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mmu_circNub1_576
Basic information of circular RNA
PanCircBase ID:
mmu_circNub1_576
mm39_Chr. Position ID:
chr5|24897804|24902421|+
Gene name:
Nub1
Transcript:
ENSMUST00000197407.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
3,4,5,6,7
Exon/intron offsets:
0,1893,2713,4198,4525
Genomic length:
4617
Exon/intron sizes in nt:
168,62,71,183,92
Flanking exon/introns:
chr5:24894508-24897804|chr5:24902421-24903662
Splice length:
576
Other database IDs:
circAtlas: mmu-Nub1_0004
Human Ortholog IDs:
Mature spliced Sequence:
GACCTTGCTAAGAAGTACTCTGAGCGGCTGGAGTGCTGTGAAAACGAAGTGGAAAACATAATCGAGGAAATCCGACGCAAAGCAATTGAGCGCGGCACTGGGAATGAACACTACCGAACAACTGGGATCGCCACCATTGAGGTGTTCCTGCCTCCAAGGCTCCGGAAGCACGATAAGAAAAGCTTGTTGGAGACCCGCTTGCATGTCACTGGTAGAGACCTGAGGTGTCAAATAGCTGAAACTTTCGGATTTCAAGAAAATTACATCAAGATCGTAATAAATAAGAAACAGCTTCAACTAGGGAAAAGCCTTGAAGAACAAGGAGTCACTCACAATGTGAAGGCGATGGTACTGGAGCTGAAACAGTCTGAAGAGGATGTGAGGAAAAACTTACAGCTAGAGGAAGAGGAACAGAACGAGGCCGAGCTGAAGGAGAGACGCATTCAGAGGACCAAACGGGGACTGGAGATCCTGGCGGAGAGAGCTGAGATGGTGGTTGATCCGGAAACGATGCCTTACTTAGACATTGCGAACCAGACAGGCAGGTCACTCAGAATTCCCCCTGCAGAAAGAAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGAGATGGTGGTTGATCCGG
59.46
TTTGCGTCGGATTTCCTCGA
60.04
172
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGAGATGGTGGTTGATCCGG
59.46
GCTTTGCGTCGGATTTCCTC
59.9
174
PCR template sequence:
GGAGAGAGCTGAGATGGTGGTTGATCCGGAAACGATGCCTTACTTAGACATTGCGAACCAGACAGGCAGGTCACTCAGAATTCCCCCTGCAGAAAGAAAAGACCTTGCTAAGAAGTACTCTGAGCGGCTGGAGTGCTGTGAAAACGAAGTGGAAAACATAATCGAGGAAATCCGACGCAAAGCAATTGAGCGCGGCACTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(1), mmu-miR-23a-3p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGCAGAAAGAAAAGACCTTGCTAAGA
siRNA sets
AAGGTCTTTTCTTTCTGCA, TCTTAGCAAGGTCTTTTCT, TTAGCAAGGTCTTTTCTTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNUB1_576_ORF_1
1.0672
0.371730133
0.983009856
807
ORF sequence:
ATGGTACTGGAGCTGAAACAGTCTGAAGAGGATGTGAGGAAAAACTTACAGCTAGAGGAAGAGGAACAGAACGAGGCCGAGCTGAAGGAGAGACGCATTCAGAGGACCAAACGGGGACTGGAGATCCTGGCGGAGAGAGCTGAGATGGTGGTTGATCCGGAAACGATGCCTTACTTAGACATTGCGAACCAGACAGGCAGGTCACTCAGAATTCCCCCTGCAGAAAGAAAAGACCTTGCTAAGAAGTACTCTGAGCGGCTGGAGTGCTGTGAAAACGAAGTGGAAAACATAATCGAGGAAATCCGACGCAAAGCAATTGAGCGCGGCACTGGGAATGAACACTACCGAACAACTGGGATCGCCACCATTGAGGTGTTCCTGCCTCCAAGGCTCCGGAAGCACGATAAGAAAAGCTTGTTGGAGACCCGCTTGCATGTCACTGGTAGAGACCTGAGGTGTCAAATAGCTGAAACTTTCGGATTTCAAGAAAATTACATCAAGATCGTAATAAATAAGAAACAGCTTCAACTAGGGAAAAGCCTTGAAGAACAAGGAGTCACTCACAATGTGAAGGCGATGGTACTGGAGCTGAAACAGTCTGAAGAGGATGTGAGGAAAAACTTACAGCTAGAGGAAGAGGAACAGAACGAGGCCGAGCTGAAGGAGAGACGCATTCAGAGGACCAAACGGGGACTGGAGATCCTGGCGGAGAGAGCTGAGATGGTGGTTGATCCGGAAACGATGCCTTACTTAGACATTGCGAACCAGACAGGCAGGTCACTCAGAATTCCCCCTGCAGAAAGAAAA
Peptide sequence:
MVLELKQSEEDVRKNLQLEEEEQNEAELKERRIQRTKRGLEILAERAEMVVDPETMPYLDIANQTGRSLRIPPAERKDLAKKYSERLECCENEVENIIEEIRRKAIERGTGNEHYRTTGIATIEVFLPPRLRKHDKKSLLETRLHVTGRDLRCQIAETFGFQENYIKIVINKKQLQLGKSLEEQGVTHNVKAMVLELKQSEEDVRKNLQLEEEEQNEAELKERRIQRTKRGLEILAERAEMVVDPETMPYLDIANQTGRSLRIPPAERK
IRESfinder result
IRESfinder score
0.274598949
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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