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mmu_ciRbm39_1414
Basic information of circular RNA
PanCircBase ID:
mmu_ciRbm39_1414
mm39_Chr. Position ID:
chr2|156019385|156020799|-
Gene name:
Rbm39
Transcript:
ENSMUST00000155837.8
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
3
Exon/intron offsets:
0
Genomic length:
1414
Exon/intron sizes in nt:
1414
Flanking exon/introns:
chr2:156019305-156020799
Splice length:
1414
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAGTAATTGAGTGACTTATCGCTGTACCGTGGTCCCCTAGGTAAAATGACTCAACTAAGAATTACCAGCTCCAGTTTGGTATAGCAAAAAGGTGAATGTAGTGGTTTGGGAAAACTGCAGGGGTCCAAGAATAATAAATTACAACCAGTCTCTGGCAAGTAAATCTTAGAAGTCTTGAAAGAAGAAATGGGTGAGATTTAAATTTTATTTTATATAAATAGATATAAGACTGGTGATAGTAAACCTGAATACAGGCAGGTATTGATCTGCTTTTCAGTTAATAATTATTAAGATTCTTGGATCCCTGAATAGAAATTGGCAAAAAAGAGGAAAAAAAACCAAGAAAAAGAACAGAAGAGAGAAAAGAAAAAAAGCAAGAGACAGTATCACAGCTTAGAGTCACTTGATGACTGTTTTACTGCTCTCCATAGTGTTTATTTTTAATTAGGCCCTGCCATAGCTTTTCACACTCAAAACTAGAAAGGAAGTATTTTGGCCAGTAATACAATATGACCCATTTCGGTATCACAGTAAAAGTCAGCACTCTTCATTCTTTGACCAGTTGGTGGTGAAAATAGCAGTGTGCATGCATGCATTGTCACTGGTGTCTCAGACCTTAAGCCTGGTAACTTAGAGATCCTACTATTGGTGATGTGTTCAAACTGTGGAATAAAAACATTGCGCTTAAACCGTTTATAAATAATACATTTGTCTTGGAGTGTAGCACGACCATGTGGTGCCTTTTGGATGAATTCTGATAGCTTTAAATAGTGTAATTTTGTAATGCTAGACTCTTGAAGCCATACTTTCTGTTTTAATGTTTCTTGTCTTAGTTTAACTTGGATATAATTCCATGTAAACAGGTATGGAAGTAGGAAATGTTTAGGCTGGACTGGTGGATTATTAATTAACTTTTCTTGGGTTCTTGGGAGTCAACATTACTAAAGCAGTGTGAATCCCTGTTTGCTTCAGGGCGAGATGTGTGACAGAGGTGGCATCAAGCTCTTACAGTCCCAACCCTCCAACGGAAATGGGCGAAGATCTCAGGAATGGCATCGGTCACAGGAAATCGATAGTGGCTGGCTGCTAGCATGGCCACTTGGGGCTTAGGCAGAAATAGAGCCATGGTACCGACAAAAGGGACAATAGCACATGGAATAAAACTCAAAATGACTTCATGTTTCATAGAAATCTTTAACCACTTCAACATTGTAATTCCGGATGACTTATTTAATACTTAAACAATGTAAGAAAGTAAAATATAACATATTAAATGTGGAAAGATTTTAATTTTTGTTTCTTGATGACTTAATTATTAGCAACAAAGTGGTTAAACGTATACCATCTAAATTTTATAGCCTTCCATGTTAAAGTAAATAAGTAATTAGTTTTAAAATTGTCTTGTATTTTCTT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCAACAAAGTGGTTAAACGT
56.87
ACCAAACTGGAGCTGGTAATTCT
59.93
177
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCAACAAAGTGGTTAAACGT
56.87
ACCAAACTGGAGCTGGTAAT
56.72
177
PCR template sequence:
TATTAGCAACAAAGTGGTTAAACGTATACCATCTAAATTTTATAGCCTTCCATGTTAAAGTAAATAAGTAATTAGTTTTAAAATTGTCTTGTATTTTCTTGTAGTAATTGAGTGACTTATCGCTGTACCGTGGTCCCCTAGGTAAAATGACTCAACTAAGAATTACCAGCTCCAGTTTGGTATAGCAAAAAGGTGAATGT
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-204-5p(1), mmu-miR-494-3p(1), mmu-miR-212-3p(1), mmu-miR-541-5p(1), mmu-miR-224-5p(1), mmu-miR-129-5p(1), mmu-miR-193b-3p(1), mmu-miR-296-3p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTTGTATTTTCTTGTAGTAATTGAGT
siRNA sets
ATTACTACAAGAAAATACA,AATTACTACAAGAAAATAC,TTACTACAAGAAAATACAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.801937743
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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