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mmu_circNell1_285
Basic information of circular RNA
PanCircBase ID:
mmu_circNell1_285
mm39_Chr. Position ID:
chr7|49869329|49929394|+
Gene name:
Nell1
Transcript:
ENSMUST00000151721.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
6,7,8
Exon/intron offsets:
0,672,59936
Genomic length:
60065
Exon/intron sizes in nt:
73,83,129
Flanking exon/introns:
chr7:49826069-49869329|chr7:49929394-50098587
Splice length:
285
Other database IDs:
CIRCpedia: MMU_CIRCpedia_21766, circAtlas: mmu-Nell1_0005
circBase: hsa_circ_0095595, circAtlas: hsa-NELL1_0005, CIRCpedia: HSA_CIRCpedia_128231
Human Ortholog IDs:
Mature spliced Sequence:
GGAATCATCCAAGATGGCAAGATCATCTTCATGCCGAACGGCTTCATCACACAGTGCCCCAACCTAAATCGCACTTGCCCAACATGCAGTGATTTCCTGAGCCTGGTTCAAGGAATAATGGATTTGCAAGAGCTTTTGGCCAAGATGACTGCAAAAGTCATAACTTCTGTGCAGAAGCACCTAAGTGTGGAGAAAACTCGGAATGCAAAAATTGGAATACAAAAGCGACTTGTGAGTGCAAGAATGGATACATCTCTGTCCAGGGCAACTCTGCATACTGTGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCGACTTGTGAGTGCAAGA
59.9
TGGGCAAGTGCGATTTAGGT
59.96
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCGACTTGTGAGTGCAAGA
59.9
CATGTTGGGCAAGTGCGATT
59.76
148
PCR template sequence:
TGTGGAGAAAACTCGGAATGCAAAAATTGGAATACAAAAGCGACTTGTGAGTGCAAGAATGGATACATCTCTGTCCAGGGCAACTCTGCATACTGTGAAGGGAATCATCCAAGATGGCAAGATCATCTTCATGCCGAACGGCTTCATCACACAGTGCCCCAACCTAAATCGCACTTGCCCAACATGCAGTGATTTCCTGA
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-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-18a-5p(1), mmu-miR-297a-5p(1), mmu-miR-129-5p(1), mmu-miR-484(1)
siRNAs for circular RNA silencing
Junction sequence
GCATACTGTGAAGGGAATCATCCAAG
siRNA sets
GATTCCCTTCACAGTATGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNELL1_285_ORF_1
0.9346
0.190706948
0.760988756
540
ORF sequence:
ATGCCGAACGGCTTCATCACACAGTGCCCCAACCTAAATCGCACTTGCCCAACATGCAGTGATTTCCTGAGCCTGGTTCAAGGAATAATGGATTTGCAAGAGCTTTTGGCCAAGATGACTGCAAAAGTCATAACTTCTGTGCAGAAGCACCTAAGTGTGGAGAAAACTCGGAATGCAAAAATTGGAATACAAAAGCGACTTGTGAGTGCAAGAATGGATACATCTCTGTCCAGGGCAACTCTGCATACTGTGAAGGGAATCATCCAAGATGGCAAGATCATCTTCATGCCGAACGGCTTCATCACACAGTGCCCCAACCTAAATCGCACTTGCCCAACATGCAGTGATTTCCTGAGCCTGGTTCAAGGAATAATGGATTTGCAAGAGCTTTTGGCCAAGATGACTGCAAAAGTCATAACTTCTGTGCAGAAGCACCTAAGTGTGGAGAAAACTCGGAATGCAAAAATTGGAATACAAAAGCGACTTGTGAGTGCAAGAATGGATACATCTCTGTCCAGGGCAACTCTGCATACTGTGAAG
Peptide sequence:
MPNGFITQCPNLNRTCPTCSDFLSLVQGIMDLQELLAKMTAKVITSVQKHLSVEKTRNAKIGIQKRLVSARMDTSLSRATLHTVKGIIQDGKIIFMPNGFITQCPNLNRTCPTCSDFLSLVQGIMDLQELLAKMTAKVITSVQKHLSVEKTRNAKIGIQKRLVSARMDTSLSRATLHTVK
IRESfinder result
IRESfinder score
0.38565254
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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