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mmu_circNf1_547
Basic information of circular RNA
PanCircBase ID:
mmu_circNf1_547
mm39_Chr. Position ID:
chr11|79439299|79444823|+
Gene name:
Nf1
Transcript:
ENSMUST00000108251.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
43,44,45,46,47
Exon/intron offsets:
0,200,934,2520,5397
Genomic length:
5524
Exon/intron sizes in nt:
6,21,15,10,21,41,127
Flanking exon/introns:
chr11:79438708-79439299|chr11:79444823-79446306
Splice length:
547
Other database IDs:
circAtlas: hsa-NF1_0159
Human Ortholog IDs:
Mature spliced Sequence:
GCATGTATGAGAGATATTCCAACATGCAAGTGGCTGGATCAGTGGACAGAACTAGCTCAAAGATTTGCGTTTCAGTATAACCCATCGCTGCAGCCAAGAGCTCTTGTGGTGTTTGGCTGTATTAGCAAACGAGTGTCTCATGGGCAGATAAAGCAGATTATCCGAATTCTTAGCAAGGCACTTGAAAGTTGTTTAAAAGGACCTGACACTTACAACAGTCAAGTTCTGATAGAATCTACGGTGATAGCACTAACAAAATTACAGCCGCTTCTTAATAAGGACTCGCCCCTGCACAAAGCCCTCTTTTGGGTTGCTGTGGCTGTGCTGCAGCTGGACGAAGTCAACTTGTATTCAGCCGGCACTGCACTTCTGGAACAAAACCTGCACACCTTGGACAGTCTCCGGATATTCAATGACAAGAGTCCGGAAGAAGTATTTATGGCGATCCGGAATCCTCTGGAATGGCACTGCAAGCAGATGGATCACTTTGTCGGACTCAACTTCAACTCTAACTTTAACTTTGCACTAGTTGGACACCTCTTAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGGAATCCTCTGGAATGGCA
59.82
TGATCCAGCCACTTGCATGT
59.96
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATCCTCTGGAATGGCACTGC
60.11
TCCACTGATCCAGCCACTTG
59.67
142
PCR template sequence:
CGGAATCCTCTGGAATGGCACTGCAAGCAGATGGATCACTTTGTCGGACTCAACTTCAACTCTAACTTTAACTTTGCACTAGTTGGACACCTCTTAAAAGGCATGTATGAGAGATATTCCAACATGCAAGTGGCTGGATCAGTGGACAGAACTAGCTCAAAGATTTGCGTTTCAGTATAACCCATCGCTGCAGCCAAGAG
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-130a-3p(1), mmu-miR-130b-3p(1), mmu-miR-301b-3p(1), mmu-miR-721(1), mmu-miR-301a-3p(1), mmu-miR-383-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CACCTCTTAAAAGGCATGTATGAGAG
siRNA sets
CATACATGCCTTTTAAGAG, TCATACATGCCTTTTAAGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNF1_547_ORF_1
0.8051
0.118053
0.767188931
621
ORF sequence:
ATGAGAGATATTCCAACATGCAAGTGGCTGGATCAGTGGACAGAACTAGCTCAAAGATTTGCGTTTCAGTATAACCCATCGCTGCAGCCAAGAGCTCTTGTGGTGTTTGGCTGTATTAGCAAACGAGTGTCTCATGGGCAGATAAAGCAGATTATCCGAATTCTTAGCAAGGCACTTGAAAGTTGTTTAAAAGGACCTGACACTTACAACAGTCAAGTTCTGATAGAATCTACGGTGATAGCACTAACAAAATTACAGCCGCTTCTTAATAAGGACTCGCCCCTGCACAAAGCCCTCTTTTGGGTTGCTGTGGCTGTGCTGCAGCTGGACGAAGTCAACTTGTATTCAGCCGGCACTGCACTTCTGGAACAAAACCTGCACACCTTGGACAGTCTCCGGATATTCAATGACAAGAGTCCGGAAGAAGTATTTATGGCGATCCGGAATCCTCTGGAATGGCACTGCAAGCAGATGGATCACTTTGTCGGACTCAACTTCAACTCTAACTTTAACTTTGCACTAGTTGGACACCTCTTAAAAGGCATGTATGAGAGATATTCCAACATGCAAGTGGCTGGATCAGTGGACAGAACTAGCTCAAAGATTTGCGTTTCAGTATAA
Peptide sequence:
MRDIPTCKWLDQWTELAQRFAFQYNPSLQPRALVVFGCISKRVSHGQIKQIIRILSKALESCLKGPDTYNSQVLIESTVIALTKLQPLLNKDSPLHKALFWVAVAVLQLDEVNLYSAGTALLEQNLHTLDSLRIFNDKSPEEVFMAIRNPLEWHCKQMDHFVGLNFNSNFNFALVGHLLKGMYERYSNMQVAGSVDRTSSKICVSV
IRESfinder result
IRESfinder score
0.509047265
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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