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mmu_circAfg3l1_864
Basic information of circular RNA
PanCircBase ID:
mmu_circAfg3l1_864
mm39_Chr. Position ID:
chr8|124207087|124216764|+
Gene name:
Afg3l1
Transcript:
ENSMUST00000001520.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
2,3,4,5,6,7,8
Exon/intron offsets:
0,722,4254,5540,7010,7852,9406
Genomic length:
9677
Exon/intron sizes in nt:
88,75,86,15,06,91,25,200
Flanking exon/introns:
chr8:124204786-124207087|chr8:124216764-124219279
Splice length:
864
Other database IDs:
circAtlas: mmu-Afg3l1_0001
Human Ortholog IDs:
Mature spliced Sequence:
GGTCATCTGGGGAGATGCTCGCAGCAGCTGGCTCTGCAGGGAAAACTGACTTCATTTTCCCCGAGGCTGTATTCAAAACCTCCCAGAGGGTTTGAGAAGTTTTTTAAGAATAAGAAGAACAGAAAAAGTGCAAGCCCAGGAAATTCAGTACCTCCAAAAAAAGAACCAAAAAATGCTGGCCCTGGAGGAGATGGAGGCAACAGAGGAGGGAAAGGAGATGATTTTCCCTGGTGGAAACGGATGCAAAAGGGAGAATTTCCTTGGGACGACAAGGACTTCCGGAGCCTGGCTGTTTTGGGGGCTGGTGTGGCTGCGGGATTTTTATATTTTTATTTCCGAGATCCCGGAAAAGAGATCACCTGGAAACACTTCGTGCAGTATTACCTGGCCAGAGGTCTGGTGGACCGGCTAGAGGTTGTGAACAAGCAGTTTGTGCGTGTTATTCCTGTTCCTGGGACGACATCTGAGAGGTTCGTGTGGTTTAACATTGGCAGTGTTGACACCTTTGAACGGAACCTCGAGTCTGCTCAGTGGGAGCTGGGCATTGAGCCCACCAACCAGGCTGCGGTGGTCTACACTACTGAGAGTGATGGCTCTTTTCTTAGAAGTCTTGTGCCCACTCTGGTCCTGGTTAGCATCCTCCTATATGCTATGAGGAGGGGTCCAATGGGGACTGGTCGCGGTGGGCGAGGAGGAGGCCTCTTCAGTGTTGGTGAGACAACAGCCAAGATCTTAAAGAACAACATCGATGTGCGGTTTGCAGATGTGGCTGGCTGTGAAGAAGCCAAACTGGAAATTATGGAGTTTGTGAATTTCCTGAAGAACCCAAAGCAATATCAGGACTTAGGAGCCAAAATTCCAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGGCTGGCTGTGAAGAAG
60.54
TCAGTTTTCCCTGCAGAGCC
60.25
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGGCTGGCTGTGAAGAAG
60.54
AGTTTTCCCTGCAGAGCCAG
60.25
147
PCR template sequence:
TGTGGCTGGCTGTGAAGAAGCCAAACTGGAAATTATGGAGTTTGTGAATTTCCTGAAGAACCCAAAGCAATATCAGGACTTAGGAGCCAAAATTCCAAAGGGTCATCTGGGGAGATGCTCGCAGCAGCTGGCTCTGCAGGGAAAACTGACTTCATTTTCCCCGAGGCTGTATTCAAAACCTCCCAGAGGGTTTGAGAAGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-199a-5p(1), mmu-miR-200b-3p(1), mmu-miR-200c-3p(1), mmu-miR-205-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-207(1), mmu-miR-350-3p(1), mmu-miR-542-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CAAAATTCCAAAGGGTCATCTGGGGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAFG3L1_864_ORF_1
0.9379
0.218203447
0.999693716
1488
ORF sequence:
ATGCAAAAGGGAGAATTTCCTTGGGACGACAAGGACTTCCGGAGCCTGGCTGTTTTGGGGGCTGGTGTGGCTGCGGGATTTTTATATTTTTATTTCCGAGATCCCGGAAAAGAGATCACCTGGAAACACTTCGTGCAGTATTACCTGGCCAGAGGTCTGGTGGACCGGCTAGAGGTTGTGAACAAGCAGTTTGTGCGTGTTATTCCTGTTCCTGGGACGACATCTGAGAGGTTCGTGTGGTTTAACATTGGCAGTGTTGACACCTTTGAACGGAACCTCGAGTCTGCTCAGTGGGAGCTGGGCATTGAGCCCACCAACCAGGCTGCGGTGGTCTACACTACTGAGAGTGATGGCTCTTTTCTTAGAAGTCTTGTGCCCACTCTGGTCCTGGTTAGCATCCTCCTATATGCTATGAGGAGGGGTCCAATGGGGACTGGTCGCGGTGGGCGAGGAGGAGGCCTCTTCAGTGTTGGTGAGACAACAGCCAAGATCTTAAAGAACAACATCGATGTGCGGTTTGCAGATGTGGCTGGCTGTGAAGAAGCCAAACTGGAAATTATGGAGTTTGTGAATTTCCTGAAGAACCCAAAGCAATATCAGGACTTAGGAGCCAAAATTCCAAAGGGTCATCTGGGGAGATGCTCGCAGCAGCTGGCTCTGCAGGGAAAACTGACTTCATTTTCCCCGAGGCTGTATTCAAAACCTCCCAGAGGGTTTGAGAAGTTTTTTAAGAATAAGAAGAACAGAAAAAGTGCAAGCCCAGGAAATTCAGTACCTCCAAAAAAAGAACCAAAAAATGCTGGCCCTGGAGGAGATGGAGGCAACAGAGGAGGGAAAGGAGATGATTTTCCCTGGTGGAAACGGATGCAAAAGGGAGAATTTCCTTGGGACGACAAGGACTTCCGGAGCCTGGCTGTTTTGGGGGCTGGTGTGGCTGCGGGATTTTTATATTTTTATTTCCGAGATCCCGGAAAAGAGATCACCTGGAAACACTTCGTGCAGTATTACCTGGCCAGAGGTCTGGTGGACCGGCTAGAGGTTGTGAACAAGCAGTTTGTGCGTGTTATTCCTGTTCCTGGGACGACATCTGAGAGGTTCGTGTGGTTTAACATTGGCAGTGTTGACACCTTTGAACGGAACCTCGAGTCTGCTCAGTGGGAGCTGGGCATTGAGCCCACCAACCAGGCTGCGGTGGTCTACACTACTGAGAGTGATGGCTCTTTTCTTAGAAGTCTTGTGCCCACTCTGGTCCTGGTTAGCATCCTCCTATATGCTATGAGGAGGGGTCCAATGGGGACTGGTCGCGGTGGGCGAGGAGGAGGCCTCTTCAGTGTTGGTGAGACAACAGCCAAGATCTTAAAGAACAACATCGATGTGCGGTTTGCAGATGTGGCTGGCTGTGAAGAAGCCAAACTGGAAATTATGGAGTTTGTGAATTTCCTGAAGAACCCAAAGCAATATCAGGACTTAGGAGCCAAAATTCCAAAG
Peptide sequence:
MQKGEFPWDDKDFRSLAVLGAGVAAGFLYFYFRDPGKEITWKHFVQYYLARGLVDRLEVVNKQFVRVIPVPGTTSERFVWFNIGSVDTFERNLESAQWELGIEPTNQAAVVYTTESDGSFLRSLVPTLVLVSILLYAMRRGPMGTGRGGRGGGLFSVGETTAKILKNNIDVRFADVAGCEEAKLEIMEFVNFLKNPKQYQDLGAKIPKGHLGRCSQQLALQGKLTSFSPRLYSKPPRGFEKFFKNKKNRKSASPGNSVPPKKEPKNAGPGGDGGNRGGKGDDFPWWKRMQKGEFPWDDKDFRSLAVLGAGVAAGFLYFYFRDPGKEITWKHFVQYYLARGLVDRLEVVNKQFVRVIPVPGTTSERFVWFNIGSVDTFERNLESAQWELGIEPTNQAAVVYTTESDGSFLRSLVPTLVLVSILLYAMRRGPMGTGRGGRGGGLFSVGETTAKILKNNIDVRFADVAGCEEAKLEIMEFVNFLKNPKQYQDLGAKIPK
IRESfinder result
IRESfinder score
0.522492707
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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