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mmu_circAfg3l1_1264
Basic information of circular RNA
PanCircBase ID:
mmu_circAfg3l1_1264
mm39_Chr. Position ID:
chr8|124207087|124220674|+
Gene name:
Afg3l1
Transcript:
ENSMUST00000001520.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
2,3,4,5,6,7,8,9,10,11
Exon/intron offsets:
0,722,4254,5540,7010,7852,9406,12192,12526,13479
Genomic length:
13587
Exon/intron sizes in nt:
8,87,58,61,50,69,12,52,00,00,00,00,000
Flanking exon/introns:
chr8:124204786-124207087|chr8:124220674-124221544
Splice length:
1264
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GGTCATCTGGGGAGATGCTCGCAGCAGCTGGCTCTGCAGGGAAAACTGACTTCATTTTCCCCGAGGCTGTATTCAAAACCTCCCAGAGGGTTTGAGAAGTTTTTTAAGAATAAGAAGAACAGAAAAAGTGCAAGCCCAGGAAATTCAGTACCTCCAAAAAAAGAACCAAAAAATGCTGGCCCTGGAGGAGATGGAGGCAACAGAGGAGGGAAAGGAGATGATTTTCCCTGGTGGAAACGGATGCAAAAGGGAGAATTTCCTTGGGACGACAAGGACTTCCGGAGCCTGGCTGTTTTGGGGGCTGGTGTGGCTGCGGGATTTTTATATTTTTATTTCCGAGATCCCGGAAAAGAGATCACCTGGAAACACTTCGTGCAGTATTACCTGGCCAGAGGTCTGGTGGACCGGCTAGAGGTTGTGAACAAGCAGTTTGTGCGTGTTATTCCTGTTCCTGGGACGACATCTGAGAGGTTCGTGTGGTTTAACATTGGCAGTGTTGACACCTTTGAACGGAACCTCGAGTCTGCTCAGTGGGAGCTGGGCATTGAGCCCACCAACCAGGCTGCGGTGGTCTACACTACTGAGAGTGATGGCTCTTTTCTTAGAAGTCTTGTGCCCACTCTGGTCCTGGTTAGCATCCTCCTATATGCTATGAGGAGGGGTCCAATGGGGACTGGTCGCGGTGGGCGAGGAGGAGGCCTCTTCAGTGTTGGTGAGACAACAGCCAAGATCTTAAAGAACAACATCGATGTGCGGTTTGCAGATGTGGCTGGCTGTGAAGAAGCCAAACTGGAAATTATGGAGTTTGTGAATTTCCTGAAGAACCCAAAGCAATATCAGGACTTAGGAGCCAAAATTCCAAAGGGAGCGATGCTCACTGGTCCACCTGGTACTGGCAAAACACTTCTTGCAAAAGCAACTGCTGGGGAGGCCAACGTGCCCTTCATCACCGTGAATGGGTCGGAATTCCTGGAAATGTTTGTTGGTGTTGGGCCAGCACGGGTCCGTGACATGTTTGCAATGGCCCGAAAACACGCTCCTTGTATTTTATTCATTGATGAGATTGATGCAATTGGCAGAAAGCGAGGCCGTGGCCACCTGGGAGGCCAGAGTGAGCAGGAAAACACTTTAAACCAGATGCTTGTGGAGATGGACGGGTTCAACTCTTCCACTAATGTGGTAGTGTTAGCCGGCACCAATCGCCCTGATATCCTTGACCCAGCCCTGACACGGCCTGGCCGGTTTGACCGTCAGATCTACATCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGTGGTAGTGTTAGCCGGC
60.11
ACAGCCTCGGGGAAAATGAA
59.6
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCACCAATCGCCCTGATAT
60.25
ACAGCCTCGGGGAAAATGAA
59.6
143
PCR template sequence:
TCTTCCACTAATGTGGTAGTGTTAGCCGGCACCAATCGCCCTGATATCCTTGACCCAGCCCTGACACGGCCTGGCCGGTTTGACCGTCAGATCTACATCGGGTCATCTGGGGAGATGCTCGCAGCAGCTGGCTCTGCAGGGAAAACTGACTTCATTTTCCCCGAGGCTGTATTCAAAACCTCCCAGAGGGTTTGAGAAGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
19
Interacting miRNAs (#binding sites)
mmu-miR-211-5p(2), 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-204-5p(1), mmu-miR-381-3p(1), mmu-miR-495-3p(1), mmu-miR-382-3p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-541-5p(1), mmu-miR-207(1), mmu-miR-350-3p(1), mmu-miR-1904(1), mmu-miR-296-3p(1), mmu-miR-542-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CAGATCTACATCGGGTCATCTGGGGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAFG3L1_1264_ORF_1
1.0821
0.256449256
0.997081359
1119
ORF sequence:
ATGCAAAAGGGAGAATTTCCTTGGGACGACAAGGACTTCCGGAGCCTGGCTGTTTTGGGGGCTGGTGTGGCTGCGGGATTTTTATATTTTTATTTCCGAGATCCCGGAAAAGAGATCACCTGGAAACACTTCGTGCAGTATTACCTGGCCAGAGGTCTGGTGGACCGGCTAGAGGTTGTGAACAAGCAGTTTGTGCGTGTTATTCCTGTTCCTGGGACGACATCTGAGAGGTTCGTGTGGTTTAACATTGGCAGTGTTGACACCTTTGAACGGAACCTCGAGTCTGCTCAGTGGGAGCTGGGCATTGAGCCCACCAACCAGGCTGCGGTGGTCTACACTACTGAGAGTGATGGCTCTTTTCTTAGAAGTCTTGTGCCCACTCTGGTCCTGGTTAGCATCCTCCTATATGCTATGAGGAGGGGTCCAATGGGGACTGGTCGCGGTGGGCGAGGAGGAGGCCTCTTCAGTGTTGGTGAGACAACAGCCAAGATCTTAAAGAACAACATCGATGTGCGGTTTGCAGATGTGGCTGGCTGTGAAGAAGCCAAACTGGAAATTATGGAGTTTGTGAATTTCCTGAAGAACCCAAAGCAATATCAGGACTTAGGAGCCAAAATTCCAAAGGGAGCGATGCTCACTGGTCCACCTGGTACTGGCAAAACACTTCTTGCAAAAGCAACTGCTGGGGAGGCCAACGTGCCCTTCATCACCGTGAATGGGTCGGAATTCCTGGAAATGTTTGTTGGTGTTGGGCCAGCACGGGTCCGTGACATGTTTGCAATGGCCCGAAAACACGCTCCTTGTATTTTATTCATTGATGAGATTGATGCAATTGGCAGAAAGCGAGGCCGTGGCCACCTGGGAGGCCAGAGTGAGCAGGAAAACACTTTAAACCAGATGCTTGTGGAGATGGACGGGTTCAACTCTTCCACTAATGTGGTAGTGTTAGCCGGCACCAATCGCCCTGATATCCTTGACCCAGCCCTGACACGGCCTGGCCGGTTTGACCGTCAGATCTACATCGGGTCATCTGGGGAGATGCTCGCAGCAGCTGGCTCTGCAGGGAAAACTGACTTCATTTTCCCCGAGGCTGTATTCAAAACCTCCCAGAGGGTTTGA
Peptide sequence:
MQKGEFPWDDKDFRSLAVLGAGVAAGFLYFYFRDPGKEITWKHFVQYYLARGLVDRLEVVNKQFVRVIPVPGTTSERFVWFNIGSVDTFERNLESAQWELGIEPTNQAAVVYTTESDGSFLRSLVPTLVLVSILLYAMRRGPMGTGRGGRGGGLFSVGETTAKILKNNIDVRFADVAGCEEAKLEIMEFVNFLKNPKQYQDLGAKIPKGAMLTGPPGTGKTLLAKATAGEANVPFITVNGSEFLEMFVGVGPARVRDMFAMARKHAPCILFIDEIDAIGRKRGRGHLGGQSEQENTLNQMLVEMDGFNSSTNVVVLAGTNRPDILDPALTRPGRFDRQIYIGSSGEMLAAAGSAGKTDFIFPEAVFKTSQRV
IRESfinder result
IRESfinder score
0.527142814
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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