top of page
mmu_circDnm3_553
Basic information of circular RNA
PanCircBase ID:
mmu_circDnm3_553
mm39_Chr. Position ID:
chr1|162102056|162141265|-
Gene name:
Dnm3
Transcript:
ENSMUST00000086074.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
13,12,11,10,9,8
Exon/intron offsets:
0,11509,21064,33380,36904,39073
Genomic length:
39209
Exon/intron sizes in nt:
5,27,18,71,39,68,136
Flanking exon/introns:
chr1:162059336-162102056|chr1:162141265-162146149
Splice length:
553
Other database IDs:
circBase: mmu_circ_0008353, CIRCpedia: MMU_CIRCpedia_11268, circAtlas: mmu-Dnm3_0014
circAtlas: hsa-DNM3_0017
Human Ortholog IDs:
Mature spliced Sequence:
GATGGTCCAACAGTTTGCTGTGGACTTTGAGAAGAGAATCGAAGGGTCAGGAGATCAAGTAGACACCTTAGAGCTCTCTGGCGGTGCTAAGATCAACCGCATTTTCCACGAACGCTTTCCTTTTGAGATAGTGAAGATGGAGTTCAATGAGAAAGAACTGAGAAGAGAAATAAGCTACGCAATCAAAAACATACATGGGATCAGGACAGGGTTGTTTACTCCAGACATGGCGTTTGAGGCAATAGTTAAAAAGCAGATAGTAAAACTGAAAGGGCCTTCCTTGAAGAGTGTGGACCTGGTAATGCAGGAGCTGATCAACACCGTGAAGAAGTGTACCAAGAGGCTGGCAAACTTCCCCAGACTCTGTGAAGAAACAGAAAGGATTGTTGCTAACCACATCCGTGAGAGAGAAGGGAAGACAAAGGACCAGGTCCTGCTACTGATTGACATTCAAGTCTCTTACATTAACACCAACCATGAGGACTTCATCGGCTTTGCAAATGCTCAGCAGAGGAGCAGTCAGGTTCACAAGAAAAGCACAATTGGAAATCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGACTTCATCGGCTTTGCA
59.96
CGCCAGAGAGCTCTAAGGTG
59.9
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGACTTCATCGGCTTTGCA
59.96
CACCGCCAGAGAGCTCTAAG
59.9
160
PCR template sequence:
AGTCTCTTACATTAACACCAACCATGAGGACTTCATCGGCTTTGCAAATGCTCAGCAGAGGAGCAGTCAGGTTCACAAGAAAAGCACAATTGGAAATCAGGATGGTCCAACAGTTTGCTGTGGACTTTGAGAAGAGAATCGAAGGGTCAGGAGATCAAGTAGACACCTTAGAGCTCTCTGGCGGTGCTAAGATCAACCGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-30e-5p(1), mmu-miR-30a-5p(1), mmu-miR-339-5p(1), mmu-miR-10a-5p(1), mmu-miR-30d-5p(1), mmu-miR-30b-5p(1), mmu-miR-29b-1-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AATTGGAAATCAGGATGGTCCAACAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDNM3_553_ORF_1
1.0771
0.235669615
0.904122764
630
ORF sequence:
ATGAGGACTTCATCGGCTTTGCAAATGCTCAGCAGAGGAGCAGTCAGGTTCACAAGAAAAGCACAATTGGAAATCAGGATGGTCCAACAGTTTGCTGTGGACTTTGAGAAGAGAATCGAAGGGTCAGGAGATCAAGTAGACACCTTAGAGCTCTCTGGCGGTGCTAAGATCAACCGCATTTTCCACGAACGCTTTCCTTTTGAGATAGTGAAGATGGAGTTCAATGAGAAAGAACTGAGAAGAGAAATAAGCTACGCAATCAAAAACATACATGGGATCAGGACAGGGTTGTTTACTCCAGACATGGCGTTTGAGGCAATAGTTAAAAAGCAGATAGTAAAACTGAAAGGGCCTTCCTTGAAGAGTGTGGACCTGGTAATGCAGGAGCTGATCAACACCGTGAAGAAGTGTACCAAGAGGCTGGCAAACTTCCCCAGACTCTGTGAAGAAACAGAAAGGATTGTTGCTAACCACATCCGTGAGAGAGAAGGGAAGACAAAGGACCAGGTCCTGCTACTGATTGACATTCAAGTCTCTTACATTAACACCAACCATGAGGACTTCATCGGCTTTGCAAATGCTCAGCAGAGGAGCAGTCAGGTTCACAAGAAAAGCACAATTGGAAATCAG
Peptide sequence:
MRTSSALQMLSRGAVRFTRKAQLEIRMVQQFAVDFEKRIEGSGDQVDTLELSGGAKINRIFHERFPFEIVKMEFNEKELRREISYAIKNIHGIRTGLFTPDMAFEAIVKKQIVKLKGPSLKSVDLVMQELINTVKKCTKRLANFPRLCEETERIVANHIREREGKTKDQVLLLIDIQVSYINTNHEDFIGFANAQQRSSQVHKKSTIGNQ
IRESfinder result
IRESfinder score
0.557974503
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page