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mmu_circCcdc88a_306
Basic information of circular RNA
PanCircBase ID:
mmu_circCcdc88a_306
mm39_Chr. Position ID:
chr11|29403118|29405516|+
Gene name:
Ccdc88a
Transcript:
ENSMUST00000040182.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
10,11
Exon/intron offsets:
0,2251
Genomic length:
2398
Exon/intron sizes in nt:
1,59,147
Flanking exon/introns:
chr11:29401103-29403118|chr11:29405516-29406457
Splice length:
306
Other database IDs:
CIRCpedia: MMU_CIRCpedia_15457
Human Ortholog IDs:
Mature spliced Sequence:
AACATGAATTTGCTTTCGGATGCTCGATCTGCTAGAATGTACCGAGATGAATTGGATGCCCTCCGAGAGAAAGCAGTCAGAGTTGATAAGCTTGAAAGTGAACTCAGTAGATATAAAGAGAGACTACATGATATTGAATTTTATAAGGCAAGAGTTGAGGAATTAAAAGAAGATAATCAAGTTTTATTAGAAACAAAAACTATGCTGGAAGACCAACTAGAAGGAACTCGGGCTCGTTCTGACAAACTACATGAATTAGAAAAAGAGAATTTACAACTAAAGGCTAAATTGCATGATATGGAGATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTCGGGCTCGTTCTGACAAA
60.32
CTTTCTCTCGGAGGGCATCC
59.89
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TAGAAGGAACTCGGGCTCGT
60.32
CTTTCTCTCGGAGGGCATCC
59.89
162
PCR template sequence:
GGAAGACCAACTAGAAGGAACTCGGGCTCGTTCTGACAAACTACATGAATTAGAAAAAGAGAATTTACAACTAAAGGCTAAATTGCATGATATGGAGATGAACATGAATTTGCTTTCGGATGCTCGATCTGCTAGAATGTACCGAGATGAATTGGATGCCCTCCGAGAGAAAGCAGTCAGAGTTGATAAGCTTGAAAGTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGATATGGAGATGAACATGAATTTGC
siRNA sets
CAAATTCATGTTCATCTCC,AAATTCATGTTCATCTCCA,AATTCATGTTCATCTCCAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCCDC88A_306_ORF_1
1.138
0.10667276
0.844191103
609
ORF sequence:
ATGAATTTGCTTTCGGATGCTCGATCTGCTAGAATGTACCGAGATGAATTGGATGCCCTCCGAGAGAAAGCAGTCAGAGTTGATAAGCTTGAAAGTGAACTCAGTAGATATAAAGAGAGACTACATGATATTGAATTTTATAAGGCAAGAGTTGAGGAATTAAAAGAAGATAATCAAGTTTTATTAGAAACAAAAACTATGCTGGAAGACCAACTAGAAGGAACTCGGGCTCGTTCTGACAAACTACATGAATTAGAAAAAGAGAATTTACAACTAAAGGCTAAATTGCATGATATGGAGATGAACATGAATTTGCTTTCGGATGCTCGATCTGCTAGAATGTACCGAGATGAATTGGATGCCCTCCGAGAGAAAGCAGTCAGAGTTGATAAGCTTGAAAGTGAACTCAGTAGATATAAAGAGAGACTACATGATATTGAATTTTATAAGGCAAGAGTTGAGGAATTAAAAGAAGATAATCAAGTTTTATTAGAAACAAAAACTATGCTGGAAGACCAACTAGAAGGAACTCGGGCTCGTTCTGACAAACTACATGAATTAGAAAAAGAGAATTTACAACTAAAGGCTAAATTGCATGATATGGAGATG
Peptide sequence:
MNLLSDARSARMYRDELDALREKAVRVDKLESELSRYKERLHDIEFYKARVEELKEDNQVLLETKTMLEDQLEGTRARSDKLHELEKENLQLKAKLHDMEMNMNLLSDARSARMYRDELDALREKAVRVDKLESELSRYKERLHDIEFYKARVEELKEDNQVLLETKTMLEDQLEGTRARSDKLHELEKENLQLKAKLHDMEM
IRESfinder result
IRESfinder score
0.496449264
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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