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mmu_circNbr1_418
Basic information of circular RNA
PanCircBase ID:
mmu_circNbr1_418
mm39_Chr. Position ID:
chr11|101465824|101466242|+
Gene name:
Nbr1
Transcript:
ENSMUST00000103099.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
1
Exon/intron indexes:
20
Exon/intron offsets:
0
Genomic length:
418
Exon/intron sizes in nt:
418
Flanking exon/introns:
chr11:101464003-101465824|chr11:101466242-101467128
Splice length:
418
Other database IDs:
CIRCpedia: MMU_CIRCpedia_529, circAtlas: mmu-Nbr1_0008
Human Ortholog IDs:
Mature spliced Sequence:
TGAAATTTGCCTTGCCTGAAGAAGGACCGCGTGGAGATGAGAGGGAGGAGATTGTCCACATTGTTGAGGAAGAAGTCGTTGAGGAAGAGGAGGAAGTCCAAGATGAAGAAGTCCAAAGTCAGTCTTCTGCTTCCTCTGAAGATTATATCATCATCCTTCCTGAGTGCTTTGATACCAGCCGCCCCCTGGGGGACTCCATGTACAGCTCTGCGCTCTCCCAGCCAGGCCTGGAGCGAGGGGCTGAAGGCGAACCTGGGATCGAGTCTGGGCTGGAACCAACTGAGGCTAGAGAGAGACTCCCAGAGAGGGAGAGCCAGCCACAGGAGCAGAGCATCAGCGACATCCTCACAACCTCACAGCCTCTGGACACGGTGCCTCTAGTCCCCGAGGTGGCAGGACTTCCAGCAGCATTGTCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCGACATCCTCACAACCT
60.04
TCCTCCTCTTCCTCAACGACT
59.92
178
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCGACATCCTCACAACCTCA
60.04
TCCTCCTCTTCCTCAACGACT
59.92
176
PCR template sequence:
CACAGGAGCAGAGCATCAGCGACATCCTCACAACCTCACAGCCTCTGGACACGGTGCCTCTAGTCCCCGAGGTGGCAGGACTTCCAGCAGCATTGTCCAGTGAAATTTGCCTTGCCTGAAGAAGGACCGCGTGGAGATGAGAGGGAGGAGATTGTCCACATTGTTGAGGAAGAAGTCGTTGAGGAAGAGGAGGAAGTCCA
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-326-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
CAGCATTGTCCAGTGAAATTTGCCTT
siRNA sets
AATTTCACTGGACAATGCT, AAATTTCACTGGACAATGC, AAGGCAAATTTCACTGGAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNBR1_418_ORF_3
0.8689
0.275774047
0.312728703
240
ORF sequence:
ATGTACAGCTCTGCGCTCTCCCAGCCAGGCCTGGAGCGAGGGGCTGAAGGCGAACCTGGGATCGAGTCTGGGCTGGAACCAACTGAGGCTAGAGAGAGACTCCCAGAGAGGGAGAGCCAGCCACAGGAGCAGAGCATCAGCGACATCCTCACAACCTCACAGCCTCTGGACACGGTGCCTCTAGTCCCCGAGGTGGCAGGACTTCCAGCAGCATTGTCCAGTGAAATTTGCCTTGCCTGA
Peptide sequence:
MYSSALSQPGLERGAEGEPGIESGLEPTEARERLPERESQPQEQSISDILTTSQPLDTVPLVPEVAGLPAALSSEICLA
IRESfinder result
IRESfinder score
0.505973628
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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