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mmu_circCdkl3_835
Basic information of circular RNA
PanCircBase ID:
mmu_circCdkl3_835
mm39_Chr. Position ID:
chr11|51916665|51923351|+
Gene name:
Cdkl3
Transcript:
ENSMUST00000109079.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
7,8,9,10,11
Exon/intron offsets:
0,920,1174,4003,6523
Genomic length:
6686
Exon/intron sizes in nt:
89,16,03,29,94,163
Flanking exon/introns:
chr11:51913704-51916665|chr11:51923351-51924340
Splice length:
835
Other database IDs:
CIRCpedia: MMU_CIRCpedia_22253, circAtlas: mmu-Cdkl3_0004
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GCTTGTTTACAAATTGATCCTGCTGAGAGGACATCATCTACTGATCTTTTGCGTCACGATTACTTTACTAGAGATGGATTTATTGAGAAATTCATACCAGAGCTGAGAGCTAAATTATTACAGGAAGCAAAGGTTAATTCATTTATAAAGCCAAAAGAGAATTTTAAAGAAAATGAACCTGTGAGAGATGAGAAGAAATCAGTTTTTACCAACACCCTGCTCTATGGAAATCCATCACTTTATGGCAAGGAAGTGGACAGAGACAAAAGGGCCAAGGAGCTCAAAGTCAGAGTCATTAAGGCCAAAGGGGGCAAAGGAGATGTCCCAGACCAGAAGAAGCCAGAGTATGAAGGCGACCACCGCCAGCAGGGCACAGCTGATGACACACAGCCCTCATCACTGGACAAGAAGCCTTCTGTCTTGGAACTGACAAACCCTCTCAATCCCAGTGAGAATTCTGACGGTGTCAAAGAAGACCCACACGCTGGGGGTTGTATGATAATGCCACCTATCAACCTGACAAGCAGTAATTTGTTGGCCGCAAATCTCAGTTCAAACCTTTCCCACCCCAATTCACGGTTAACTGAAAGAACAAAAAAGAGACGCACTTCTTCACAAACTATTGGACAGACTTTGTCTAATAGCAGACAAGAGGACACAGGTCCCACACAAGTCCAAACAGAGAAAGGTGCATTTAATGAGCGAACAGGTCAGAATGACCAAATATCGAGTGGGAACAAAAGAAAGCTGAATTTTCCCAAATGCGACAGGAAAGAATTCCATTTCCCTGAACTGCCATTCACAGTGCAGGCGAAGGAGATGAAAGGGATGGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCCAAATGCGACAGGAAAGA
59.93
ATCGTGACGCAAAAGATCAGT
58.31
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTCCCAAATGCGACAGGAAAG
59.11
TCGTGACGCAAAAGATCAGT
57.85
140
PCR template sequence:
AACAAAAGAAAGCTGAATTTTCCCAAATGCGACAGGAAAGAATTCCATTTCCCTGAACTGCCATTCACAGTGCAGGCGAAGGAGATGAAAGGGATGGAAGGCTTGTTTACAAATTGATCCTGCTGAGAGGACATCATCTACTGATCTTTTGCGTCACGATTACTTTACTAGAGATGGATTTATTGAGAAATTCATACCAG
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-211-5p(1), mmu-miR-204-5p(1), mmu-miR-328-3p(1), mmu-miR-370-3p(1), mmu-miR-669d-5p(1), mmu-miR-3065-5p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AAAGGGATGGAAGGCTTGTTTACAAA
siRNA sets
TAAACAAGCCTTCCATCCC, AAACAAGCCTTCCATCCCT, TTTGTAAACAAGCCTTCCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDKL3_835_ORF_1
0.6161
-0.004725257
0.170861596
357
ORF sequence:
ATGATAATGCCACCTATCAACCTGACAAGCAGTAATTTGTTGGCCGCAAATCTCAGTTCAAACCTTTCCCACCCCAATTCACGGTTAACTGAAAGAACAAAAAAGAGACGCACTTCTTCACAAACTATTGGACAGACTTTGTCTAATAGCAGACAAGAGGACACAGGTCCCACACAAGTCCAAACAGAGAAAGGTGCATTTAATGAGCGAACAGGTCAGAATGACCAAATATCGAGTGGGAACAAAAGAAAGCTGAATTTTCCCAAATGCGACAGGAAAGAATTCCATTTCCCTGAACTGCCATTCACAGTGCAGGCGAAGGAGATGAAAGGGATGGAAGGCTTGTTTACAAATTGA
Peptide sequence:
MIMPPINLTSSNLLAANLSSNLSHPNSRLTERTKKRRTSSQTIGQTLSNSRQEDTGPTQVQTEKGAFNERTGQNDQISSGNKRKLNFPKCDRKEFHFPELPFTVQAKEMKGMEGLFTN
IRESfinder result
IRESfinder score
0.560299562
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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