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mmu_circNf1_1707
Basic information of circular RNA
PanCircBase ID:
mmu_circNf1_1707
mm39_Chr. Position ID:
chr11|79331673|79339162|+
Gene name:
Nf1
Transcript:
ENSMUST00000219057.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
19,20,21,22,23,24,25,26,27,28
Exon/intron offsets:
0,781,1043,2921,3752,4176,4868,5958,6636,7277
Genomic length:
7489
Exon/intron sizes in nt:
25,07,48,44,41,14,01,20,00,00,00,00,000
Flanking exon/introns:
chr11:79329674-79331673|chr11:79339162-79344628
Splice length:
1707
Other database IDs:
circAtlas: mmu-Nf1_0090
Human Ortholog IDs:
Mature spliced Sequence:
GATAGCACAGCAGGGTGCAGTGGAACCCCACCTATATGCCGACAAGCCCAGACCAAGCTAGAAGTGGCCTTATACATGTTTCTGTGGAATCCTGACACTGAAGCTGTTCTGGTTGCTATGTCCTGTTTCCGCCACCTCTGTGAAGAAGCAGATATTCGATGTGGGGTAGATGAAGTGTCAGTACACAACTTCTTGCCCAACTATAACACATTCATGGAATTTGCCTCAGTCAGCAATATGATGTCAACAGGAAGAGCAGCGCTTCAGAAAAGAGTGATGGCCCTGCTAAGGCGCATTGAGCACCCTACTGCAGGAAACATTGAGGCCTGGGAAGATACACATGCAAAGTGGGAACAGGCTACAAAACTAATCCTTAACTACCCAAAAGCCAAAATGGAAGATGGCCAGGCTGCAGAAAGTCTTCATAAGACCATTGTTAAGAGACGGATGTCCCATGTCAGTGGAGGAGGCTCCATAGACTTGTCTGACACAGACTCCCTGCAGGAGTGGATCAACATGACTGGCTTCCTTTGTGCCCTTGGTGGGGTGTGCCTGCAACAGAGAAGCAGCTCTGGCCTAGCGACATACAGCCCACCTATGGGCGCTGTCAGTGAACGCAAAGGGTCTATGATTTCTGTAATGTCTTCTGAAGGGAATATTGATTCACCTGTCAGCAGATTTATGGACCGGCTTCTGTCCTTAATGGTGTGTAACCACGAGAAAGTGGGGCTTCAGATACGGACCAATGTTAAGGACCTGGTGGGTCTGGAGTTGAGTCCTGCTCTGTATCCAATGCTGTTTAACAAACTGAAGAATACCATCAGCAAGTTTTTTGACTCTCAAGGACAGGTATTACTAAGTGACAGCAATACTCAGTTTGTAGAGCAAACCATAGCCATAATGAAAAACCTACTGGATAATCATACTGAAGGCAGCTCTGAGCATCTGGGACAAGCGAGCATTGAGACAATGATGCTAAATCTGGTCAGATACGTTCGTGTTCTTGGGAATATGGTCCATGCAATACAAATAAAAACAAAATTGTGTCAGTTAGTTGAAGTCATGATGGCAAGAAGAGATGACCTCTCGTTTTGTCAAGAGATGAAATTTAGGAATAAGATGGTAGAATATCTAACAGACTGGGTTATGGGAACATCAAACCAAGCAGCAGATGATGACATAAAATGTCTTACGAGAGATCTGGACCAAGCAAGCATGGAAGCAGTAGTTTCTCTCCTCGCTGGTCTTCCACTGCAGCCCGAAGAAGGAGATGGGGTGGAGCTGATGGAGGCCAAATCACAGTTATTCCTTAAGTACTTCACATTATTTATGAACCTTTTGAATGACTGTAGTGAAGTTGAAGATGAAAATGCACAAACGGGTGGCAGGAAACGTGGCATGTCTCGGAGGCTGGCATCCCTGAGGCACTGTACAGTGCTTGCAATGTCAAACTTACTCAATGCTAATGTGGACAGTGGACTCATGCACTCCATAGGCTTAGGTTATCACAAGGATCTTCAGACAAGAGCTACGTTTATGGAAGTTCTGACAAAAATCCTTCAACAAGGAACAGAATTCGATACACTTGCGGAAACGGTGTTGGCAGATCGATTTGAGAGACTTGTGGAACTGGTCACAATGATGGGAGACCAGGGAGAACTCCCTATAGCTATGGCTCTTGCCAATGTGGTCCCTTGTTCTCAGTGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGACTTGTGGAACTGGTCACA
59.16
GTCTGGGCTTGTCGGCATAT
60.18
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGACTTGTGGAACTGGTCACA
59.16
TAGCTTGGTCTGGGCTTGTC
59.68
150
PCR template sequence:
TCGATTTGAGAGACTTGTGGAACTGGTCACAATGATGGGAGACCAGGGAGAACTCCCTATAGCTATGGCTCTTGCCAATGTGGTCCCTTGTTCTCAGTGGGATAGCACAGCAGGGTGCAGTGGAACCCCACCTATATGCCGACAAGCCCAGACCAAGCTAGAAGTGGCCTTATACATGTTTCTGTGGAATCCTGACACTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-miR-31-5p(2), mmu-miR-7b-5p(1), mmu-miR-103-3p(1), mmu-miR-223-3p(1), mmu-miR-335-5p(1), mmu-miR-7a-5p(1), mmu-miR-185-5p(1), mmu-miR-758-3p(1), mmu-miR-362-5p(1), mmu-miR-107-3p(1), mmu-miR-1198-5p(1), mmu-miR-129-5p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTGTTCTCAGTGGGATAGCACAGCAG
siRNA sets
CTGCTGTGCTATCCCACTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNF1_1707_ORF_1
0.9885
0.118967453
0.999999999
3339
ORF sequence:
ATGTTTCTGTGGAATCCTGACACTGAAGCTGTTCTGGTTGCTATGTCCTGTTTCCGCCACCTCTGTGAAGAAGCAGATATTCGATGTGGGGTAGATGAAGTGTCAGTACACAACTTCTTGCCCAACTATAACACATTCATGGAATTTGCCTCAGTCAGCAATATGATGTCAACAGGAAGAGCAGCGCTTCAGAAAAGAGTGATGGCCCTGCTAAGGCGCATTGAGCACCCTACTGCAGGAAACATTGAGGCCTGGGAAGATACACATGCAAAGTGGGAACAGGCTACAAAACTAATCCTTAACTACCCAAAAGCCAAAATGGAAGATGGCCAGGCTGCAGAAAGTCTTCATAAGACCATTGTTAAGAGACGGATGTCCCATGTCAGTGGAGGAGGCTCCATAGACTTGTCTGACACAGACTCCCTGCAGGAGTGGATCAACATGACTGGCTTCCTTTGTGCCCTTGGTGGGGTGTGCCTGCAACAGAGAAGCAGCTCTGGCCTAGCGACATACAGCCCACCTATGGGCGCTGTCAGTGAACGCAAAGGGTCTATGATTTCTGTAATGTCTTCTGAAGGGAATATTGATTCACCTGTCAGCAGATTTATGGACCGGCTTCTGTCCTTAATGGTGTGTAACCACGAGAAAGTGGGGCTTCAGATACGGACCAATGTTAAGGACCTGGTGGGTCTGGAGTTGAGTCCTGCTCTGTATCCAATGCTGTTTAACAAACTGAAGAATACCATCAGCAAGTTTTTTGACTCTCAAGGACAGGTATTACTAAGTGACAGCAATACTCAGTTTGTAGAGCAAACCATAGCCATAATGAAAAACCTACTGGATAATCATACTGAAGGCAGCTCTGAGCATCTGGGACAAGCGAGCATTGAGACAATGATGCTAAATCTGGTCAGATACGTTCGTGTTCTTGGGAATATGGTCCATGCAATACAAATAAAAACAAAATTGTGTCAGTTAGTTGAAGTCATGATGGCAAGAAGAGATGACCTCTCGTTTTGTCAAGAGATGAAATTTAGGAATAAGATGGTAGAATATCTAACAGACTGGGTTATGGGAACATCAAACCAAGCAGCAGATGATGACATAAAATGTCTTACGAGAGATCTGGACCAAGCAAGCATGGAAGCAGTAGTTTCTCTCCTCGCTGGTCTTCCACTGCAGCCCGAAGAAGGAGATGGGGTGGAGCTGATGGAGGCCAAATCACAGTTATTCCTTAAGTACTTCACATTATTTATGAACCTTTTGAATGACTGTAGTGAAGTTGAAGATGAAAATGCACAAACGGGTGGCAGGAAACGTGGCATGTCTCGGAGGCTGGCATCCCTGAGGCACTGTACAGTGCTTGCAATGTCAAACTTACTCAATGCTAATGTGGACAGTGGACTCATGCACTCCATAGGCTTAGGTTATCACAAGGATCTTCAGACAAGAGCTACGTTTATGGAAGTTCTGACAAAAATCCTTCAACAAGGAACAGAATTCGATACACTTGCGGAAACGGTGTTGGCAGATCGATTTGAGAGACTTGTGGAACTGGTCACAATGATGGGAGACCAGGGAGAACTCCCTATAGCTATGGCTCTTGCCAATGTGGTCCCTTGTTCTCAGTGGGATAGCACAGCAGGGTGCAGTGGAACCCCACCTATATGCCGACAAGCCCAGACCAAGCTAGAAGTGGCCTTATACATGTTTCTGTGGAATCCTGACACTGAAGCTGTTCTGGTTGCTATGTCCTGTTTCCGCCACCTCTGTGAAGAAGCAGATATTCGATGTGGGGTAGATGAAGTGTCAGTACACAACTTCTTGCCCAACTATAACACATTCATGGAATTTGCCTCAGTCAGCAATATGATGTCAACAGGAAGAGCAGCGCTTCAGAAAAGAGTGATGGCCCTGCTAAGGCGCATTGAGCACCCTACTGCAGGAAACATTGAGGCCTGGGAAGATACACATGCAAAGTGGGAACAGGCTACAAAACTAATCCTTAACTACCCAAAAGCCAAAATGGAAGATGGCCAGGCTGCAGAAAGTCTTCATAAGACCATTGTTAAGAGACGGATGTCCCATGTCAGTGGAGGAGGCTCCATAGACTTGTCTGACACAGACTCCCTGCAGGAGTGGATCAACATGACTGGCTTCCTTTGTGCCCTTGGTGGGGTGTGCCTGCAACAGAGAAGCAGCTCTGGCCTAGCGACATACAGCCCACCTATGGGCGCTGTCAGTGAACGCAAAGGGTCTATGATTTCTGTAATGTCTTCTGAAGGGAATATTGATTCACCTGTCAGCAGATTTATGGACCGGCTTCTGTCCTTAATGGTGTGTAACCACGAGAAAGTGGGGCTTCAGATACGGACCAATGTTAAGGACCTGGTGGGTCTGGAGTTGAGTCCTGCTCTGTATCCAATGCTGTTTAACAAACTGAAGAATACCATCAGCAAGTTTTTTGACTCTCAAGGACAGGTATTACTAAGTGACAGCAATACTCAGTTTGTAGAGCAAACCATAGCCATAATGAAAAACCTACTGGATAATCATACTGAAGGCAGCTCTGAGCATCTGGGACAAGCGAGCATTGAGACAATGATGCTAAATCTGGTCAGATACGTTCGTGTTCTTGGGAATATGGTCCATGCAATACAAATAAAAACAAAATTGTGTCAGTTAGTTGAAGTCATGATGGCAAGAAGAGATGACCTCTCGTTTTGTCAAGAGATGAAATTTAGGAATAAGATGGTAGAATATCTAACAGACTGGGTTATGGGAACATCAAACCAAGCAGCAGATGATGACATAAAATGTCTTACGAGAGATCTGGACCAAGCAAGCATGGAAGCAGTAGTTTCTCTCCTCGCTGGTCTTCCACTGCAGCCCGAAGAAGGAGATGGGGTGGAGCTGATGGAGGCCAAATCACAGTTATTCCTTAAGTACTTCACATTATTTATGAACCTTTTGAATGACTGTAGTGAAGTTGAAGATGAAAATGCACAAACGGGTGGCAGGAAACGTGGCATGTCTCGGAGGCTGGCATCCCTGAGGCACTGTACAGTGCTTGCAATGTCAAACTTACTCAATGCTAATGTGGACAGTGGACTCATGCACTCCATAGGCTTAGGTTATCACAAGGATCTTCAGACAAGAGCTACGTTTATGGAAGTTCTGACAAAAATCCTTCAACAAGGAACAGAATTCGATACACTTGCGGAAACGGTGTTGGCAGATCGATTTGAGAGACTTGTGGAACTGGTCACAATGATGGGAGACCAGGGAGAACTCCCTATAGCTATGGCTCTTGCCAATGTGGTCCCTTGTTCTCAGTGG
Peptide sequence:
MFLWNPDTEAVLVAMSCFRHLCEEADIRCGVDEVSVHNFLPNYNTFMEFASVSNMMSTGRAALQKRVMALLRRIEHPTAGNIEAWEDTHAKWEQATKLILNYPKAKMEDGQAAESLHKTIVKRRMSHVSGGGSIDLSDTDSLQEWINMTGFLCALGGVCLQQRSSSGLATYSPPMGAVSERKGSMISVMSSEGNIDSPVSRFMDRLLSLMVCNHEKVGLQIRTNVKDLVGLELSPALYPMLFNKLKNTISKFFDSQGQVLLSDSNTQFVEQTIAIMKNLLDNHTEGSSEHLGQASIETMMLNLVRYVRVLGNMVHAIQIKTKLCQLVEVMMARRDDLSFCQEMKFRNKMVEYLTDWVMGTSNQAADDDIKCLTRDLDQASMEAVVSLLAGLPLQPEEGDGVELMEAKSQLFLKYFTLFMNLLNDCSEVEDENAQTGGRKRGMSRRLASLRHCTVLAMSNLLNANVDSGLMHSIGLGYHKDLQTRATFMEVLTKILQQGTEFDTLAETVLADRFERLVELVTMMGDQGELPIAMALANVVPCSQWDSTAGCSGTPPICRQAQTKLEVALYMFLWNPDTEAVLVAMSCFRHLCEEADIRCGVDEVSVHNFLPNYNTFMEFASVSNMMSTGRAALQKRVMALLRRIEHPTAGNIEAWEDTHAKWEQATKLILNYPKAKMEDGQAAESLHKTIVKRRMSHVSGGGSIDLSDTDSLQEWINMTGFLCALGGVCLQQRSSSGLATYSPPMGAVSERKGSMISVMSSEGNIDSPVSRFMDRLLSLMVCNHEKVGLQIRTNVKDLVGLELSPALYPMLFNKLKNTISKFFDSQGQVLLSDSNTQFVEQTIAIMKNLLDNHTEGSSEHLGQASIETMMLNLVRYVRVLGNMVHAIQIKTKLCQLVEVMMARRDDLSFCQEMKFRNKMVEYLTDWVMGTSNQAADDDIKCLTRDLDQASMEAVVSLLAGLPLQPEEGDGVELMEAKSQLFLKYFTLFMNLLNDCSEVEDENAQTGGRKRGMSRRLASLRHCTVLAMSNLLNANVDSGLMHSIGLGYHKDLQTRATFMEVLTKILQQGTEFDTLAETVLADRFERLVELVTMMGDQGELPIAMALANVVPCSQW
IRESfinder result
IRESfinder score
0.441072093
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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