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mmu_circAfg3l2_766
Basic information of circular RNA
PanCircBase ID:
mmu_circAfg3l2_766
mm39_Chr. Position ID:
chr18|67556014|67567299|-
Gene name:
Afg3l2
Transcript:
ENSMUST00000025408.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
10,9,8,7,6
Exon/intron offsets:
0,2944,6036,8709,11210
Genomic length:
11285
Exon/intron sizes in nt:
154,138,274,125,75
Flanking exon/introns:
chr18:67554385-67556014|chr18:67567299-67573251
Splice length:
766
Other database IDs:
circBase: mmu_circ_0007463, CIRCpedia: MMU_CIRCpedia_40521, circAtlas: mmu-Afg3l2_0004
circAtlas: hsa-AFG3L2_0006, CIRCpedia: HSA_CIRCpedia_121284
Human Ortholog IDs:
Mature spliced Sequence:
GTGGACAGACTAGAAGTTGTCAACAAGCGTTTTGTTCGTGTGACCTTTACACCAGGAAAAACTCCGGTTGATGGGCAATACGTCTGGTTTAATATTGGCAGTGTTGACACATTTGAGCGGAATCTGGAGACTTTGCAGCAAGAATTGGGCATAGAAGGGGAGAACCGGGTCCCTGTGGTTTATATTGCTGAGAGCGATGGCTCCTTCCTGCTGAGCATGTTGCCCACCGTACTCATTATCGCTTTTCTACTCTACACCATAAGAAGAGGGCCCGCTGGCATTGGTCGGACCGGCCGGGGAATGGGTGGACTCTTCAGCGTTGGGGAAACCACAGCCAAGGTCTTAAAGGATGAGATAGATGTGAAGTTTAAAGATGTGGCTGGCTGTGAGGAGGCCAAGCTAGAAATAATGGAATTCGTGAATTTCTTGAAAAACCCAAAGCAATATCAAGACCTAGGAGCAAAAATCCCAAAGGGTGCCATTCTCACCGGTCCCCCAGGTACTGGGAAGACGCTGCTAGCTAAGGCCACAGCTGGAGAAGCCAATGTCCCCTTTATCACTGTGAGCGGATCTGAGTTTCTGGAGATGTTTGTTGGCGTTGGTCCAGCCAGAGTCCGAGACTTATTTGCCCTTGCTCGGAAGAATGCGCCTTGCATTCTCTTCATTGATGAGATTGATGCTGTGGGAAGGAAGCGCGGCAGAGGCAACTTCGGTGGGCAGAGCGAGCAGGAGAACACACTCAACCAGCTGCTTGTGGAGATGGACG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGATGCTGTGGGAAGGAAGC
60.32
ATTGCCCATCAACCGGAGTT
59.96
171
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGATGCTGTGGGAAGGAAGC
60.32
TGCCCATCAACCGGAGTTTT
60.18
169
PCR template sequence:
GATGAGATTGATGCTGTGGGAAGGAAGCGCGGCAGAGGCAACTTCGGTGGGCAGAGCGAGCAGGAGAACACACTCAACCAGCTGCTTGTGGAGATGGACGGTGGACAGACTAGAAGTTGTCAACAAGCGTTTTGTTCGTGTGACCTTTACACCAGGAAAAACTCCGGTTGATGGGCAATACGTCTGGTTTAATATTGGCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-495-3p(1), mmu-miR-129-5p(1), mmu-miR-207(1), mmu-miR-300-3p(1), mmu-miR-452-3p(1), mmu-miR-3065-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GTGGAGATGGACGGTGGACAGACTAG
siRNA sets
TGTCCACCGTCCATCTCCA, CTGTCCACCGTCCATCTCC, CTAGTCTGTCCACCGTCCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAFG3L2_766_ORF_1
1.0172
0.221116734
0.980637391
888
ORF sequence:
ATGCGCCTTGCATTCTCTTCATTGATGAGATTGATGCTGTGGGAAGGAAGCGCGGCAGAGGCAACTTCGGTGGGCAGAGCGAGCAGGAGAACACACTCAACCAGCTGCTTGTGGAGATGGACGGTGGACAGACTAGAAGTTGTCAACAAGCGTTTTGTTCGTGTGACCTTTACACCAGGAAAAACTCCGGTTGATGGGCAATACGTCTGGTTTAATATTGGCAGTGTTGACACATTTGAGCGGAATCTGGAGACTTTGCAGCAAGAATTGGGCATAGAAGGGGAGAACCGGGTCCCTGTGGTTTATATTGCTGAGAGCGATGGCTCCTTCCTGCTGAGCATGTTGCCCACCGTACTCATTATCGCTTTTCTACTCTACACCATAAGAAGAGGGCCCGCTGGCATTGGTCGGACCGGCCGGGGAATGGGTGGACTCTTCAGCGTTGGGGAAACCACAGCCAAGGTCTTAAAGGATGAGATAGATGTGAAGTTTAAAGATGTGGCTGGCTGTGAGGAGGCCAAGCTAGAAATAATGGAATTCGTGAATTTCTTGAAAAACCCAAAGCAATATCAAGACCTAGGAGCAAAAATCCCAAAGGGTGCCATTCTCACCGGTCCCCCAGGTACTGGGAAGACGCTGCTAGCTAAGGCCACAGCTGGAGAAGCCAATGTCCCCTTTATCACTGTGAGCGGATCTGAGTTTCTGGAGATGTTTGTTGGCGTTGGTCCAGCCAGAGTCCGAGACTTATTTGCCCTTGCTCGGAAGAATGCGCCTTGCATTCTCTTCATTGATGAGATTGATGCTGTGGGAAGGAAGCGCGGCAGAGGCAACTTCGGTGGGCAGAGCGAGCAGGAGAACACACTCAACCAGCTGCTTGTGGAGATGGAC
Peptide sequence:
MRLAFSSLMRLMLWEGSAAEATSVGRASRRTHSTSCLWRWTVDRLEVVNKRFVRVTFTPGKTPVDGQYVWFNIGSVDTFERNLETLQQELGIEGENRVPVVYIAESDGSFLLSMLPTVLIIAFLLYTIRRGPAGIGRTGRGMGGLFSVGETTAKVLKDEIDVKFKDVAGCEEAKLEIMEFVNFLKNPKQYQDLGAKIPKGAILTGPPGTGKTLLAKATAGEANVPFITVSGSEFLEMFVGVGPARVRDLFALARKNAPCILFIDEIDAVGRKRGRGNFGGQSEQENTLNQLLVEMD
IRESfinder result
IRESfinder score
0.408658686
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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