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mmu_circSec23a_391
Basic information of circular RNA
PanCircBase ID:
mmu_circSec23a_391
mm39_Chr. Position ID:
chr12|59051275|59054021|-
Gene name:
Sec23a
Transcript:
ENSMUST00000021375.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
4,3,2
Exon/intron offsets:
0,769,2500
Genomic length:
2746
Exon/intron sizes in nt:
87,58,246
Flanking exon/introns:
chr12:59048841-59051275|chr12:59054021-59058631
Splice length:
391
Other database IDs:
CIRCpedia: MMU_CIRCpedia_228343, circAtlas: mmu-Sec23a_0017
Human Ortholog IDs:
Mature spliced Sequence:
ACAGAAATAAGAATCAAGTGCTACCATGACAACCTATTTGGAATTTATCCAACAAAATGAAGAACGAGATGGGGTCCGGTTCAGTTGGAATGTTTGGCCATCGAGTCGTCTGGAAGCTACAAGAATGGTTGTCCCAGTGGCAGCCCTGTTTACACCTCTGAAGGAGAGACCCGACCTACCACCCATCCAGTACGAGCCTGTCCTGTGCAGTAGGACCACTTGCCGTGCAGTTTTGAATCCTTTATGCCAAGTGGATTATCGAGCAAAACTCTGGGCTTGCAACTTTTGTTACCAAAGGAATCAGTTTCCACCTACATATGCTGGGATATCTGAATTGAACCAGCCTGCAGAGCTTTTACCTCAGTTTTCAAGCATTGAATATGTAGTTCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCAGCCTGCAGAGCTTTTA
59.6
ATTCCAACTGAACCGGACCC
59.96
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AACCAGCCTGCAGAGCTTTT
60.47
ATTCCAACTGAACCGGACCC
59.96
145
PCR template sequence:
CCAAAGGAATCAGTTTCCACCTACATATGCTGGGATATCTGAATTGAACCAGCCTGCAGAGCTTTTACCTCAGTTTTCAAGCATTGAATATGTAGTTCTGACAGAAATAAGAATCAAGTGCTACCATGACAACCTATTTGGAATTTATCCAACAAAATGAAGAACGAGATGGGGTCCGGTTCAGTTGGAATGTTTGGCCA
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-9-5p(1), mmu-miR-30e-5p(1), mmu-miR-30a-5p(1), mmu-miR-30d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATATGTAGTTCTGACAGAAATAAGAA
siRNA sets
ATTTCTGTCAGAACTACAT,TTTCTGTCAGAACTACATA,TCTTATTTCTGTCAGAACT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSEC23A_391_ORF_1
0.4776
-0.002523704
0.212582147
426
ORF sequence:
ATGACAACCTATTTGGAATTTATCCAACAAAATGAAGAACGAGATGGGGTCCGGTTCAGTTGGAATGTTTGGCCATCGAGTCGTCTGGAAGCTACAAGAATGGTTGTCCCAGTGGCAGCCCTGTTTACACCTCTGAAGGAGAGACCCGACCTACCACCCATCCAGTACGAGCCTGTCCTGTGCAGTAGGACCACTTGCCGTGCAGTTTTGAATCCTTTATGCCAAGTGGATTATCGAGCAAAACTCTGGGCTTGCAACTTTTGTTACCAAAGGAATCAGTTTCCACCTACATATGCTGGGATATCTGAATTGAACCAGCCTGCAGAGCTTTTACCTCAGTTTTCAAGCATTGAATATGTAGTTCTGACAGAAATAAGAATCAAGTGCTACCATGACAACCTATTTGGAATTTATCCAACAAAATGA
Peptide sequence:
MTTYLEFIQQNEERDGVRFSWNVWPSSRLEATRMVVPVAALFTPLKERPDLPPIQYEPVLCSRTTCRAVLNPLCQVDYRAKLWACNFCYQRNQFPPTYAGISELNQPAELLPQFSSIEYVVLTEIRIKCYHDNLFGIYPTK
IRESfinder result
IRESfinder score
0.686726108
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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