top of page
mmu_circNipbl_786
Basic information of circular RNA
PanCircBase ID:
mmu_circNipbl_786
mm39_Chr. Position ID:
chr15|8321620|8326362|-
Gene name:
Nipbl
Transcript:
ENSMUST00000052965.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
46,45,44,43
Exon/intron offsets:
0,947,3374,4595
Genomic length:
4742
Exon/intron sizes in nt:
1,89,17,52,75,147
Flanking exon/introns:
chr15:8321074-8321620|chr15:8326362-8330178
Splice length:
786
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AAAACAGAAGTGACTATGCTCTTGTACATAGCAGACAATCTAGCCTGTTTTCCATACCAGACTCAGGAAGAGCCGCTGTTTATAATGCACCACATAGACATTACGCTCTCTGTTTCCGGTAGTAACCTATTGCAGTCATTCAAGGAGTCTATGGTAAAAGACAAAAGGAAAGAGAGGAAAACGTCCCCTGCTAAAGAGAACGAGTCCAGTGAGAGTGAAGAAGAAGTGTCCAGACCTCGGAAGTCTCGAAAGCGGGTAGATTCGGAGTCAGACTCAGACTCTGAAGATGATATAAATTCAGTGATGAAGTGTTTGCCGGAAAATTCAGCCCCTTTGATTGAATTCGCAAATGTTTCCCAGGGTATTTTATTACTTCTTATGTTAAAGCAGCACCTGAAGAATCTCTGTGGATTTTCTGATAGTAAAATTCAAAAATATTCTCCATCTGAATCTGCAAAAGTGTATGATAAAGCCATTAATCGGAAAACAGGGGTTCATTTTCATCCCAAACAAACACTGGACTTCCTGCGAAGTGACATGGCTAATTCCAAACTGACGGAGGATGTGAAGAGGAGCATCGTAAGGCAGTACTTAGACTTTAAACTTCTCATGGAACATCTAGACCCTGATGAAGAAGAAGAGGAAGGAGAGGTGTCAGCTAGCACCAATGCTCGGAACAAAGCAATTACCTCGCTGCTTGGAGGAGGCAGCCCTAAAAATAACACAGCAGCAGACACAGAAGATGAGGAGAGTGATGGGGAGGATAGAGGAGGAGGCACTTCAGGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACACAGCAGCAGACACAGAA
59.82
AAACAGCGGCTCTTCCTGAG
60.32
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AACACAGCAGCAGACACAGA
59.82
AAACAGCGGCTCTTCCTGAG
60.32
147
PCR template sequence:
TACCTCGCTGCTTGGAGGAGGCAGCCCTAAAAATAACACAGCAGCAGACACAGAAGATGAGGAGAGTGATGGGGAGGATAGAGGAGGAGGCACTTCAGGGAAAACAGAAGTGACTATGCTCTTGTACATAGCAGACAATCTAGCCTGTTTTCCATACCAGACTCAGGAAGAGCCGCTGTTTATAATGCACCACATAGACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-207(2), mmu-miR-221-3p(1), mmu-miR-135a-5p(1), mmu-miR-223-3p(1), mmu-miR-503-5p(1), mmu-miR-149-5p(1), mmu-miR-5101(1), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
AGGCACTTCAGGGAAAACAGAAGTGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNIPBL_786_ORF_1
0.9812
0.186690887
0.999805318
1557
ORF sequence:
ATGCTCTTGTACATAGCAGACAATCTAGCCTGTTTTCCATACCAGACTCAGGAAGAGCCGCTGTTTATAATGCACCACATAGACATTACGCTCTCTGTTTCCGGTAGTAACCTATTGCAGTCATTCAAGGAGTCTATGGTAAAAGACAAAAGGAAAGAGAGGAAAACGTCCCCTGCTAAAGAGAACGAGTCCAGTGAGAGTGAAGAAGAAGTGTCCAGACCTCGGAAGTCTCGAAAGCGGGTAGATTCGGAGTCAGACTCAGACTCTGAAGATGATATAAATTCAGTGATGAAGTGTTTGCCGGAAAATTCAGCCCCTTTGATTGAATTCGCAAATGTTTCCCAGGGTATTTTATTACTTCTTATGTTAAAGCAGCACCTGAAGAATCTCTGTGGATTTTCTGATAGTAAAATTCAAAAATATTCTCCATCTGAATCTGCAAAAGTGTATGATAAAGCCATTAATCGGAAAACAGGGGTTCATTTTCATCCCAAACAAACACTGGACTTCCTGCGAAGTGACATGGCTAATTCCAAACTGACGGAGGATGTGAAGAGGAGCATCGTAAGGCAGTACTTAGACTTTAAACTTCTCATGGAACATCTAGACCCTGATGAAGAAGAAGAGGAAGGAGAGGTGTCAGCTAGCACCAATGCTCGGAACAAAGCAATTACCTCGCTGCTTGGAGGAGGCAGCCCTAAAAATAACACAGCAGCAGACACAGAAGATGAGGAGAGTGATGGGGAGGATAGAGGAGGAGGCACTTCAGGGAAAACAGAAGTGACTATGCTCTTGTACATAGCAGACAATCTAGCCTGTTTTCCATACCAGACTCAGGAAGAGCCGCTGTTTATAATGCACCACATAGACATTACGCTCTCTGTTTCCGGTAGTAACCTATTGCAGTCATTCAAGGAGTCTATGGTAAAAGACAAAAGGAAAGAGAGGAAAACGTCCCCTGCTAAAGAGAACGAGTCCAGTGAGAGTGAAGAAGAAGTGTCCAGACCTCGGAAGTCTCGAAAGCGGGTAGATTCGGAGTCAGACTCAGACTCTGAAGATGATATAAATTCAGTGATGAAGTGTTTGCCGGAAAATTCAGCCCCTTTGATTGAATTCGCAAATGTTTCCCAGGGTATTTTATTACTTCTTATGTTAAAGCAGCACCTGAAGAATCTCTGTGGATTTTCTGATAGTAAAATTCAAAAATATTCTCCATCTGAATCTGCAAAAGTGTATGATAAAGCCATTAATCGGAAAACAGGGGTTCATTTTCATCCCAAACAAACACTGGACTTCCTGCGAAGTGACATGGCTAATTCCAAACTGACGGAGGATGTGAAGAGGAGCATCGTAAGGCAGTACTTAGACTTTAAACTTCTCATGGAACATCTAGACCCTGATGAAGAAGAAGAGGAAGGAGAGGTGTCAGCTAGCACCAATGCTCGGAACAAAGCAATTACCTCGCTGCTTGGAGGAGGCAGCCCTAAAAATAACACAGCAGCAGACACAGAAGATGAGGAGAGTGATGGGGAGGATAGAGGAGGAGGCACTTCAGGG
Peptide sequence:
MLLYIADNLACFPYQTQEEPLFIMHHIDITLSVSGSNLLQSFKESMVKDKRKERKTSPAKENESSESEEEVSRPRKSRKRVDSESDSDSEDDINSVMKCLPENSAPLIEFANVSQGILLLLMLKQHLKNLCGFSDSKIQKYSPSESAKVYDKAINRKTGVHFHPKQTLDFLRSDMANSKLTEDVKRSIVRQYLDFKLLMEHLDPDEEEEEGEVSASTNARNKAITSLLGGGSPKNNTAADTEDEESDGEDRGGGTSGKTEVTMLLYIADNLACFPYQTQEEPLFIMHHIDITLSVSGSNLLQSFKESMVKDKRKERKTSPAKENESSESEEEVSRPRKSRKRVDSESDSDSEDDINSVMKCLPENSAPLIEFANVSQGILLLLMLKQHLKNLCGFSDSKIQKYSPSESAKVYDKAINRKTGVHFHPKQTLDFLRSDMANSKLTEDVKRSIVRQYLDFKLLMEHLDPDEEEEEGEVSASTNARNKAITSLLGGGSPKNNTAADTEDEESDGEDRGGGTSG
IRESfinder result
IRESfinder score
0.653842933
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page