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mmu_circCdkl4_709
Basic information of circular RNA
PanCircBase ID:
mmu_circCdkl4_709
mm39_Chr. Position ID:
chr17|80851048|80868003|-
Gene name:
Cdkl4
Transcript:
ENSMUST00000086545.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,4072,7206,12687,16730
Genomic length:
16955
Exon/intron sizes in nt:
19,89,17,31,22,225
Flanking exon/introns:
chr17:80847015-80851048|chr17:80868003-80871153
Splice length:
709
Other database IDs:
CIRCpedia: MMU_CIRCpedia_30532
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_344426
Human Ortholog IDs:
Mature spliced Sequence:
GTGCAACGCTGAACTTCAAGTCGACCGGTACACTAAAATTAAGTCGCTGTAACTAAAATGGAAAAGTATGAAAAGCTAGCTAAGATCGGAGAAGGGTCTTATGGCGTTGTATTCAAGTGCAGAAACAAATCTTCTGGACAAGTAGTAGCGATCAAAAAATTCGTGGAATCTGAAGATGATCGTGTCGTTAGGAAAATAGCCCTGCGGGAAATCCGTATGCTGAAGCAGTTGAAACACCCAAACCTCGTGAACCTCATCGAGGTGTTCAGAAGAAAGAGAAAGATGCATCTAGTTTTTGAGTACTGTGATCACACACTGTTAAACGAGCTGGAGAGAAACCCAAACGGAGTTTCTGATGGAGTGATTAAAAGTGTGCTATGGCAAACCCTTCAAGCCCTTAACTTCTGTCACAAGCACAATTGTATTCATCGGGATGTAAAACCTGAAAACATCCTAATAACCAAGCAAGGGATGATAAAGATTTGTGACTTTGGATTTGCACGAATTCTAATTCCAGGAGACGCCTACACAGACTATGTTGCCACCAGGTGGTACCGAGCCCCCGAACTTCTCGTGGGAGACACGAAGTACGGTTCCTCTGTAGACGTGTGGGCCGTCGGCTGTGTTTTTGCAGAGCTCCTGACGGGTCAGCCACTCTGGCCGGGAAAATCCGACGTGGACCAGCTTTACCTGATCATCAGGACGTTGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTTTGCAGAGCTCCTGACGG
60.6
CCCTTCTCCGATCTTAGCTAGC
59.77
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTTTGCAGAGCTCCTGACGG
60.6
ACCCTTCTCCGATCTTAGCT
57.54
180
PCR template sequence:
TGGGCCGTCGGCTGTGTTTTTGCAGAGCTCCTGACGGGTCAGCCACTCTGGCCGGGAAAATCCGACGTGGACCAGCTTTACCTGATCATCAGGACGTTGGGTGCAACGCTGAACTTCAAGTCGACCGGTACACTAAAATTAAGTCGCTGTAACTAAAATGGAAAAGTATGAAAAGCTAGCTAAGATCGGAGAAGGGTCTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(1), mmu-miR-19b-3p(1), mmu-miR-101a-3p(1), mmu-miR-19a-3p(1), mmu-miR-298-5p(1), mmu-miR-320-3p(1), mmu-miR-676-3p(1), mmu-miR-425-5p(1), mmu-miR-224-5p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATCAGGACGTTGGGTGCAACGCTGAA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDKL4_709_ORF_1
1.0204
0.168793158
0.918385378
708
ORF sequence:
ATGGAAAAGTATGAAAAGCTAGCTAAGATCGGAGAAGGGTCTTATGGCGTTGTATTCAAGTGCAGAAACAAATCTTCTGGACAAGTAGTAGCGATCAAAAAATTCGTGGAATCTGAAGATGATCGTGTCGTTAGGAAAATAGCCCTGCGGGAAATCCGTATGCTGAAGCAGTTGAAACACCCAAACCTCGTGAACCTCATCGAGGTGTTCAGAAGAAAGAGAAAGATGCATCTAGTTTTTGAGTACTGTGATCACACACTGTTAAACGAGCTGGAGAGAAACCCAAACGGAGTTTCTGATGGAGTGATTAAAAGTGTGCTATGGCAAACCCTTCAAGCCCTTAACTTCTGTCACAAGCACAATTGTATTCATCGGGATGTAAAACCTGAAAACATCCTAATAACCAAGCAAGGGATGATAAAGATTTGTGACTTTGGATTTGCACGAATTCTAATTCCAGGAGACGCCTACACAGACTATGTTGCCACCAGGTGGTACCGAGCCCCCGAACTTCTCGTGGGAGACACGAAGTACGGTTCCTCTGTAGACGTGTGGGCCGTCGGCTGTGTTTTTGCAGAGCTCCTGACGGGTCAGCCACTCTGGCCGGGAAAATCCGACGTGGACCAGCTTTACCTGATCATCAGGACGTTGGGTGCAACGCTGAACTTCAAGTCGACCGGTACACTAAAATTAAGTCGCTGTAACTAA
Peptide sequence:
MEKYEKLAKIGEGSYGVVFKCRNKSSGQVVAIKKFVESEDDRVVRKIALREIRMLKQLKHPNLVNLIEVFRRKRKMHLVFEYCDHTLLNELERNPNGVSDGVIKSVLWQTLQALNFCHKHNCIHRDVKPENILITKQGMIKICDFGFARILIPGDAYTDYVATRWYRAPELLVGDTKYGSSVDVWAVGCVFAELLTGQPLWPGKSDVDQLYLIIRTLGATLNFKSTGTLKLSRCN
IRESfinder result
IRESfinder score
0.454890554
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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