATGTCATGTGGGGGCAGGTAGTAGCTTGGTTCTACGTGGCAGCTGTTGAATATGTTGTAAGGCTGTGTGGACCAGCAGAGGCAGGCAAAGAAAGGGTGAGCATACTGTTGCTGCTGAAGCCAGGATAGCCCTACAACCTGTCCAGAAGGCTGGACCCAGGTTGGGCCAGCCGCCTTTTTTGCGTCGTCTTCAGCTCTGGCCAGAGTCACGGGAGGGTCAGGGAGGGGGAGACTAGAAGAGGAGGGAGTCAGGGCTGTGGCTGTCCTCGGGGCCTGGCCCCTCTGTGTCATAGGCTGGACATCTTTCTGAGCATTTGTGGCACTCTTCTTAGAGATAATGTCCGAGTTTTCTTACATACCTGTAGCTGTTTTTGCTTTTCTGTTTTGAAGTCAGTTTGTGTCTTGACGTGTCCCTTGCAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCTGTAGCTGTTTTTGCTT
55.77
AGTACTCACCCAGACCAGCT
59.88
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCTGTAGCTGTTTTTGCTT
55.77
CAGTACTCACCCAGACCAGC
59.75
152
PCR template sequence:
CACTCTTCTTAGAGATAATGTCCGAGTTTTCTTACATACCTGTAGCTGTTTTTGCTTTTCTGTTTTGAAGTCAGTTTGTGTCTTGACGTGTCCCTTGCAAGTGAGTGGTGGCCAGAGTGTGCTAATAGGGGCCTAAAGGCCTCACCTCTTTCTCGCTTCTCTCAGGCTAGCTGGTCTGGGTGAGTACTGGCAACCCTGTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
23
Interacting miRNAs (#binding sites)
mmu-miR-214-3p(2), mmu-miR-1187(2), mmu-miR-15a-5p(1), mmu-miR-150-5p(1), mmu-miR-30e-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-143-3p(1), mmu-miR-495-3p(1), mmu-miR-30b-5p(1), mmu-miR-191-5p(1), mmu-miR-351-5p(1), mmu-miR-22-3p(1), mmu-miR-483-5p(1), mmu-miR-362-5p(1), mmu-miR-324-3p(1), mmu-miR-297a-5p(1), mmu-miR-499-5p(1), mmu-miR-466a-5p(1), mmu-miR-466p-5p(1), mmu-miR-673-5p(1), mmu-miR-3470b(1), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
GTGTCCCTTGCAAGTGAGTGGTGGCC
siRNA sets
ACTCACTTGCAAGGGACAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.681027789
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page