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mmu_circTomm34_571
Basic information of circular RNA
PanCircBase ID:
mmu_circTomm34_571
mm39_Chr. Position ID:
chr2|163900585|163908589|-
Gene name:
Tomm34
Transcript:
ENSMUST00000018466.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,4,3,2
Exon/intron offsets:
0,2173,6226,7904
Genomic length:
8004
Exon/intron sizes in nt:
1,48,17,01,53,100
Flanking exon/introns:
chr2:163896747-163900585|chr2:163908589-163912386
Splice length:
571
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTTCTGCAGACCCCGAAGAAGAAAGTGTTCTGTACTCCAACCGTGCAGCGTGCTACTTGAAGGATGGGAACTGCACAGATTGCATCAAAGATTGCACTTCCGCGCTGGCCTTGGTTCCCTTCAGCATCAAGCCCTTGCTGCGCAGAGCATCTGCATATGAAGCCCTGGAGAAGTACGCCCTGGCCTACGTTGACTATAAGACTGTGCTGCAGATCGATAACAGTGTGGCATCCGCCCTGGAAGGCATCAACAGAATAACCAGAGCTCTCATGGACTCCCTGGGACCTGAGTGGCGCCTGAAGCTGCCCCCTATCCCTGTGGTGCCTGTTTCAGCCCAGAAGAGATGGAATTCCTTGCCTTCAGATAACCACAAAGAGACAGCTAAAACCAAATCCAAAGAAGCCACAGCTACGAAGAGCAGAGTGCCTTCTGCTGGGGATGTGGAGAGAGCCAAAGCTCTGAAGGAAGAAGGCAATGACCTTGTAAAGAAGGGCAACCATAAGAAAGCTATTGAGAAGTACAGTGAGAGCCTCTTGTGTAGTAGCCTGGAGTCTGCCACATACAGCAACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGAGAAGTACAGTGAGAGCCTC
58.91
ATCTGTGCAGTTCCCATCCT
58.71
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGAGAAGTACAGTGAGAGCCT
57.84
ATCTGTGCAGTTCCCATCCT
58.71
140
PCR template sequence:
GCAATGACCTTGTAAAGAAGGGCAACCATAAGAAAGCTATTGAGAAGTACAGTGAGAGCCTCTTGTGTAGTAGCCTGGAGTCTGCCACATACAGCAACAGGTTCTGCAGACCCCGAAGAAGAAAGTGTTCTGTACTCCAACCGTGCAGCGTGCTACTTGAAGGATGGGAACTGCACAGATTGCATCAAAGATTGCACTTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-130a-3p(1), mmu-miR-130b-3p(1), mmu-miR-297a-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
CATACAGCAACAGGTTCTGCAGACCC
siRNA sets
GGTCTGCAGAACCTGTTGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTOMM34_571_ORF_1
0.5857
0.155235761
0.447193739
462
ORF sequence:
ATGGACTCCCTGGGACCTGAGTGGCGCCTGAAGCTGCCCCCTATCCCTGTGGTGCCTGTTTCAGCCCAGAAGAGATGGAATTCCTTGCCTTCAGATAACCACAAAGAGACAGCTAAAACCAAATCCAAAGAAGCCACAGCTACGAAGAGCAGAGTGCCTTCTGCTGGGGATGTGGAGAGAGCCAAAGCTCTGAAGGAAGAAGGCAATGACCTTGTAAAGAAGGGCAACCATAAGAAAGCTATTGAGAAGTACAGTGAGAGCCTCTTGTGTAGTAGCCTGGAGTCTGCCACATACAGCAACAGGTTCTGCAGACCCCGAAGAAGAAAGTGTTCTGTACTCCAACCGTGCAGCGTGCTACTTGAAGGATGGGAACTGCACAGATTGCATCAAAGATTGCACTTCCGCGCTGGCCTTGGTTCCCTTCAGCATCAAGCCCTTGCTGCGCAGAGCATCTGCATATGA
Peptide sequence:
MDSLGPEWRLKLPPIPVVPVSAQKRWNSLPSDNHKETAKTKSKEATATKSRVPSAGDVERAKALKEEGNDLVKKGNHKKAIEKYSESLLCSSLESATYSNRFCRPRRRKCSVLQPCSVLLEGWELHRLHQRLHFRAGLGSLQHQALAAQSICI
IRESfinder result
IRESfinder score
0.558142696
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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