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mmu_circAmotl1_1108
Basic information of circular RNA
PanCircBase ID:
mmu_circAmotl1_1108
mm39_Chr. Position ID:
chr9|14504049|14507896|-
Gene name:
Amotl1
Transcript:
ENSMUST00000013220.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,2
Exon/intron offsets:
0,3697
Genomic length:
3847
Exon/intron sizes in nt:
958,150
Flanking exon/introns:
chr9:14486735-14504049|chr9:14507896-14526029
Splice length:
1108
Other database IDs:
circBase: mmu_circ_0015414, CIRCpedia: MMU_CIRCpedia_9621, circAtlas: mmu-Amotl1_0002
circBase: hsa_circ_0000350, circAtlas: hsa-AMOTL1_0001, CIRCpedia: HSA_CIRCpedia_6130
Human Ortholog IDs:
Mature spliced Sequence:
CTCCTCCTCCCATCTGCTACAGCCCCAGCAGTCCTGTGCAGATTCTAGAAGACCCCGCCTACTTCTACCCAGACTTGCAGCTCTATTCTGGGAGGCATGAAGCATCTACTTTGACAGTGGAGGCAAGTGGAGGCCTAAGGGGGAAAAGCGTAGAGGACCCTCTCTCCAGCTTCCACTCCCCGAACTTCCTGAGGACGCCCGAGGTGGAAATGAGAGGTTCTGAGGATGTAGCCTCTGGAAGAGTGTTACAGCGGCTGATCCAGGAACAACTGCGCTATGGCACCCCAACTGAGAACATGAACCTGCTGGCCATTCAGCACCAGGCCACAGGGAGTGCAGGGCCAGCCCACGCCACCACCAACTTTTCTTCCACGGAAACCCTCACTCAAGAAGATCCACAAATGGTCTATCAGTCGGCCCGCCAAGAACCGCAGGGTCAAGAGCATCAGGGAGACAATACGGTGATGGAGAAGCAGGTCCGGTCCACACAGCCTCAGCAGAACAACGAGGAGCTCCCCACGTATGAGGAAGCCAAGGCCCAGTCCCAGTTCTTCAGGGGACAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAACAGCAGCAGCAACAGCAGCAGGGACAGGGGCCCCTTAGCCACACTTATTACATGGCCGGAGGTACCAGTCAGAAGTCCCGCACTGAGGGGAGGCCCACAGTGAACCGGGCCAACAGTGGACAGGCGCATAAGGATGAGGCCCTGAAAGAACTAAAGCAGGGCCATGTCCGGTCCCTCAGTGAGAGGATCATGCAGCTGTCACTGGAGAGGAATGGGGCTAAGCAACACCTCCCCAGCTCTGGAAATGGAAAGAGCTTCAAAGCTGGAGGAGAGCCATCCCCAGCTCAGCCTGTCTGTAAAGCACTGGACCCTCGTGGCCCTCCACCTGAATACCCCTTCAAGACCAAGCCAATGAAATCCCCAGTCAGCAAGAACCAAGATCACGGTCTTTACTACAATGACCAGCACCCTGGGGTACTCCATGAGATGGTCAAACCTTACCCAGCACCTCAGCCTGCGAGAACAGAAGTGGCCGTCCTGAGGTATCAGCCACCCCCGGAGTATGGCGTCACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCAGCCTGCGAGAACAGAAG
60.04
GCCTCCCAGAATAGAGCTGC
60.25
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTCAGCCTGCGAGAACAGAA
60.04
GCCTCCCAGAATAGAGCTGC
60.25
163
PCR template sequence:
TACTCCATGAGATGGTCAAACCTTACCCAGCACCTCAGCCTGCGAGAACAGAAGTGGCCGTCCTGAGGTATCAGCCACCCCCGGAGTATGGCGTCACCAGCTCCTCCTCCCATCTGCTACAGCCCCAGCAGTCCTGTGCAGATTCTAGAAGACCCCGCCTACTTCTACCCAGACTTGCAGCTCTATTCTGGGAGGCATGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-328-3p(2), mmu-miR-221-3p(1), mmu-miR-370-3p(1), mmu-miR-342-5p(1), mmu-miR-705(1)
siRNAs for circular RNA silencing
Junction sequence
ATGGCGTCACCAGCTCCTCCTCCCAT
siRNA sets
GAGGAGGAGCTGGTGACGC, AGGAGGAGCTGGTGACGCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAMOTL1_1108_ORF_1
1.0501
0.360872222
0.997991641
1119
ORF sequence:
ATGGCGTCACCAGCTCCTCCTCCCATCTGCTACAGCCCCAGCAGTCCTGTGCAGATTCTAGAAGACCCCGCCTACTTCTACCCAGACTTGCAGCTCTATTCTGGGAGGCATGAAGCATCTACTTTGACAGTGGAGGCAAGTGGAGGCCTAAGGGGGAAAAGCGTAGAGGACCCTCTCTCCAGCTTCCACTCCCCGAACTTCCTGAGGACGCCCGAGGTGGAAATGAGAGGTTCTGAGGATGTAGCCTCTGGAAGAGTGTTACAGCGGCTGATCCAGGAACAACTGCGCTATGGCACCCCAACTGAGAACATGAACCTGCTGGCCATTCAGCACCAGGCCACAGGGAGTGCAGGGCCAGCCCACGCCACCACCAACTTTTCTTCCACGGAAACCCTCACTCAAGAAGATCCACAAATGGTCTATCAGTCGGCCCGCCAAGAACCGCAGGGTCAAGAGCATCAGGGAGACAATACGGTGATGGAGAAGCAGGTCCGGTCCACACAGCCTCAGCAGAACAACGAGGAGCTCCCCACGTATGAGGAAGCCAAGGCCCAGTCCCAGTTCTTCAGGGGACAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAACAGCAGCAGCAACAGCAGCAGGGACAGGGGCCCCTTAGCCACACTTATTACATGGCCGGAGGTACCAGTCAGAAGTCCCGCACTGAGGGGAGGCCCACAGTGAACCGGGCCAACAGTGGACAGGCGCATAAGGATGAGGCCCTGAAAGAACTAAAGCAGGGCCATGTCCGGTCCCTCAGTGAGAGGATCATGCAGCTGTCACTGGAGAGGAATGGGGCTAAGCAACACCTCCCCAGCTCTGGAAATGGAAAGAGCTTCAAAGCTGGAGGAGAGCCATCCCCAGCTCAGCCTGTCTGTAAAGCACTGGACCCTCGTGGCCCTCCACCTGAATACCCCTTCAAGACCAAGCCAATGAAATCCCCAGTCAGCAAGAACCAAGATCACGGTCTTTACTACAATGACCAGCACCCTGGGGTACTCCATGAGATGGTCAAACCTTACCCAGCACCTCAGCCTGCGAGAACAGAAGTGGCCGTCCTGAGGTATCAGCCACCCCCGGAGTATGGCGTCACC
Peptide sequence:
MASPAPPPICYSPSSPVQILEDPAYFYPDLQLYSGRHEASTLTVEASGGLRGKSVEDPLSSFHSPNFLRTPEVEMRGSEDVASGRVLQRLIQEQLRYGTPTENMNLLAIQHQATGSAGPAHATTNFSSTETLTQEDPQMVYQSARQEPQGQEHQGDNTVMEKQVRSTQPQQNNEELPTYEEAKAQSQFFRGQQQQQQQQQQQQQQQQQQGQGPLSHTYYMAGGTSQKSRTEGRPTVNRANSGQAHKDEALKELKQGHVRSLSERIMQLSLERNGAKQHLPSSGNGKSFKAGGEPSPAQPVCKALDPRGPPPEYPFKTKPMKSPVSKNQDHGLYYNDQHPGVLHEMVKPYPAPQPARTEVAVLRYQPPPEYGVT
IRESfinder result
IRESfinder score
0.393301454
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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