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mmu_circNdufs1_1138
Basic information of circular RNA
PanCircBase ID:
mmu_circNdufs1_1138
mm39_Chr. Position ID:
chr1|63196290|63210073|-
Gene name:
Ndufs1
Transcript:
ENSMUST00000027111.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
11,10,9,8,7,6,5,4,3,2
Exon/intron offsets:
0,2618,3748,6535,7598,7817,9159,12097,12918,13717
Genomic length:
13783
Exon/intron sizes in nt:
146,115,135,186,131,82,77,108,92,66
Flanking exon/introns:
chr1:63195491-63196290|chr1:63210073-63215744
Splice length:
1138
Other database IDs:
circAtlas: hsa-NDUFS1_0107
Human Ortholog IDs:
Mature spliced Sequence:
CCATCATGTTAAGGATACCTATAAAAAGGGCCTTGATAGGCCTTTCTAATTCTCCTAAAGGATATGTTCGCACAACTGGCACAGCAGCAAGTAACTTGATTGAAGTATTTGTTGATGGTCAGTCTGTCATGGTGGAACCAGGAACCACTGTTCTGCAGGCTTGCGAGAAGGTCGGCATGCAAATCCCTCGATTCTGTTACCATGAAAGGTTGTCTGTTGCTGGAAATTGCAGGATGTGCCTGGTAGAGATTGAGAAAGCTCCAAAGGTTGTCGCTGCTTGTGCTATGCCTGTAATGAAGGGCTGGAATATCTTGACAAACTCGGAAAAATCTAAGAAAGCCAGAGAAGGTGTGATGGAGTTCTTATTAGCAAATCACCCATTGGATTGTCCTATTTGTGACCAGGGAGGTGAATGTGATCTGCAGGACCAGTCCATGATGTTTGGAAGTGATAGGAGCCGATTTCTAGAGGGGAAGCGTGCTGTGGAGGACAAGAACATTGGGCCCCTAGTAAAGACCATCATGACTAGATGCATCCAGTGTACCCGGTGCATCAGGTTTGCAAGTGAGATTGCAGGAGTAGATGATTTGGGAACAACAGGAAGAGGAAATGACATGCAAGTTGGCACATACATTGAAAAAATGTTTATGTCTGAACTGTCTGGGAATGTCATTGATATCTGCCCTGTAGGGGCCCTAACCTCTAAGCCTTATGCCTTTACTGCCCGGCCTTGGGAAACAAGAAAGACAGAGTCCATTGATGTAATGGATGCAGTGGGAAGTAACATTGTGGTTAGCACAAGAACTGGAGAGGTAATGAGGATTTTGCCAAGAATGCATGAAGATATTAATGAAGAATGGATCTCTGATAAAACCAGGTTTGCTTATGATGGACTAAAACGTCAAAGACTTACTGAACCAATGGTCAGAAACGAAAAAGGGCTTTTAACTTATACCTCCTGGGAAGATGCACTCTCTCGTGTAGCTGGAATGTTACAGAATTTTGAAGGCAATGCTGTGGCAGCGATTGCAGGAGGCTTGGTGGATGCTGAAGCCTTAGTAGCTCTGAAAGACTTGCTTAATAAAGTTGACTCTGACAACTTATGCACTGAAGAGATCTTCCCCACTGAAGGAGCTGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGTGGATGCTGAAGCCTTA
59.01
GCCAGTTGTGCGAACATATCC
59.94
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGTGGATGCTGAAGCCTTAGT
60.07
GCCAGTTGTGCGAACATATCC
59.94
179
PCR template sequence:
TGGTGGATGCTGAAGCCTTAGTAGCTCTGAAAGACTTGCTTAATAAAGTTGACTCTGACAACTTATGCACTGAAGAGATCTTCCCCACTGAAGGAGCTGGCCATCATGTTAAGGATACCTATAAAAAGGGCCTTGATAGGCCTTTCTAATTCTCCTAAAGGATATGTTCGCACAACTGGCACAGCAGCAAGTAACTTGAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-181a-5p(1), mmu-miR-205-5p(1), mmu-miR-152-3p(1), mmu-miR-216a-5p(1), mmu-miR-217-5p(1), mmu-miR-181b-5p(1), mmu-miR-503-5p(1), mmu-miR-433-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-501-3p(1), mmu-miR-382-5p(1), mmu-miR-541-5p(1), mmu-miR-297a-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-452-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGAAGGAGCTGGCCATCATGTTAAG
siRNA sets
TTAACATGATGGCCAGCTC, TAACATGATGGCCAGCTCC, CTTAACATGATGGCCAGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNDUFS1_1138_ORF_1
0.9945
0.071104579
0.9953837
1182
ORF sequence:
ATGTTAAGGATACCTATAAAAAGGGCCTTGATAGGCCTTTCTAATTCTCCTAAAGGATATGTTCGCACAACTGGCACAGCAGCAAGTAACTTGATTGAAGTATTTGTTGATGGTCAGTCTGTCATGGTGGAACCAGGAACCACTGTTCTGCAGGCTTGCGAGAAGGTCGGCATGCAAATCCCTCGATTCTGTTACCATGAAAGGTTGTCTGTTGCTGGAAATTGCAGGATGTGCCTGGTAGAGATTGAGAAAGCTCCAAAGGTTGTCGCTGCTTGTGCTATGCCTGTAATGAAGGGCTGGAATATCTTGACAAACTCGGAAAAATCTAAGAAAGCCAGAGAAGGTGTGATGGAGTTCTTATTAGCAAATCACCCATTGGATTGTCCTATTTGTGACCAGGGAGGTGAATGTGATCTGCAGGACCAGTCCATGATGTTTGGAAGTGATAGGAGCCGATTTCTAGAGGGGAAGCGTGCTGTGGAGGACAAGAACATTGGGCCCCTAGTAAAGACCATCATGACTAGATGCATCCAGTGTACCCGGTGCATCAGGTTTGCAAGTGAGATTGCAGGAGTAGATGATTTGGGAACAACAGGAAGAGGAAATGACATGCAAGTTGGCACATACATTGAAAAAATGTTTATGTCTGAACTGTCTGGGAATGTCATTGATATCTGCCCTGTAGGGGCCCTAACCTCTAAGCCTTATGCCTTTACTGCCCGGCCTTGGGAAACAAGAAAGACAGAGTCCATTGATGTAATGGATGCAGTGGGAAGTAACATTGTGGTTAGCACAAGAACTGGAGAGGTAATGAGGATTTTGCCAAGAATGCATGAAGATATTAATGAAGAATGGATCTCTGATAAAACCAGGTTTGCTTATGATGGACTAAAACGTCAAAGACTTACTGAACCAATGGTCAGAAACGAAAAAGGGCTTTTAACTTATACCTCCTGGGAAGATGCACTCTCTCGTGTAGCTGGAATGTTACAGAATTTTGAAGGCAATGCTGTGGCAGCGATTGCAGGAGGCTTGGTGGATGCTGAAGCCTTAGTAGCTCTGAAAGACTTGCTTAATAAAGTTGACTCTGACAACTTATGCACTGAAGAGATCTTCCCCACTGAAGGAGCTGGCCATCATGTTAAGGATACCTATAAAAAGGGCCTTGATAGGCCTTTCTAA
Peptide sequence:
MLRIPIKRALIGLSNSPKGYVRTTGTAASNLIEVFVDGQSVMVEPGTTVLQACEKVGMQIPRFCYHERLSVAGNCRMCLVEIEKAPKVVAACAMPVMKGWNILTNSEKSKKAREGVMEFLLANHPLDCPICDQGGECDLQDQSMMFGSDRSRFLEGKRAVEDKNIGPLVKTIMTRCIQCTRCIRFASEIAGVDDLGTTGRGNDMQVGTYIEKMFMSELSGNVIDICPVGALTSKPYAFTARPWETRKTESIDVMDAVGSNIVVSTRTGEVMRILPRMHEDINEEWISDKTRFAYDGLKRQRLTEPMVRNEKGLLTYTSWEDALSRVAGMLQNFEGNAVAAIAGGLVDAEALVALKDLLNKVDSDNLCTEEIFPTEGAGHHVKDTYKKGLDRPF
IRESfinder result
IRESfinder score
0.514018271
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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