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mmu_circDdx6_446
Basic information of circular RNA
PanCircBase ID:
mmu_circDdx6_446
mm39_Chr. Position ID:
chr9|44524124|44535918|+
Gene name:
Ddx6
Transcript:
ENSMUST00000170489.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
3,4,5,6
Exon/intron offsets:
0,1384,10791,11647
Genomic length:
11794
Exon/intron sizes in nt:
64,10,51,30,147
Flanking exon/introns:
chr9:44518889-44524124|chr9:44535918-44537684
Splice length:
446
Other database IDs:
CIRCpedia: MMU_CIRCpedia_20353, circAtlas: mmu-Ddx6_0008
circAtlas: hsa-DDX6_0019, CIRCpedia: HSA_CIRCpedia_3420
Human Ortholog IDs:
Mature spliced Sequence:
ACCTGGTGATGACTGGAAAAAGACATTAAAACTCCCTCCAAAGGATCTAAGAATCAAAACTTCGGATGTGACCTCCACAAAAGGAAATGAGTTTGAAGATTACTGTTTGAAACGAGAGTTGCTAATGGGAATTTTTGAAATGGGCTGGGAAAAACCATCTCCTATCCAGGAGGAGAGCATTCCCATTGCTTTATCTGGTAGGGATATCTTAGCTAGAGCAAAAAATGGAACAGGCAAAAGCGGTGCCTACCTCATCCCCTTACTTGAAAGGCTGGACCTGAAGAAGGACAATATTCAAGCAATGGTGATTGTTCCCACTAGAGAACTTGCTCTACAGGTCAGTCAGATTTGCATCCAGGTCAGCAAACACATGGGAGGGGCCAAAGTGATGGCAACCACCGGAGGAACCAATTTACGAGATGACATAATGAGGCTTGATGATACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAAAGTGATGGCAACCACCG
60.04
GTGGAGGTCACATCCGAAGT
59.39
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCATCCAGGTCAGCAAACA
60.18
GTGGAGGTCACATCCGAAGT
59.39
175
PCR template sequence:
ATTTGCATCCAGGTCAGCAAACACATGGGAGGGGCCAAAGTGATGGCAACCACCGGAGGAACCAATTTACGAGATGACATAATGAGGCTTGATGATACAGACCTGGTGATGACTGGAAAAAGACATTAAAACTCCCTCCAAAGGATCTAAGAATCAAAACTTCGGATGTGACCTCCACAAAAGGAAATGAGTTTGAAGAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-26a-5p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-340-5p(1), mmu-miR-1198-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTTGATGATACAGACCTGGTGATGAC
siRNA sets
CATCACCAGGTCTGTATCA,ATCACCAGGTCTGTATCAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDDX6_446_ORF_1
0.9419
0.149520372
0.408995949
351
ORF sequence:
ATGGGAATTTTTGAAATGGGCTGGGAAAAACCATCTCCTATCCAGGAGGAGAGCATTCCCATTGCTTTATCTGGTAGGGATATCTTAGCTAGAGCAAAAAATGGAACAGGCAAAAGCGGTGCCTACCTCATCCCCTTACTTGAAAGGCTGGACCTGAAGAAGGACAATATTCAAGCAATGGTGATTGTTCCCACTAGAGAACTTGCTCTACAGGTCAGTCAGATTTGCATCCAGGTCAGCAAACACATGGGAGGGGCCAAAGTGATGGCAACCACCGGAGGAACCAATTTACGAGATGACATAATGAGGCTTGATGATACAGACCTGGTGATGACTGGAAAAAGACATTAA
Peptide sequence:
MGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTDLVMTGKRH
IRESfinder result
IRESfinder score
0.456844787
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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