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mmu_circNploc4_420
Basic information of circular RNA
PanCircBase ID:
mmu_circNploc4_420
mm39_Chr. Position ID:
chr11|120309894|120323954|-
Gene name:
Nploc4
Transcript:
ENSMUST00000044271.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,4,3,2
Exon/intron offsets:
0,2296,9455,13979
Genomic length:
14060
Exon/intron sizes in nt:
49,177,113,81
Flanking exon/introns:
chr11:120309165-120309894|chr11:120323954-120328324
Splice length:
420
Other database IDs:
circAtlas: mmu-Nploc4_0033
circBase: hsa_circ_0046206, circAtlas: hsa-NPLOC4_0092, CIRCpedia: HSA_CIRCpedia_22779
Human Ortholog IDs:
Mature spliced Sequence:
ATAATCCGTGTCCAGTCCCCTGATGGCGTGAAGAGGATCACAGCTACGAAGAGAGAGACGGCTGCCACCTTCCTGAAAAAGGTTGCAAAGGAGTTTGGCTTCCAAAACAACGGCTTCTCAGTTTACATCAATAGAAACAAGACTGGAGAGATAACAGCATCGTCCAGCAAATCCCTCCATTTGCTAAAAATCAAGCATGGCGATTTGTTGTTCCTGTTTCCCTCAAGCCTTGCTGGACCCTCGTCTGAAATGGAAACATCGACCTCGGTAGGGTTAAAGGCCTTTGGTGCTCCTAACGTGGTTGAAGATGAGATCGATCAATACCTCAGCAAGCAGGATGGGAAGATTTACCGGAGCCGAGACCCACAGCTATGCCGCCATGGTCCCTTGGGCAAGTGTGTGCATTGTGTCCCACTGGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCAAGCAGGATGGGAAGA
60.03
GCCGTCTCTCTCTTCGTAGC
59.97
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCAGCAAGCAGGATGGGAAG
60.03
GCCGTCTCTCTCTTCGTAGC
59.97
157
PCR template sequence:
ATACCTCAGCAAGCAGGATGGGAAGATTTACCGGAGCCGAGACCCACAGCTATGCCGCCATGGTCCCTTGGGCAAGTGTGTGCATTGTGTCCCACTGGAGATAATCCGTGTCCAGTCCCCTGATGGCGTGAAGAGGATCACAGCTACGAAGAGAGAGACGGCTGCCACCTTCCTGAAAAAGGTTGCAAAGGAGTTTGGCT
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
TGTCCCACTGGAGATAATCCGTGTCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNPLOC4_420_ORF_1
0.9571
0.274228593
0.870248243
591
ORF sequence:
ATGGAAACATCGACCTCGGTAGGGTTAAAGGCCTTTGGTGCTCCTAACGTGGTTGAAGATGAGATCGATCAATACCTCAGCAAGCAGGATGGGAAGATTTACCGGAGCCGAGACCCACAGCTATGCCGCCATGGTCCCTTGGGCAAGTGTGTGCATTGTGTCCCACTGGAGATAATCCGTGTCCAGTCCCCTGATGGCGTGAAGAGGATCACAGCTACGAAGAGAGAGACGGCTGCCACCTTCCTGAAAAAGGTTGCAAAGGAGTTTGGCTTCCAAAACAACGGCTTCTCAGTTTACATCAATAGAAACAAGACTGGAGAGATAACAGCATCGTCCAGCAAATCCCTCCATTTGCTAAAAATCAAGCATGGCGATTTGTTGTTCCTGTTTCCCTCAAGCCTTGCTGGACCCTCGTCTGAAATGGAAACATCGACCTCGGTAGGGTTAAAGGCCTTTGGTGCTCCTAACGTGGTTGAAGATGAGATCGATCAATACCTCAGCAAGCAGGATGGGAAGATTTACCGGAGCCGAGACCCACAGCTATGCCGCCATGGTCCCTTGGGCAAGTGTGTGCATTGTGTCCCACTGGAG
Peptide sequence:
METSTSVGLKAFGAPNVVEDEIDQYLSKQDGKIYRSRDPQLCRHGPLGKCVHCVPLEIIRVQSPDGVKRITATKRETAATFLKKVAKEFGFQNNGFSVYINRNKTGEITASSSKSLHLLKIKHGDLLFLFPSSLAGPSSEMETSTSVGLKAFGAPNVVEDEIDQYLSKQDGKIYRSRDPQLCRHGPLGKCVHCVPLE
IRESfinder result
IRESfinder score
0.399731545
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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