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mmu_circAfg1l_609
Basic information of circular RNA
PanCircBase ID:
mmu_circAfg1l_609
mm39_Chr. Position ID:
chr10|42291544|42330526|-
Gene name:
Afg1l
Transcript:
ENSMUST00000041024.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,9629,10937,22805,38758
Genomic length:
38982
Exon/intron sizes in nt:
1,00,13,11,02,52,224
Flanking exon/introns:
chr10:42276395-42291544|chr10:42330526-42354258
Splice length:
609
Other database IDs:
circBase: mmu_circ_0002209, CIRCpedia: MMU_CIRCpedia_19863, circAtlas: mmu-Lace1_0002
circBase: hsa_circ_0130214, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_53238
Human Ortholog IDs:
Mature spliced Sequence:
CCTACACAGTCCAGACATCCGAGGGTGTACGCCCAACAGCCGCTTCTGAGGCCCGTTTGAAAGCCTTGGCTGTTTGCCACGGGCCTCTGGACCACTACGACTTTCTGATCAAATCTCAGGAGCTGAGGGAGGATGAACATCAAAGAAGAGTCGTTCAGTGTTTGCAGAAGTTACAGGAGGACCTTAAAGGATACAGCATAGAGGAAGGAGGGCTCTTTTCAAAGCTTTTTTCAAGGAACAAACCTCCAAAGGGCCTCTATGTTTATGGAGACGTTGGTACAGGAAAAACAATGGTGATGGACATGTTTTATGCATATGTGGAAACGAAGAGAAAGAAGCGGGTCCATTTTCACGGCTTCATGCTGGACGTGCACAGAAGGATACACCACCTTAAACAGAGTTTGCCAAAAAGGAAGGCGGGATTCATGGCTAAGTCATATGACCCGATAGCTCCCATAGCCGAGGAAATCAGTCAAGAAACTTCTCTCCTATGTTTTGATGAATTTCAGGTCACTGACATCGCCGACGCCATGATTCTGAAACAGCTTTTTGAAAATCTGTTCAAAAACGGGGTCGTCGTTGTGGCAACATCCAACAGACCACCGGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCGACGCCATGATTCTGAAAC
59.94
TTCAAACGGGCCTCAGAAGC
60.89
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCGACGCCATGATTCTGAAAC
59.94
GCTTTCAAACGGGCCTCAGA
60.89
151
PCR template sequence:
GTCACTGACATCGCCGACGCCATGATTCTGAAACAGCTTTTTGAAAATCTGTTCAAAAACGGGGTCGTCGTTGTGGCAACATCCAACAGACCACCGGAAGCCTACACAGTCCAGACATCCGAGGGTGTACGCCCAACAGCCGCTTCTGAGGCCCGTTTGAAAGCCTTGGCTGTTTGCCACGGGCCTCTGGACCACTACGA
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-320-3p(1), mmu-miR-383-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGACCACCGGAAGCCTACACAGTCCA
siRNA sets
CTGTGTAGGCTTCCGGTGG, TGTGTAGGCTTCCGGTGGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAFG1L_609_ORF_1
1.1498
0.191688381
0.987130154
927
ORF sequence:
ATGGTGATGGACATGTTTTATGCATATGTGGAAACGAAGAGAAAGAAGCGGGTCCATTTTCACGGCTTCATGCTGGACGTGCACAGAAGGATACACCACCTTAAACAGAGTTTGCCAAAAAGGAAGGCGGGATTCATGGCTAAGTCATATGACCCGATAGCTCCCATAGCCGAGGAAATCAGTCAAGAAACTTCTCTCCTATGTTTTGATGAATTTCAGGTCACTGACATCGCCGACGCCATGATTCTGAAACAGCTTTTTGAAAATCTGTTCAAAAACGGGGTCGTCGTTGTGGCAACATCCAACAGACCACCGGAAGCCTACACAGTCCAGACATCCGAGGGTGTACGCCCAACAGCCGCTTCTGAGGCCCGTTTGAAAGCCTTGGCTGTTTGCCACGGGCCTCTGGACCACTACGACTTTCTGATCAAATCTCAGGAGCTGAGGGAGGATGAACATCAAAGAAGAGTCGTTCAGTGTTTGCAGAAGTTACAGGAGGACCTTAAAGGATACAGCATAGAGGAAGGAGGGCTCTTTTCAAAGCTTTTTTCAAGGAACAAACCTCCAAAGGGCCTCTATGTTTATGGAGACGTTGGTACAGGAAAAACAATGGTGATGGACATGTTTTATGCATATGTGGAAACGAAGAGAAAGAAGCGGGTCCATTTTCACGGCTTCATGCTGGACGTGCACAGAAGGATACACCACCTTAAACAGAGTTTGCCAAAAAGGAAGGCGGGATTCATGGCTAAGTCATATGACCCGATAGCTCCCATAGCCGAGGAAATCAGTCAAGAAACTTCTCTCCTATGTTTTGATGAATTTCAGGTCACTGACATCGCCGACGCCATGATTCTGAAACAGCTTTTTGAAAATCTGTTCAAAAACGGGGTCGTCGTTGTGGCAACATCCAACAGACCACCGGAA
Peptide sequence:
MVMDMFYAYVETKRKKRVHFHGFMLDVHRRIHHLKQSLPKRKAGFMAKSYDPIAPIAEEISQETSLLCFDEFQVTDIADAMILKQLFENLFKNGVVVVATSNRPPEAYTVQTSEGVRPTAASEARLKALAVCHGPLDHYDFLIKSQELREDEHQRRVVQCLQKLQEDLKGYSIEEGGLFSKLFSRNKPPKGLYVYGDVGTGKTMVMDMFYAYVETKRKKRVHFHGFMLDVHRRIHHLKQSLPKRKAGFMAKSYDPIAPIAEEISQETSLLCFDEFQVTDIADAMILKQLFENLFKNGVVVVATSNRPPE
IRESfinder result
IRESfinder score
0.561198007
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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