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mmu_circCdc42bpa_619
Basic information of circular RNA
PanCircBase ID:
mmu_circCdc42bpa_619
mm39_Chr. Position ID:
chr1|179894715|179902257|+
Gene name:
Cdc42bpa
Transcript:
ENSMUST00000097453.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
8,9,10,11
Exon/intron offsets:
0,2146,5194,7419
Genomic length:
7542
Exon/intron sizes in nt:
24,98,01,67,123
Flanking exon/introns:
chr1:179892731-179894715|chr1:179902257-179911936
Splice length:
619
Other database IDs:
CIRCpedia: MMU_CIRCpedia_226776, circAtlas: mmu-Cdc42bpa_0062
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_348085
Human Ortholog IDs:
Mature spliced Sequence:
GAGCGGTTTCAGTTTCCAGCCCAAGTGACAGACGTGTCCGAAAATGCTAAAGATCTTATTCGAAGACTCATTTGTAGTAGAGAACATCGACTTGGCCAAAATGGAATAGAAGACTTTAAGAAGCATCCATTCTTCAGTGGAATTGATTGGGATAACATTCGGAATTGTGAAGCACCTTACATCCCAGAAGTTAGTAGCCCGACAGATACGTCAAATTTTGATGTGGATGACGACTGTTTAAAAAATTCTGAAACAATGCCCCCACCAACACATACTGCATTTTCTGGCCATCATCTACCATTTGTTGGTTTTACATATACTAGTAGCTGTGTTCTTTCTGATCGGAGCTGTTTAAGAGTCACAGCAGGCCCCACCTCATTGGACCTTGATGTCAGTGTCCAGAGGACTCTAGACAATAACTTAGCAACTGAGGCTTATGAAAGGAGAATTAAGCGGCTTGAGCAGGAAAAGCTTGAACTGACTAGAAAACTTCAAGAGTCAACACAGACTGTTCAAGCTCTGCAATATTCAACTGTTGATGGTCCACTAACGGCAAGCAAAGATTTAGAAATTAAAAGTCTGAAAGAAGAGATTGAAAAACTAAGGAAACAAGTAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGGTCCACTAACGGCAAGC
60.68
TGGCCAAGTCGATGTTCTCT
59.02
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGTCCACTAACGGCAAGCAA
60.89
TGGCCAAGTCGATGTTCTCT
59.02
177
PCR template sequence:
CTGCAATATTCAACTGTTGATGGTCCACTAACGGCAAGCAAAGATTTAGAAATTAAAAGTCTGAAAGAAGAGATTGAAAAACTAAGGAAACAAGTAGCAGGAGCGGTTTCAGTTTCCAGCCCAAGTGACAGACGTGTCCGAAAATGCTAAAGATCTTATTCGAAGACTCATTTGTAGTAGAGAACATCGACTTGGCCAAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-18a-5p(1), mmu-miR-132-3p(1), mmu-miR-212-3p(1), mmu-miR-383-5p(1), mmu-miR-1198-5p(1), mmu-miR-3061-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAACAAGTAGCAGGAGCGGTTTCAGT
siRNA sets
AAACCGCTCCTGCTACTTG, AACCGCTCCTGCTACTTGT, TGAAACCGCTCCTGCTACT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDC42BPA_619_ORF_1
1.0429
-0.070138117
0.347098932
414
ORF sequence:
ATGCCCCCACCAACACATACTGCATTTTCTGGCCATCATCTACCATTTGTTGGTTTTACATATACTAGTAGCTGTGTTCTTTCTGATCGGAGCTGTTTAAGAGTCACAGCAGGCCCCACCTCATTGGACCTTGATGTCAGTGTCCAGAGGACTCTAGACAATAACTTAGCAACTGAGGCTTATGAAAGGAGAATTAAGCGGCTTGAGCAGGAAAAGCTTGAACTGACTAGAAAACTTCAAGAGTCAACACAGACTGTTCAAGCTCTGCAATATTCAACTGTTGATGGTCCACTAACGGCAAGCAAAGATTTAGAAATTAAAAGTCTGAAAGAAGAGATTGAAAAACTAAGGAAACAAGTAGCAGGAGCGGTTTCAGTTTCCAGCCCAAGTGACAGACGTGTCCGAAAATGCTAA
Peptide sequence:
MPPPTHTAFSGHHLPFVGFTYTSSCVLSDRSCLRVTAGPTSLDLDVSVQRTLDNNLATEAYERRIKRLEQEKLELTRKLQESTQTVQALQYSTVDGPLTASKDLEIKSLKEEIEKLRKQVAGAVSVSSPSDRRVRKC
IRESfinder result
IRESfinder score
0.685187219
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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