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mmu_circPrkdc_1527
Basic information of circular RNA
PanCircBase ID:
mmu_circPrkdc_1527
mm39_Chr. Position ID:
chr16|15547702|15577715|+
Gene name:
Prkdc
Transcript:
ENSMUST00000023352.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
43,44,45,46,47,48,49,50,51,52,53,54
Exon/intron offsets:
0,601,1711,4142,5061,6914,7981,9593,10360,22897,29646,29863
Genomic length:
30013
Exon/intron sizes in nt:
1,69,66,73,14,91,38,12,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr16:15545626-15547702|chr16:15577715-15585731
Splice length:
1527
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTTGTGCCATGATGCATTTACAGAGAACATGGTGGGGGAGAGCCAGTTGCTGGAGAAGAGAAGACTTTATCATTGTGCTGCATACAACTGTGCCATTTCTCTGATAAGCTGTGTCTTCAATGAGTTGAAATTTTACCAAGGTTTTTTATTTAATGAAAAACCAGAAAAGAACTTGTTTATTTTTGAAAATTTGATAGACCTGAAACGTTGCTATACATTTCCTATAGAAGTTGAGGTTCCTATGGAAAGAAAGAAAAAGTACATTGAAATTAGGAAAGAGGCCAGGGATGCAGCAAATGGGGCTTCAGGCAGTCCTCATTATATGTCTTCATTGTCATATTTGACAGACAGTAGCCTAAGTGAAGAAATGAGTCAATTTGATTTCTCAACTGGAGTTCAGAGCTATTCATACAGTTCTCAAGATCGTAAACCTACCACTGGCCATTTTCAGAGACGGGAGCATCAAGATTCCATGACCCAGGATGACATCATGGAGTTAGAGATGGATGAGCTCAATCAACATGAATGTATGGCTCCCATGATAGCCCTGATTAAGCACATGCAGAGAAATGTGATTGCACCTAAGGGAGAAGAGGGTTCAATACCAAAAGATCTTCCACCGTGGATGAAATTTCTTCATGACAAACTAGGAAATGCATCAGTATCTTTAAATATCCGTCTCTTCTTAGCCAAGCTTGTTATTAATACAGAAGAGGTCTTTCGCCCTTATGCAAAGCACTGGCTCAGCCCCCTGCTACAGCTAGCTGTTTGCGAGAACAACAGAGAAGGAATTCACTACATGATGGTAGAAATAGTAGCTACCATTCTCTCTTGGACTGGCTTGGCTACACCTACAGGAGTCCCTAAAGATGAAGTGTTAGCAAATCGATTGCTTCGTTTTCTAATGAAGCATGTCTTCCATCCCAAAAGAGCTGTGTTTAGGCACAACCTTGAAATTATTAAAACCCTTGTTGAATGCTGGAAGGAGTGTCTTTCCATCCCTTACAGGTTAATATTTGAAAAATTTTCCCATAAGGACCCTAATTCTAAAGACAATTCTGTGGGAATTCAGTTATTAGGCATTGTGATAGCTAATAACTTGCCTCCCTATGACCCAAATTGTGACATAACCAGTGCCATGTATTTTGAAGCTTTAGTCAATAACATGTCCTTTGTGAAGTATAAAGAAGTATATGCAGCTGCAGCAGAAGTTTTAGGACTTATTCTTCAATACATTACTGAGAGAAAACACGTGATAGCAGAGTTGGTATGTGAACTGGTTATAAAACAACTGAAGCAACATCAAAATACTATGGAAGACAAATTTATTGTTTGCTTAAACAAAATAGCGAAGGGCTTCCCTCCTCTTGCTGACAGGTTCTTGAATGCTTTGTTCTTTCTGCTGCCAAAATTTCATGGAGTAATGAAGACACTTTGTCTGGAAGTTGTACTTTGTCGAGCAGAGGAGATCACAGGCCTATACTTACAGTTAAAGAGTAAAGACTTTCTTCAAGTCATGAGACATAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGCAGAGGAGATCACAGGC
59.9
GGCACAGTTGTATGCAGCAC
60.11
164
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGAGCAGAGGAGATCACAGG
59.61
GGCACAGTTGTATGCAGCAC
60.11
165
PCR template sequence:
AGACACTTTGTCTGGAAGTTGTACTTTGTCGAGCAGAGGAGATCACAGGCCTATACTTACAGTTAAAGAGTAAAGACTTTCTTCAAGTCATGAGACATAGGTTGTGCCATGATGCATTTACAGAGAACATGGTGGGGGAGAGCCAGTTGCTGGAGAAGAGAAGACTTTATCATTGTGCTGCATACAACTGTGCCATTTCT
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-539-5p(1), mmu-miR-335-3p(1), mmu-miR-350-3p(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
TCATGAGACATAGGTTGTGCCATGAT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPRKDC_1527_ORF_1
0.8719
-0.002716626
0.999999986
3024
ORF sequence:
ATGGTGGGGGAGAGCCAGTTGCTGGAGAAGAGAAGACTTTATCATTGTGCTGCATACAACTGTGCCATTTCTCTGATAAGCTGTGTCTTCAATGAGTTGAAATTTTACCAAGGTTTTTTATTTAATGAAAAACCAGAAAAGAACTTGTTTATTTTTGAAAATTTGATAGACCTGAAACGTTGCTATACATTTCCTATAGAAGTTGAGGTTCCTATGGAAAGAAAGAAAAAGTACATTGAAATTAGGAAAGAGGCCAGGGATGCAGCAAATGGGGCTTCAGGCAGTCCTCATTATATGTCTTCATTGTCATATTTGACAGACAGTAGCCTAAGTGAAGAAATGAGTCAATTTGATTTCTCAACTGGAGTTCAGAGCTATTCATACAGTTCTCAAGATCGTAAACCTACCACTGGCCATTTTCAGAGACGGGAGCATCAAGATTCCATGACCCAGGATGACATCATGGAGTTAGAGATGGATGAGCTCAATCAACATGAATGTATGGCTCCCATGATAGCCCTGATTAAGCACATGCAGAGAAATGTGATTGCACCTAAGGGAGAAGAGGGTTCAATACCAAAAGATCTTCCACCGTGGATGAAATTTCTTCATGACAAACTAGGAAATGCATCAGTATCTTTAAATATCCGTCTCTTCTTAGCCAAGCTTGTTATTAATACAGAAGAGGTCTTTCGCCCTTATGCAAAGCACTGGCTCAGCCCCCTGCTACAGCTAGCTGTTTGCGAGAACAACAGAGAAGGAATTCACTACATGATGGTAGAAATAGTAGCTACCATTCTCTCTTGGACTGGCTTGGCTACACCTACAGGAGTCCCTAAAGATGAAGTGTTAGCAAATCGATTGCTTCGTTTTCTAATGAAGCATGTCTTCCATCCCAAAAGAGCTGTGTTTAGGCACAACCTTGAAATTATTAAAACCCTTGTTGAATGCTGGAAGGAGTGTCTTTCCATCCCTTACAGGTTAATATTTGAAAAATTTTCCCATAAGGACCCTAATTCTAAAGACAATTCTGTGGGAATTCAGTTATTAGGCATTGTGATAGCTAATAACTTGCCTCCCTATGACCCAAATTGTGACATAACCAGTGCCATGTATTTTGAAGCTTTAGTCAATAACATGTCCTTTGTGAAGTATAAAGAAGTATATGCAGCTGCAGCAGAAGTTTTAGGACTTATTCTTCAATACATTACTGAGAGAAAACACGTGATAGCAGAGTTGGTATGTGAACTGGTTATAAAACAACTGAAGCAACATCAAAATACTATGGAAGACAAATTTATTGTTTGCTTAAACAAAATAGCGAAGGGCTTCCCTCCTCTTGCTGACAGGTTCTTGAATGCTTTGTTCTTTCTGCTGCCAAAATTTCATGGAGTAATGAAGACACTTTGTCTGGAAGTTGTACTTTGTCGAGCAGAGGAGATCACAGGCCTATACTTACAGTTAAAGAGTAAAGACTTTCTTCAAGTCATGAGACATAGGTTGTGCCATGATGCATTTACAGAGAACATGGTGGGGGAGAGCCAGTTGCTGGAGAAGAGAAGACTTTATCATTGTGCTGCATACAACTGTGCCATTTCTCTGATAAGCTGTGTCTTCAATGAGTTGAAATTTTACCAAGGTTTTTTATTTAATGAAAAACCAGAAAAGAACTTGTTTATTTTTGAAAATTTGATAGACCTGAAACGTTGCTATACATTTCCTATAGAAGTTGAGGTTCCTATGGAAAGAAAGAAAAAGTACATTGAAATTAGGAAAGAGGCCAGGGATGCAGCAAATGGGGCTTCAGGCAGTCCTCATTATATGTCTTCATTGTCATATTTGACAGACAGTAGCCTAAGTGAAGAAATGAGTCAATTTGATTTCTCAACTGGAGTTCAGAGCTATTCATACAGTTCTCAAGATCGTAAACCTACCACTGGCCATTTTCAGAGACGGGAGCATCAAGATTCCATGACCCAGGATGACATCATGGAGTTAGAGATGGATGAGCTCAATCAACATGAATGTATGGCTCCCATGATAGCCCTGATTAAGCACATGCAGAGAAATGTGATTGCACCTAAGGGAGAAGAGGGTTCAATACCAAAAGATCTTCCACCGTGGATGAAATTTCTTCATGACAAACTAGGAAATGCATCAGTATCTTTAAATATCCGTCTCTTCTTAGCCAAGCTTGTTATTAATACAGAAGAGGTCTTTCGCCCTTATGCAAAGCACTGGCTCAGCCCCCTGCTACAGCTAGCTGTTTGCGAGAACAACAGAGAAGGAATTCACTACATGATGGTAGAAATAGTAGCTACCATTCTCTCTTGGACTGGCTTGGCTACACCTACAGGAGTCCCTAAAGATGAAGTGTTAGCAAATCGATTGCTTCGTTTTCTAATGAAGCATGTCTTCCATCCCAAAAGAGCTGTGTTTAGGCACAACCTTGAAATTATTAAAACCCTTGTTGAATGCTGGAAGGAGTGTCTTTCCATCCCTTACAGGTTAATATTTGAAAAATTTTCCCATAAGGACCCTAATTCTAAAGACAATTCTGTGGGAATTCAGTTATTAGGCATTGTGATAGCTAATAACTTGCCTCCCTATGACCCAAATTGTGACATAACCAGTGCCATGTATTTTGAAGCTTTAGTCAATAACATGTCCTTTGTGAAGTATAAAGAAGTATATGCAGCTGCAGCAGAAGTTTTAGGACTTATTCTTCAATACATTACTGAGAGAAAACACGTGATAGCAGAGTTGGTATGTGAACTGGTTATAAAACAACTGAAGCAACATCAAAATACTATGGAAGACAAATTTATTGTTTGCTTAAACAAAATAGCGAAGGGCTTCCCTCCTCTTGCTGACAGGTTCTTGAATGCTTTGTTCTTTCTGCTGCCAAAATTTCATGGAGTAATGAAGACACTTTGTCTGGAAGTTGTACTTTGTCGAGCAGAGGAGATCACAGGCCTATACTTACAGTTAAAGAGTAAAGACTTTCTTCAAGTCATGAGACAT
Peptide sequence:
MVGESQLLEKRRLYHCAAYNCAISLISCVFNELKFYQGFLFNEKPEKNLFIFENLIDLKRCYTFPIEVEVPMERKKKYIEIRKEARDAANGASGSPHYMSSLSYLTDSSLSEEMSQFDFSTGVQSYSYSSQDRKPTTGHFQRREHQDSMTQDDIMELEMDELNQHECMAPMIALIKHMQRNVIAPKGEEGSIPKDLPPWMKFLHDKLGNASVSLNIRLFLAKLVINTEEVFRPYAKHWLSPLLQLAVCENNREGIHYMMVEIVATILSWTGLATPTGVPKDEVLANRLLRFLMKHVFHPKRAVFRHNLEIIKTLVECWKECLSIPYRLIFEKFSHKDPNSKDNSVGIQLLGIVIANNLPPYDPNCDITSAMYFEALVNNMSFVKYKEVYAAAAEVLGLILQYITERKHVIAELVCELVIKQLKQHQNTMEDKFIVCLNKIAKGFPPLADRFLNALFFLLPKFHGVMKTLCLEVVLCRAEEITGLYLQLKSKDFLQVMRHRLCHDAFTENMVGESQLLEKRRLYHCAAYNCAISLISCVFNELKFYQGFLFNEKPEKNLFIFENLIDLKRCYTFPIEVEVPMERKKKYIEIRKEARDAANGASGSPHYMSSLSYLTDSSLSEEMSQFDFSTGVQSYSYSSQDRKPTTGHFQRREHQDSMTQDDIMELEMDELNQHECMAPMIALIKHMQRNVIAPKGEEGSIPKDLPPWMKFLHDKLGNASVSLNIRLFLAKLVINTEEVFRPYAKHWLSPLLQLAVCENNREGIHYMMVEIVATILSWTGLATPTGVPKDEVLANRLLRFLMKHVFHPKRAVFRHNLEIIKTLVECWKECLSIPYRLIFEKFSHKDPNSKDNSVGIQLLGIVIANNLPPYDPNCDITSAMYFEALVNNMSFVKYKEVYAAAAEVLGLILQYITERKHVIAELVCELVIKQLKQHQNTMEDKFIVCLNKIAKGFPPLADRFLNALFFLLPKFHGVMKTLCLEVVLCRAEEITGLYLQLKSKDFLQVMRH
IRESfinder result
IRESfinder score
0.76759521
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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