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mmu_circTrim25_466
Basic information of circular RNA
PanCircBase ID:
mmu_circTrim25_466
mm39_Chr. Position ID:
chr11|88899944|88904364|+
Gene name:
Trim25
Transcript:
ENSMUST00000000284.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
3,4,5
Exon/intron offsets:
0,1686,4357
Genomic length:
4420
Exon/intron sizes in nt:
234,169,63
Flanking exon/introns:
chr11:88895650-88899944|chr11:88904364-88906358
Splice length:
466
Other database IDs:
circAtlas: mmu-Trim25_0011
Human Ortholog IDs:
Mature spliced Sequence:
GATTCTATGAAGAGGAAGATGGAACAGCTGAGACAGGAGTATATGGAAATGAAGGCTGTCATCGACGCAGCAGAGACCAGCTCCTTGCGCAAGTTAAAGGAGGAGGAGAAGAGAGTCTACGGAAAATTCGACACCATCTACCAGGTTCTCGTCAAGAAGAAGAGTGAGATGCAGAAACTGAAGGCAGAGGTTGAGCTCATTATGGACAAAGGGGATGAGTTTGAGTTTCTGGAGAAAGCTGCAAAATTGCAAGGAGAGTCAACAAAACCAGTCTACATCCCTAAGATAGATCTGGATCATGATTTGATAATGGGAATCTACCAAGGGGCGGCGGACCTCAAGAGTGAACTGAAGCACTCCATTAAGAAGCTACAGAAGAAGTCTGAGGAGCACAATGGCTCAGGTAACAAGGGAGACCAGACACAGTCCACTTTTAAACCCGTACAACCTTCGAAGAAGACCATTC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTCTGAGGAGCACAATGGC
60.04
CAAGGAGCTGGTCTCTGCTG
60.39
174
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGAGACCAGACACAGTCCAC
59.68
CAAGGAGCTGGTCTCTGCTG
60.39
142
PCR template sequence:
AAGCTACAGAAGAAGTCTGAGGAGCACAATGGCTCAGGTAACAAGGGAGACCAGACACAGTCCACTTTTAAACCCGTACAACCTTCGAAGAAGACCATTCGATTCTATGAAGAGGAAGATGGAACAGCTGAGACAGGAGTATATGGAAATGAAGGCTGTCATCGACGCAGCAGAGACCAGCTCCTTGCGCAAGTTAAAGG
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-205-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
AAGAAGACCATTCGATTCTATGAAGA
siRNA sets
TTCATAGAATCGAATGGTC, TCTTCATAGAATCGAATGG, CTTCATAGAATCGAATGGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTRIM25_466_ORF_1
1.0981
0.378071453
0.94519339
627
ORF sequence:
ATGAAGAGGAAGATGGAACAGCTGAGACAGGAGTATATGGAAATGAAGGCTGTCATCGACGCAGCAGAGACCAGCTCCTTGCGCAAGTTAAAGGAGGAGGAGAAGAGAGTCTACGGAAAATTCGACACCATCTACCAGGTTCTCGTCAAGAAGAAGAGTGAGATGCAGAAACTGAAGGCAGAGGTTGAGCTCATTATGGACAAAGGGGATGAGTTTGAGTTTCTGGAGAAAGCTGCAAAATTGCAAGGAGAGTCAACAAAACCAGTCTACATCCCTAAGATAGATCTGGATCATGATTTGATAATGGGAATCTACCAAGGGGCGGCGGACCTCAAGAGTGAACTGAAGCACTCCATTAAGAAGCTACAGAAGAAGTCTGAGGAGCACAATGGCTCAGGTAACAAGGGAGACCAGACACAGTCCACTTTTAAACCCGTACAACCTTCGAAGAAGACCATTCGATTCTATGAAGAGGAAGATGGAACAGCTGAGACAGGAGTATATGGAAATGAAGGCTGTCATCGACGCAGCAGAGACCAGCTCCTTGCGCAAGTTAAAGGAGGAGGAGAAGAGAGTCTACGGAAAATTCGACACCATCTACCAGGTTCTCGTCAAGAAGAAGAGTGA
Peptide sequence:
MKRKMEQLRQEYMEMKAVIDAAETSSLRKLKEEEKRVYGKFDTIYQVLVKKKSEMQKLKAEVELIMDKGDEFEFLEKAAKLQGESTKPVYIPKIDLDHDLIMGIYQGAADLKSELKHSIKKLQKKSEEHNGSGNKGDQTQSTFKPVQPSKKTIRFYEEEDGTAETGVYGNEGCHRRSRDQLLAQVKGGGEESLRKIRHHLPGSRQEEE
IRESfinder result
IRESfinder score
0.383959435
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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