top of page
mmu_circCcdc39_677
Basic information of circular RNA
PanCircBase ID:
mmu_circCcdc39_677
mm39_Chr. Position ID:
chr3|33884805|33892113|-
Gene name:
Ccdc39
Transcript:
ENSMUST00000029222.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
8,7,6,5,4
Exon/intron offsets:
0,1871,6059,6283,7149
Genomic length:
7308
Exon/intron sizes in nt:
1,04,19,21,29,93,159
Flanking exon/introns:
chr3:33884306-33884805|chr3:33892113-33893226
Splice length:
677
Other database IDs:
CIRCpedia: MMU_CIRCpedia_17000, circAtlas: mmu-Ccdc39_0003
Human Ortholog IDs:
Mature spliced Sequence:
AACAATATATTTAAAACTACTCAAAAGCTGGATGACTTGAAATGTCAGATGAACTGGGACCAGCAAGCCTTGGAGGCCTGGCTGGAAGAATCGGCTCACAAAGACAGTGACTCTCTGACCCTTCAGAAGTACTCTCAGCAAGACGATAACAAAATCAGGGCCCTGACTCTGCAGTTAGAAAAGCTGACCATGGAGTATAACGAGAAGAGGAAGCTTCTAGACAGTGAACTGACAGAGACGCTAAGTGCGCAGTTAGAATTAGATAAAGCTGCACAGGATTTCCGGAAGATTCACTTAGAACGGCAGGAGCTCATTCAGCAGTGGGAGAACACCATTGAGCAGATGCAGAGGCGGGATCAGGAGATAGACAACTGTGCCCTGGCATTATCACGAATAAAGCAGGAAGCAAGAGAAAAAGAAGGCGTGGTGAAAGAGAAGATCAAGTTTCTGGAAAATGAGGTTGAGAACAACATAGAATACGAGAGAAAAATTTCTGTTGCTGAGCGGAAAGTGTCCAAGTGCAGGATGGACTACCAGCGTCACGAAGGCAACAGAAGTCAGCTGAAGGATGAGCTGGATACTTTAAAAACCACTCTCAACAGAACATCCAGTGACTTACAAGCTCTGAGGAAAAACATTTCCAAAGTAAAGAAGGACATCTTTGACGAAACATTAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCACTCTCAACAGAACATCCA
59.29
TGCTGGTCCCAGTTCATCTG
59.67
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCACTCTCAACAGAACATCCA
59.29
GCTTGCTGGTCCCAGTTCAT
60.61
157
PCR template sequence:
ATACTTTAAAAACCACTCTCAACAGAACATCCAGTGACTTACAAGCTCTGAGGAAAAACATTTCCAAAGTAAAGAAGGACATCTTTGACGAAACATTAAGAACAATATATTTAAAACTACTCAAAAGCTGGATGACTTGAAATGTCAGATGAACTGGGACCAGCAAGCCTTGGAGGCCTGGCTGGAAGAATCGGCTCACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-140-5p(1), mmu-miR-224-5p(1), mmu-miR-802-5p(1), mmu-miR-540-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACGAAACATTAAGAACAATATATTTA
siRNA sets
AAATATATTGTTCTTAATG, TAAATATATTGTTCTTAAT, ATTGTTCTTAATGTTTCGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCCDC39_677_ORF_1
1.0844
0.331212659
0.949007771
669
ORF sequence:
ATGAACTGGGACCAGCAAGCCTTGGAGGCCTGGCTGGAAGAATCGGCTCACAAAGACAGTGACTCTCTGACCCTTCAGAAGTACTCTCAGCAAGACGATAACAAAATCAGGGCCCTGACTCTGCAGTTAGAAAAGCTGACCATGGAGTATAACGAGAAGAGGAAGCTTCTAGACAGTGAACTGACAGAGACGCTAAGTGCGCAGTTAGAATTAGATAAAGCTGCACAGGATTTCCGGAAGATTCACTTAGAACGGCAGGAGCTCATTCAGCAGTGGGAGAACACCATTGAGCAGATGCAGAGGCGGGATCAGGAGATAGACAACTGTGCCCTGGCATTATCACGAATAAAGCAGGAAGCAAGAGAAAAAGAAGGCGTGGTGAAAGAGAAGATCAAGTTTCTGGAAAATGAGGTTGAGAACAACATAGAATACGAGAGAAAAATTTCTGTTGCTGAGCGGAAAGTGTCCAAGTGCAGGATGGACTACCAGCGTCACGAAGGCAACAGAAGTCAGCTGAAGGATGAGCTGGATACTTTAAAAACCACTCTCAACAGAACATCCAGTGACTTACAAGCTCTGAGGAAAAACATTTCCAAAGTAAAGAAGGACATCTTTGACGAAACATTAAGAACAATATATTTAAAACTACTCAAAAGCTGGATGACTTGA
Peptide sequence:
MNWDQQALEAWLEESAHKDSDSLTLQKYSQQDDNKIRALTLQLEKLTMEYNEKRKLLDSELTETLSAQLELDKAAQDFRKIHLERQELIQQWENTIEQMQRRDQEIDNCALALSRIKQEAREKEGVVKEKIKFLENEVENNIEYERKISVAERKVSKCRMDYQRHEGNRSQLKDELDTLKTTLNRTSSDLQALRKNISKVKKDIFDETLRTIYLKLLKSWMT
IRESfinder result
IRESfinder score
0.511652044
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page