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mmu_circPrkcb_1042
Basic information of circular RNA
PanCircBase ID:
mmu_circPrkcb_1042
mm39_Chr. Position ID:
chr7|122127698|122200053|+
Gene name:
Prkcb
Transcript:
ENSMUST00000143692.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
8,9,10,11,12,13,14,15,16
Exon/intron offsets:
0,16157,39658,53954,55922,61569,66127,66490,72214
Genomic length:
72355
Exon/intron sizes in nt:
97,14,71,74,92,63,13,90,00,00,000
Flanking exon/introns:
chr7:122117402-122127698|chr7:122200053-122226878
Splice length:
1042
Other database IDs:
CIRCpedia: MMU_CIRCpedia_5800, circAtlas: mmu-Prkcb_0045
circBase: hsa_circ_0038656, circAtlas: hsa-PRKCB_0080
Human Ortholog IDs:
Mature spliced Sequence:
GTTCAAGTTACTAAGCCAGGAAGAGGGTGAATACTTCAATGTGCCCGTGCCGCCCGAAGGAAGCGAGGGCAATGAAGAGCTGCGGCAGAAGTTTGAGAGAGCCAAGATTGGCCAAGGTACCAAGGCTCCAGAAGAAAAGACAGCTAACACTATCTCCAAATTTGACAACAATGGCAACAGGGACCGGATGAAACTGACCGATTTTAACTTCCTGATGGTGCTGGGGAAAGGCAGCTTTGGCAAGGTCATGCTCTCAGAGCGGAAGGGTACAGATGAACTCTATGCCGTGAAGATCCTGAAGAAGGACGTGGTGATCCAAGATGACGATGTGGAGTGCACCATGGTGGAGAAGCGGGTGCTGGCCCTGCCTGGGAAGCCCCCGTTCCTGACTCAGCTCCATTCCTGCTTCCAGACCATGGACCGCCTGTACTTTGTGATGGAGTATGTGAACGGGGGTGACCTCATGTACCACATCCAACAAGTTGGCCGTTTCAAGGAGCCCCATGCTGTATTTTACGCCGCAGAGATTGCCATCGGTCTGTTCTTCTTGCAGAGCAAGGGCATTATTTACCGCGACCTGAAACTTGACAACGTGATGCTGGATTCTGAGGGGCACATCAAAATCGCTGACTTTGGCATGTGTAAGGAGAACATCTGGGATGGGGTGACAACCAAGACATTCTGTGGCACTCCGGACTACATTGCTCCAGAGATCATTGCTTATCAGCCCTACGGGAAGTCTGTGGACTGGTGGGCATTTGGAGTCCTGCTGTATGAAATGTTGGCTGGCCAGGCACCGTTTGAAGGGGAGGATGAGGATGAACTCTTCCAGTCAATCATGGAACACAATGTGGCGTATCCCAAGTCCATGTCCAAGGAAGCCGTGGCAATCTGCAAAGGGCTAATGACCAAACACCCAGGCAAGCGCCTGGGTTGTGGGCCTGAAGGGGAACGAGACATTAAGGAGCATGCGTTTTTCCGGTATATTGACTGGGAGAAACTCGAACGCAAGGAGATTCAGCCACCTTATAAACCAAAAGCT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGGAGCATGCGTTTTTCCG
59.76
TTCATTGCCCTCGCTTCCTT
59.96
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGGAGAAACTCGAACGCAA
59.89
TTCTGCCGCAGCTCTTCATT
60.32
141
PCR template sequence:
TGAAGGGGAACGAGACATTAAGGAGCATGCGTTTTTCCGGTATATTGACTGGGAGAAACTCGAACGCAAGGAGATTCAGCCACCTTATAAACCAAAAGCTGTTCAAGTTACTAAGCCAGGAAGAGGGTGAATACTTCAATGTGCCCGTGCCGCCCGAAGGAAGCGAGGGCAATGAAGAGCTGCGGCAGAAGTTTGAGAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-221-3p(1), mmu-miR-223-3p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-1198-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TAAACCAAAAGCTGTTCAAGTTACTA
siRNA sets
TAACTTGAACAGCTTTTGG,AACTTGAACAGCTTTTGGT,GTAACTTGAACAGCTTTTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPRKCB_1042_ORF_1
1.2362
0.441133683
0.998956476
1116
ORF sequence:
ATGCGTTTTTCCGGTATATTGACTGGGAGAAACTCGAACGCAAGGAGATTCAGCCACCTTATAAACCAAAAGCTGTTCAAGTTACTAAGCCAGGAAGAGGGTGAATACTTCAATGTGCCCGTGCCGCCCGAAGGAAGCGAGGGCAATGAAGAGCTGCGGCAGAAGTTTGAGAGAGCCAAGATTGGCCAAGGTACCAAGGCTCCAGAAGAAAAGACAGCTAACACTATCTCCAAATTTGACAACAATGGCAACAGGGACCGGATGAAACTGACCGATTTTAACTTCCTGATGGTGCTGGGGAAAGGCAGCTTTGGCAAGGTCATGCTCTCAGAGCGGAAGGGTACAGATGAACTCTATGCCGTGAAGATCCTGAAGAAGGACGTGGTGATCCAAGATGACGATGTGGAGTGCACCATGGTGGAGAAGCGGGTGCTGGCCCTGCCTGGGAAGCCCCCGTTCCTGACTCAGCTCCATTCCTGCTTCCAGACCATGGACCGCCTGTACTTTGTGATGGAGTATGTGAACGGGGGTGACCTCATGTACCACATCCAACAAGTTGGCCGTTTCAAGGAGCCCCATGCTGTATTTTACGCCGCAGAGATTGCCATCGGTCTGTTCTTCTTGCAGAGCAAGGGCATTATTTACCGCGACCTGAAACTTGACAACGTGATGCTGGATTCTGAGGGGCACATCAAAATCGCTGACTTTGGCATGTGTAAGGAGAACATCTGGGATGGGGTGACAACCAAGACATTCTGTGGCACTCCGGACTACATTGCTCCAGAGATCATTGCTTATCAGCCCTACGGGAAGTCTGTGGACTGGTGGGCATTTGGAGTCCTGCTGTATGAAATGTTGGCTGGCCAGGCACCGTTTGAAGGGGAGGATGAGGATGAACTCTTCCAGTCAATCATGGAACACAATGTGGCGTATCCCAAGTCCATGTCCAAGGAAGCCGTGGCAATCTGCAAAGGGCTAATGACCAAACACCCAGGCAAGCGCCTGGGTTGTGGGCCTGAAGGGGAACGAGACATTAAGGAGCATGCGTTTTTCCGGTATATTGACTGGGAGAAACTCGAACGCAAGGAGATTCAGCCACCTTATAAACCAAAAGCT
Peptide sequence:
MRFSGILTGRNSNARRFSHLINQKLFKLLSQEEGEYFNVPVPPEGSEGNEELRQKFERAKIGQGTKAPEEKTANTISKFDNNGNRDRMKLTDFNFLMVLGKGSFGKVMLSERKGTDELYAVKILKKDVVIQDDDVECTMVEKRVLALPGKPPFLTQLHSCFQTMDRLYFVMEYVNGGDLMYHIQQVGRFKEPHAVFYAAEIAIGLFFLQSKGIIYRDLKLDNVMLDSEGHIKIADFGMCKENIWDGVTTKTFCGTPDYIAPEIIAYQPYGKSVDWWAFGVLLYEMLAGQAPFEGEDEDELFQSIMEHNVAYPKSMSKEAVAICKGLMTKHPGKRLGCGPEGERDIKEHAFFRYIDWEKLERKEIQPPYKPKA
IRESfinder result
IRESfinder score
0.315814808
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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