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mmu_circCkap5_630
Basic information of circular RNA
PanCircBase ID:
mmu_circCkap5_630
mm39_Chr. Position ID:
chr2|91394664|91400617|+
Gene name:
Ckap5
Transcript:
ENSMUST00000111338.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
12,13,14,15,16
Exon/intron offsets:
0,1301,3817,4317,5860
Genomic length:
5953
Exon/intron sizes in nt:
129,183,114,111,93
Flanking exon/introns:
chr2:91393458-91394664|chr2:91400617-91402692
Splice length:
630
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CACATCAATGATTCTGCTCCTGAAGTCAGAGATGCTGCATTTGAAGCACTGGGTACAGCTTTGAAGGTGGTTGGTGAGAAATCAGTAAACCCATTTTTAGCTGATGTTGACAAACTCAAACTTGATAGGATCAAAGAATGTTCAGAAAAAGTAGAACTGGTTCATGGTAAAAAATCTGGACTTGCAACTGAAAAGAAGGAATCCAAGCCTCTACCTGGAAGGGCTGCAGCATCAGGGGCTGCAGGGGACAAAGACACAAAAGATGTTTCAGGACCCAAACCAGGACCGTTAAAAAAAACACCTACTGCTAAGGCTGGTGGACCATCTAAGAAAGGTAAAACAACTGCACCAGGTGGCTCAGCAAGTGCCGGGACAAAGAATAAGAAAGGATTGGAGACCAAAGAAATAGTGGAGCCAGAACTCTCAATTGAAGTATGTGAAGAGAAAGCTTCAGCTGTTCTTCCCCCAACCTGTATTCAGCTTCTAGACAGCAGCAACTGGAAGGAAAGGCTGGCCTGTATGGAAGAATTCCAAAAGGCTGTTGAACTAATGGAGCGAACTGAGATGCCGTGCCAGGCATTGGTGAAGATGCTAGCAAAAAAACCTGGATGGAAAGAAACTAATTTTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGGAGCGAACTGAGATGCC
60.18
AGCTGTACCCAGTGCTTCAA
59.24
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATGGAGCGAACTGAGATGCC
60.18
AAGCTGTACCCAGTGCTTCA
59.24
142
PCR template sequence:
CCAAAAGGCTGTTGAACTAATGGAGCGAACTGAGATGCCGTGCCAGGCATTGGTGAAGATGCTAGCAAAAAAACCTGGATGGAAAGAAACTAATTTTCAGCACATCAATGATTCTGCTCCTGAAGTCAGAGATGCTGCATTTGAAGCACTGGGTACAGCTTTGAAGGTGGTTGGTGAGAAATCAGTAAACCCATTTTTAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-149-5p(1), mmu-miR-136-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AACTAATTTTCAGCACATCAATGATT
siRNA sets
TTGATGTGCTGAAAATTAG, ATTGATGTGCTGAAAATTA, AATCATTGATGTGCTGAAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCKAP5_630_ORF_1
1.1077
0.090234092
0.924394117
741
ORF sequence:
ATGGAAGAATTCCAAAAGGCTGTTGAACTAATGGAGCGAACTGAGATGCCGTGCCAGGCATTGGTGAAGATGCTAGCAAAAAAACCTGGATGGAAAGAAACTAATTTTCAGCACATCAATGATTCTGCTCCTGAAGTCAGAGATGCTGCATTTGAAGCACTGGGTACAGCTTTGAAGGTGGTTGGTGAGAAATCAGTAAACCCATTTTTAGCTGATGTTGACAAACTCAAACTTGATAGGATCAAAGAATGTTCAGAAAAAGTAGAACTGGTTCATGGTAAAAAATCTGGACTTGCAACTGAAAAGAAGGAATCCAAGCCTCTACCTGGAAGGGCTGCAGCATCAGGGGCTGCAGGGGACAAAGACACAAAAGATGTTTCAGGACCCAAACCAGGACCGTTAAAAAAAACACCTACTGCTAAGGCTGGTGGACCATCTAAGAAAGGTAAAACAACTGCACCAGGTGGCTCAGCAAGTGCCGGGACAAAGAATAAGAAAGGATTGGAGACCAAAGAAATAGTGGAGCCAGAACTCTCAATTGAAGTATGTGAAGAGAAAGCTTCAGCTGTTCTTCCCCCAACCTGTATTCAGCTTCTAGACAGCAGCAACTGGAAGGAAAGGCTGGCCTGTATGGAAGAATTCCAAAAGGCTGTTGAACTAATGGAGCGAACTGAGATGCCGTGCCAGGCATTGGTGAAGATGCTAGCAAAAAAACCTGGATGGAAAGAAACTAATTTTCAG
Peptide sequence:
MEEFQKAVELMERTEMPCQALVKMLAKKPGWKETNFQHINDSAPEVRDAAFEALGTALKVVGEKSVNPFLADVDKLKLDRIKECSEKVELVHGKKSGLATEKKESKPLPGRAAASGAAGDKDTKDVSGPKPGPLKKTPTAKAGGPSKKGKTTAPGGSASAGTKNKKGLETKEIVEPELSIEVCEEKASAVLPPTCIQLLDSSNWKERLACMEEFQKAVELMERTEMPCQALVKMLAKKPGWKETNFQ
IRESfinder result
IRESfinder score
0.505741424
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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