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mmu_circTrim25_499
Basic information of circular RNA
PanCircBase ID:
mmu_circTrim25_499
mm39_Chr. Position ID:
chr11|88895554|88901799|+
Gene name:
Trim25
Transcript:
ENSMUST00000100627.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
2,3,4
Exon/intron offsets:
0,4390,6076
Genomic length:
6245
Exon/intron sizes in nt:
9,62,34,169
Flanking exon/introns:
chr11:88890908-88895554|chr11:88901799-88904301
Splice length:
499
Other database IDs:
circAtlas: mmu-Trim25_0004
Human Ortholog IDs:
Mature spliced Sequence:
TACAAACTGAGGAATAAACTCACTATCATGCACAGCCACATCAATGGGGCAACCAAAGCATTGGAGGATGTGAGATCCAAGCAACAGTGTGTGCAGGATTCTATGAAGAGGAAGATGGAACAGCTGAGACAGGAGTATATGGAAATGAAGGCTGTCATCGACGCAGCAGAGACCAGCTCCTTGCGCAAGTTAAAGGAGGAGGAGAAGAGAGTCTACGGAAAATTCGACACCATCTACCAGGTTCTCGTCAAGAAGAAGAGTGAGATGCAGAAACTGAAGGCAGAGGTTGAGCTCATTATGGACAAAGGGGATGAGTTTGAGTTTCTGGAGAAAGCTGCAAAATTGCAAGGAGAGTCAACAAAACCAGTCTACATCCCTAAGATAGATCTGGATCATGATTTGATAATGGGAATCTACCAAGGGGCGGCGGACCTCAAGAGTGAACTGAAGCACTCCATTAAGAAGCTACAGAAGAAGTCTGAGGAGCACAATGGCTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCGGACCTCAAGAGTGAACT
59.68
ATCCTGCACACACTGTTGCT
60.18
172
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCGGACCTCAAGAGTGAACT
59.68
CTGCACACACTGTTGCTTGG
60.25
169
PCR template sequence:
TTGATAATGGGAATCTACCAAGGGGCGGCGGACCTCAAGAGTGAACTGAAGCACTCCATTAAGAAGCTACAGAAGAAGTCTGAGGAGCACAATGGCTCAGTACAAACTGAGGAATAAACTCACTATCATGCACAGCCACATCAATGGGGCAACCAAAGCATTGGAGGATGTGAGATCCAAGCAACAGTGTGTGCAGGATT
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-9-5p(1), mmu-miR-205-5p(1), mmu-miR-207(1), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
CACAATGGCTCAGTACAAACTGAGGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTRIM25_499_ORF_1
1.2061
0.430406574
0.916437639
507
ORF sequence:
ATGGCTCAGTACAAACTGAGGAATAAACTCACTATCATGCACAGCCACATCAATGGGGCAACCAAAGCATTGGAGGATGTGAGATCCAAGCAACAGTGTGTGCAGGATTCTATGAAGAGGAAGATGGAACAGCTGAGACAGGAGTATATGGAAATGAAGGCTGTCATCGACGCAGCAGAGACCAGCTCCTTGCGCAAGTTAAAGGAGGAGGAGAAGAGAGTCTACGGAAAATTCGACACCATCTACCAGGTTCTCGTCAAGAAGAAGAGTGAGATGCAGAAACTGAAGGCAGAGGTTGAGCTCATTATGGACAAAGGGGATGAGTTTGAGTTTCTGGAGAAAGCTGCAAAATTGCAAGGAGAGTCAACAAAACCAGTCTACATCCCTAAGATAGATCTGGATCATGATTTGATAATGGGAATCTACCAAGGGGCGGCGGACCTCAAGAGTGAACTGAAGCACTCCATTAAGAAGCTACAGAAGAAGTCTGAGGAGCACAATGGCTCA
Peptide sequence:
MAQYKLRNKLTIMHSHINGATKALEDVRSKQQCVQDSMKRKMEQLRQEYMEMKAVIDAAETSSLRKLKEEEKRVYGKFDTIYQVLVKKKSEMQKLKAEVELIMDKGDEFEFLEKAAKLQGESTKPVYIPKIDLDHDLIMGIYQGAADLKSELKHSIKKLQKKSEEHNGS
IRESfinder result
IRESfinder score
0.351523381
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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