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mmu_circNploc4_199
Basic information of circular RNA
PanCircBase ID:
mmu_circNploc4_199
mm39_Chr. Position ID:
chr11|120299598|120300509|-
Gene name:
Nploc4
Transcript:
ENSMUST00000044271.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
11,10
Exon/intron offsets:
0,839
Genomic length:
911
Exon/intron sizes in nt:
127,72
Flanking exon/introns:
chr11:120295192-120299598|chr11:120300509-120302483
Splice length:
199
Other database IDs:
CIRCpedia: MMU_CIRCpedia_5103, circAtlas: mmu-Nploc4_0003
circBase: hsa_circ_0046192, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_22763
Human Ortholog IDs:
Mature spliced Sequence:
GTTGGATGGATATTCACGGACCTTGTCTCAGAAGACACCCGAAAGGGTACAGTCCGATACAGTCGGAATAAGGACACCTATTTCCTGAGTTCAGAAGAATGCATCACTGCAGGAGACTTTCAAAACAAGCACCCCAACATTTGCCGGCTCTCTCCCGATGGTCATTTTGGATCCAAGTTTGTTACTGCAGTGGCCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACAAGCACCCCAACATTTGC
59.89
CCCTTTCGGGTGTCTTCTGA
59.31
122
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACAAGCACCCCAACATTTGC
59.89
ATCGGACTGTACCCTTTCGG
59.18
133
PCR template sequence:
GCATCACTGCAGGAGACTTTCAAAACAAGCACCCCAACATTTGCCGGCTCTCTCCCGATGGTCATTTTGGATCCAAGTTTGTTACTGCAGTGGCCACAGGTTGGATGGATATTCACGGACCTTGTCTCAGAAGACACCCGAAAGGGTACAGTCCGATACAGTCGGAATAAGGACACCTATTTCCTGAGTTCAGAAGAA
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-495-3p(1), mmu-miR-342-5p(1), mmu-miR-802-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCAGTGGCCACAGGTTGGATGGATAT
siRNA sets
ATCCAACCTGTGGCCACTG, CATCCAACCTGTGGCCACT, TCCAACCTGTGGCCACTGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNPLOC4_199_ORF_1
0.5866
0.181435211
0.156056518
240
ORF sequence:
ATGGTCATTTTGGATCCAAGTTTGTTACTGCAGTGGCCACAGGTTGGATGGATATTCACGGACCTTGTCTCAGAAGACACCCGAAAGGGTACAGTCCGATACAGTCGGAATAAGGACACCTATTTCCTGAGTTCAGAAGAATGCATCACTGCAGGAGACTTTCAAAACAAGCACCCCAACATTTGCCGGCTCTCTCCCGATGGTCATTTTGGATCCAAGTTTGTTACTGCAGTGGCCACA
Peptide sequence:
MVILDPSLLLQWPQVGWIFTDLVSEDTRKGTVRYSRNKDTYFLSSEECITAGDFQNKHPNICRLSPDGHFGSKFVTAVAT
IRESfinder result
IRESfinder score
0.683199237
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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