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mmu_circNploc4_371
Basic information of circular RNA
PanCircBase ID:
mmu_circNploc4_371
mm39_Chr. Position ID:
chr11|120312190|120323954|-
Gene name:
Nploc4
Transcript:
ENSMUST00000044271.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
4,3,2
Exon/intron offsets:
0,7159,11683
Genomic length:
11764
Exon/intron sizes in nt:
177,113,81
Flanking exon/introns:
chr11:120309943-120312190|chr11:120323954-120328324
Splice length:
371
Other database IDs:
CIRCpedia: MMU_CIRCpedia_212477, circAtlas: mmu-Nploc4_0001
circBase: hsa_circ_0046209, circAtlas: hsa-NPLOC4_0001, CIRCpedia: HSA_CIRCpedia_22782
Human Ortholog IDs:
Mature spliced Sequence:
ATAATCCGTGTCCAGTCCCCTGATGGCGTGAAGAGGATCACAGCTACGAAGAGAGAGACGGCTGCCACCTTCCTGAAAAAGGTTGCAAAGGAGTTTGGCTTCCAAAACAACGGCTTCTCAGTTTACATCAATAGAAACAAGACTGGAGAGATAACAGCATCGTCCAGCAAATCCCTCCATTTGCTAAAAATCAAGCATGGCGATTTGTTGTTCCTGTTTCCCTCAAGCCTTGCTGGACCCTCGTCTGAAATGGAAACATCGACCTCGGTAGGGTTAAAGGCCTTTGGTGCTCCTAACGTGGTTGAAGATGAGATCGATCAATACCTCAGCAAGCAGGATGGGAAGATTTACCGGAGCCGAGACCCACAGCT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGTGCTCCTAACGTGGTTGA
59.97
GCCGTCTCTCTCTTCGTAGC
59.97
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGCCTTTGGTGCTCCTAAC
59.96
GCCGTCTCTCTCTTCGTAGC
59.97
156
PCR template sequence:
GGTTAAAGGCCTTTGGTGCTCCTAACGTGGTTGAAGATGAGATCGATCAATACCTCAGCAAGCAGGATGGGAAGATTTACCGGAGCCGAGACCCACAGCTATAATCCGTGTCCAGTCCCCTGATGGCGTGAAGAGGATCACAGCTACGAAGAGAGAGACGGCTGCCACCTTCCTGAAAAAGGTTGCAAAGGAGTTTGGCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-541-5p(1), mmu-miR-3065-5p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAGACCCACAGCTATAATCCGTGTCC
siRNA sets
GATTATAGCTGTGGGTCTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNPLOC4_371_ORF_1
0.8362
0.365580886
0.213913412
126
ORF sequence:
ATGGAAACATCGACCTCGGTAGGGTTAAAGGCCTTTGGTGCTCCTAACGTGGTTGAAGATGAGATCGATCAATACCTCAGCAAGCAGGATGGGAAGATTTACCGGAGCCGAGACCCACAGCTATAA
Peptide sequence:
METSTSVGLKAFGAPNVVEDEIDQYLSKQDGKIYRSRDPQL
IRESfinder result
IRESfinder score
0.428318076
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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