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mmu_circPrkcb_418
Basic information of circular RNA
PanCircBase ID:
mmu_circPrkcb_418
mm39_Chr. Position ID:
chr7|122127698|122167530|+
Gene name:
Prkcb
Transcript:
ENSMUST00000143692.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
8,9,10
Exon/intron offsets:
0,16157,39658
Genomic length:
39832
Exon/intron sizes in nt:
9,71,47,174
Flanking exon/introns:
chr7:122117402-122127698|chr7:122167530-122181652
Splice length:
418
Other database IDs:
CIRCpedia: MMU_CIRCpedia_37096, circAtlas: mmu-Prkcb_0016
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_143933
Human Ortholog IDs:
Mature spliced Sequence:
GTTCAAGTTACTAAGCCAGGAAGAGGGTGAATACTTCAATGTGCCCGTGCCGCCCGAAGGAAGCGAGGGCAATGAAGAGCTGCGGCAGAAGTTTGAGAGAGCCAAGATTGGCCAAGGTACCAAGGCTCCAGAAGAAAAGACAGCTAACACTATCTCCAAATTTGACAACAATGGCAACAGGGACCGGATGAAACTGACCGATTTTAACTTCCTGATGGTGCTGGGGAAAGGCAGCTTTGGCAAGGTCATGCTCTCAGAGCGGAAGGGTACAGATGAACTCTATGCCGTGAAGATCCTGAAGAAGGACGTGGTGATCCAAGATGACGATGTGGAGTGCACCATGGTGGAGAAGCGGGTGCTGGCCCTGCCTGGGAAGCCCCCGTTCCTGACTCAGCTCCATTCCTGCTTCCAGACCATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGTGCACCATGGTGGAGAA
59.96
TTCATTGCCCTCGCTTCCTT
59.96
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTGCACCATGGTGGAGAAG
59.96
TTCATTGCCCTCGCTTCCTT
59.96
162
PCR template sequence:
AGATGACGATGTGGAGTGCACCATGGTGGAGAAGCGGGTGCTGGCCCTGCCTGGGAAGCCCCCGTTCCTGACTCAGCTCCATTCCTGCTTCCAGACCATGGTTCAAGTTACTAAGCCAGGAAGAGGGTGAATACTTCAATGTGCCCGTGCCGCCCGAAGGAAGCGAGGGCAATGAAGAGCTGCGGCAGAAGTTTGAGAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-223-3p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTTCCAGACCATGGTTCAAGTTACTA
siRNA sets
TAGTAACTTGAACCATGGT, TAACTTGAACCATGGTCTG, ACTTGAACCATGGTCTGGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPRKCB_418_ORF_1
1.2542
0.479352239
0.713621133
261
ORF sequence:
ATGAAACTGACCGATTTTAACTTCCTGATGGTGCTGGGGAAAGGCAGCTTTGGCAAGGTCATGCTCTCAGAGCGGAAGGGTACAGATGAACTCTATGCCGTGAAGATCCTGAAGAAGGACGTGGTGATCCAAGATGACGATGTGGAGTGCACCATGGTGGAGAAGCGGGTGCTGGCCCTGCCTGGGAAGCCCCCGTTCCTGACTCAGCTCCATTCCTGCTTCCAGACCATGGTTCAAGTTACTAAGCCAGGAAGAGGGTGA
Peptide sequence:
MKLTDFNFLMVLGKGSFGKVMLSERKGTDELYAVKILKKDVVIQDDDVECTMVEKRVLALPGKPPFLTQLHSCFQTMVQVTKPGRG
IRESfinder result
IRESfinder score
0.278515823
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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