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mmu_circCse1l_401
Basic information of circular RNA
PanCircBase ID:
mmu_circCse1l_401
mm39_Chr. Position ID:
chr2|166774052|166779359|+
Gene name:
Cse1l
Transcript:
ENSMUST00000002790.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
14,15,16,17
Exon/intron offsets:
0,2620,3790,5209
Genomic length:
5307
Exon/intron sizes in nt:
62,137,104,98
Flanking exon/introns:
chr2:166772586-166774052|chr2:166779359-166781554
Splice length:
401
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TGAATGAGTTTCCTGTGCTTAAAGCTGATGGTATCAAATATATTATGATTTTTAGGAATCAAGTACCAAAAGAGCACCTCCTAGTCTCTATTCCCCTCTTGATCAGTCACCTGGAGGCTGAGAGTATTGTCGTCCACACTTATGCCGCACATGCTCTCGAAAGGCTGTTCACTATGAGAGGGTCAAACAATACCACTCTTTTTACAGCTGCAGAAATCGCACCGTTTGTTGAGATTCTGCTAACAAACCTTTTCAAAGCTCTCACACTTCCTGGCTCTTCAGAAAATGAATATATTATGAAAGCTATCATGAGAAGTTTCTCCCTCCTGCAAGAGGCCATCATCCCCTATATCCCCACTCTCATCACGCAGCTCACACAGAAGCTGCTGGCTGTTAGTAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTGCAAGAGGCCATCATC
59.82
GACTAGGAGGTGCTCTTTTGGT
59.7
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTCCTGCAAGAGGCCATCAT
59.82
GACTAGGAGGTGCTCTTTTGGT
59.7
164
PCR template sequence:
AGCTATCATGAGAAGTTTCTCCCTCCTGCAAGAGGCCATCATCCCCTATATCCCCACTCTCATCACGCAGCTCACACAGAAGCTGCTGGCTGTTAGTAAGTGAATGAGTTTCCTGTGCTTAAAGCTGATGGTATCAAATATATTATGATTTTTAGGAATCAAGTACCAAAAGAGCACCTCCTAGTCTCTATTCCCCTCTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-134-5p(1), mmu-miR-216a-5p(1), mmu-miR-495-3p(1), mmu-miR-384-3p(1), mmu-miR-1187(1), mmu-miR-5101(1)
siRNAs for circular RNA silencing
Junction sequence
GGCTGTTAGTAAGTGAATGAGTTTCC
siRNA sets
AAACTCATTCACTTACTAA, AACTCATTCACTTACTAAC, CATTCACTTACTAACAGCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCSE1L_401_ORF_1
1.1311
0.061250924
0.42309112
360
ORF sequence:
ATGATTTTTAGGAATCAAGTACCAAAAGAGCACCTCCTAGTCTCTATTCCCCTCTTGATCAGTCACCTGGAGGCTGAGAGTATTGTCGTCCACACTTATGCCGCACATGCTCTCGAAAGGCTGTTCACTATGAGAGGGTCAAACAATACCACTCTTTTTACAGCTGCAGAAATCGCACCGTTTGTTGAGATTCTGCTAACAAACCTTTTCAAAGCTCTCACACTTCCTGGCTCTTCAGAAAATGAATATATTATGAAAGCTATCATGAGAAGTTTCTCCCTCCTGCAAGAGGCCATCATCCCCTATATCCCCACTCTCATCACGCAGCTCACACAGAAGCTGCTGGCTGTTAGTAAGTGA
Peptide sequence:
MIFRNQVPKEHLLVSIPLLISHLEAESIVVHTYAAHALERLFTMRGSNNTTLFTAAEIAPFVEILLTNLFKALTLPGSSENEYIMKAIMRSFSLLQEAIIPYIPTLITQLTQKLLAVSK
IRESfinder result
IRESfinder score
0.723365559
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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