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mmu_circCdc42bpb_287
Basic information of circular RNA
PanCircBase ID:
mmu_circCdc42bpb_287
mm39_Chr. Position ID:
chr12|111289236|111289607|-
Gene name:
Cdc42bpb
Transcript:
ENSMUST00000041965.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
11,10
Exon/intron offsets:
0,204
Genomic length:
371
Exon/intron sizes in nt:
120,167
Flanking exon/introns:
chr12:111288038-111289236|chr12:111289607-111291417
Splice length:
287
Other database IDs:
CIRCpedia: MMU_CIRCpedia_38862, circAtlas: mmu-Cdc42bpb_0007
circAtlas: hsa-CDC42BPB_0100, CIRCpedia: HSA_CIRCpedia_85322
Human Ortholog IDs:
Mature spliced Sequence:
CTGCTTTTCTGACCGGGGCTCTCTGAAGAGCATGACTCAGTCTAACACGCTAACCAAAGACGAAGATGTGCAGCGGGACTTGGAGAACAGCTTGCAGATCGAAGCGTACGAGCGAAGGATACGGAGGCTGGAGCAGGAGAAGCTGGAGCTCAGCCGGAAGCTGCAAGAATCCACCCAGACTGTGCAGTCCCTTCACGGTTCCACACGGGCCCTGGGCAACTCAAACCGCGACAAGGAAATCAAGAGGCTGAATGAAGAGCTTGAACGCATGAAGAGTAAAATGGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAACTCAAACCGCGACAAGG
60.04
AAGCTGTTCTCCAAGTCCCG
59.96
164
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTCAAACCGCGACAAGGAA
60.18
AAGCTGTTCTCCAAGTCCCG
59.96
162
PCR template sequence:
TCCCTTCACGGTTCCACACGGGCCCTGGGCAACTCAAACCGCGACAAGGAAATCAAGAGGCTGAATGAAGAGCTTGAACGCATGAAGAGTAAAATGGCAGCTGCTTTTCTGACCGGGGCTCTCTGAAGAGCATGACTCAGTCTAACACGCTAACCAAAGACGAAGATGTGCAGCGGGACTTGGAGAACAGCTTGCAGATC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
AGTAAAATGGCAGCTGCTTTTCTGAC
siRNA sets
AAAGCAGCTGCCATTTTAC, AAAAGCAGCTGCCATTTTA, AAGCAGCTGCCATTTTACT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDC42BPB_287_ORF_1
1.1964
0.506229251
0.745185126
282
ORF sequence:
ATGACTCAGTCTAACACGCTAACCAAAGACGAAGATGTGCAGCGGGACTTGGAGAACAGCTTGCAGATCGAAGCGTACGAGCGAAGGATACGGAGGCTGGAGCAGGAGAAGCTGGAGCTCAGCCGGAAGCTGCAAGAATCCACCCAGACTGTGCAGTCCCTTCACGGTTCCACACGGGCCCTGGGCAACTCAAACCGCGACAAGGAAATCAAGAGGCTGAATGAAGAGCTTGAACGCATGAAGAGTAAAATGGCAGCTGCTTTTCTGACCGGGGCTCTCTGA
Peptide sequence:
MTQSNTLTKDEDVQRDLENSLQIEAYERRIRRLEQEKLELSRKLQESTQTVQSLHGSTRALGNSNRDKEIKRLNEELERMKSKMAAAFLTGAL
IRESfinder result
IRESfinder score
0.179878847
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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