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mmu_circDdx5_284
Basic information of circular RNA
PanCircBase ID:
mmu_circDdx5_284
mm39_Chr. Position ID:
chr11|106675239|106675878|-
Gene name:
Ddx5
Transcript:
ENSMUST00000021062.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
9,8
Exon/intron offsets:
0,466
Genomic length:
639
Exon/intron sizes in nt:
1,11,173
Flanking exon/introns:
chr11:106674988-106675239|chr11:106675878-106675961
Splice length:
284
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CCTGATAGGCAAACACTAATGTGGAGTGCAACTTGGCCAAAAGAAGTAAGACAGCTTGCTGAAGATTTCCTGAAAGACTATATTCATATCAATATTGGTGCACTGGAACTGAGTGCAAACCATAACATTCTTCAGATTGTGGATGTATGTCATGATGTCGAAAAGGATGAAAAGCTTATTCGTCTGATGGAAGAAATCATGAGTGAGAAGGAGAATAAAACTATTGTTTTTGTTGAAACCAAAAGAAGATGTGATGAACTTACCAGAAAAATGAGGAGAGATGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGGAAGAAATCATGAGTGAGAAGGA
60.07
TTTTGGCCAAGTTGCACTCC
59.54
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATGGAAGAAATCATGAGTGAGAAGG
58.88
TTTTGGCCAAGTTGCACTCC
59.54
140
PCR template sequence:
TGATGGAAGAAATCATGAGTGAGAAGGAGAATAAAACTATTGTTTTTGTTGAAACCAAAAGAAGATGTGATGAACTTACCAGAAAAATGAGGAGAGATGGCCTGATAGGCAAACACTAATGTGGAGTGCAACTTGGCCAAAAGAAGTAAGACAGCTTGCTGAAGATTTCCTGAAAGACTATATTCATATCAATATTGGTG
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-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-433-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-3065-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGAGGAGAGATGGCCTGATAGGCAAA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDDX5_284_ORF_1
1.0566
0.079427496
0.28698157
285
ORF sequence:
ATGTGGAGTGCAACTTGGCCAAAAGAAGTAAGACAGCTTGCTGAAGATTTCCTGAAAGACTATATTCATATCAATATTGGTGCACTGGAACTGAGTGCAAACCATAACATTCTTCAGATTGTGGATGTATGTCATGATGTCGAAAAGGATGAAAAGCTTATTCGTCTGATGGAAGAAATCATGAGTGAGAAGGAGAATAAAACTATTGTTTTTGTTGAAACCAAAAGAAGATGTGATGAACTTACCAGAAAAATGAGGAGAGATGGCCTGATAGGCAAACACTAA
Peptide sequence:
MWSATWPKEVRQLAEDFLKDYIHINIGALELSANHNILQIVDVCHDVEKDEKLIRLMEEIMSEKENKTIVFVETKRRCDELTRKMRRDGLIGKH
IRESfinder result
IRESfinder score
0.391132757
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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