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mmu_circPrkdc_651
Basic information of circular RNA
PanCircBase ID:
mmu_circPrkdc_651
mm39_Chr. Position ID:
chr16|15589887|15595024|+
Gene name:
Prkdc
Transcript:
ENSMUST00000023352.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
58,59,60,61
Exon/intron offsets:
0,1575,3833,5005
Genomic length:
5137
Exon/intron sizes in nt:
1,90,21,61,13,132
Flanking exon/introns:
chr16:15587865-15589887|chr16:15595024-15597241
Splice length:
651
Other database IDs:
circAtlas: mmu-Prkdc_0019
CIRCpedia: HSA_CIRCpedia_89226
Human Ortholog IDs:
Mature spliced Sequence:
GAATATACTATAGATCCTGACTGGCGTTTTCGTAGTACTGTTCTTACTCCGATGTTTATTGAGACCCAGGCCTCTCCAAGTATTCTCCATACCCAAACCCAAGAAGGGCCCCTCTCAGACCAAAGGCAGAAGCCTGGACAAGTGCGGGCCACCCAACAACAATATGATTTCACTCCAACACAAGCTTCAGTTGAAAGGAGCTCATTTGATTGGCTGACTGGGAGCAGCATTGACCTACTGGCGGATCACACCGTCTTCTCTTCAGAGACCTTGTCTTCCTCCTTGCTGTTTTCCCACAAAAGGACTGAAAAGTCACAGAGAATGTCTTGTAAGTCAGTAGGACCGGACTTTGGAACAAAAAAGCTGGGCCTTCCTGATGATGAGGTGGATAACCAAGTGAAAAGTGGCACTCCGAGCCAGGCAGATATTCTGAGATTGCGCAGAAGATTTTTAAAGGACCGAGAAAAGTTGAGTTTGCTGTATGCCAAAAGGGGCCTCATGGAACAAAAACTAGAGAAGGATATCAAGAGTGAGTTTAAAATGAAGCAGGATGCGCAGGTTGTTCTGTACAGAAGTTATCGTCATGGCGATCTTCCTGATATCCAGATCCAGCACAGTGGTCTGATCACCCCCTTGCAGGCTGTGGCCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGTCATGGCGATCTTCCTGA
59.9
ATACTTGGAGAGGCCTGGGT
59.96
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCGTCATGGCGATCTTCCTG
59.9
ATACTTGGAGAGGCCTGGGT
59.96
156
PCR template sequence:
TGCGCAGGTTGTTCTGTACAGAAGTTATCGTCATGGCGATCTTCCTGATATCCAGATCCAGCACAGTGGTCTGATCACCCCCTTGCAGGCTGTGGCCCAGGAATATACTATAGATCCTGACTGGCGTTTTCGTAGTACTGTTCTTACTCCGATGTTTATTGAGACCCAGGCCTCTCCAAGTATTCTCCATACCCAAACCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-101a-3p(1), mmu-miR-7a-5p(1), mmu-miR-149-5p(1), mmu-miR-383-5p(1), mmu-miR-669d-5p(1), mmu-miR-3087-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGCTGTGGCCCAGGAATATACTATAG
siRNA sets
TATAGTATATTCCTGGGCC, CTATAGTATATTCCTGGGC, TATATTCCTGGGCCACAGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPRKDC_651_ORF_1
0.9447
0.163587089
0.997933272
1251
ORF sequence:
ATGTTTATTGAGACCCAGGCCTCTCCAAGTATTCTCCATACCCAAACCCAAGAAGGGCCCCTCTCAGACCAAAGGCAGAAGCCTGGACAAGTGCGGGCCACCCAACAACAATATGATTTCACTCCAACACAAGCTTCAGTTGAAAGGAGCTCATTTGATTGGCTGACTGGGAGCAGCATTGACCTACTGGCGGATCACACCGTCTTCTCTTCAGAGACCTTGTCTTCCTCCTTGCTGTTTTCCCACAAAAGGACTGAAAAGTCACAGAGAATGTCTTGTAAGTCAGTAGGACCGGACTTTGGAACAAAAAAGCTGGGCCTTCCTGATGATGAGGTGGATAACCAAGTGAAAAGTGGCACTCCGAGCCAGGCAGATATTCTGAGATTGCGCAGAAGATTTTTAAAGGACCGAGAAAAGTTGAGTTTGCTGTATGCCAAAAGGGGCCTCATGGAACAAAAACTAGAGAAGGATATCAAGAGTGAGTTTAAAATGAAGCAGGATGCGCAGGTTGTTCTGTACAGAAGTTATCGTCATGGCGATCTTCCTGATATCCAGATCCAGCACAGTGGTCTGATCACCCCCTTGCAGGCTGTGGCCCAGGAATATACTATAGATCCTGACTGGCGTTTTCGTAGTACTGTTCTTACTCCGATGTTTATTGAGACCCAGGCCTCTCCAAGTATTCTCCATACCCAAACCCAAGAAGGGCCCCTCTCAGACCAAAGGCAGAAGCCTGGACAAGTGCGGGCCACCCAACAACAATATGATTTCACTCCAACACAAGCTTCAGTTGAAAGGAGCTCATTTGATTGGCTGACTGGGAGCAGCATTGACCTACTGGCGGATCACACCGTCTTCTCTTCAGAGACCTTGTCTTCCTCCTTGCTGTTTTCCCACAAAAGGACTGAAAAGTCACAGAGAATGTCTTGTAAGTCAGTAGGACCGGACTTTGGAACAAAAAAGCTGGGCCTTCCTGATGATGAGGTGGATAACCAAGTGAAAAGTGGCACTCCGAGCCAGGCAGATATTCTGAGATTGCGCAGAAGATTTTTAAAGGACCGAGAAAAGTTGAGTTTGCTGTATGCCAAAAGGGGCCTCATGGAACAAAAACTAGAGAAGGATATCAAGAGTGAGTTTAAAATGAAGCAGGATGCGCAGGTTGTTCTGTACAGAAGTTATCGTCATGGCGATCTTCCTGATATCCAGATCCAGCACAGTGGTCTGATCACCCCCTTGCAGGCTGTGGCCCAG
Peptide sequence:
MFIETQASPSILHTQTQEGPLSDQRQKPGQVRATQQQYDFTPTQASVERSSFDWLTGSSIDLLADHTVFSSETLSSSLLFSHKRTEKSQRMSCKSVGPDFGTKKLGLPDDEVDNQVKSGTPSQADILRLRRRFLKDREKLSLLYAKRGLMEQKLEKDIKSEFKMKQDAQVVLYRSYRHGDLPDIQIQHSGLITPLQAVAQEYTIDPDWRFRSTVLTPMFIETQASPSILHTQTQEGPLSDQRQKPGQVRATQQQYDFTPTQASVERSSFDWLTGSSIDLLADHTVFSSETLSSSLLFSHKRTEKSQRMSCKSVGPDFGTKKLGLPDDEVDNQVKSGTPSQADILRLRRRFLKDREKLSLLYAKRGLMEQKLEKDIKSEFKMKQDAQVVLYRSYRHGDLPDIQIQHSGLITPLQAVAQ
IRESfinder result
IRESfinder score
0.61725234
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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