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mmu_circCdkl3_1817
Basic information of circular RNA
PanCircBase ID:
mmu_circCdkl3_1817
mm39_Chr. Position ID:
chr11|51895736|51926847|+
Gene name:
Cdkl3
Transcript:
ENSMUST00000109080.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
2,3,4,5,6,7,8,9,10,11,12,13
Exon/intron offsets:
0,6221,13367,14820,17828,20929,21849,22103,24932,27452,28604,31037
Genomic length:
31111
Exon/intron sizes in nt:
183,195,179,113,140,89,160,329,94,163,98,74
Flanking exon/introns:
chr11:51895244-51895736|chr11:51926847-51928257
Splice length:
1817
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TAGAAGCCAGGCTTGAAAATGGAGATGTATGAAACCCTTGGAAAAGTGGGAGAGGGAAGTTATGGAACGGTCATGAAATGCAAACATAAGGACACTGGGCGAATAGTGGCCATTAAGATTTTCTATGAGAAACCAGAAAAATCTGTCAACAAAATTGCAACGAGAGAAATAAAGTTTCTAAAGCAATTTCGGCATGAAAACCTGGTCAATTTGATTGAAGTTTTTAGACAAAAGAAGAAAATTCATTTGGTATTTGAGTTTATTGACCACACGGTCTTAGATGAGCTGCAGCACTACTGTCACGGACTAGAGAGTAAGCGGCTGAGAAAGTACCTCTTCCAGATCCTTCGCGCCATTGAGTACCTGCATAATAATAATATTATCCATCGAGATATAAAGCCTGAGAATATTTTAGTCTCCCAGTCAGGAATTACGAAGCTGTGTGATTTTGGGTTTGCGAGGACACTAGCAGCTCCTGGAGACGTTTACACAGACTACGTGGCCACACGCTGGTACAGAGCTCCAGAGCTGGTGTTGAAAGACACCTCCTACGGAAAGCCAGTGGACATCTGGGCTTTGGGCTGTATGATCATTGAAATGGCCACTGGCCATCCCTTCCTTCCTAGCAGTTCCGATTTGGATTTGCTCCACAAGATTGTTTTAAAAGTAGGCAACCTGACCCCGCACCTGCACAATATCTTTTCCAAGAGTCCCATCTTTGCTGGGGTGGTTCTTCCTCAAGTTCAACACCCAAAAACCGCAAGAAAGAAATACCCCAAGCTCAATGGATTGCTGGCAGATATAGTTCATGCTTGTTTACAAATTGATCCTGCTGAGAGGACATCATCTACTGATCTTTTGCGTCACGATTACTTTACTAGAGATGGATTTATTGAGAAATTCATACCAGAGCTGAGAGCTAAATTATTACAGGAAGCAAAGGTTAATTCATTTATAAAGCCAAAAGAGAATTTTAAAGAAAATGAACCTGTGAGAGATGAGAAGAAATCAGTTTTTACCAACACCCTGCTCTATGGAAATCCATCACTTTATGGCAAGGAAGTGGACAGAGACAAAAGGGCCAAGGAGCTCAAAGTCAGAGTCATTAAGGCCAAAGGGGGCAAAGGAGATGTCCCAGACCAGAAGAAGCCAGAGTATGAAGGCGACCACCGCCAGCAGGGCACAGCTGATGACACACAGCCCTCATCACTGGACAAGAAGCCTTCTGTCTTGGAACTGACAAACCCTCTCAATCCCAGTGAGAATTCTGACGGTGTCAAAGAAGACCCACACGCTGGGGGTTGTATGATAATGCCACCTATCAACCTGACAAGCAGTAATTTGTTGGCCGCAAATCTCAGTTCAAACCTTTCCCACCCCAATTCACGGTTAACTGAAAGAACAAAAAAGAGACGCACTTCTTCACAAACTATTGGACAGACTTTGTCTAATAGCAGACAAGAGGACACAGGTCCCACACAAGTCCAAACAGAGAAAGGTGCATTTAATGAGCGAACAGGTCAGAATGACCAAATATCGAGTGGGAACAAAAGAAAGCTGAATTTTCCCAAATGCGACAGGAAAGAATTCCATTTCCCTGAACTGCCATTCACAGTGCAGGCGAAGGAGATGAAAGGGATGGAAGTTAAACAGATAAAAGTGCTGAAGAGAGAATCAAAGAAAACAGATTCATCTAAAATACCAACTTTACTTAGTATGGACCCAAATCAAGAAAAACAAGAGACAGAACCCTGTGTGACTGTGAATGAGTGGCCTGATCAAGAGAGGAGAGAGCCTACAGGAAGAGGAGGCCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GACTGTGAATGAGTGGCCTGA
60
GCCCAGTGTCCTTATGTTTGC
59.8
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGCCTGATCAAGAGAGGAGA
59.99
GCCCAGTGTCCTTATGTTTGC
59.8
147
PCR template sequence:
TGGACCCAAATCAAGAAAAACAAGAGACAGAACCCTGTGTGACTGTGAATGAGTGGCCTGATCAAGAGAGGAGAGAGCCTACAGGAAGAGGAGGCCACAGTAGAAGCCAGGCTTGAAAATGGAGATGTATGAAACCCTTGGAAAAGTGGGAGAGGGAAGTTATGGAACGGTCATGAAATGCAAACATAAGGACACTGGGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-669d-5p(2), mmu-miR-27b-3p(1), mmu-miR-30e-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-30a-5p(1), mmu-miR-328-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-382-3p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-370-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-3065-5p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAGGAGGCCACAGTAGAAGCCAGGCT
siRNA sets
CTTCTACTGTGGCCTCCTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDKL3_1817_ORF_1
0.8791
0.130976548
0.999951791
1815
ORF sequence:
ATGGAGATGTATGAAACCCTTGGAAAAGTGGGAGAGGGAAGTTATGGAACGGTCATGAAATGCAAACATAAGGACACTGGGCGAATAGTGGCCATTAAGATTTTCTATGAGAAACCAGAAAAATCTGTCAACAAAATTGCAACGAGAGAAATAAAGTTTCTAAAGCAATTTCGGCATGAAAACCTGGTCAATTTGATTGAAGTTTTTAGACAAAAGAAGAAAATTCATTTGGTATTTGAGTTTATTGACCACACGGTCTTAGATGAGCTGCAGCACTACTGTCACGGACTAGAGAGTAAGCGGCTGAGAAAGTACCTCTTCCAGATCCTTCGCGCCATTGAGTACCTGCATAATAATAATATTATCCATCGAGATATAAAGCCTGAGAATATTTTAGTCTCCCAGTCAGGAATTACGAAGCTGTGTGATTTTGGGTTTGCGAGGACACTAGCAGCTCCTGGAGACGTTTACACAGACTACGTGGCCACACGCTGGTACAGAGCTCCAGAGCTGGTGTTGAAAGACACCTCCTACGGAAAGCCAGTGGACATCTGGGCTTTGGGCTGTATGATCATTGAAATGGCCACTGGCCATCCCTTCCTTCCTAGCAGTTCCGATTTGGATTTGCTCCACAAGATTGTTTTAAAAGTAGGCAACCTGACCCCGCACCTGCACAATATCTTTTCCAAGAGTCCCATCTTTGCTGGGGTGGTTCTTCCTCAAGTTCAACACCCAAAAACCGCAAGAAAGAAATACCCCAAGCTCAATGGATTGCTGGCAGATATAGTTCATGCTTGTTTACAAATTGATCCTGCTGAGAGGACATCATCTACTGATCTTTTGCGTCACGATTACTTTACTAGAGATGGATTTATTGAGAAATTCATACCAGAGCTGAGAGCTAAATTATTACAGGAAGCAAAGGTTAATTCATTTATAAAGCCAAAAGAGAATTTTAAAGAAAATGAACCTGTGAGAGATGAGAAGAAATCAGTTTTTACCAACACCCTGCTCTATGGAAATCCATCACTTTATGGCAAGGAAGTGGACAGAGACAAAAGGGCCAAGGAGCTCAAAGTCAGAGTCATTAAGGCCAAAGGGGGCAAAGGAGATGTCCCAGACCAGAAGAAGCCAGAGTATGAAGGCGACCACCGCCAGCAGGGCACAGCTGATGACACACAGCCCTCATCACTGGACAAGAAGCCTTCTGTCTTGGAACTGACAAACCCTCTCAATCCCAGTGAGAATTCTGACGGTGTCAAAGAAGACCCACACGCTGGGGGTTGTATGATAATGCCACCTATCAACCTGACAAGCAGTAATTTGTTGGCCGCAAATCTCAGTTCAAACCTTTCCCACCCCAATTCACGGTTAACTGAAAGAACAAAAAAGAGACGCACTTCTTCACAAACTATTGGACAGACTTTGTCTAATAGCAGACAAGAGGACACAGGTCCCACACAAGTCCAAACAGAGAAAGGTGCATTTAATGAGCGAACAGGTCAGAATGACCAAATATCGAGTGGGAACAAAAGAAAGCTGAATTTTCCCAAATGCGACAGGAAAGAATTCCATTTCCCTGAACTGCCATTCACAGTGCAGGCGAAGGAGATGAAAGGGATGGAAGTTAAACAGATAAAAGTGCTGAAGAGAGAATCAAAGAAAACAGATTCATCTAAAATACCAACTTTACTTAGTATGGACCCAAATCAAGAAAAACAAGAGACAGAACCCTGTGTGACTGTGAATGAGTGGCCTGATCAAGAGAGGAGAGAGCCTACAGGAAGAGGAGGCCACAGTAGAAGCCAGGCTTGA
Peptide sequence:
MEMYETLGKVGEGSYGTVMKCKHKDTGRIVAIKIFYEKPEKSVNKIATREIKFLKQFRHENLVNLIEVFRQKKKIHLVFEFIDHTVLDELQHYCHGLESKRLRKYLFQILRAIEYLHNNNIIHRDIKPENILVSQSGITKLCDFGFARTLAAPGDVYTDYVATRWYRAPELVLKDTSYGKPVDIWALGCMIIEMATGHPFLPSSSDLDLLHKIVLKVGNLTPHLHNIFSKSPIFAGVVLPQVQHPKTARKKYPKLNGLLADIVHACLQIDPAERTSSTDLLRHDYFTRDGFIEKFIPELRAKLLQEAKVNSFIKPKENFKENEPVRDEKKSVFTNTLLYGNPSLYGKEVDRDKRAKELKVRVIKAKGGKGDVPDQKKPEYEGDHRQQGTADDTQPSSLDKKPSVLELTNPLNPSENSDGVKEDPHAGGCMIMPPINLTSSNLLAANLSSNLSHPNSRLTERTKKRRTSSQTIGQTLSNSRQEDTGPTQVQTEKGAFNERTGQNDQISSGNKRKLNFPKCDRKEFHFPELPFTVQAKEMKGMEVKQIKVLKRESKKTDSSKIPTLLSMDPNQEKQETEPCVTVNEWPDQERREPTGRGGHSRSQA
IRESfinder result
IRESfinder score
0.615075632
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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