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mmu_circSec24a_382
Basic information of circular RNA
PanCircBase ID:
mmu_circSec24a_382
mm39_Chr. Position ID:
chr11|51607265|51612760|-
Gene name:
Sec24a
Transcript:
ENSMUST00000109097.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
13,12,11
Exon/intron offsets:
0,1285,5376
Genomic length:
5495
Exon/intron sizes in nt:
2,07,56,119
Flanking exon/introns:
chr11:51606072-51607265|chr11:51612760-51614410
Splice length:
382
Other database IDs:
CIRCpedia: MMU_CIRCpedia_22155, circAtlas: mmu-Sec24a_0011
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GCTTCCTGGCAACACTAGGACAAAAATCGGTTTCATAACATTTGATAGCACTATCCATTTCTACAGTCTTCAGGAAGGTCTCTCCCAGCCTCAGATGCTAATAGTTTCAGATATTGACGATGTTTTTATCCCTATGCCAGAGAACTTACTAGTAAACTTAAATGAAAGTAAAGAGCTTGTTCAAGATTTACTGAAAACGCTGCCACAAATGTTTACGAAGACGCTGGAGACCCAGAGTGCCTTGGGTCCTGCACTTCAGGCTGCATTCAAGCTGATATCACCAACTGGTGGTCGAATGTCTGTCTTCCAAACACAACTCCCAACGCTTGGTGTAGGAGCTCTGAAACCACGAGAGGAACCCAACCAAAGGTCATCTGCTAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AACGCTTGGTGTAGGAGCTC
60.04
TAGCATCTGAGGCTGGGAGA
59.74
161
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AACGCTTGGTGTAGGAGCTC
60.04
ATCTGAGGCTGGGAGAGACC
60.4
157
PCR template sequence:
AACTGGTGGTCGAATGTCTGTCTTCCAAACACAACTCCCAACGCTTGGTGTAGGAGCTCTGAAACCACGAGAGGAACCCAACCAAAGGTCATCTGCTAAGGCTTCCTGGCAACACTAGGACAAAAATCGGTTTCATAACATTTGATAGCACTATCCATTTCTACAGTCTTCAGGAAGGTCTCTCCCAGCCTCAGATGCTA
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-30e-5p(1), mmu-miR-7a-5p(1), mmu-miR-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GTCATCTGCTAAGGCTTCCTGGCAAC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSEC24A_382_ORF_1
1.0528
0.043118847
0.285234869
306
ORF sequence:
ATGCTAATAGTTTCAGATATTGACGATGTTTTTATCCCTATGCCAGAGAACTTACTAGTAAACTTAAATGAAAGTAAAGAGCTTGTTCAAGATTTACTGAAAACGCTGCCACAAATGTTTACGAAGACGCTGGAGACCCAGAGTGCCTTGGGTCCTGCACTTCAGGCTGCATTCAAGCTGATATCACCAACTGGTGGTCGAATGTCTGTCTTCCAAACACAACTCCCAACGCTTGGTGTAGGAGCTCTGAAACCACGAGAGGAACCCAACCAAAGGTCATCTGCTAAGGCTTCCTGGCAACACTAG
Peptide sequence:
MLIVSDIDDVFIPMPENLLVNLNESKELVQDLLKTLPQMFTKTLETQSALGPALQAAFKLISPTGGRMSVFQTQLPTLGVGALKPREEPNQRSSAKASWQH
IRESfinder result
IRESfinder score
0.623652307
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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