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mmu_circAifm1_447
Basic information of circular RNA
PanCircBase ID:
mmu_circAifm1_447
mm39_Chr. Position ID:
chrX|47583615|47588748|-
Gene name:
Aifm1
Transcript:
ENSMUST00000143466.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,5,4,3
Exon/intron offsets:
0,2341,2595,5033
Genomic length:
5133
Exon/intron sizes in nt:
91,13,11,25,100
Flanking exon/introns:
chrX:47575107-47583615|chrX:47588748-47593686
Splice length:
447
Other database IDs:
CIRCpedia: MMU_CIRCpedia_212221, circAtlas: mmu-Aifm1_0001
Human Ortholog IDs:
Mature spliced Sequence:
GCCTACAAAACTATAAAAGAAGACCAAAAAAGATACAATGAAAGAGTGATGGGATTAGGACTGTCCCCAGAAGAGAAACAGAGAAGAGCCATTGCCTCCGCTACAGAGGGAGGCTCAGTTCCTCAGATCAGGGCACCAAGTCACGTCCCTTTCCTGCTGATTGGTGGAGGGACTGCTGCTTTTGCAGCAGCCAGATCCATCCGGGCTCGGGATCCTGGGGCCAGGGTCCTGATTGTATCTGAAGACCCTGAACTGCCATACATGCGACCTCCTCTTTCAAAAGAATTGTGGTTTTCAGATGATCCAAATGTCACAAAGACACTGCAATTCAGACAGTGGAATGGAAAAGAGAGAAGCATATATTTCCAGCCACCTTCTTTCTATGTCTCTGCTCAGGACCTGCCTAATATTGAGAACGGTGGTGTGGCTGTCCTCACTGGGAAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGTCTCTGCTCAGGACCTG
58.81
AGGCAATGGCTCTTCTCTGT
59.01
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTCTCTGCTCAGGACCTGC
59.78
AGGCAATGGCTCTTCTCTGT
59.01
160
PCR template sequence:
AGAGAGAAGCATATATTTCCAGCCACCTTCTTTCTATGTCTCTGCTCAGGACCTGCCTAATATTGAGAACGGTGGTGTGGCTGTCCTCACTGGGAAAAAGGCCTACAAAACTATAAAAGAAGACCAAAAAAGATACAATGAAAGAGTGATGGGATTAGGACTGTCCCCAGAAGAGAAACAGAGAAGAGCCATTGCCTCCG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-322-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CACTGGGAAAAAGGCCTACAAAACTA
siRNA sets
GTTTTGTAGGCCTTTTTCC,TTTTGTAGGCCTTTTTCCC,TTTGTAGGCCTTTTTCCCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAIFM1_447_ORF_1
1.0004
0.118146824
0.960244613
846
ORF sequence:
ATGGGATTAGGACTGTCCCCAGAAGAGAAACAGAGAAGAGCCATTGCCTCCGCTACAGAGGGAGGCTCAGTTCCTCAGATCAGGGCACCAAGTCACGTCCCTTTCCTGCTGATTGGTGGAGGGACTGCTGCTTTTGCAGCAGCCAGATCCATCCGGGCTCGGGATCCTGGGGCCAGGGTCCTGATTGTATCTGAAGACCCTGAACTGCCATACATGCGACCTCCTCTTTCAAAAGAATTGTGGTTTTCAGATGATCCAAATGTCACAAAGACACTGCAATTCAGACAGTGGAATGGAAAAGAGAGAAGCATATATTTCCAGCCACCTTCTTTCTATGTCTCTGCTCAGGACCTGCCTAATATTGAGAACGGTGGTGTGGCTGTCCTCACTGGGAAAAAGGCCTACAAAACTATAAAAGAAGACCAAAAAAGATACAATGAAAGAGTGATGGGATTAGGACTGTCCCCAGAAGAGAAACAGAGAAGAGCCATTGCCTCCGCTACAGAGGGAGGCTCAGTTCCTCAGATCAGGGCACCAAGTCACGTCCCTTTCCTGCTGATTGGTGGAGGGACTGCTGCTTTTGCAGCAGCCAGATCCATCCGGGCTCGGGATCCTGGGGCCAGGGTCCTGATTGTATCTGAAGACCCTGAACTGCCATACATGCGACCTCCTCTTTCAAAAGAATTGTGGTTTTCAGATGATCCAAATGTCACAAAGACACTGCAATTCAGACAGTGGAATGGAAAAGAGAGAAGCATATATTTCCAGCCACCTTCTTTCTATGTCTCTGCTCAGGACCTGCCTAATATTGAGAACGGTGGTGTGGCTGTCCTCACTGGGAAAAAG
Peptide sequence:
MGLGLSPEEKQRRAIASATEGGSVPQIRAPSHVPFLLIGGGTAAFAAARSIRARDPGARVLIVSEDPELPYMRPPLSKELWFSDDPNVTKTLQFRQWNGKERSIYFQPPSFYVSAQDLPNIENGGVAVLTGKKAYKTIKEDQKRYNERVMGLGLSPEEKQRRAIASATEGGSVPQIRAPSHVPFLLIGGGTAAFAAARSIRARDPGARVLIVSEDPELPYMRPPLSKELWFSDDPNVTKTLQFRQWNGKERSIYFQPPSFYVSAQDLPNIENGGVAVLTGKK
IRESfinder result
IRESfinder score
0.613066439
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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