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mmu_circJade3_729
Basic information of circular RNA
PanCircBase ID:
mmu_circJade3_729
mm39_Chr. Position ID:
chrX|20345752|20365832|+
Gene name:
Jade3
Transcript:
ENSMUST00000115384.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,7,8,9
Exon/intron offsets:
0,10188,14643,19912
Genomic length:
20080
Exon/intron sizes in nt:
1,58,19,12,12,168
Flanking exon/introns:
chrX:20328430-20345752|chrX:20365832-20368634
Splice length:
729
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTATTCCGAAAGGACCTCATCAGTGCCATGAAAATTCCTGACTCTCACCATGTTAATCCTGACAGCTATTACCTCTTTACTGACACATGGAAAGAAGAATGGGAAAAAGGAGTCCAAGTACCAGCCAATCCAGACTCTGTTCCAACGCCGTCTCTCAGGATTATATCTGAAAAAGTAAAGGAGATGCTTTTTGTCCGGCCCCGGAAATATATCCGTTGCTCCAGCCCAGAGTCTGCAGAACCTGGCTATATCAATACCCTGGAGCAAGCAGCATCTACATGCCGCTATGACCTAGATGACATGGATATCTTTTGGCTTCAGGAACTCAATGAAGACCTTGGAGAAATGGGTTATGGCCCAATTGATGAGACTCTTATGGAAAAGACAATAGAAGTTCTGGAACGCCACTGCCATGAAAATATGAACCATGCTATTGAAACAGTGGAAGGGCTAGGAATAGAATATGATGAAGATGTGATCTGTGATGTGTGCCGGTCTCCAGACAGTGAAGAAGGGAATGATATGGTATTCTGTGATAAGTGTAACGTCTGTGTACATCAGGCTTGCTATGGCATTCTCAAGATTCCAGAAGGTAGTTGGCTGTGCCGCTCCTGTGTCCTGGGCATTTATCCACAGTGTGTTTTATGTCCTAAGAAAGGTGGAGCCATGAAGACCACCAGAACAGGGACTAAATGGGCTCATGTCAGCTGTGCCCTGTGGATTCCAGAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGGTGGAGCCATGAAGACC
59.67
AGCTGTCAGGATTAACATGGTGA
59.74
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGGTGGAGCCATGAAGACC
59.67
GCTGTCAGGATTAACATGGTGA
58.39
140
PCR template sequence:
TCCACAGTGTGTTTTATGTCCTAAGAAAGGTGGAGCCATGAAGACCACCAGAACAGGGACTAAATGGGCTCATGTCAGCTGTGCCCTGTGGATTCCAGAAGTATTCCGAAAGGACCTCATCAGTGCCATGAAAATTCCTGACTCTCACCATGTTAATCCTGACAGCTATTACCTCTTTACTGACACATGGAAAGAAGAAT
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-let-7b-5p(1), mmu-let-7c-5p(1), mmu-miR-183-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GTGGATTCCAGAAGTATTCCGAAAGG
siRNA sets
GAATACTTCTGGAATCCAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCJADE3_729_ORF_1
0.9884
0.170214616
0.999491421
1431
ORF sequence:
ATGAAAATTCCTGACTCTCACCATGTTAATCCTGACAGCTATTACCTCTTTACTGACACATGGAAAGAAGAATGGGAAAAAGGAGTCCAAGTACCAGCCAATCCAGACTCTGTTCCAACGCCGTCTCTCAGGATTATATCTGAAAAAGTAAAGGAGATGCTTTTTGTCCGGCCCCGGAAATATATCCGTTGCTCCAGCCCAGAGTCTGCAGAACCTGGCTATATCAATACCCTGGAGCAAGCAGCATCTACATGCCGCTATGACCTAGATGACATGGATATCTTTTGGCTTCAGGAACTCAATGAAGACCTTGGAGAAATGGGTTATGGCCCAATTGATGAGACTCTTATGGAAAAGACAATAGAAGTTCTGGAACGCCACTGCCATGAAAATATGAACCATGCTATTGAAACAGTGGAAGGGCTAGGAATAGAATATGATGAAGATGTGATCTGTGATGTGTGCCGGTCTCCAGACAGTGAAGAAGGGAATGATATGGTATTCTGTGATAAGTGTAACGTCTGTGTACATCAGGCTTGCTATGGCATTCTCAAGATTCCAGAAGGTAGTTGGCTGTGCCGCTCCTGTGTCCTGGGCATTTATCCACAGTGTGTTTTATGTCCTAAGAAAGGTGGAGCCATGAAGACCACCAGAACAGGGACTAAATGGGCTCATGTCAGCTGTGCCCTGTGGATTCCAGAAGTATTCCGAAAGGACCTCATCAGTGCCATGAAAATTCCTGACTCTCACCATGTTAATCCTGACAGCTATTACCTCTTTACTGACACATGGAAAGAAGAATGGGAAAAAGGAGTCCAAGTACCAGCCAATCCAGACTCTGTTCCAACGCCGTCTCTCAGGATTATATCTGAAAAAGTAAAGGAGATGCTTTTTGTCCGGCCCCGGAAATATATCCGTTGCTCCAGCCCAGAGTCTGCAGAACCTGGCTATATCAATACCCTGGAGCAAGCAGCATCTACATGCCGCTATGACCTAGATGACATGGATATCTTTTGGCTTCAGGAACTCAATGAAGACCTTGGAGAAATGGGTTATGGCCCAATTGATGAGACTCTTATGGAAAAGACAATAGAAGTTCTGGAACGCCACTGCCATGAAAATATGAACCATGCTATTGAAACAGTGGAAGGGCTAGGAATAGAATATGATGAAGATGTGATCTGTGATGTGTGCCGGTCTCCAGACAGTGAAGAAGGGAATGATATGGTATTCTGTGATAAGTGTAACGTCTGTGTACATCAGGCTTGCTATGGCATTCTCAAGATTCCAGAAGGTAGTTGGCTGTGCCGCTCCTGTGTCCTGGGCATTTATCCACAGTGTGTTTTATGTCCTAAGAAAGGTGGAGCCATGAAGACCACCAGAACAGGGACTAAATGGGCTCATGTCAGCTGTGCCCTGTGGATTCCAGAA
Peptide sequence:
MKIPDSHHVNPDSYYLFTDTWKEEWEKGVQVPANPDSVPTPSLRIISEKVKEMLFVRPRKYIRCSSPESAEPGYINTLEQAASTCRYDLDDMDIFWLQELNEDLGEMGYGPIDETLMEKTIEVLERHCHENMNHAIETVEGLGIEYDEDVICDVCRSPDSEEGNDMVFCDKCNVCVHQACYGILKIPEGSWLCRSCVLGIYPQCVLCPKKGGAMKTTRTGTKWAHVSCALWIPEVFRKDLISAMKIPDSHHVNPDSYYLFTDTWKEEWEKGVQVPANPDSVPTPSLRIISEKVKEMLFVRPRKYIRCSSPESAEPGYINTLEQAASTCRYDLDDMDIFWLQELNEDLGEMGYGPIDETLMEKTIEVLERHCHENMNHAIETVEGLGIEYDEDVICDVCRSPDSEEGNDMVFCDKCNVCVHQACYGILKIPEGSWLCRSCVLGIYPQCVLCPKKGGAMKTTRTGTKWAHVSCALWIPE
IRESfinder result
IRESfinder score
0.403250784
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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