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mmu_circSzt2_249
Basic information of circular RNA
PanCircBase ID:
mmu_circSzt2_249
mm39_Chr. Position ID:
chr4|118254809|118255452|-
Gene name:
Szt2
Transcript:
ENSMUST00000075406.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
7,6
Exon/intron offsets:
0,501
Genomic length:
643
Exon/intron sizes in nt:
1,07,142
Flanking exon/introns:
chr4:118251227-118254809|chr4:118255452-118256227
Splice length:
249
Other database IDs:
circAtlas: mmu-Szt2_0005
Human Ortholog IDs:
Mature spliced Sequence:
GCAGAAGACCAGTCCCCAGAGTCAGGGGAGTCCTTGGGACGGAAGGTAGGAGTCTCCATGGTGACAGCTGATCTTGGGCTGGTCAGTATGATTCGTCAGGGCATCTTGGCGCTGCAGTTACTGCCCTCAAATTCTAGTGCAGGTATCATTGTGATCACAGACGGGGTGACCAGTGTCCCTGATGTTGCTGTGTGTGAGACACTACTGAACCAGCTCCGCAGTGGCACTGTGGCATGCTCTTTTGTGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGTGACCAGTGTCCCTGATG
60.04
AGACTCCTACCTTCCGTCCC
60.03
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGTGACCAGTGTCCCTGATG
60.04
AGCCCAAGATCAGCTGTCAC
60.04
165
PCR template sequence:
TGTGATCACAGACGGGGTGACCAGTGTCCCTGATGTTGCTGTGTGTGAGACACTACTGAACCAGCTCCGCAGTGGCACTGTGGCATGCTCTTTTGTGCAGGCAGAAGACCAGTCCCCAGAGTCAGGGGAGTCCTTGGGACGGAAGGTAGGAGTCTCCATGGTGACAGCTGATCTTGGGCTGGTCAGTATGATTCGTCAGG
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-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-377-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTCTTTTGTGCAGGCAGAAGACCAGT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSZT2_249_ORF_1
1.0749
0.268742629
0.736012185
441
ORF sequence:
ATGGTGACAGCTGATCTTGGGCTGGTCAGTATGATTCGTCAGGGCATCTTGGCGCTGCAGTTACTGCCCTCAAATTCTAGTGCAGGTATCATTGTGATCACAGACGGGGTGACCAGTGTCCCTGATGTTGCTGTGTGTGAGACACTACTGAACCAGCTCCGCAGTGGCACTGTGGCATGCTCTTTTGTGCAGGCAGAAGACCAGTCCCCAGAGTCAGGGGAGTCCTTGGGACGGAAGGTAGGAGTCTCCATGGTGACAGCTGATCTTGGGCTGGTCAGTATGATTCGTCAGGGCATCTTGGCGCTGCAGTTACTGCCCTCAAATTCTAGTGCAGGTATCATTGTGATCACAGACGGGGTGACCAGTGTCCCTGATGTTGCTGTGTGTGAGACACTACTGAACCAGCTCCGCAGTGGCACTGTGGCATGCTCTTTTGTGCAG
Peptide sequence:
MVTADLGLVSMIRQGILALQLLPSNSSAGIIVITDGVTSVPDVAVCETLLNQLRSGTVACSFVQAEDQSPESGESLGRKVGVSMVTADLGLVSMIRQGILALQLLPSNSSAGIIVITDGVTSVPDVAVCETLLNQLRSGTVACSFVQ
IRESfinder result
IRESfinder score
0.650032642
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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