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mmu_circAfg3l2_474
Basic information of circular RNA
PanCircBase ID:
mmu_circAfg3l2_474
mm39_Chr. Position ID:
chr18|67562050|67567299|-
Gene name:
Afg3l2
Transcript:
ENSMUST00000025408.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
8,7,6
Exon/intron offsets:
0,2673,5174
Genomic length:
5249
Exon/intron sizes in nt:
274,125,75
Flanking exon/introns:
chr18:67559096-67562050|chr18:67567299-67573251
Splice length:
474
Other database IDs:
CIRCpedia: MMU_CIRCpedia_26772, circAtlas: mmu-Afg3l2_0001
circAtlas: hsa-AFG3L2_0002, CIRCpedia: HSA_CIRCpedia_374995
Human Ortholog IDs:
Mature spliced Sequence:
GTGGACAGACTAGAAGTTGTCAACAAGCGTTTTGTTCGTGTGACCTTTACACCAGGAAAAACTCCGGTTGATGGGCAATACGTCTGGTTTAATATTGGCAGTGTTGACACATTTGAGCGGAATCTGGAGACTTTGCAGCAAGAATTGGGCATAGAAGGGGAGAACCGGGTCCCTGTGGTTTATATTGCTGAGAGCGATGGCTCCTTCCTGCTGAGCATGTTGCCCACCGTACTCATTATCGCTTTTCTACTCTACACCATAAGAAGAGGGCCCGCTGGCATTGGTCGGACCGGCCGGGGAATGGGTGGACTCTTCAGCGTTGGGGAAACCACAGCCAAGGTCTTAAAGGATGAGATAGATGTGAAGTTTAAAGATGTGGCTGGCTGTGAGGAGGCCAAGCTAGAAATAATGGAATTCGTGAATTTCTTGAAAAACCCAAAGCAATATCAAGACCTAGGAGCAAAAATCCCAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGTGAGGAGGCCAAGCTAG
59.82
ATTGCCCATCAACCGGAGTT
59.96
170
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGAGGAGGCCAAGCTAGA
60.25
ATTGCCCATCAACCGGAGTT
59.96
169
PCR template sequence:
TGTGGCTGGCTGTGAGGAGGCCAAGCTAGAAATAATGGAATTCGTGAATTTCTTGAAAAACCCAAAGCAATATCAAGACCTAGGAGCAAAAATCCCAAAGGTGGACAGACTAGAAGTTGTCAACAAGCGTTTTGTTCGTGTGACCTTTACACCAGGAAAAACTCCGGTTGATGGGCAATACGTCTGGTTTAATATTGGCA
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-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-129-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAAAATCCCAAAGGTGGACAGACTAG
siRNA sets
TAGTCTGTCCACCTTTGGG, CTAGTCTGTCCACCTTTGG, AGTCTGTCCACCTTTGGGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAFG3L2_474_ORF_1
1.0842
0.242708561
0.953718968
732
ORF sequence:
ATGTTGCCCACCGTACTCATTATCGCTTTTCTACTCTACACCATAAGAAGAGGGCCCGCTGGCATTGGTCGGACCGGCCGGGGAATGGGTGGACTCTTCAGCGTTGGGGAAACCACAGCCAAGGTCTTAAAGGATGAGATAGATGTGAAGTTTAAAGATGTGGCTGGCTGTGAGGAGGCCAAGCTAGAAATAATGGAATTCGTGAATTTCTTGAAAAACCCAAAGCAATATCAAGACCTAGGAGCAAAAATCCCAAAGGTGGACAGACTAGAAGTTGTCAACAAGCGTTTTGTTCGTGTGACCTTTACACCAGGAAAAACTCCGGTTGATGGGCAATACGTCTGGTTTAATATTGGCAGTGTTGACACATTTGAGCGGAATCTGGAGACTTTGCAGCAAGAATTGGGCATAGAAGGGGAGAACCGGGTCCCTGTGGTTTATATTGCTGAGAGCGATGGCTCCTTCCTGCTGAGCATGTTGCCCACCGTACTCATTATCGCTTTTCTACTCTACACCATAAGAAGAGGGCCCGCTGGCATTGGTCGGACCGGCCGGGGAATGGGTGGACTCTTCAGCGTTGGGGAAACCACAGCCAAGGTCTTAAAGGATGAGATAGATGTGAAGTTTAAAGATGTGGCTGGCTGTGAGGAGGCCAAGCTAGAAATAATGGAATTCGTGAATTTCTTGAAAAACCCAAAGCAATATCAAGACCTAGGAGCAAAAATCCCAAAG
Peptide sequence:
MLPTVLIIAFLLYTIRRGPAGIGRTGRGMGGLFSVGETTAKVLKDEIDVKFKDVAGCEEAKLEIMEFVNFLKNPKQYQDLGAKIPKVDRLEVVNKRFVRVTFTPGKTPVDGQYVWFNIGSVDTFERNLETLQQELGIEGENRVPVVYIAESDGSFLLSMLPTVLIIAFLLYTIRRGPAGIGRTGRGMGGLFSVGETTAKVLKDEIDVKFKDVAGCEEAKLEIMEFVNFLKNPKQYQDLGAKIPK
IRESfinder result
IRESfinder score
0.476685872
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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