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mmu_circCdkl3_557
Basic information of circular RNA
PanCircBase ID:
mmu_circCdkl3_557
mm39_Chr. Position ID:
chr11|51895736|51909282|+
Gene name:
Cdkl3
Transcript:
ENSMUST00000109080.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
2,3,4
Exon/intron offsets:
0,6221,13367
Genomic length:
13546
Exon/intron sizes in nt:
18,31,95,179
Flanking exon/introns:
chr11:51895244-51895736|chr11:51909282-51910556
Splice length:
557
Other database IDs:
circAtlas: mmu-Cdkl3_0014
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
TAGAAGCCAGGCTTGAAAATGGAGATGTATGAAACCCTTGGAAAAGTGGGAGAGGGAAGTTATGGAACGGTCATGAAATGCAAACATAAGGACACTGGGCGAATAGTGGCCATTAAGATTTTCTATGAGAAACCAGAAAAATCTGTCAACAAAATTGCAACGAGAGAAATAAAGTTTCTAAAGCAATTTCGGCATGAAAACCTGGTCAATTTGATTGAAGTTTTTAGACAAAAGAAGAAAATTCATTTGGTATTTGAGTTTATTGACCACACGGTCTTAGATGAGCTGCAGCACTACTGTCACGGACTAGAGAGTAAGCGGCTGAGAAAGTACCTCTTCCAGATCCTTCGCGCCATTGAGTACCTGCATAATAATAATATTATCCATCGAGATATAAAGCCTGAGAATATTTTAGTCTCCCAGTCAGGAATTACGAAGCTGTGTGATTTTGGGTTTGCGAGGACACTAGCAGCTCCTGGAGACGTTTACACAGACTACGTGGCCACACGCTGGTACAGAGCTCCAGAGCTGGTGTTGAAAGACACCTCCTACGGAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACACTAGCAGCTCCTGGAGA
59.96
CCTCTCCCACTTTTCCAAGGG
60.27
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACACTAGCAGCTCCTGGAGA
59.96
CCCTCTCCCACTTTTCCAAGG
60.27
151
PCR template sequence:
CGAGGACACTAGCAGCTCCTGGAGACGTTTACACAGACTACGTGGCCACACGCTGGTACAGAGCTCCAGAGCTGGTGTTGAAAGACACCTCCTACGGAAATAGAAGCCAGGCTTGAAAATGGAGATGTATGAAACCCTTGGAAAAGTGGGAGAGGGAAGTTATGGAACGGTCATGAAATGCAAACATAAGGACACTGGGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-29b-1-5p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-669d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CCTCCTACGGAAATAGAAGCCAGGCT
siRNA sets
AGCCTGGCTTCTATTTCCG, TGGCTTCTATTTCCGTAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDKL3_557_ORF_1
1.0436
0.171314373
0.798519495
555
ORF sequence:
ATGGAGATGTATGAAACCCTTGGAAAAGTGGGAGAGGGAAGTTATGGAACGGTCATGAAATGCAAACATAAGGACACTGGGCGAATAGTGGCCATTAAGATTTTCTATGAGAAACCAGAAAAATCTGTCAACAAAATTGCAACGAGAGAAATAAAGTTTCTAAAGCAATTTCGGCATGAAAACCTGGTCAATTTGATTGAAGTTTTTAGACAAAAGAAGAAAATTCATTTGGTATTTGAGTTTATTGACCACACGGTCTTAGATGAGCTGCAGCACTACTGTCACGGACTAGAGAGTAAGCGGCTGAGAAAGTACCTCTTCCAGATCCTTCGCGCCATTGAGTACCTGCATAATAATAATATTATCCATCGAGATATAAAGCCTGAGAATATTTTAGTCTCCCAGTCAGGAATTACGAAGCTGTGTGATTTTGGGTTTGCGAGGACACTAGCAGCTCCTGGAGACGTTTACACAGACTACGTGGCCACACGCTGGTACAGAGCTCCAGAGCTGGTGTTGAAAGACACCTCCTACGGAAATAGAAGCCAGGCTTGA
Peptide sequence:
MEMYETLGKVGEGSYGTVMKCKHKDTGRIVAIKIFYEKPEKSVNKIATREIKFLKQFRHENLVNLIEVFRQKKKIHLVFEFIDHTVLDELQHYCHGLESKRLRKYLFQILRAIEYLHNNNIIHRDIKPENILVSQSGITKLCDFGFARTLAAPGDVYTDYVATRWYRAPELVLKDTSYGNRSQA
IRESfinder result
IRESfinder score
0.602863521
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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