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mmu_ciSec16b_527
Basic information of circular RNA
PanCircBase ID:
mmu_ciSec16b_527
mm39_Chr. Position ID:
chr1|157334430|157334957|+
Gene name:
Sec16b
Transcript:
ENSMUST00000086130.9
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
1
Exon/intron offsets:
0
Genomic length:
527
Exon/intron sizes in nt:
527
Flanking exon/introns:
chr1:157334430-157334955
Splice length:
527
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTACTTATTTTCACCACTAACAACTTCACCCAAACCAAACCCAAGCAGAAGAAAACTAAGAGGGAATGTAATTTTTACTGGAGACCCTTCTAACAGATTCATTTGAAAAAGCATGTAGTTTGAACCAGGGAAGACAGGCATTCAGGCCAGCACATGGTTTCATCAGAATGAAGAACTTGACAGGATCCTGTTTGGAAAAAAAAAAAAAAAAACAACAACAAAAAACAACAAAAAAACAACCACCCTCAAGTTCAATGGTGGCTGAGGCTGGTTTAGACCCTCACTCTGTACAGTGACTGCATACCCTGGCAGGGGCCTTGCCTTGTTGGCTGGAATGCACGGCTAATGTGCATGTAATTTCAACTTTCACAGGAATTTAGGCAAGTTTGATTATGGTTAGATGAAAGGAGACTTGGCAATTACAGTGTTTGGGGAGAGGATAGAGCCCGTTAAATATTTTAAGGAGGATTCAAGCTGGTTAAAGCTGACTTAGAGACAATGTGGAAACTTCTGTTCTCAAGCT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGGGGAGAGGATAGAGCCC
60.1
CTGCTTGGGTTTGGTTTGGG
59.89
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTGGGGAGAGGATAGAGCCC
60.1
GCTTGGGTTTGGTTTGGGTG
60.18
145
PCR template sequence:
AGTGTTTGGGGAGAGGATAGAGCCCGTTAAATATTTTAAGGAGGATTCAAGCTGGTTAAAGCTGACTTAGAGACAATGTGGAAACTTCTGTTCTCAAGCTGTAAGTACTTATTTTCACCACTAACAACTTCACCCAAACCAAACCCAAGCAGAAGAAAACTAAGAGGGAATGTAATTTTTACTGGAGACCCTTCTAACAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-141-3p(1), mmu-miR-382-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGTTCTCAAGCTGTAAGTACTTATT
siRNA sets
TACTTACAGCTTGAGAACA, GTACTTACAGCTTGAGAAC, ACTTACAGCTTGAGAACAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CISEC16B_527_ORF_1
0.8004
-0.365536464
0.013392238
135
ORF sequence:
ATGTGGAAACTTCTGTTCTCAAGCTGTAAGTACTTATTTTCACCACTAACAACTTCACCCAAACCAAACCCAAGCAGAAGAAAACTAAGAGGGAATGTAATTTTTACTGGAGACCCTTCTAACAGATTCATTTGA
Peptide sequence:
MWKLLFSSCKYLFSPLTTSPKPNPSRRKLRGNVIFTGDPSNRFI
IRESfinder result
IRESfinder score
0.831966945
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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