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mmu_circDnm3_777
Basic information of circular RNA
PanCircBase ID:
mmu_circDnm3_777
mm39_Chr. Position ID:
chr1|161962025|162141265|-
Gene name:
Dnm3
Transcript:
ENSMUST00000086074.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
15,14,13,12,11,10,9,8
Exon/intron offsets:
0,97197,140031,151540,161095,173411,176935,179104
Genomic length:
179240
Exon/intron sizes in nt:
1,10,11,45,27,18,71,39,00,000
Flanking exon/introns:
chr1:161911713-161962025|chr1:162141265-162146149
Splice length:
777
Other database IDs:
CIRCpedia: MMU_CIRCpedia_11254, circAtlas: mmu-Dnm3_0022
CIRCpedia: HSA_CIRCpedia_159993
Human Ortholog IDs:
Mature spliced Sequence:
GATGGTCCAACAGTTTGCTGTGGACTTTGAGAAGAGAATCGAAGGGTCAGGAGATCAAGTAGACACCTTAGAGCTCTCTGGCGGTGCTAAGATCAACCGCATTTTCCACGAACGCTTTCCTTTTGAGATAGTGAAGATGGAGTTCAATGAGAAAGAACTGAGAAGAGAAATAAGCTACGCAATCAAAAACATACATGGGATCAGGACAGGGTTGTTTACTCCAGACATGGCGTTTGAGGCAATAGTTAAAAAGCAGATAGTAAAACTGAAAGGGCCTTCCTTGAAGAGTGTGGACCTGGTAATGCAGGAGCTGATCAACACCGTGAAGAAGTGTACCAAGAGGCTGGCAAACTTCCCCAGACTCTGTGAAGAAACAGAAAGGATTGTTGCTAACCACATCCGTGAGAGAGAAGGGAAGACAAAGGACCAGGTCCTGCTACTGATTGACATTCAAGTCTCTTACATTAACACCAACCATGAGGACTTCATCGGCTTTGCAAATGCTCAGCAGAGGAGCAGTCAGGTTCACAAGAAAAGCACAATTGGAAATCAGGTGATTCGTAAGGGCTGGCTGACCGTCAGCAACATTGGCATCATGAAAGGGGGCTCGAAGGGCTACTGGTTTGTCCTCACTGCAGAAAGCCTGTCCTGGTATAAAGACGATGAGGAGAAAGAAAAGAAATATATGCTTCCCCTGGACAACCTGAAGGTCCGGGATGTGGAGAAGGGCTTCATGTCCAGCAAGCACGTCTTCGCACTCTTCAACACCGAGCAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGAAGGGCTTCATGTCCAGC
60.03
CACCGCCAGAGAGCTCTAAG
59.9
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGATGTGGAGAAGGGCTTC
60.11
CGCCAGAGAGCTCTAAGGTG
59.9
147
PCR template sequence:
AGAAATATATGCTTCCCCTGGACAACCTGAAGGTCCGGGATGTGGAGAAGGGCTTCATGTCCAGCAAGCACGTCTTCGCACTCTTCAACACCGAGCAAAGGATGGTCCAACAGTTTGCTGTGGACTTTGAGAAGAGAATCGAAGGGTCAGGAGATCAAGTAGACACCTTAGAGCTCTCTGGCGGTGCTAAGATCAACCGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
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), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
ACACCGAGCAAAGGATGGTCCAACAG
siRNA sets
GTTGGACCATCCTTTGCTC, CTGTTGGACCATCCTTTGC, TTGGACCATCCTTTGCTCG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDNM3_777_ORF_1
1.1948
0.355962622
0.999931621
1551
ORF sequence:
ATGGTCCAACAGTTTGCTGTGGACTTTGAGAAGAGAATCGAAGGGTCAGGAGATCAAGTAGACACCTTAGAGCTCTCTGGCGGTGCTAAGATCAACCGCATTTTCCACGAACGCTTTCCTTTTGAGATAGTGAAGATGGAGTTCAATGAGAAAGAACTGAGAAGAGAAATAAGCTACGCAATCAAAAACATACATGGGATCAGGACAGGGTTGTTTACTCCAGACATGGCGTTTGAGGCAATAGTTAAAAAGCAGATAGTAAAACTGAAAGGGCCTTCCTTGAAGAGTGTGGACCTGGTAATGCAGGAGCTGATCAACACCGTGAAGAAGTGTACCAAGAGGCTGGCAAACTTCCCCAGACTCTGTGAAGAAACAGAAAGGATTGTTGCTAACCACATCCGTGAGAGAGAAGGGAAGACAAAGGACCAGGTCCTGCTACTGATTGACATTCAAGTCTCTTACATTAACACCAACCATGAGGACTTCATCGGCTTTGCAAATGCTCAGCAGAGGAGCAGTCAGGTTCACAAGAAAAGCACAATTGGAAATCAGGTGATTCGTAAGGGCTGGCTGACCGTCAGCAACATTGGCATCATGAAAGGGGGCTCGAAGGGCTACTGGTTTGTCCTCACTGCAGAAAGCCTGTCCTGGTATAAAGACGATGAGGAGAAAGAAAAGAAATATATGCTTCCCCTGGACAACCTGAAGGTCCGGGATGTGGAGAAGGGCTTCATGTCCAGCAAGCACGTCTTCGCACTCTTCAACACCGAGCAAAGGATGGTCCAACAGTTTGCTGTGGACTTTGAGAAGAGAATCGAAGGGTCAGGAGATCAAGTAGACACCTTAGAGCTCTCTGGCGGTGCTAAGATCAACCGCATTTTCCACGAACGCTTTCCTTTTGAGATAGTGAAGATGGAGTTCAATGAGAAAGAACTGAGAAGAGAAATAAGCTACGCAATCAAAAACATACATGGGATCAGGACAGGGTTGTTTACTCCAGACATGGCGTTTGAGGCAATAGTTAAAAAGCAGATAGTAAAACTGAAAGGGCCTTCCTTGAAGAGTGTGGACCTGGTAATGCAGGAGCTGATCAACACCGTGAAGAAGTGTACCAAGAGGCTGGCAAACTTCCCCAGACTCTGTGAAGAAACAGAAAGGATTGTTGCTAACCACATCCGTGAGAGAGAAGGGAAGACAAAGGACCAGGTCCTGCTACTGATTGACATTCAAGTCTCTTACATTAACACCAACCATGAGGACTTCATCGGCTTTGCAAATGCTCAGCAGAGGAGCAGTCAGGTTCACAAGAAAAGCACAATTGGAAATCAGGTGATTCGTAAGGGCTGGCTGACCGTCAGCAACATTGGCATCATGAAAGGGGGCTCGAAGGGCTACTGGTTTGTCCTCACTGCAGAAAGCCTGTCCTGGTATAAAGACGATGAGGAGAAAGAAAAGAAATATATGCTTCCCCTGGACAACCTGAAGGTCCGGGATGTGGAGAAGGGCTTCATGTCCAGCAAGCACGTCTTCGCACTCTTCAACACCGAGCAA
Peptide sequence:
MVQQFAVDFEKRIEGSGDQVDTLELSGGAKINRIFHERFPFEIVKMEFNEKELRREISYAIKNIHGIRTGLFTPDMAFEAIVKKQIVKLKGPSLKSVDLVMQELINTVKKCTKRLANFPRLCEETERIVANHIREREGKTKDQVLLLIDIQVSYINTNHEDFIGFANAQQRSSQVHKKSTIGNQVIRKGWLTVSNIGIMKGGSKGYWFVLTAESLSWYKDDEEKEKKYMLPLDNLKVRDVEKGFMSSKHVFALFNTEQRMVQQFAVDFEKRIEGSGDQVDTLELSGGAKINRIFHERFPFEIVKMEFNEKELRREISYAIKNIHGIRTGLFTPDMAFEAIVKKQIVKLKGPSLKSVDLVMQELINTVKKCTKRLANFPRLCEETERIVANHIREREGKTKDQVLLLIDIQVSYINTNHEDFIGFANAQQRSSQVHKKSTIGNQVIRKGWLTVSNIGIMKGGSKGYWFVLTAESLSWYKDDEEKEKKYMLPLDNLKVRDVEKGFMSSKHVFALFNTEQ
IRESfinder result
IRESfinder score
0.491003702
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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