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mmu_circPrkdc_1170
Basic information of circular RNA
PanCircBase ID:
mmu_circPrkdc_1170
mm39_Chr. Position ID:
chr16|15480846|15493230|+
Gene name:
Prkdc
Transcript:
ENSMUST00000023352.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
11,12,13,14,15,16,17,18,19
Exon/intron offsets:
0,1225,4606,6299,7530,9274,10986,11456,12297
Genomic length:
12384
Exon/intron sizes in nt:
147,165,169,50,126,153,113,160,87
Flanking exon/introns:
chr16:15474277-15480846|chr16:15493230-15494767
Splice length:
1170
Other database IDs:
circAtlas: mmu-Prkdc_0109
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_69408
Human Ortholog IDs:
Mature spliced Sequence:
ATTTCGTTTACTGTGGCAGAAGATGCAGAGTTGCATAAGAGCAGGCTGAAGTACTTTATGGAACAGTTCTATGGAATCATCAGAAATACAGACTCGAACAACAAGGAATTAGCCATTGCTATTCGCGGATATGGACTATTTGCAGGACCTTGCAAGGTTATAAATGCAAAAGATGTTGACTTCATGTACGTGGAGCTCATTCAGCGCTGTAAGCAGATGTTCCTCACCCACGCAGATGCTTCTGAGGATCATGTTTACCAGATGCCAAGTTTCCTTCAGTCTATTGCAAGTGTCTTGCTTTACCTTGACACGGTTCCGGAGGTATATACTCCAGTACTGGAACATCTCATGGTGGTACAGATAGACAGCTTCCCTCAGTATAGTCCCAAAATGCAGTTGGTGTGCTGTAAAGCAATAATAAAACTTTTCCTAGCCTTATCAGAGAAAGGACCAGTTCACTGGAATTGCATTAGTGCTGTGGTGCACCAAGGTTTAATTAGAATATGTTCTAAACCAGTGGTCCTTCAAAAGGATGTTGAGTCTAGGTCTGATAACCGTTCGGCCTCCGAGGAAGTCAGAACTGGCAGGTGGAAAGTACCTACGTACAAAGACTATGTGGATCTTTTTCAGCATCTTTTAGGCTGTGACCAGATGGAGGATTTTATTTTAGGAGATGAAACATTTCTCTTTGTGAACTCCTCCCTTAAAAGTCTGAATCATTTACTCTATGATGAATTTATAAGATCAGTTTTGAAGATTGTGGAAAAATTGGATCTTACACTGGAAAAACAGACTGTTGGAGAGCAGGAGGATGGAAGCACTGCTGATGTCTGGGTGATCCCAACTTCAGATCCAGCAGCTAATTTGCACCCTGCTAAACCAAGTGATTTTTCAGCTCTCATTAACCTGGTGGAGTTTTGCAGGGAGATTCTTCCTAGGAAACATGTAGGCTTTTTTGAGCCATGGGTGTACTCATTTGCATATGAGTTAATTTTGCAGTCTACACGATTGCCACTCATCAGTGGTTTCTACAAATTGCTTTCTATTGCAGTGAAAAATGCCAGGAAAATAAAATATTTTGAGGGAATCAGCCCAAAGAGTCTGAAACATTCTCCTGAAGATACAGAAAAGTATTCTTGCTTTGCTTTATTTGCAAAGTTTGGCAAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGAATCAGCCCAAAGAGTCTGA
60.03
TACTTCAGCCTGCTCTTATGCA
59.5
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGAATCAGCCCAAAGAGTCTG
58.64
TACTTCAGCCTGCTCTTATGCA
59.5
140
PCR template sequence:
AAAATATTTTGAGGGAATCAGCCCAAAGAGTCTGAAACATTCTCCTGAAGATACAGAAAAGTATTCTTGCTTTGCTTTATTTGCAAAGTTTGGCAAAGAGATTTCGTTTACTGTGGCAGAAGATGCAGAGTTGCATAAGAGCAGGCTGAAGTACTTTATGGAACAGTTCTATGGAATCATCAGAAATACAGACTCGAACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-137-3p(1), mmu-miR-30e-5p(1), mmu-miR-31-5p(1), mmu-miR-30a-5p(1), mmu-miR-217-5p(1), mmu-miR-30b-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-680(1), mmu-miR-690(1), mmu-miR-384-3p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTTTGGCAAAGAGATTTCGTTTACTG
siRNA sets
TAAACGAAATCTCTTTGCC, AAACGAAATCTCTTTGCCA, AACGAAATCTCTTTGCCAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPRKDC_1170_ORF_1
0.812
0.043007056
0.999997408
2283
ORF sequence:
ATGGAACAGTTCTATGGAATCATCAGAAATACAGACTCGAACAACAAGGAATTAGCCATTGCTATTCGCGGATATGGACTATTTGCAGGACCTTGCAAGGTTATAAATGCAAAAGATGTTGACTTCATGTACGTGGAGCTCATTCAGCGCTGTAAGCAGATGTTCCTCACCCACGCAGATGCTTCTGAGGATCATGTTTACCAGATGCCAAGTTTCCTTCAGTCTATTGCAAGTGTCTTGCTTTACCTTGACACGGTTCCGGAGGTATATACTCCAGTACTGGAACATCTCATGGTGGTACAGATAGACAGCTTCCCTCAGTATAGTCCCAAAATGCAGTTGGTGTGCTGTAAAGCAATAATAAAACTTTTCCTAGCCTTATCAGAGAAAGGACCAGTTCACTGGAATTGCATTAGTGCTGTGGTGCACCAAGGTTTAATTAGAATATGTTCTAAACCAGTGGTCCTTCAAAAGGATGTTGAGTCTAGGTCTGATAACCGTTCGGCCTCCGAGGAAGTCAGAACTGGCAGGTGGAAAGTACCTACGTACAAAGACTATGTGGATCTTTTTCAGCATCTTTTAGGCTGTGACCAGATGGAGGATTTTATTTTAGGAGATGAAACATTTCTCTTTGTGAACTCCTCCCTTAAAAGTCTGAATCATTTACTCTATGATGAATTTATAAGATCAGTTTTGAAGATTGTGGAAAAATTGGATCTTACACTGGAAAAACAGACTGTTGGAGAGCAGGAGGATGGAAGCACTGCTGATGTCTGGGTGATCCCAACTTCAGATCCAGCAGCTAATTTGCACCCTGCTAAACCAAGTGATTTTTCAGCTCTCATTAACCTGGTGGAGTTTTGCAGGGAGATTCTTCCTAGGAAACATGTAGGCTTTTTTGAGCCATGGGTGTACTCATTTGCATATGAGTTAATTTTGCAGTCTACACGATTGCCACTCATCAGTGGTTTCTACAAATTGCTTTCTATTGCAGTGAAAAATGCCAGGAAAATAAAATATTTTGAGGGAATCAGCCCAAAGAGTCTGAAACATTCTCCTGAAGATACAGAAAAGTATTCTTGCTTTGCTTTATTTGCAAAGTTTGGCAAAGAGATTTCGTTTACTGTGGCAGAAGATGCAGAGTTGCATAAGAGCAGGCTGAAGTACTTTATGGAACAGTTCTATGGAATCATCAGAAATACAGACTCGAACAACAAGGAATTAGCCATTGCTATTCGCGGATATGGACTATTTGCAGGACCTTGCAAGGTTATAAATGCAAAAGATGTTGACTTCATGTACGTGGAGCTCATTCAGCGCTGTAAGCAGATGTTCCTCACCCACGCAGATGCTTCTGAGGATCATGTTTACCAGATGCCAAGTTTCCTTCAGTCTATTGCAAGTGTCTTGCTTTACCTTGACACGGTTCCGGAGGTATATACTCCAGTACTGGAACATCTCATGGTGGTACAGATAGACAGCTTCCCTCAGTATAGTCCCAAAATGCAGTTGGTGTGCTGTAAAGCAATAATAAAACTTTTCCTAGCCTTATCAGAGAAAGGACCAGTTCACTGGAATTGCATTAGTGCTGTGGTGCACCAAGGTTTAATTAGAATATGTTCTAAACCAGTGGTCCTTCAAAAGGATGTTGAGTCTAGGTCTGATAACCGTTCGGCCTCCGAGGAAGTCAGAACTGGCAGGTGGAAAGTACCTACGTACAAAGACTATGTGGATCTTTTTCAGCATCTTTTAGGCTGTGACCAGATGGAGGATTTTATTTTAGGAGATGAAACATTTCTCTTTGTGAACTCCTCCCTTAAAAGTCTGAATCATTTACTCTATGATGAATTTATAAGATCAGTTTTGAAGATTGTGGAAAAATTGGATCTTACACTGGAAAAACAGACTGTTGGAGAGCAGGAGGATGGAAGCACTGCTGATGTCTGGGTGATCCCAACTTCAGATCCAGCAGCTAATTTGCACCCTGCTAAACCAAGTGATTTTTCAGCTCTCATTAACCTGGTGGAGTTTTGCAGGGAGATTCTTCCTAGGAAACATGTAGGCTTTTTTGAGCCATGGGTGTACTCATTTGCATATGAGTTAATTTTGCAGTCTACACGATTGCCACTCATCAGTGGTTTCTACAAATTGCTTTCTATTGCAGTGAAAAATGCCAGGAAAATAAAATATTTTGAGGGAATCAGCCCAAAGAGTCTGAAACATTCTCCTGAAGATACAGAAAAGTATTCTTGCTTTGCTTTATTTGCAAAGTTTGGCAAAGAG
Peptide sequence:
MEQFYGIIRNTDSNNKELAIAIRGYGLFAGPCKVINAKDVDFMYVELIQRCKQMFLTHADASEDHVYQMPSFLQSIASVLLYLDTVPEVYTPVLEHLMVVQIDSFPQYSPKMQLVCCKAIIKLFLALSEKGPVHWNCISAVVHQGLIRICSKPVVLQKDVESRSDNRSASEEVRTGRWKVPTYKDYVDLFQHLLGCDQMEDFILGDETFLFVNSSLKSLNHLLYDEFIRSVLKIVEKLDLTLEKQTVGEQEDGSTADVWVIPTSDPAANLHPAKPSDFSALINLVEFCREILPRKHVGFFEPWVYSFAYELILQSTRLPLISGFYKLLSIAVKNARKIKYFEGISPKSLKHSPEDTEKYSCFALFAKFGKEISFTVAEDAELHKSRLKYFMEQFYGIIRNTDSNNKELAIAIRGYGLFAGPCKVINAKDVDFMYVELIQRCKQMFLTHADASEDHVYQMPSFLQSIASVLLYLDTVPEVYTPVLEHLMVVQIDSFPQYSPKMQLVCCKAIIKLFLALSEKGPVHWNCISAVVHQGLIRICSKPVVLQKDVESRSDNRSASEEVRTGRWKVPTYKDYVDLFQHLLGCDQMEDFILGDETFLFVNSSLKSLNHLLYDEFIRSVLKIVEKLDLTLEKQTVGEQEDGSTADVWVIPTSDPAANLHPAKPSDFSALINLVEFCREILPRKHVGFFEPWVYSFAYELILQSTRLPLISGFYKLLSIAVKNARKIKYFEGISPKSLKHSPEDTEKYSCFALFAKFGKE
IRESfinder result
IRESfinder score
0.724436649
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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