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mmu_circAfg3l2_388
Basic information of circular RNA
PanCircBase ID:
mmu_circAfg3l2_388
mm39_Chr. Position ID:
chr18|67554055|67556168|-
Gene name:
Afg3l2
Transcript:
ENSMUST00000025408.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
12,11,10
Exon/intron offsets:
0,222,1959
Genomic length:
2113
Exon/intron sizes in nt:
12,61,08,154
Flanking exon/introns:
chr18:67548679-67554055|chr18:67556168-67558958
Splice length:
388
Other database IDs:
circAtlas: mmu-Afg3l2_0009
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_23144
Human Ortholog IDs:
Mature spliced Sequence:
GTCCGAGACTTATTTGCCCTTGCTCGGAAGAATGCGCCTTGCATTCTCTTCATTGATGAGATTGATGCTGTGGGAAGGAAGCGCGGCAGAGGCAACTTCGGTGGGCAGAGCGAGCAGGAGAACACACTCAACCAGCTGCTTGTGGAGATGGACGGCTTCAACACAACCACCAATGTGGTCATCCTGGCAGGCACAAATCGACCAGACATCCTGGATCCAGCTCTGTTGAGACCAGGCCGCTTTGACAGGCAGATTTTTATTGGACCCCCAGACATAAAAGGACGAGCCTCAATCTTCAAAGTTCACCTTCGACCATTGAAGCTGGACAGTGCCTTGGAAAAAGATAAATTGGCCAGAAAACTGGCGTCCTTAACTCCAGGGTTTTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGAAGCTGGACAGTGCCTT
59.82
GCTTCCTTCCCACAGCATCA
60.32
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATTGAAGCTGGACAGTGCCT
59.6
GCTTCCTTCCCACAGCATCA
60.32
156
PCR template sequence:
TCAATCTTCAAAGTTCACCTTCGACCATTGAAGCTGGACAGTGCCTTGGAAAAAGATAAATTGGCCAGAAAACTGGCGTCCTTAACTCCAGGGTTTTCAGGTCCGAGACTTATTTGCCCTTGCTCGGAAGAATGCGCCTTGCATTCTCTTCATTGATGAGATTGATGCTGTGGGAAGGAAGCGCGGCAGAGGCAACTTCG
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-300-3p(1), mmu-miR-452-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCAGGGTTTTCAGGTCCGAGACTTAT
siRNA sets
TAAGTCTCGGACCTGAAAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAFG3L2_388_ORF_1
0.6642
0.130079991
0.205703777
297
ORF sequence:
ATGGACGGCTTCAACACAACCACCAATGTGGTCATCCTGGCAGGCACAAATCGACCAGACATCCTGGATCCAGCTCTGTTGAGACCAGGCCGCTTTGACAGGCAGATTTTTATTGGACCCCCAGACATAAAAGGACGAGCCTCAATCTTCAAAGTTCACCTTCGACCATTGAAGCTGGACAGTGCCTTGGAAAAAGATAAATTGGCCAGAAAACTGGCGTCCTTAACTCCAGGGTTTTCAGGTCCGAGACTTATTTGCCCTTGCTCGGAAGAATGCGCCTTGCATTCTCTTCATTGA
Peptide sequence:
MDGFNTTTNVVILAGTNRPDILDPALLRPGRFDRQIFIGPPDIKGRASIFKVHLRPLKLDSALEKDKLARKLASLTPGFSGPRLICPCSEECALHSLH
IRESfinder result
IRESfinder score
0.626448886
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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