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mmu_ciRimbp2_1356
Basic information of circular RNA
PanCircBase ID:
mmu_ciRimbp2_1356
mm39_Chr. Position ID:
chr5|128863866|128865222|-
Gene name:
Rimbp2
Transcript:
ENSMUST00000199537.5
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
9
Exon/intron offsets:
0
Genomic length:
1356
Exon/intron sizes in nt:
1356
Flanking exon/introns:
chr5:128863862-128865222
Splice length:
1356
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTTGTATACTCCTACCAAGTTGGTCCCTGTACTCTTGGGGTGTCGTGTGACCTGTTCCTGCACCTGGCAGCTCTTCCGGAGAGCACTCTAGGACCTCAGCCTGGGACTGTTGTCCTGAACTGGGCGGGGCCTGTTTTTTTGATACCACATCCCAGCCTAAGGCTATGTGTGTATGCTTTGGGGTAGGGGCAGGGGGGTTATTGTAACTGTACAGATTGAGGATAGGAGTGAGATTTGGGCATATTCCCATCGTGGCTAATGAGATGTGCACTATAGGTCACCTATAAGGTGCCCCTTCCCACCAGGCCCAGGGGACTAGGACCCAGGACTGAATTGGCCCCAGGACCTGCCCATCTCTCCCAGGTATCCACCTGCCAGCTGCCCAGATGTTTGTGGCAAGCCTGAGTTTCTCCATGAGGAGGCATCTGGGCCTATTGGCACAGCCCTCTGAGTTTCAGGTTGCCCTGTGGGTCTTAAGATGGTCACCCCTGGGACTGTCTGCTAAGGCTGAGGTATTCTTTCCCATTAGGTTTCCTCTAGCCAGGGCCTGAGTCAGGAGAGTGAGGATACATGACCAAGGGTGAACACTGGAGTTGCAGTTGCACGGCAGGATGTTTCTAACGCATGTCTAACCCTGTGCATCTCCATGAGGGCATAGAGCTACCCTGACCTCAGGCACCTAGCACCTTGTAAGACACTAGAGCATCAGACTGTCTGTGAAATCTGATTTGCTCAACAGCGGCTATTGACACAATACATAGGCATGAACTTGGGACCTCAAACATAAAGGGCGCTCTGAGGCTCAGGGAGACTGGAACCAGGCCTGCACTGGGATGACTGGGTGATACTTGTGGCCAAGAGGCACAGGATCCCAGTGTGGCCTCAGAGCAGCCCCATAGGAGAGCTTAGTGGCTGCTAGGCTAGTCCAGAGACCCTTCCCAGGCTAATGCCCCAATGTCATAGTCATTGCCCAAACTAAAGGTGAGTCGAGCAAGGGAGGACAAAGGCTCCTATTAAGGCCTGTGGTCCCCTCTAGTGAAGCTGAGAGTGATGCAGGCCTCAGGGAGAGGAGAGGGGAGGGGGAGATCTGGCTTTGGGAGCCTGGATCTCATGGGAACCACCCTCTAGAGCAGCCTAGAGTCACGTACTTAGGAAGTCATAGCATCTTTCACGTATCTGCCCTGAGGGAGGCTGCAGTGCTCAGTGTATGAGAGGCCTCCTCAGGGTACCACTGGGGAAATCTCCTTGATGTCCTCGGCACTCAGGGGCCCAGGATACCAACAGTGCATGCTCCTGGTGTCCCCTCCAGCCCCTCCCCACACACCCATTCATCGGTGGTCCCTTTCTCTTTC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCAGGATACCAACAGTGCA
59.67
CAGGAACAGGTCACACGACA
59.9
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCCAGGATACCAACAGTGCA
59.67
AGGAACAGGTCACACGACAC
59.9
147
PCR template sequence:
CCTCGGCACTCAGGGGCCCAGGATACCAACAGTGCATGCTCCTGGTGTCCCCTCCAGCCCCTCCCCACACACCCATTCATCGGTGGTCCCTTTCTCTTTCGTAAGTTGTATACTCCTACCAAGTTGGTCCCTGTACTCTTGGGGTGTCGTGTGACCTGTTCCTGCACCTGGCAGCTCTTCCGGAGAGCACTCTAGGACCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-199a-5p(1), mmu-miR-132-3p(1), mmu-miR-185-5p(1), mmu-miR-434-5p(1), mmu-miR-351-5p(1), mmu-miR-125a-5p(1), mmu-miR-494-3p(1), mmu-miR-22-3p(1), mmu-miR-127-5p(1), mmu-miR-212-3p(1), mmu-miR-192-5p(1), mmu-miR-215-5p(1), mmu-miR-670-5p(1), mmu-miR-697(1), mmu-miR-344-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCCTTTCTCTTTCGTAAGTTGTATAC
siRNA sets
ATACAACTTACGAAAGAGA, GTATACAACTTACGAAAGA, TACAACTTACGAAAGAGAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRIMBP2_1356_ORF_3
0.7298
-0.082651588
0.029088385
108
ORF sequence:
ATGTCCTCGGCACTCAGGGGCCCAGGATACCAACAGTGCATGCTCCTGGTGTCCCCTCCAGCCCCTCCCCACACACCCATTCATCGGTGGTCCCTTTCTCTTTCGTAA
Peptide sequence:
MSSALRGPGYQQCMLLVSPPAPPHTPIHRWSLSLS
IRESfinder result
IRESfinder score
0.573116726
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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