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mmu_circCkap5_1510
Basic information of circular RNA
PanCircBase ID:
mmu_circCkap5_1510
mm39_Chr. Position ID:
chr2|91385611|91400617|+
Gene name:
Ckap5
Transcript:
ENSMUST00000111338.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
5,6,7,8,9,10,11,12,13,14,15,16
Exon/intron offsets:
0,1233,2308,3782,5540,7487,7682,9053,10354,12870,13370,14913
Genomic length:
15006
Exon/intron sizes in nt:
172,133,101,114,105,90,165,129,183,114,111,93
Flanking exon/introns:
chr2:91381103-91385611|chr2:91400617-91402692
Splice length:
1510
Other database IDs:
CIRCpedia: MMU_CIRCpedia_225656, circAtlas: mmu-Ckap5_0081
Human Ortholog IDs:
Mature spliced Sequence:
TGAATTTGGTTCCAAAATCATCTCACTTAAGCCAATTATTAAAGTGTTGCCAAAACTATTTGAATCTCGAGACAAGGCTGTTCGGGATGAAGCCAAATTATTTGCTATAGAGATTTATCGATGGAATCGAGATGCTGTGAAACACACACTACAAAATATAAATTCTGTCCAGTTGAAAGAATTAGAAGAAGAGTGGGTCAAGCTGCCAACAGGTGCTCCTAAGCCCAGTCGGTTTCTGCGTTCCCAACAAGAACTAGAAGCTAAACTGGAACAGCAACAGTCTGCTGGTGGAGATGCAGAAGGGGGTGGTGATGATGGTGATGAGGTACCACAGGTAGATGCTTATGAGCTTCTGGATGCGGTAGAGATCCTTTCCAAACTTCCCAAAGACTTTTATGACAAAATTGAGGCAAAGAAATGGCAAGAGAGAAAAGAAGCTCTGGAGGCTGTAGAAGTACTAGTGAAAAACCCCAAGCTGGAAGCAGGCGATTACGCAGATTTAGTGAAAGCATTAAAAAAGGTTGTTGGAAAGGACACCAATGTCATGTTGGTAGCTTTGGCAGCAAAATGTCTTACTGGCTTAGCTGTTGGGCTCAGAAAGAAATTTGGACAATATGCAGGACATGTTGTGCCAACAATTTTGGAAAAATTCAAAGAAAAGAAGCCTCAAGTGGTACAAGCCCTGCAGGAGGCAATTGATGCAATCTTCCTCACTACCACACTACAGAACATCAGTGAGGATGTCTTAGCAGTAATGGATAATAAAAATCCCACCATCAAGCAGCAGACATCACTTTTTATTGCAAGAAGCTTTCGTCACTGCACTTCCTCTACATTGCCGAAGAGTCTACTAAAACCCTTTTGTGCTGCTCTACTTAAGCACATCAATGATTCTGCTCCTGAAGTCAGAGATGCTGCATTTGAAGCACTGGGTACAGCTTTGAAGGTGGTTGGTGAGAAATCAGTAAACCCATTTTTAGCTGATGTTGACAAACTCAAACTTGATAGGATCAAAGAATGTTCAGAAAAAGTAGAACTGGTTCATGGTAAAAAATCTGGACTTGCAACTGAAAAGAAGGAATCCAAGCCTCTACCTGGAAGGGCTGCAGCATCAGGGGCTGCAGGGGACAAAGACACAAAAGATGTTTCAGGACCCAAACCAGGACCGTTAAAAAAAACACCTACTGCTAAGGCTGGTGGACCATCTAAGAAAGGTAAAACAACTGCACCAGGTGGCTCAGCAAGTGCCGGGACAAAGAATAAGAAAGGATTGGAGACCAAAGAAATAGTGGAGCCAGAACTCTCAATTGAAGTATGTGAAGAGAAAGCTTCAGCTGTTCTTCCCCCAACCTGTATTCAGCTTCTAGACAGCAGCAACTGGAAGGAAAGGCTGGCCTGTATGGAAGAATTCCAAAAGGCTGTTGAACTAATGGAGCGAACTGAGATGCCGTGCCAGGCATTGGTGAAGATGCTAGCAAAAAAACCTGGATGGAAAGAAACTAATTTTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGGAGCGAACTGAGATGCC
60.18
CATCCCGAACAGCCTTGTCT
60.04
170
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATGGAGCGAACTGAGATGCC
60.18
TCATCCCGAACAGCCTTGTC
60.04
171
PCR template sequence:
CCAAAAGGCTGTTGAACTAATGGAGCGAACTGAGATGCCGTGCCAGGCATTGGTGAAGATGCTAGCAAAAAAACCTGGATGGAAAGAAACTAATTTTCAGTGAATTTGGTTCCAAAATCATCTCACTTAAGCCAATTATTAAAGTGTTGCCAAAACTATTTGAATCTCGAGACAAGGCTGTTCGGGATGAAGCCAAATTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-15b-5p(1), mmu-miR-149-5p(1), mmu-miR-136-5p(1), mmu-miR-96-5p(1), mmu-miR-27a-5p(1), mmu-miR-673-5p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AACTAATTTTCAGTGAATTTGGTTCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCKAP5_1510_ORF_1
1.0666
0.04806467
0.979345693
969
ORF sequence:
ATGTTGGTAGCTTTGGCAGCAAAATGTCTTACTGGCTTAGCTGTTGGGCTCAGAAAGAAATTTGGACAATATGCAGGACATGTTGTGCCAACAATTTTGGAAAAATTCAAAGAAAAGAAGCCTCAAGTGGTACAAGCCCTGCAGGAGGCAATTGATGCAATCTTCCTCACTACCACACTACAGAACATCAGTGAGGATGTCTTAGCAGTAATGGATAATAAAAATCCCACCATCAAGCAGCAGACATCACTTTTTATTGCAAGAAGCTTTCGTCACTGCACTTCCTCTACATTGCCGAAGAGTCTACTAAAACCCTTTTGTGCTGCTCTACTTAAGCACATCAATGATTCTGCTCCTGAAGTCAGAGATGCTGCATTTGAAGCACTGGGTACAGCTTTGAAGGTGGTTGGTGAGAAATCAGTAAACCCATTTTTAGCTGATGTTGACAAACTCAAACTTGATAGGATCAAAGAATGTTCAGAAAAAGTAGAACTGGTTCATGGTAAAAAATCTGGACTTGCAACTGAAAAGAAGGAATCCAAGCCTCTACCTGGAAGGGCTGCAGCATCAGGGGCTGCAGGGGACAAAGACACAAAAGATGTTTCAGGACCCAAACCAGGACCGTTAAAAAAAACACCTACTGCTAAGGCTGGTGGACCATCTAAGAAAGGTAAAACAACTGCACCAGGTGGCTCAGCAAGTGCCGGGACAAAGAATAAGAAAGGATTGGAGACCAAAGAAATAGTGGAGCCAGAACTCTCAATTGAAGTATGTGAAGAGAAAGCTTCAGCTGTTCTTCCCCCAACCTGTATTCAGCTTCTAGACAGCAGCAACTGGAAGGAAAGGCTGGCCTGTATGGAAGAATTCCAAAAGGCTGTTGAACTAATGGAGCGAACTGAGATGCCGTGCCAGGCATTGGTGAAGATGCTAGCAAAAAAACCTGGATGGAAAGAAACTAATTTTCAGTGA
Peptide sequence:
MLVALAAKCLTGLAVGLRKKFGQYAGHVVPTILEKFKEKKPQVVQALQEAIDAIFLTTTLQNISEDVLAVMDNKNPTIKQQTSLFIARSFRHCTSSTLPKSLLKPFCAALLKHINDSAPEVRDAAFEALGTALKVVGEKSVNPFLADVDKLKLDRIKECSEKVELVHGKKSGLATEKKESKPLPGRAAASGAAGDKDTKDVSGPKPGPLKKTPTAKAGGPSKKGKTTAPGGSASAGTKNKKGLETKEIVEPELSIEVCEEKASAVLPPTCIQLLDSSNWKERLACMEEFQKAVELMERTEMPCQALVKMLAKKPGWKETNFQ
IRESfinder result
IRESfinder score
0.461865053
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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