top of page
mmu_circPrkdc_1319
Basic information of circular RNA
PanCircBase ID:
mmu_circPrkdc_1319
mm39_Chr. Position ID:
chr16|15545447|15558194|+
Gene name:
Prkdc
Transcript:
ENSMUST00000023352.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
42,43,44,45,46,47,48,49,50,51
Exon/intron offsets:
0,2255,2856,3966,6397,7316,9169,10236,11848,12615
Genomic length:
12747
Exon/intron sizes in nt:
1,79,16,96,67,31,49,13,00,00,00,00,00,000
Flanking exon/introns:
chr16:15544573-15545447|chr16:15558194-15570599
Splice length:
1319
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CTAAATGAATTTACTTTTGACACTCAAATCACCAAGAAGATGTGCTATTACAAGATGCTAGCTGTGATGTATTCTCGTCTTTTAAAAGATGATGTTCACTCTAAAGAAGCTAAAATTAATCAAGCTTTTCATGGCTCCCGTGTTGCAGAAGGAAATGAACTCACAAAGACACTTCTTAAGTTGTGCCATGATGCATTTACAGAGAACATGGTGGGGGAGAGCCAGTTGCTGGAGAAGAGAAGACTTTATCATTGTGCTGCATACAACTGTGCCATTTCTCTGATAAGCTGTGTCTTCAATGAGTTGAAATTTTACCAAGGTTTTTTATTTAATGAAAAACCAGAAAAGAACTTGTTTATTTTTGAAAATTTGATAGACCTGAAACGTTGCTATACATTTCCTATAGAAGTTGAGGTTCCTATGGAAAGAAAGAAAAAGTACATTGAAATTAGGAAAGAGGCCAGGGATGCAGCAAATGGGGCTTCAGGCAGTCCTCATTATATGTCTTCATTGTCATATTTGACAGACAGTAGCCTAAGTGAAGAAATGAGTCAATTTGATTTCTCAACTGGAGTTCAGAGCTATTCATACAGTTCTCAAGATCGTAAACCTACCACTGGCCATTTTCAGAGACGGGAGCATCAAGATTCCATGACCCAGGATGACATCATGGAGTTAGAGATGGATGAGCTCAATCAACATGAATGTATGGCTCCCATGATAGCCCTGATTAAGCACATGCAGAGAAATGTGATTGCACCTAAGGGAGAAGAGGGTTCAATACCAAAAGATCTTCCACCGTGGATGAAATTTCTTCATGACAAACTAGGAAATGCATCAGTATCTTTAAATATCCGTCTCTTCTTAGCCAAGCTTGTTATTAATACAGAAGAGGTCTTTCGCCCTTATGCAAAGCACTGGCTCAGCCCCCTGCTACAGCTAGCTGTTTGCGAGAACAACAGAGAAGGAATTCACTACATGATGGTAGAAATAGTAGCTACCATTCTCTCTTGGACTGGCTTGGCTACACCTACAGGAGTCCCTAAAGATGAAGTGTTAGCAAATCGATTGCTTCGTTTTCTAATGAAGCATGTCTTCCATCCCAAAAGAGCTGTGTTTAGGCACAACCTTGAAATTATTAAAACCCTTGTTGAATGCTGGAAGGAGTGTCTTTCCATCCCTTACAGGTTAATATTTGAAAAATTTTCCCATAAGGACCCTAATTCTAAAGACAATTCTGTGGGAATTCAGTTATTAGGCATTGTGATAGCTAATAACTTGCCTCCCTATGACCCAAATTGTGACATAACCAGTGCCAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGTGGGAATTCAGTTATTAGGCA
60.05
ACGAGAATACATCACAGCTAGCA
59.62
161
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGGGAATTCAGTTATTAGGCA
57.81
ACGAGAATACATCACAGCTAGCA
59.62
159
PCR template sequence:
CTAATTCTAAAGACAATTCTGTGGGAATTCAGTTATTAGGCATTGTGATAGCTAATAACTTGCCTCCCTATGACCCAAATTGTGACATAACCAGTGCCATCTAAATGAATTTACTTTTGACACTCAAATCACCAAGAAGATGTGCTATTACAAGATGCTAGCTGTGATGTATTCTCGTCTTTTAAAAGATGATGTTCACT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
16
Interacting miRNAs (#binding sites)
mmu-miR-183-5p(2), mmu-miR-7b-5p(1), mmu-miR-146a-5p(1), mmu-miR-7a-5p(1), mmu-miR-185-5p(1), mmu-miR-434-3p(1), mmu-miR-433-3p(1), mmu-miR-218-5p(1), mmu-miR-207(1), mmu-miR-673-5p(1), mmu-miR-539-5p(1), mmu-miR-335-3p(1), mmu-miR-146b-5p(1), mmu-miR-338-3p(1), mmu-miR-181d-5p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TAACCAGTGCCATCTAAATGAATTTA
siRNA sets
TAAATTCATTTAGATGGCA, AATTCATTTAGATGGCACT, ATTCATTTAGATGGCACTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPRKDC_1319_ORF_1
0.8784
0.018959911
0.996570937
1284
ORF sequence:
ATGTGCTATTACAAGATGCTAGCTGTGATGTATTCTCGTCTTTTAAAAGATGATGTTCACTCTAAAGAAGCTAAAATTAATCAAGCTTTTCATGGCTCCCGTGTTGCAGAAGGAAATGAACTCACAAAGACACTTCTTAAGTTGTGCCATGATGCATTTACAGAGAACATGGTGGGGGAGAGCCAGTTGCTGGAGAAGAGAAGACTTTATCATTGTGCTGCATACAACTGTGCCATTTCTCTGATAAGCTGTGTCTTCAATGAGTTGAAATTTTACCAAGGTTTTTTATTTAATGAAAAACCAGAAAAGAACTTGTTTATTTTTGAAAATTTGATAGACCTGAAACGTTGCTATACATTTCCTATAGAAGTTGAGGTTCCTATGGAAAGAAAGAAAAAGTACATTGAAATTAGGAAAGAGGCCAGGGATGCAGCAAATGGGGCTTCAGGCAGTCCTCATTATATGTCTTCATTGTCATATTTGACAGACAGTAGCCTAAGTGAAGAAATGAGTCAATTTGATTTCTCAACTGGAGTTCAGAGCTATTCATACAGTTCTCAAGATCGTAAACCTACCACTGGCCATTTTCAGAGACGGGAGCATCAAGATTCCATGACCCAGGATGACATCATGGAGTTAGAGATGGATGAGCTCAATCAACATGAATGTATGGCTCCCATGATAGCCCTGATTAAGCACATGCAGAGAAATGTGATTGCACCTAAGGGAGAAGAGGGTTCAATACCAAAAGATCTTCCACCGTGGATGAAATTTCTTCATGACAAACTAGGAAATGCATCAGTATCTTTAAATATCCGTCTCTTCTTAGCCAAGCTTGTTATTAATACAGAAGAGGTCTTTCGCCCTTATGCAAAGCACTGGCTCAGCCCCCTGCTACAGCTAGCTGTTTGCGAGAACAACAGAGAAGGAATTCACTACATGATGGTAGAAATAGTAGCTACCATTCTCTCTTGGACTGGCTTGGCTACACCTACAGGAGTCCCTAAAGATGAAGTGTTAGCAAATCGATTGCTTCGTTTTCTAATGAAGCATGTCTTCCATCCCAAAAGAGCTGTGTTTAGGCACAACCTTGAAATTATTAAAACCCTTGTTGAATGCTGGAAGGAGTGTCTTTCCATCCCTTACAGGTTAATATTTGAAAAATTTTCCCATAAGGACCCTAATTCTAAAGACAATTCTGTGGGAATTCAGTTATTAGGCATTGTGATAGCTAATAACTTGCCTCCCTATGACCCAAATTGTGACATAACCAGTGCCATCTAA
Peptide sequence:
MCYYKMLAVMYSRLLKDDVHSKEAKINQAFHGSRVAEGNELTKTLLKLCHDAFTENMVGESQLLEKRRLYHCAAYNCAISLISCVFNELKFYQGFLFNEKPEKNLFIFENLIDLKRCYTFPIEVEVPMERKKKYIEIRKEARDAANGASGSPHYMSSLSYLTDSSLSEEMSQFDFSTGVQSYSYSSQDRKPTTGHFQRREHQDSMTQDDIMELEMDELNQHECMAPMIALIKHMQRNVIAPKGEEGSIPKDLPPWMKFLHDKLGNASVSLNIRLFLAKLVINTEEVFRPYAKHWLSPLLQLAVCENNREGIHYMMVEIVATILSWTGLATPTGVPKDEVLANRLLRFLMKHVFHPKRAVFRHNLEIIKTLVECWKECLSIPYRLIFEKFSHKDPNSKDNSVGIQLLGIVIANNLPPYDPNCDITSAI
IRESfinder result
IRESfinder score
0.740199697
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page