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mmu_circAtf1_340
Basic information of circular RNA
PanCircBase ID:
mmu_circAtf1_340
mm39_Chr. Position ID:
chr15|100151974|100152394|+
Gene name:
Atf1
Transcript:
ENSMUST00000023769.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
5,6
Exon/intron offsets:
0,260
Genomic length:
420
Exon/intron sizes in nt:
180,160
Flanking exon/introns:
chr15:100150080-100151974|chr15:100152394-100157695
Splice length:
340
Other database IDs:
CIRCpedia: MMU_CIRCpedia_223880, circAtlas: mmu-Atf1_0001
circBase: hsa_circ_0026285, circAtlas: hsa-ATF1_0001, CIRCpedia: HSA_CIRCpedia_8753
Human Ortholog IDs:
Mature spliced Sequence:
TTGCCATTGCCCCAAACGGAGCCTTACAGTTGGCCAGTCCAAGCACGGATGGAGTGCAGGCACTGCAGACATTAACCATGACAAATTCAAGCAGTACTCAGCAGGGGACGATCCTCCAGTATGCACAGACCTCTGACGGACAGCAGATACTCGTCCCGAGCAACCAGGTGGTTGTACAGACTGCATCAGGAGATATGCAGACCTACCAGATCCGTACCACGCCGTCTGCCACGTCTCTCCCGCAGACCGTGGTGATGACTTCTCCTGTGACTCTTGCATCTCAGACAACAAAGACAGATGACCCTCAACTAAGAAGAGAAATACGACTGATGAAAAACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGACCGTGGTGATGACTT
60.32
TGGACTGGCCAACTGTAAGG
59.6
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGACCGTGGTGATGACTT
60.32
CTCCATCCGTGCTTGGACTG
60.74
153
PCR template sequence:
CGCAGACCGTGGTGATGACTTCTCCTGTGACTCTTGCATCTCAGACAACAAAGACAGATGACCCTCAACTAAGAAGAGAAATACGACTGATGAAAAACAGTTGCCATTGCCCCAAACGGAGCCTTACAGTTGGCCAGTCCAAGCACGGATGGAGTGCAGGCACTGCAGACATTAACCATGACAAATTCAAGCAGTACTCA
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-185-5p(1), mmu-miR-193b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGATGAAAAACAGTTGCCATTGCCCC
siRNA sets
CAATGGCAACTGTTTTTCA, AATGGCAACTGTTTTTCAT, ATGGCAACTGTTTTTCATC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATF1_340_ORF_1
0.8943
0.212003749
0.53746966
399
ORF sequence:
ATGACAAATTCAAGCAGTACTCAGCAGGGGACGATCCTCCAGTATGCACAGACCTCTGACGGACAGCAGATACTCGTCCCGAGCAACCAGGTGGTTGTACAGACTGCATCAGGAGATATGCAGACCTACCAGATCCGTACCACGCCGTCTGCCACGTCTCTCCCGCAGACCGTGGTGATGACTTCTCCTGTGACTCTTGCATCTCAGACAACAAAGACAGATGACCCTCAACTAAGAAGAGAAATACGACTGATGAAAAACAGTTGCCATTGCCCCAAACGGAGCCTTACAGTTGGCCAGTCCAAGCACGGATGGAGTGCAGGCACTGCAGACATTAACCATGACAAATTCAAGCAGTACTCAGCAGGGGACGATCCTCCAGTATGCACAGACCTCTGA
Peptide sequence:
MTNSSSTQQGTILQYAQTSDGQQILVPSNQVVVQTASGDMQTYQIRTTPSATSLPQTVVMTSPVTLASQTTKTDDPQLRREIRLMKNSCHCPKRSLTVGQSKHGWSAGTADINHDKFKQYSAGDDPPVCTDL
IRESfinder result
IRESfinder score
0.344796025
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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