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mmu_ciRbm39_970
Basic information of circular RNA
PanCircBase ID:
mmu_ciRbm39_970
mm39_Chr. Position ID:
chr2|156019829|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:
970
Exon/intron sizes in nt:
970
Flanking exon/introns:
chr2:156019305-156020799
Splice length:
970
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAGTAATTGAGTGACTTATCGCTGTACCGTGGTCCCCTAGGTAAAATGACTCAACTAAGAATTACCAGCTCCAGTTTGGTATAGCAAAAAGGTGAATGTAGTGGTTTGGGAAAACTGCAGGGGTCCAAGAATAATAAATTACAACCAGTCTCTGGCAAGTAAATCTTAGAAGTCTTGAAAGAAGAAATGGGTGAGATTTAAATTTTATTTTATATAAATAGATATAAGACTGGTGATAGTAAACCTGAATACAGGCAGGTATTGATCTGCTTTTCAGTTAATAATTATTAAGATTCTTGGATCCCTGAATAGAAATTGGCAAAAAAGAGGAAAAAAAACCAAGAAAAAGAACAGAAGAGAGAAAAGAAAAAAAGCAAGAGACAGTATCACAGCTTAGAGTCACTTGATGACTGTTTTACTGCTCTCCATAGTGTTTATTTTTAATTAGGCCCTGCCATAGCTTTTCACACTCAAAACTAGAAAGGAAGTATTTTGGCCAGTAATACAATATGACCCATTTCGGTATCACAGTAAAAGTCAGCACTCTTCATTCTTTGACCAGTTGGTGGTGAAAATAGCAGTGTGCATGCATGCATTGTCACTGGTGTCTCAGACCTTAAGCCTGGTAACTTAGAGATCCTACTATTGGTGATGTGTTCAAACTGTGGAATAAAAACATTGCGCTTAAACCGTTTATAAATAATACATTTGTCTTGGAGTGTAGCACGACCATGTGGTGCCTTTTGGATGAATTCTGATAGCTTTAAATAGTGTAATTTTGTAATGCTAGACTCTTGAAGCCATACTTTCTGTTTTAATGTTTCTTGTCTTAGTTTAACTTGGATATAATTCCATGTAAACAGGTATGGAAGTAGGAAATGTTTAGGCTGGACTGGTGGATTATTAATTAACTTTTCTTGGGTTCTTGGGAGTCAACATTACTAAAGCAGTGTGAATCCCTGTTTGCTT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTTTAGGCTGGACTGGTGG
59.6
GCTATACCAAACTGGAGCTGGT
60.09
176
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTTTAGGCTGGACTGGTGG
59.6
TGCTATACCAAACTGGAGCTGG
60.09
177
PCR template sequence:
AAGTAGGAAATGTTTAGGCTGGACTGGTGGATTATTAATTAACTTTTCTTGGGTTCTTGGGAGTCAACATTACTAAAGCAGTGTGAATCCCTGTTTGCTTGTAGTAATTGAGTGACTTATCGCTGTACCGTGGTCCCCTAGGTAAAATGACTCAACTAAGAATTACCAGCTCCAGTTTGGTATAGCAAAAAGGTGAATGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
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-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCCCTGTTTGCTTGTAGTAATTGAGT
siRNA sets
ATTACTACAAGCAAACAGG, AATTACTACAAGCAAACAG, TTACTACAAGCAAACAGGG
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
0.830656621
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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