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mmu_circTns3_219
Basic information of circular RNA
PanCircBase ID:
mmu_circTns3_219
mm39_Chr. Position ID:
chr11|8398689|8400156|-
Gene name:
Tns3
Transcript:
ENSMUST00000239091.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
24,23
Exon/intron offsets:
0,1380
Genomic length:
1467
Exon/intron sizes in nt:
132,87
Flanking exon/introns:
chr11:8395741-8398689|chr11:8400156-8400854
Splice length:
219
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATAGCCCAAATGATAAACTCGTGATTGTGAAATTTGTTCAAGACACTTCGAAGTTCTGGTACAAGGCAGACATCTCAAGAGAACAAGCCATTGCCATGCTGAAGGACAAAGCCCCCGGGTCATTCATCGTGAGGGACAGTCACTCCTTCCGAGGGGCCTACGGCCTGGCCATGAAGGTGGCCACACCTCCTCCGTCTGTCCTGCACCTCAACAAGAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GACAGTCACTCCTTCCGAGG
59.47
TGCCTTGTACCAGAACTTCGA
59.31
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGACAGTCACTCCTTCCGAG
59.47
TGCCTTGTACCAGAACTTCGA
59.31
154
PCR template sequence:
TCATTCATCGTGAGGGACAGTCACTCCTTCCGAGGGGCCTACGGCCTGGCCATGAAGGTGGCCACACCTCCTCCGTCTGTCCTGCACCTCAACAAGAAAGATAGCCCAAATGATAAACTCGTGATTGTGAAATTTGTTCAAGACACTTCGAAGTTCTGGTACAAGGCAGACATCTCAAGAGAACAAGCCATTGCCATGCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(1), mmu-miR-205-5p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTCAACAAGAAAGATAGCCCAAATGA
siRNA sets
TTTGGGCTATCTTTCTTGT, TCATTTGGGCTATCTTTCT, TTGGGCTATCTTTCTTGTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTNS3_219_ORF_1
1.2988
0.470167695
0.825238681
342
ORF sequence:
ATGCTGAAGGACAAAGCCCCCGGGTCATTCATCGTGAGGGACAGTCACTCCTTCCGAGGGGCCTACGGCCTGGCCATGAAGGTGGCCACACCTCCTCCGTCTGTCCTGCACCTCAACAAGAAAGATAGCCCAAATGATAAACTCGTGATTGTGAAATTTGTTCAAGACACTTCGAAGTTCTGGTACAAGGCAGACATCTCAAGAGAACAAGCCATTGCCATGCTGAAGGACAAAGCCCCCGGGTCATTCATCGTGAGGGACAGTCACTCCTTCCGAGGGGCCTACGGCCTGGCCATGAAGGTGGCCACACCTCCTCCGTCTGTCCTGCACCTCAACAAGAAA
Peptide sequence:
MLKDKAPGSFIVRDSHSFRGAYGLAMKVATPPPSVLHLNKKDSPNDKLVIVKFVQDTSKFWYKADISREQAIAMLKDKAPGSFIVRDSHSFRGAYGLAMKVATPPPSVLHLNKK
IRESfinder result
IRESfinder score
0.536762331
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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