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mmu_circUbr3_835
Basic information of circular RNA
PanCircBase ID:
mmu_circUbr3_835
mm39_Chr. Position ID:
chr2|69830801|69848916|+
Gene name:
Ubr3
Transcript:
ENSMUST00000055758.16
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
30,31,32,33,34,35,36
Exon/intron offsets:
0,2896,8645,12632,15674,15882,17935
Genomic length:
18115
Exon/intron sizes in nt:
8,61,06,10,41,25,10,81,00,000
Flanking exon/introns:
chr2:69824156-69830801|chr2:69848916-69850794
Splice length:
835
Other database IDs:
circAtlas: mmu-Ubr3_0081
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_114136
Human Ortholog IDs:
Mature spliced Sequence:
AACCAATCTGGAGCTGGAACTGATTCATAGAGGAGGCAGTCTCTGCTCCGGTGGTCCAAGCACAGCGGGGAAAAGATCTTGTCTGAATCAGCTGTTCCATGTATTAGCCTTGCACATGCGGCTTTATACCATTGATTCTGAATATAATCCATGGAAAAAACTCACCCAGTTAGTGGAAGATATGAATTCACAGGTGGGGAATGAAGACCAGCAGCCAGAAGTTCCAATTCTTTATCATGATGTGACATCCCTTCTGCTCATCCAGATCTTAATGATGCCACAACCCTTACGTAAAGAGCACTTCACCTGCATTGTGAAAGTACTCTTCACCCTGCTGTACACACAGGCCCTGGCGGCGCTCTCAGTTAAGGGCACTGAAGAGGACCGGTCAGCCTGGAAACACGCCGGGGCTCTTAGAAAGGATACATGTGATGCAGAAAAGTGTTACGAAGTGCTGTTGAGCTTTGTTATAAGTGAGCTGTCTAAAGGGAAGTTATATTATGAAGAAGGCGCTCAGGAGTGTGCGATGGTCAGTCCTATTGCTTGGTCTCCTGAGTCCATGGAAAGATACATACAGGATTTCTGCTTGCCTTTCCTCAGGGTCAGCAGCCTTCTTCAGCACCACCTCTTTGGGGAAGACTTACCCAGTTGCCAGGAAGAAGAAGAATTTTCAGTCCTTGCCAGCTGCCTGGGACTTCTGCCAACTTTTTACCAAACAGATCACCCGTTCATCAGTGCCTCGTGTCTGGACTGGCCAGTTGCAGCGTTTGACATTATAACTCAGTGGTGTTTTGAGATAACATCATTTACGGAGAGACACGCAGAGCAAGGAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGTTGCAGCGTTTGACAT
59.69
ATCTTTTCCCCGCTGTGCTT
60.25
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGTTGCAGCGTTTGACAT
59.69
GATCTTTTCCCCGCTGTGCT
60.68
159
PCR template sequence:
TGCCTCGTGTCTGGACTGGCCAGTTGCAGCGTTTGACATTATAACTCAGTGGTGTTTTGAGATAACATCATTTACGGAGAGACACGCAGAGCAAGGAAAGAACCAATCTGGAGCTGGAACTGATTCATAGAGGAGGCAGTCTCTGCTCCGGTGGTCCAAGCACAGCGGGGAAAAGATCTTGTCTGAATCAGCTGTTCCAT
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-32-5p(1), mmu-miR-351-5p(1), mmu-miR-218-5p(1), mmu-miR-297a-5p(1), mmu-miR-339-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAGCAAGGAAAGAACCAATCTGGAG
siRNA sets
TTGGTTCTTTCCTTGCTCT, ATTGGTTCTTTCCTTGCTC, GATTGGTTCTTTCCTTGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUBR3_835_ORF_1
0.7958
0.094712228
0.880505932
750
ORF sequence:
ATGCGGCTTTATACCATTGATTCTGAATATAATCCATGGAAAAAACTCACCCAGTTAGTGGAAGATATGAATTCACAGGTGGGGAATGAAGACCAGCAGCCAGAAGTTCCAATTCTTTATCATGATGTGACATCCCTTCTGCTCATCCAGATCTTAATGATGCCACAACCCTTACGTAAAGAGCACTTCACCTGCATTGTGAAAGTACTCTTCACCCTGCTGTACACACAGGCCCTGGCGGCGCTCTCAGTTAAGGGCACTGAAGAGGACCGGTCAGCCTGGAAACACGCCGGGGCTCTTAGAAAGGATACATGTGATGCAGAAAAGTGTTACGAAGTGCTGTTGAGCTTTGTTATAAGTGAGCTGTCTAAAGGGAAGTTATATTATGAAGAAGGCGCTCAGGAGTGTGCGATGGTCAGTCCTATTGCTTGGTCTCCTGAGTCCATGGAAAGATACATACAGGATTTCTGCTTGCCTTTCCTCAGGGTCAGCAGCCTTCTTCAGCACCACCTCTTTGGGGAAGACTTACCCAGTTGCCAGGAAGAAGAAGAATTTTCAGTCCTTGCCAGCTGCCTGGGACTTCTGCCAACTTTTTACCAAACAGATCACCCGTTCATCAGTGCCTCGTGTCTGGACTGGCCAGTTGCAGCGTTTGACATTATAACTCAGTGGTGTTTTGAGATAACATCATTTACGGAGAGACACGCAGAGCAAGGAAAGAACCAATCTGGAGCTGGAACTGATTCATAG
Peptide sequence:
MRLYTIDSEYNPWKKLTQLVEDMNSQVGNEDQQPEVPILYHDVTSLLLIQILMMPQPLRKEHFTCIVKVLFTLLYTQALAALSVKGTEEDRSAWKHAGALRKDTCDAEKCYEVLLSFVISELSKGKLYYEEGAQECAMVSPIAWSPESMERYIQDFCLPFLRVSSLLQHHLFGEDLPSCQEEEEFSVLASCLGLLPTFYQTDHPFISASCLDWPVAAFDIITQWCFEITSFTERHAEQGKNQSGAGTDS
IRESfinder result
IRESfinder score
0.65257815
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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