top of page
mmu_circSbno1_921
Basic information of circular RNA
PanCircBase ID:
mmu_circSbno1_921
mm39_Chr. Position ID:
chr5|124529984|124536572|-
Gene name:
Sbno1
Transcript:
ENSMUST00000065263.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
20,19,18,17,16,15
Exon/intron offsets:
0,652,917,1879,3973,6490
Genomic length:
6588
Exon/intron sizes in nt:
132,176,168,195,152,98
Flanking exon/introns:
chr5:124526723-124529984|chr5:124536572-124538066
Splice length:
921
Other database IDs:
circBase: mmu_circ_0012127, CIRCpedia: MMU_CIRCpedia_6307, circAtlas: mmu-Sbno1_0038
CIRCpedia: HSA_CIRCpedia_178171
Human Ortholog IDs:
Mature spliced Sequence:
TGTGTTGTAATTGGTCTTCAGTCTACAGGAGAAGCCAGAACTTTAGAGGCCTTGGAAGAGGGAGGAGGAGAACTAAATGATTTTGTTTCAACTGCCAAAGGGGTATTGCAGTCACTGATTGAAAAACACTTCCCTGCTCCAGACAGGAAGAAACTTTATAGTTTGCTAGGAATCGATTTGACAGCCCCAAGTAACAACAGTTCACCAAGAGATAGTCCTTGTAAAGAAAATAAAATAAAGAAGCGGAAAGGTGAAGAAATCACTCGAGAAGCCAAAAAAGCACGAAAAGTTGGTGGCCTCACAGGAAGCAGCTCTGACGACAGTGGAAGTGAGTCTGTGTCTGATAATGACGAAAGCGACTATGAGAGCTCTAAAAACATGAGCTCTGGGGATGATGACGATTTCAATCCCTTCAGAGATGAGTCCAGTGAAGACAATGAGGATGATCCGTGGTTAATTAGGAAAGACCATAAGAAAAGCAAAGATAAAAAAAAGAAGAAAAGTATAGATCCAGATTCCATTCAAAGTGCCTTGTTAGCATCAGGTCTTGGATCAAAGCGGCCTAGTTTCTCCTCTGCACCAGTCATCTCGCCTGCTTCCAACAGTGCACCAGCCAACAGTAACAGCAACAGCAACAGCAGCCTTGTAACAAGTCAAGATGCTGTCGAAAGGGCGCAACAGATGAAGAAAGACCTGCTTGATAAACTAGAAAAATTGGCTGAAGACCTCCCTCCTAACACCCTGGATGAACTTATCGATGAACTTGGTGGTCCTGAAAATGTGGCTGAGATGACTGGCCGCAAAGGGCGGGTAGTGAGCAATGATGACGGAAGCATATCCTACGAGTCGAGGTCTGAACTTGATGTGCCTGTGGAGATTCTAAACATCACAGAGAAGCAAAGGTTCATGGATGGAGACAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTACGAGTCGAGGTCTGA
59.1
TCCTCCTCCCTCTTCCAAGG
59.96
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACGAGTCGAGGTCTGAACTTG
59.73
TCCTCCTCCCTCTTCCAAGG
59.96
149
PCR template sequence:
TGATGACGGAAGCATATCCTACGAGTCGAGGTCTGAACTTGATGTGCCTGTGGAGATTCTAAACATCACAGAGAAGCAAAGGTTCATGGATGGAGACAAGTGTGTTGTAATTGGTCTTCAGTCTACAGGAGAAGCCAGAACTTTAGAGGCCTTGGAAGAGGGAGGAGGAGAACTAAATGATTTTGTTTCAACTGCCAAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-124-3p(1), mmu-miR-298-5p(1), mmu-miR-138-5p(1), mmu-miR-381-3p(1), mmu-miR-434-5p(1), mmu-miR-541-5p(1), mmu-miR-384-3p(1), mmu-miR-207(1), mmu-miR-544-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGATGGAGACAAGTGTGTTGTAATTG
siRNA sets
TTACAACACACTTGTCTCC, TACAACACACTTGTCTCCA, ATTACAACACACTTGTCTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSBNO1_921_ORF_1
1.1195
0.267876893
0.99978735
1464
ORF sequence:
ATGAGCTCTGGGGATGATGACGATTTCAATCCCTTCAGAGATGAGTCCAGTGAAGACAATGAGGATGATCCGTGGTTAATTAGGAAAGACCATAAGAAAAGCAAAGATAAAAAAAAGAAGAAAAGTATAGATCCAGATTCCATTCAAAGTGCCTTGTTAGCATCAGGTCTTGGATCAAAGCGGCCTAGTTTCTCCTCTGCACCAGTCATCTCGCCTGCTTCCAACAGTGCACCAGCCAACAGTAACAGCAACAGCAACAGCAGCCTTGTAACAAGTCAAGATGCTGTCGAAAGGGCGCAACAGATGAAGAAAGACCTGCTTGATAAACTAGAAAAATTGGCTGAAGACCTCCCTCCTAACACCCTGGATGAACTTATCGATGAACTTGGTGGTCCTGAAAATGTGGCTGAGATGACTGGCCGCAAAGGGCGGGTAGTGAGCAATGATGACGGAAGCATATCCTACGAGTCGAGGTCTGAACTTGATGTGCCTGTGGAGATTCTAAACATCACAGAGAAGCAAAGGTTCATGGATGGAGACAAGTGTGTTGTAATTGGTCTTCAGTCTACAGGAGAAGCCAGAACTTTAGAGGCCTTGGAAGAGGGAGGAGGAGAACTAAATGATTTTGTTTCAACTGCCAAAGGGGTATTGCAGTCACTGATTGAAAAACACTTCCCTGCTCCAGACAGGAAGAAACTTTATAGTTTGCTAGGAATCGATTTGACAGCCCCAAGTAACAACAGTTCACCAAGAGATAGTCCTTGTAAAGAAAATAAAATAAAGAAGCGGAAAGGTGAAGAAATCACTCGAGAAGCCAAAAAAGCACGAAAAGTTGGTGGCCTCACAGGAAGCAGCTCTGACGACAGTGGAAGTGAGTCTGTGTCTGATAATGACGAAAGCGACTATGAGAGCTCTAAAAACATGAGCTCTGGGGATGATGACGATTTCAATCCCTTCAGAGATGAGTCCAGTGAAGACAATGAGGATGATCCGTGGTTAATTAGGAAAGACCATAAGAAAAGCAAAGATAAAAAAAAGAAGAAAAGTATAGATCCAGATTCCATTCAAAGTGCCTTGTTAGCATCAGGTCTTGGATCAAAGCGGCCTAGTTTCTCCTCTGCACCAGTCATCTCGCCTGCTTCCAACAGTGCACCAGCCAACAGTAACAGCAACAGCAACAGCAGCCTTGTAACAAGTCAAGATGCTGTCGAAAGGGCGCAACAGATGAAGAAAGACCTGCTTGATAAACTAGAAAAATTGGCTGAAGACCTCCCTCCTAACACCCTGGATGAACTTATCGATGAACTTGGTGGTCCTGAAAATGTGGCTGAGATGACTGGCCGCAAAGGGCGGGTAGTGAGCAATGATGACGGAAGCATATCCTACGAGTCGAGGTCTGAACTTGATGTGCCTGTGGAGATTCTAAACATCACAGAGAAGCAAAGGTTCATGGATGGAGACAAG
Peptide sequence:
MSSGDDDDFNPFRDESSEDNEDDPWLIRKDHKKSKDKKKKKSIDPDSIQSALLASGLGSKRPSFSSAPVISPASNSAPANSNSNSNSSLVTSQDAVERAQQMKKDLLDKLEKLAEDLPPNTLDELIDELGGPENVAEMTGRKGRVVSNDDGSISYESRSELDVPVEILNITEKQRFMDGDKCVVIGLQSTGEARTLEALEEGGGELNDFVSTAKGVLQSLIEKHFPAPDRKKLYSLLGIDLTAPSNNSSPRDSPCKENKIKKRKGEEITREAKKARKVGGLTGSSSDDSGSESVSDNDESDYESSKNMSSGDDDDFNPFRDESSEDNEDDPWLIRKDHKKSKDKKKKKSIDPDSIQSALLASGLGSKRPSFSSAPVISPASNSAPANSNSNSNSSLVTSQDAVERAQQMKKDLLDKLEKLAEDLPPNTLDELIDELGGPENVAEMTGRKGRVVSNDDGSISYESRSELDVPVEILNITEKQRFMDGDK
IRESfinder result
IRESfinder score
0.497220314
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page