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mmu_circTnip1_412
Basic information of circular RNA
PanCircBase ID:
mmu_circTnip1_412
mm39_Chr. Position ID:
chr11|54814923|54820044|-
Gene name:
Tnip1
Transcript:
ENSMUST00000108889.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
11,10,9,8
Exon/intron offsets:
0,278,2606,4997
Genomic length:
5121
Exon/intron sizes in nt:
1,32,66,90,124
Flanking exon/introns:
chr11:54811715-54814923|chr11:54820044-54821590
Splice length:
412
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GGAGGAAAACACGGAGCTCAAGAAACTGTTGATGAACAGCAGCTGCAAAGAGGGACTCTGTGGGCAGCCCAGCTCCCCAAAGCCAGAGGGTGCTGGCAAGAAGGGCGTGGCTGGACAGCAGCAGGCCAGTGTGATGGCGAGTAAAGTCCCTGAAGCGGGGGCCTTTGGAGCAGCTGAGAAGAAGGTGAAGTTGCTAGAACAGCAACGCATGGAGCTGCTGGAAGTGAACAAGCAGTGGGACCAGCATTTCCGGTCCATGAAGCAGCAGTATGAGCAGAAGATCACAGAGCTTCGCCAGAAGCTGGTGGACCTGCAGAAACAGGTAACTGAGCTGGAGGCCGAACGGGAGCAGAAGCAGCGTGACTTTGACCGGAAACTCCTCCTGGCCAAATCGAAGATAGAGATGGAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TAACTGAGCTGGAGGCCGAA
60.9
ACAGAGTCCCTCTTTGCAGC
59.96
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TAACTGAGCTGGAGGCCGAA
60.9
CCTCTTTGCAGCTGCTGTTC
59.76
142
PCR template sequence:
GCAGAAACAGGTAACTGAGCTGGAGGCCGAACGGGAGCAGAAGCAGCGTGACTTTGACCGGAAACTCCTCCTGGCCAAATCGAAGATAGAGATGGAAGAGGGAGGAAAACACGGAGCTCAAGAAACTGTTGATGAACAGCAGCTGCAAAGAGGGACTCTGTGGGCAGCCCAGCTCCCCAAAGCCAGAGGGTGCTGGCAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-1904(2), mmu-miR-370-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAGATGGAAGAGGGAGGAAAACACG
siRNA sets
TTTTCCTCCCTCTTCCATC, TTCCTCCCTCTTCCATCTC, TTTCCTCCCTCTTCCATCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTNIP1_412_ORF_1
1.1333
0.441584453
0.919766044
525
ORF sequence:
ATGAACAGCAGCTGCAAAGAGGGACTCTGTGGGCAGCCCAGCTCCCCAAAGCCAGAGGGTGCTGGCAAGAAGGGCGTGGCTGGACAGCAGCAGGCCAGTGTGATGGCGAGTAAAGTCCCTGAAGCGGGGGCCTTTGGAGCAGCTGAGAAGAAGGTGAAGTTGCTAGAACAGCAACGCATGGAGCTGCTGGAAGTGAACAAGCAGTGGGACCAGCATTTCCGGTCCATGAAGCAGCAGTATGAGCAGAAGATCACAGAGCTTCGCCAGAAGCTGGTGGACCTGCAGAAACAGGTAACTGAGCTGGAGGCCGAACGGGAGCAGAAGCAGCGTGACTTTGACCGGAAACTCCTCCTGGCCAAATCGAAGATAGAGATGGAAGAGGGAGGAAAACACGGAGCTCAAGAAACTGTTGATGAACAGCAGCTGCAAAGAGGGACTCTGTGGGCAGCCCAGCTCCCCAAAGCCAGAGGGTGCTGGCAAGAAGGGCGTGGCTGGACAGCAGCAGGCCAGTGTGATGGCGAGTAA
Peptide sequence:
MNSSCKEGLCGQPSSPKPEGAGKKGVAGQQQASVMASKVPEAGAFGAAEKKVKLLEQQRMELLEVNKQWDQHFRSMKQQYEQKITELRQKLVDLQKQVTELEAEREQKQRDFDRKLLLAKSKIEMEEGGKHGAQETVDEQQLQRGTLWAAQLPKARGCWQEGRGWTAAGQCDGE
IRESfinder result
IRESfinder score
0.226264136
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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