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mmu_circAmfr_436
Basic information of circular RNA
PanCircBase ID:
mmu_circAmfr_436
mm39_Chr. Position ID:
chr8|94709939|94712100|-
Gene name:
Amfr
Transcript:
ENSMUST00000053766.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
9,8,7
Exon/intron offsets:
0,1522,2027
Genomic length:
2161
Exon/intron sizes in nt:
19,11,11,134
Flanking exon/introns:
chr8:94707049-94709939|chr8:94712100-94714001
Splice length:
436
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TTATTTGGCAACATCTGGTTATCTATGGCTAGCTTGGTCATCTTTATGCAACTTCGTTACCTGTTCCATGAGGTACAGCGTCGAATCCGTCGACACAAGAATTATTTGCGAGTGGTAGGAAACATGGAAGCCAGGTTTGCTGTTGCAACTCCAGAGGAACTAGCTGTCAATAATGATGACTGTGCAATCTGCTGGGACTCCATGCAGGCTGCAAGGAAACTGCCCTGTGGACATCTTTTTCACAACTCCTGCCTTCGTTCTTGGCTAGAACAAGACACCTCTTGTCCAACATGCAGAATGTCTCTTAATATTGCTGATGGCAGTCGTGCCAGGGAAGACCATCAAGGAGAGAACCTGGACGAGAACTTGGTTCCTGTAGCAGCTGCCGAAGGCAGGCCTCGCTTGAACCAGCACAATCACTTCTTCCACTTCGATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGGTTCCTGTAGCAGCTGC
60.61
CGACGCTGTACCTCATGGAA
59.83
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTGGTTCCTGTAGCAGCTGC
60.61
TTCGACGCTGTACCTCATGG
59.83
155
PCR template sequence:
GACCATCAAGGAGAGAACCTGGACGAGAACTTGGTTCCTGTAGCAGCTGCCGAAGGCAGGCCTCGCTTGAACCAGCACAATCACTTCTTCCACTTCGATGTTATTTGGCAACATCTGGTTATCTATGGCTAGCTTGGTCATCTTTATGCAACTTCGTTACCTGTTCCATGAGGTACAGCGTCGAATCCGTCGACACAAGA
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-32-5p(1), mmu-miR-363-3p(1), mmu-miR-153-3p(1), mmu-miR-325-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTCCACTTCGATGTTATTTGGCAACA
siRNA sets
AAATAACATCGAAGTGGAA, CCAAATAACATCGAAGTGG, TTGCCAAATAACATCGAAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAMFR_436_ORF_1
1.0593
0.147373367
0.625514887
444
ORF sequence:
ATGGCTAGCTTGGTCATCTTTATGCAACTTCGTTACCTGTTCCATGAGGTACAGCGTCGAATCCGTCGACACAAGAATTATTTGCGAGTGGTAGGAAACATGGAAGCCAGGTTTGCTGTTGCAACTCCAGAGGAACTAGCTGTCAATAATGATGACTGTGCAATCTGCTGGGACTCCATGCAGGCTGCAAGGAAACTGCCCTGTGGACATCTTTTTCACAACTCCTGCCTTCGTTCTTGGCTAGAACAAGACACCTCTTGTCCAACATGCAGAATGTCTCTTAATATTGCTGATGGCAGTCGTGCCAGGGAAGACCATCAAGGAGAGAACCTGGACGAGAACTTGGTTCCTGTAGCAGCTGCCGAAGGCAGGCCTCGCTTGAACCAGCACAATCACTTCTTCCACTTCGATGTTATTTGGCAACATCTGGTTATCTATGGCTAG
Peptide sequence:
MASLVIFMQLRYLFHEVQRRIRRHKNYLRVVGNMEARFAVATPEELAVNNDDCAICWDSMQAARKLPCGHLFHNSCLRSWLEQDTSCPTCRMSLNIADGSRAREDHQGENLDENLVPVAAAEGRPRLNQHNHFFHFDVIWQHLVIYG
IRESfinder result
IRESfinder score
0.521598116
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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