top of page
mmu_circNub1_814
Basic information of circular RNA
PanCircBase ID:
mmu_circNub1_814
mm39_Chr. Position ID:
chr5|24894377|24903769|+
Gene name:
Nub1
Transcript:
ENSMUST00000068825.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
2,3,4,5,6,7,8
Exon/intron offsets:
0,3427,5320,6140,7625,7952,9285
Genomic length:
9392
Exon/intron sizes in nt:
1,31,16,86,27,11,83,92,000
Flanking exon/introns:
chr5:24891020-24894377|chr5:24903769-24906347
Splice length:
814
Other database IDs:
circAtlas: mmu-Nub1_0009
Human Ortholog IDs:
Mature spliced Sequence:
TTTTACTTTCAAGGATGGCGCAGAAGAAATATCTTCAAGCAAAACTGACTCAGTTTCTAAGGGAAGACAGAATTCAACTTTGGAAACCTCCATATACTAAAGAAAATAAGGAAGTTGGTTTGGCCGTAAAGGACCTTGCTAAGAAGTACTCTGAGCGGCTGGAGTGCTGTGAAAACGAAGTGGAAAACATAATCGAGGAAATCCGACGCAAAGCAATTGAGCGCGGCACTGGGAATGAACACTACCGAACAACTGGGATCGCCACCATTGAGGTGTTCCTGCCTCCAAGGCTCCGGAAGCACGATAAGAAAAGCTTGTTGGAGACCCGCTTGCATGTCACTGGTAGAGACCTGAGGTGTCAAATAGCTGAAACTTTCGGATTTCAAGAAAATTACATCAAGATCGTAATAAATAAGAAACAGCTTCAACTAGGGAAAAGCCTTGAAGAACAAGGAGTCACTCACAATGTGAAGGCGATGGTACTGGAGCTGAAACAGTCTGAAGAGGATGTGAGGAAAAACTTACAGCTAGAGGAAGAGGAACAGAACGAGGCCGAGCTGAAGGAGAGACGCATTCAGAGGACCAAACGGGGACTGGAGATCCTGGCGGAGAGAGCTGAGATGGTGGTTGATCCGGAAACGATGCCTTACTTAGACATTGCGAACCAGACAGGCAGGTCACTCAGAATTCCCCCTGCAGAAAGAAAAGCCCTTATGTTAGCTATGGGATATCACGAGAAGGGCAGAGCTTTCCTGAAAAGAAAAGAGTATGGAATAGCCCTGCCCTGCCTCCTGGACGCTGACAGATACTTCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACGAGAAGGGCAGAGCTTTC
60.04
TCCAAAGTTGAATTCTGTCTTCCC
59.17
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACGAGAAGGGCAGAGCTTTC
60.04
CCAAAGTTGAATTCTGTCTTCCCT
59.17
165
PCR template sequence:
TGTTAGCTATGGGATATCACGAGAAGGGCAGAGCTTTCCTGAAAAGAAAAGAGTATGGAATAGCCCTGCCCTGCCTCCTGGACGCTGACAGATACTTCTGTTTTACTTTCAAGGATGGCGCAGAAGAAATATCTTCAAGCAAAACTGACTCAGTTTCTAAGGGAAGACAGAATTCAACTTTGGAAACCTCCATATACTAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(1), mmu-miR-709(1), mmu-miR-23a-3p(1), mmu-miR-362-5p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACAGATACTTCTGTTTTACTTTCAAG
siRNA sets
AAAGTAAAACAGAAGTATC, TTGAAAGTAAAACAGAAGT, AAGTAAAACAGAAGTATCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNUB1_814_ORF_1
1.0265
0.231660005
0.983202973
900
ORF sequence:
ATGGCGCAGAAGAAATATCTTCAAGCAAAACTGACTCAGTTTCTAAGGGAAGACAGAATTCAACTTTGGAAACCTCCATATACTAAAGAAAATAAGGAAGTTGGTTTGGCCGTAAAGGACCTTGCTAAGAAGTACTCTGAGCGGCTGGAGTGCTGTGAAAACGAAGTGGAAAACATAATCGAGGAAATCCGACGCAAAGCAATTGAGCGCGGCACTGGGAATGAACACTACCGAACAACTGGGATCGCCACCATTGAGGTGTTCCTGCCTCCAAGGCTCCGGAAGCACGATAAGAAAAGCTTGTTGGAGACCCGCTTGCATGTCACTGGTAGAGACCTGAGGTGTCAAATAGCTGAAACTTTCGGATTTCAAGAAAATTACATCAAGATCGTAATAAATAAGAAACAGCTTCAACTAGGGAAAAGCCTTGAAGAACAAGGAGTCACTCACAATGTGAAGGCGATGGTACTGGAGCTGAAACAGTCTGAAGAGGATGTGAGGAAAAACTTACAGCTAGAGGAAGAGGAACAGAACGAGGCCGAGCTGAAGGAGAGACGCATTCAGAGGACCAAACGGGGACTGGAGATCCTGGCGGAGAGAGCTGAGATGGTGGTTGATCCGGAAACGATGCCTTACTTAGACATTGCGAACCAGACAGGCAGGTCACTCAGAATTCCCCCTGCAGAAAGAAAAGCCCTTATGTTAGCTATGGGATATCACGAGAAGGGCAGAGCTTTCCTGAAAAGAAAAGAGTATGGAATAGCCCTGCCCTGCCTCCTGGACGCTGACAGATACTTCTGTTTTACTTTCAAGGATGGCGCAGAAGAAATATCTTCAAGCAAAACTGACTCAGTTTCTAAGGGAAGACAGAATTCAACTTTGGAAACCTCCATATACTAA
Peptide sequence:
MAQKKYLQAKLTQFLREDRIQLWKPPYTKENKEVGLAVKDLAKKYSERLECCENEVENIIEEIRRKAIERGTGNEHYRTTGIATIEVFLPPRLRKHDKKSLLETRLHVTGRDLRCQIAETFGFQENYIKIVINKKQLQLGKSLEEQGVTHNVKAMVLELKQSEEDVRKNLQLEEEEQNEAELKERRIQRTKRGLEILAERAEMVVDPETMPYLDIANQTGRSLRIPPAERKALMLAMGYHEKGRAFLKRKEYGIALPCLLDADRYFCFTFKDGAEEISSSKTDSVSKGRQNSTLETSIY
IRESfinder result
IRESfinder score
0.362312706
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page