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mmu_circNf1_863
Basic information of circular RNA
PanCircBase ID:
mmu_circNf1_863
mm39_Chr. Position ID:
chr11|79302321|79325750|+
Gene name:
Nf1
Transcript:
ENSMUST00000219057.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
9,10,11,12,13,14,15,16
Exon/intron offsets:
0,559,1188,2745,7056,14017,17082,23349
Genomic length:
23429
Exon/intron sizes in nt:
174,123,75,30,132,135,114,80
Flanking exon/introns:
chr11:79300377-79302321|chr11:79325750-79327515
Splice length:
863
Other database IDs:
CIRCpedia: MMU_CIRCpedia_30139, circAtlas: mmu-Nf1_0097
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
AAGCTGTTTCTGGACAGTTTACGGAAAGCACTCGCTGGCCATGGAGGAAGCAGGCAGCTGACTGAGAGTGCTGCCATTGCTTGTGTCAAGTTGTGTAAAGCAAGTACTTACATCAACTGGGAAGATAATTCTGTCATTTTCCTACTGGTTCAGTCCATGGTAGTTGATCTTAAGAACCTGCTTTTTAATCCAAGTAAACCATTCTCTAGAGGCAGTCAGCCTGCAGATGTGGACCTCATGATTGACTGTCTTGTCTCTTGCTTTCGGATAAGCCCTCACAACAACCAACACTTTAAGATCTGCCTGGCTCAGAATTCACCTTCTACATTTCACTATGTGTTGGTAAACTCACTGCACCGCATCATCACCAATAGCACTTTCAAGCATGGACTTGGCACTGCTTCTGCGTTGGATTGGTGGCCTAAGATTGATGCTGTATATTGTCACTCAGTTGAACTTCGCAATATGTTTGGTGAAACACTTCATAAAGCAGTGCAAGGCTGTGGAGCGCACCCAGCAATACGAATGGCACCAAGTCTCACCTTTAAAGAAAAGGTAACAAGCCTTAAATTTAAAGAAAAGCCTACAGACCTAGAGACAAGGAGCTACAAATGTCTTCTTTTGTCCATGGTGAAACTGATTCATGCAGACCCAAAGCTTTTGCTTTGTAATCCAAGAAAACAGGGCCCTGAAACTCAGAGCAGTACAGCAGAACTAATTACAGGGCTCGTACAACTGGTTCCTCAGTCACACATGCCAGAGGTCGCTCAGGAGGCTATGGAGGCTTTGCTGGTCCTTCATCAGTTAGATAGCATTGATCTCTGGAATCCTGACGCTCCTGTAGAGACATTCTGGGAAATCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGGCTTTGCTGGTCCTTCA
60.25
TTGACACAAGCAATGGCAGC
59.97
172
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TATGGAGGCTTTGCTGGTCC
59.74
TTGACACAAGCAATGGCAGC
59.97
176
PCR template sequence:
TCGCTCAGGAGGCTATGGAGGCTTTGCTGGTCCTTCATCAGTTAGATAGCATTGATCTCTGGAATCCTGACGCTCCTGTAGAGACATTCTGGGAAATCAGAAGCTGTTTCTGGACAGTTTACGGAAAGCACTCGCTGGCCATGGAGGAAGCAGGCAGCTGACTGAGAGTGCTGCCATTGCTTGTGTCAAGTTGTGTAAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-134-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-106b-5p(1), mmu-miR-203-3p(1), mmu-miR-27a-5p(1), mmu-miR-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCTGGGAAATCAGAAGCTGTTTCTGG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNF1_863_ORF_1
0.8404
0.03403689
0.876607376
768
ORF sequence:
ATGGTAGTTGATCTTAAGAACCTGCTTTTTAATCCAAGTAAACCATTCTCTAGAGGCAGTCAGCCTGCAGATGTGGACCTCATGATTGACTGTCTTGTCTCTTGCTTTCGGATAAGCCCTCACAACAACCAACACTTTAAGATCTGCCTGGCTCAGAATTCACCTTCTACATTTCACTATGTGTTGGTAAACTCACTGCACCGCATCATCACCAATAGCACTTTCAAGCATGGACTTGGCACTGCTTCTGCGTTGGATTGGTGGCCTAAGATTGATGCTGTATATTGTCACTCAGTTGAACTTCGCAATATGTTTGGTGAAACACTTCATAAAGCAGTGCAAGGCTGTGGAGCGCACCCAGCAATACGAATGGCACCAAGTCTCACCTTTAAAGAAAAGGTAACAAGCCTTAAATTTAAAGAAAAGCCTACAGACCTAGAGACAAGGAGCTACAAATGTCTTCTTTTGTCCATGGTGAAACTGATTCATGCAGACCCAAAGCTTTTGCTTTGTAATCCAAGAAAACAGGGCCCTGAAACTCAGAGCAGTACAGCAGAACTAATTACAGGGCTCGTACAACTGGTTCCTCAGTCACACATGCCAGAGGTCGCTCAGGAGGCTATGGAGGCTTTGCTGGTCCTTCATCAGTTAGATAGCATTGATCTCTGGAATCCTGACGCTCCTGTAGAGACATTCTGGGAAATCAGAAGCTGTTTCTGGACAGTTTACGGAAAGCACTCGCTGGCCATGGAGGAAGCAGGCAGCTGA
Peptide sequence:
MVVDLKNLLFNPSKPFSRGSQPADVDLMIDCLVSCFRISPHNNQHFKICLAQNSPSTFHYVLVNSLHRIITNSTFKHGLGTASALDWWPKIDAVYCHSVELRNMFGETLHKAVQGCGAHPAIRMAPSLTFKEKVTSLKFKEKPTDLETRSYKCLLLSMVKLIHADPKLLLCNPRKQGPETQSSTAELITGLVQLVPQSHMPEVAQEAMEALLVLHQLDSIDLWNPDAPVETFWEIRSCFWTVYGKHSLAMEEAGS
IRESfinder result
IRESfinder score
0.716317631
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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