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mmu_circSec24a_444
Basic information of circular RNA
PanCircBase ID:
mmu_circSec24a_444
mm39_Chr. Position ID:
chr11|51599761|51604516|-
Gene name:
Sec24a
Transcript:
ENSMUST00000109097.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
17,16,15
Exon/intron offsets:
0,3254,4596
Genomic length:
4755
Exon/intron sizes in nt:
11,11,74,159
Flanking exon/introns:
chr11:51598130-51599761|chr11:51604516-51605951
Splice length:
444
Other database IDs:
CIRCpedia: MMU_CIRCpedia_229792
circBase: hsa_circ_0073998, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_50254
Human Ortholog IDs:
Mature spliced Sequence:
GCTGCATCTCTCGGTACTCAGCGGGTAGTGTGTATTACTATCCCTCGTACCATCACCAGCACAACCCAGTGCAAGTACAGAAACTACAGAAGGAACTACACAGGTACCTCACTCGGAAGATTGGATTTGAGGCAGTCATGAGGATCCGGTGCACCAAAGGTCTTTCCATTCATACTTTCCATGGGAACTTCTTCGTCCGTTCTACAGACTTACTGTCTCTTCCCAATGTCAACCCAGATGCTGGGTATGCGGTCCAGATGTCAGTAGAAGAGAGTCTCACTGACACTCAGCTGGTTTCCTTCCAGTCAGCACTCTTATATACATCAAGCAAAGGTGAAAGAAGAATCCGTGTGCATACTTTGTGTTTGCCGGTAGTTTCTACCCTGAATGAAGTCTTTCTTGGAGCTGATGTGCAAGCAATTTCAGGGTTATTAGCCAATATGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCCGGTAGTTTCTACCCTG
59.1
GGGTTGTGCTGGTGATGGTA
59.96
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCATACTTTGTGTTTGCCGGT
60
GGGTTGTGCTGGTGATGGTA
59.96
159
PCR template sequence:
ATCCGTGTGCATACTTTGTGTTTGCCGGTAGTTTCTACCCTGAATGAAGTCTTTCTTGGAGCTGATGTGCAAGCAATTTCAGGGTTATTAGCCAATATGGGCTGCATCTCTCGGTACTCAGCGGGTAGTGTGTATTACTATCCCTCGTACCATCACCAGCACAACCCAGTGCAAGTACAGAAACTACAGAAGGAACTACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-138-5p(1), mmu-miR-127-3p(1), mmu-miR-680(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTAGCCAATATGGGCTGCATCTCTCG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSEC24A_444_ORF_1
0.7575
0.07938054
0.867793603
750
ORF sequence:
ATGAGGATCCGGTGCACCAAAGGTCTTTCCATTCATACTTTCCATGGGAACTTCTTCGTCCGTTCTACAGACTTACTGTCTCTTCCCAATGTCAACCCAGATGCTGGGTATGCGGTCCAGATGTCAGTAGAAGAGAGTCTCACTGACACTCAGCTGGTTTCCTTCCAGTCAGCACTCTTATATACATCAAGCAAAGGTGAAAGAAGAATCCGTGTGCATACTTTGTGTTTGCCGGTAGTTTCTACCCTGAATGAAGTCTTTCTTGGAGCTGATGTGCAAGCAATTTCAGGGTTATTAGCCAATATGGGCTGCATCTCTCGGTACTCAGCGGGTAGTGTGTATTACTATCCCTCGTACCATCACCAGCACAACCCAGTGCAAGTACAGAAACTACAGAAGGAACTACACAGGTACCTCACTCGGAAGATTGGATTTGAGGCAGTCATGAGGATCCGGTGCACCAAAGGTCTTTCCATTCATACTTTCCATGGGAACTTCTTCGTCCGTTCTACAGACTTACTGTCTCTTCCCAATGTCAACCCAGATGCTGGGTATGCGGTCCAGATGTCAGTAGAAGAGAGTCTCACTGACACTCAGCTGGTTTCCTTCCAGTCAGCACTCTTATATACATCAAGCAAAGGTGAAAGAAGAATCCGTGTGCATACTTTGTGTTTGCCGGTAGTTTCTACCCTGAATGAAGTCTTTCTTGGAGCTGATGTGCAAGCAATTTCAGGGTTATTAGCCAATATG
Peptide sequence:
MRIRCTKGLSIHTFHGNFFVRSTDLLSLPNVNPDAGYAVQMSVEESLTDTQLVSFQSALLYTSSKGERRIRVHTLCLPVVSTLNEVFLGADVQAISGLLANMGCISRYSAGSVYYYPSYHHQHNPVQVQKLQKELHRYLTRKIGFEAVMRIRCTKGLSIHTFHGNFFVRSTDLLSLPNVNPDAGYAVQMSVEESLTDTQLVSFQSALLYTSSKGERRIRVHTLCLPVVSTLNEVFLGADVQAISGLLANM
IRESfinder result
IRESfinder score
0.620721171
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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