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mmu_circPlcb4_820
Basic information of circular RNA
PanCircBase ID:
mmu_circPlcb4_820
mm39_Chr. Position ID:
chr2|135780179|135796919|+
Gene name:
Plcb4
Transcript:
ENSMUST00000134310.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
9,10,11,12,13,14,15,16
Exon/intron offsets:
0,950,1687,8786,11952,13733,16086,16655
Genomic length:
16740
Exon/intron sizes in nt:
82,101,58,109,211,94,80,85
Flanking exon/introns:
chr2:135774222-135780179|chr2:135796919-135799974
Splice length:
820
Other database IDs:
circAtlas: mmu-Plcb4_0023
Human Ortholog IDs:
Mature spliced Sequence:
TATCACTAGAACCTTCGCATCAGGGAAAACAGAAAAGGTGATCTTTCAAGCCCTCAAGGAACTAGGTCTTCCCAGTGGAAAGAATGATGAAATTGAACCTGCTGCATTTACTTATGAAAAGTTCTATGAACTGACACAAAAGATTTGTCCTCGGACAGATATAGAAGATCTTTTTAAAAAAATCAATGGAGACAAAACTGATTATTTAACGGTAGACCAATTAGTGAGCTTTCTAAACGAACATCAGCGAGATCCTCGGCTGAATGAAATTTTATTCCCATTTTATGATGCTAAAAGAGCAATGCAGATCATTGAAATGTATGAGCCTGATGAAGAGCTGAAGAAAAAAGGCCTCATATCCAGTGATGGATTCTGCAGATATCTGATGTCAGATGAAAATGCCCCTGTCTTCTTAGATCGCTTAGAACTTTACCAGGAGATGGACCACCCGCTGGCTCATTACTTCATCAGTTCCTCCCACAACACCTATCTCACTGGCCGGCAATTTGGAGGAAAGTCTTCAGTGGAAATGTACAGACAAGTTCTCCTGGCTGGTTGCAGGTGTGTTGAACTTGACTGTTGGGATGGAAAAGGTGAAGATCAGGAACCGATAATAACTCACGGAAAAGCAATGTGTACAGACATCCTTTTTAAGGATGTAATCCAGGCCATCAAGGAAACGGCGTTTGTCACATCAGAATACCCTGTCATTCTCTCCTTCGAAAACCACTGCAGCAAATATCAACAGTACAAGATGTCCAAGTATTGTGAAGATCTATTTGGGGATCTCCTGTTGAAACAAGCACTTGAGTCGCATCCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGAAAACCACTGCAGCAAAT
57.86
AGACCTAGTTCCTTGAGGGCT
59.92
169
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGAAAACCACTGCAGCAAAT
57.86
GACCTAGTTCCTTGAGGGCT
58.43
168
PCR template sequence:
CGAAAACCACTGCAGCAAATATCAACAGTACAAGATGTCCAAGTATTGTGAAGATCTATTTGGGGATCTCCTGTTGAAACAAGCACTTGAGTCGCATCCATATCACTAGAACCTTCGCATCAGGGAAAACAGAAAAGGTGATCTTTCAAGCCCTCAAGGAACTAGGTCTTCCCAGTGGAAAGAATGATGAAATTGAACCT
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-140-5p(1), mmu-miR-7b-5p(1), mmu-miR-223-3p(1), mmu-miR-33-5p(1), mmu-miR-7a-5p(1), mmu-miR-185-5p(1), mmu-miR-136-5p(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGAGTCGCATCCATATCACTAGAACC
siRNA sets
GTTCTAGTGATATGGATGC, CTAGTGATATGGATGCGAC, TAGTGATATGGATGCGACT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPLCB4_820_ORF_1
0.8168
0.163887019
0.672118336
528
ORF sequence:
ATGCAGATCATTGAAATGTATGAGCCTGATGAAGAGCTGAAGAAAAAAGGCCTCATATCCAGTGATGGATTCTGCAGATATCTGATGTCAGATGAAAATGCCCCTGTCTTCTTAGATCGCTTAGAACTTTACCAGGAGATGGACCACCCGCTGGCTCATTACTTCATCAGTTCCTCCCACAACACCTATCTCACTGGCCGGCAATTTGGAGGAAAGTCTTCAGTGGAAATGTACAGACAAGTTCTCCTGGCTGGTTGCAGGTGTGTTGAACTTGACTGTTGGGATGGAAAAGGTGAAGATCAGGAACCGATAATAACTCACGGAAAAGCAATGTGTACAGACATCCTTTTTAAGGATGTAATCCAGGCCATCAAGGAAACGGCGTTTGTCACATCAGAATACCCTGTCATTCTCTCCTTCGAAAACCACTGCAGCAAATATCAACAGTACAAGATGTCCAAGTATTGTGAAGATCTATTTGGGGATCTCCTGTTGAAACAAGCACTTGAGTCGCATCCATATCACTAG
Peptide sequence:
MQIIEMYEPDEELKKKGLISSDGFCRYLMSDENAPVFLDRLELYQEMDHPLAHYFISSSHNTYLTGRQFGGKSSVEMYRQVLLAGCRCVELDCWDGKGEDQEPIITHGKAMCTDILFKDVIQAIKETAFVTSEYPVILSFENHCSKYQQYKMSKYCEDLFGDLLLKQALESHPYH
IRESfinder result
IRESfinder score
0.613985472
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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