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mmu_circCdc42bpa_370
Basic information of circular RNA
PanCircBase ID:
mmu_circCdc42bpa_370
mm39_Chr. Position ID:
chr1|179896861|179902257|+
Gene name:
Cdc42bpa
Transcript:
ENSMUST00000097453.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
9,10,11
Exon/intron offsets:
0,3048,5273
Genomic length:
5396
Exon/intron sizes in nt:
8,01,67,123
Flanking exon/introns:
chr1:179894964-179896861|chr1:179902257-179911936
Splice length:
370
Other database IDs:
CIRCpedia: MMU_CIRCpedia_12253
Human Ortholog IDs:
Mature spliced Sequence:
GAAACAATGCCCCCACCAACACATACTGCATTTTCTGGCCATCATCTACCATTTGTTGGTTTTACATATACTAGTAGCTGTGTTCTTTCTGATCGGAGCTGTTTAAGAGTCACAGCAGGCCCCACCTCATTGGACCTTGATGTCAGTGTCCAGAGGACTCTAGACAATAACTTAGCAACTGAGGCTTATGAAAGGAGAATTAAGCGGCTTGAGCAGGAAAAGCTTGAACTGACTAGAAAACTTCAAGAGTCAACACAGACTGTTCAAGCTCTGCAATATTCAACTGTTGATGGTCCACTAACGGCAAGCAAAGATTTAGAAATTAAAAGTCTGAAAGAAGAGATTGAAAAACTAAGGAAACAAGTAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGGTCCACTAACGGCAAGC
60.68
TCCGATCAGAAAGAACACAGCT
59.7
178
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGATGGTCCACTAACGGCAA
59.31
TCCGATCAGAAAGAACACAGCT
59.7
180
PCR template sequence:
CTGCAATATTCAACTGTTGATGGTCCACTAACGGCAAGCAAAGATTTAGAAATTAAAAGTCTGAAAGAAGAGATTGAAAAACTAAGGAAACAAGTAGCAGGAAACAATGCCCCCACCAACACATACTGCATTTTCTGGCCATCATCTACCATTTGTTGGTTTTACATATACTAGTAGCTGTGTTCTTTCTGATCGGAGCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-383-5p(1), mmu-miR-1198-5p(1), mmu-miR-3061-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAACAAGTAGCAGGAAACAATGCCCC
siRNA sets
TTGTTTCCTGCTACTTGTT, CATTGTTTCCTGCTACTTG, ATTGTTTCCTGCTACTTGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDC42BPA_370_ORF_1
0.8087
-0.106027723
0.26322512
438
ORF sequence:
ATGCCCCCACCAACACATACTGCATTTTCTGGCCATCATCTACCATTTGTTGGTTTTACATATACTAGTAGCTGTGTTCTTTCTGATCGGAGCTGTTTAAGAGTCACAGCAGGCCCCACCTCATTGGACCTTGATGTCAGTGTCCAGAGGACTCTAGACAATAACTTAGCAACTGAGGCTTATGAAAGGAGAATTAAGCGGCTTGAGCAGGAAAAGCTTGAACTGACTAGAAAACTTCAAGAGTCAACACAGACTGTTCAAGCTCTGCAATATTCAACTGTTGATGGTCCACTAACGGCAAGCAAAGATTTAGAAATTAAAAGTCTGAAAGAAGAGATTGAAAAACTAAGGAAACAAGTAGCAGGAAACAATGCCCCCACCAACACATACTGCATTTTCTGGCCATCATCTACCATTTGTTGGTTTTACATATACTAG
Peptide sequence:
MPPPTHTAFSGHHLPFVGFTYTSSCVLSDRSCLRVTAGPTSLDLDVSVQRTLDNNLATEAYERRIKRLEQEKLELTRKLQESTQTVQALQYSTVDGPLTASKDLEIKSLKEEIEKLRKQVAGNNAPTNTYCIFWPSSTICWFYIY
IRESfinder result
IRESfinder score
0.685974565
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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