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mmu_circCkap5_687
Basic information of circular RNA
PanCircBase ID:
mmu_circCkap5_687
mm39_Chr. Position ID:
chr2|91395965|91402878|+
Gene name:
Ckap5
Transcript:
ENSMUST00000111338.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
13,14,15,16,17
Exon/intron offsets:
0,2516,3016,4559,6727
Genomic length:
6913
Exon/intron sizes in nt:
1,83,11,41,11,93,186
Flanking exon/introns:
chr2:91394793-91395965|chr2:91402878-91403317
Splice length:
687
Other database IDs:
circAtlas: mmu-Ckap5_0116
Human Ortholog IDs:
Mature spliced Sequence:
ATCAAAGAATGTTCAGAAAAAGTAGAACTGGTTCATGGTAAAAAATCTGGACTTGCAACTGAAAAGAAGGAATCCAAGCCTCTACCTGGAAGGGCTGCAGCATCAGGGGCTGCAGGGGACAAAGACACAAAAGATGTTTCAGGACCCAAACCAGGACCGTTAAAAAAAACACCTACTGCTAAGGCTGGTGGACCATCTAAGAAAGGTAAAACAACTGCACCAGGTGGCTCAGCAAGTGCCGGGACAAAGAATAAGAAAGGATTGGAGACCAAAGAAATAGTGGAGCCAGAACTCTCAATTGAAGTATGTGAAGAGAAAGCTTCAGCTGTTCTTCCCCCAACCTGTATTCAGCTTCTAGACAGCAGCAACTGGAAGGAAAGGCTGGCCTGTATGGAAGAATTCCAAAAGGCTGTTGAACTAATGGAGCGAACTGAGATGCCGTGCCAGGCATTGGTGAAGATGCTAGCAAAAAAACCTGGATGGAAAGAAACTAATTTTCAGGTGATGCAGATGAAGCTTCACATTGTTGCTTTGATTGCCCAGAAGGGAAATTTTTCTAAAACGTCTGCTCAGATTGTATTAGATGGCCTTGTAGACAAGATTGGAGATGTGAAATGTGGGAACAATGCAAAAGAAGCCATGACAGCAATAGCTGAAGCGTGCATGCTGCCCTGGACAGCTGAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCAAAAGAAGCCATGACAGCA
60
CCTTCCAGGTAGAGGCTTGG
59.46
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCAAAAGAAGCCATGACAGCA
60
CCCTTCCAGGTAGAGGCTTG
59.46
154
PCR template sequence:
CCTTGTAGACAAGATTGGAGATGTGAAATGTGGGAACAATGCAAAAGAAGCCATGACAGCAATAGCTGAAGCGTGCATGCTGCCCTGGACAGCTGAGCAGATCAAAGAATGTTCAGAAAAAGTAGAACTGGTTCATGGTAAAAAATCTGGACTTGCAACTGAAAAGAAGGAATCCAAGCCTCTACCTGGAAGGGCTGCAG
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-9-5p(1), mmu-miR-103-3p(1), mmu-miR-135a-5p(1), mmu-miR-33-5p(1), mmu-miR-149-5p(1), mmu-miR-136-5p(1), mmu-miR-107-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GACAGCTGAGCAGATCAAAGAATGTT
siRNA sets
TTCTTTGATCTGCTCAGCT, AACATTCTTTGATCTGCTC, CTTTGATCTGCTCAGCTGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCKAP5_687_ORF_1
1.0583
0.118995098
0.986349412
984
ORF sequence:
ATGGAAGAATTCCAAAAGGCTGTTGAACTAATGGAGCGAACTGAGATGCCGTGCCAGGCATTGGTGAAGATGCTAGCAAAAAAACCTGGATGGAAAGAAACTAATTTTCAGGTGATGCAGATGAAGCTTCACATTGTTGCTTTGATTGCCCAGAAGGGAAATTTTTCTAAAACGTCTGCTCAGATTGTATTAGATGGCCTTGTAGACAAGATTGGAGATGTGAAATGTGGGAACAATGCAAAAGAAGCCATGACAGCAATAGCTGAAGCGTGCATGCTGCCCTGGACAGCTGAGCAGATCAAAGAATGTTCAGAAAAAGTAGAACTGGTTCATGGTAAAAAATCTGGACTTGCAACTGAAAAGAAGGAATCCAAGCCTCTACCTGGAAGGGCTGCAGCATCAGGGGCTGCAGGGGACAAAGACACAAAAGATGTTTCAGGACCCAAACCAGGACCGTTAAAAAAAACACCTACTGCTAAGGCTGGTGGACCATCTAAGAAAGGTAAAACAACTGCACCAGGTGGCTCAGCAAGTGCCGGGACAAAGAATAAGAAAGGATTGGAGACCAAAGAAATAGTGGAGCCAGAACTCTCAATTGAAGTATGTGAAGAGAAAGCTTCAGCTGTTCTTCCCCCAACCTGTATTCAGCTTCTAGACAGCAGCAACTGGAAGGAAAGGCTGGCCTGTATGGAAGAATTCCAAAAGGCTGTTGAACTAATGGAGCGAACTGAGATGCCGTGCCAGGCATTGGTGAAGATGCTAGCAAAAAAACCTGGATGGAAAGAAACTAATTTTCAGGTGATGCAGATGAAGCTTCACATTGTTGCTTTGATTGCCCAGAAGGGAAATTTTTCTAAAACGTCTGCTCAGATTGTATTAGATGGCCTTGTAGACAAGATTGGAGATGTGAAATGTGGGAACAATGCAAAAGAAGCCATGACAGCAATAGCTGAAGCGTGCATGCTGCCCTGGACAGCTGAGCAG
Peptide sequence:
MEEFQKAVELMERTEMPCQALVKMLAKKPGWKETNFQVMQMKLHIVALIAQKGNFSKTSAQIVLDGLVDKIGDVKCGNNAKEAMTAIAEACMLPWTAEQIKECSEKVELVHGKKSGLATEKKESKPLPGRAAASGAAGDKDTKDVSGPKPGPLKKTPTAKAGGPSKKGKTTAPGGSASAGTKNKKGLETKEIVEPELSIEVCEEKASAVLPPTCIQLLDSSNWKERLACMEEFQKAVELMERTEMPCQALVKMLAKKPGWKETNFQVMQMKLHIVALIAQKGNFSKTSAQIVLDGLVDKIGDVKCGNNAKEAMTAIAEACMLPWTAEQ
IRESfinder result
IRESfinder score
0.413814001
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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