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mmu_circDdx3y_434
Basic information of circular RNA
PanCircBase ID:
mmu_circDdx3y_434
mm39_Chr. Position ID:
chrY|1278896|1282948|-
Gene name:
Ddx3y
Transcript:
ENSMUST00000091190.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,5,4,3
Exon/intron offsets:
0,526,1413,4004
Genomic length:
4052
Exon/intron sizes in nt:
100,156,130,48
Flanking exon/introns:
chrY:1269840-1278896|chrY:1282948-1284321
Splice length:
434
Other database IDs:
circBase: hsa_circ_0008297, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_66461
Human Ortholog IDs:
Mature spliced Sequence:
AAGGGCGCTATATACCTCCTCACTTAAGGAACAGAGAAACATCTAAAGGGGTCTGTGATAAGGACAGTTCAGGATGGAGCTGTAGTAAAGATAAAGATGCCTACAGCAGTTTTGGATCTCGTGATTCCAGAGGGAAGCCCAATTATTTCAGTGATCGTGGAAGTGGATCCAGGGGAAGGTTCGATGATCATGGTCGAAATGACTATGATGGTATTGGTGGTCGTGACCGAACTGGATTTGGCAAATTTGAACGGAGTGGTCATAGTCGTTGGAGTGACAGATCAGATGAAGATGACTGGTCAAAACCACTTCCACCAAGTGAACGCTTAGAGCAAGAACTTTTTTCTGGAGGAAACACAGGGATTAACTTTGAGAAATATGATGATATACCAGTAGAAGCAACTGGAAATAATTGTCCTCCTCACATTGAAAAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTCTGGAGGAAACACAGGGA
58.19
GCTCCATCCTGAACTGTCCT
59.09
171
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTCTGGAGGAAACACAGGGA
58.19
AGCTCCATCCTGAACTGTCC
59.09
172
PCR template sequence:
AGAACTTTTTTCTGGAGGAAACACAGGGATTAACTTTGAGAAATATGATGATATACCAGTAGAAGCAACTGGAAATAATTGTCCTCCTCACATTGAAAATAAGGGCGCTATATACCTCCTCACTTAAGGAACAGAGAAACATCTAAAGGGGTCTGTGATAAGGACAGTTCAGGATGGAGCTGTAGTAAAGATAAAGATGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-140-5p(1), mmu-miR-207(1), mmu-miR-202-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCACATTGAAAATAAGGGCGCTATAT
siRNA sets
TATAGCGCCCTTATTTTCA, ATATAGCGCCCTTATTTTC, ATAGCGCCCTTATTTTCAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.462941012
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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