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mmu_circLrch3_552
Basic information of circular RNA
PanCircBase ID:
mmu_circLrch3_552
mm39_Chr. Position ID:
chr16|32814131|32826111|+
Gene name:
Lrch3
Transcript:
ENSMUST00000023491.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
15,16,17,18,19,20
Exon/intron offsets:
0,1186,2044,3620,4742,11902
Genomic length:
11980
Exon/intron sizes in nt:
72,49,108,107,138,78
Flanking exon/introns:
chr16:32810688-32814131|chr16:32826111-32832710
Splice length:
552
Other database IDs:
circAtlas: mmu-Lrch3_0054
circBase: hsa_circ_0068761, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_45146
Human Ortholog IDs:
Mature spliced Sequence:
TCACTGTCAGGGTTGGATGGAGTGAGCTGCGTGGCTACCCGGCCTCATTCTTCTGCCTTCACACCTCTCAAGAGCGAAAACAGAGTTGATGTCACCTCAAGCTTTCCTATGACAGAGACAGTCCATCATTCCCCTGCGTATTCCTTTCCTGCTGCTACCCAGAGAAATCAGCCCCAGCGCCCTGAAAGCTTCCTTTTCCGAGCTGCTGTCAGGGCAGAAGCTAATAAAGGTCGTGCATCCCCGCTTCTCCTGTCATCTGCACCTGCAACTGATCCTACAGATGCTATAACAAGACAGAGAGAAGAAGAGCTGAAATTAATAGATCAGCTACGAAAACACATTGAGTACCGGTTGAAAGTCTCTTTGCCCTGTGACCTTGGAGCAGCTCTAACTGACGGTGTTGTACTTTGCCACTTGGCCAATCATGTTCGGCCTCGATCTGTCCCAAGCATTCATGTCCCATCCCCAGCCGTGCCTAAATTAACGATGGCAAAGTGCAGGCGGAATGTGGAGAACTTCCTGGATGCTTGCAGAAAAATCGGTGTACCCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCCAGCCGTGCCTAAATTA
60.11
GAAGAATGAGGCCGGGTAGC
60.53
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCCCAGCCGTGCCTAAATTA
60.11
CAGAAGAATGAGGCCGGGTA
59.17
144
PCR template sequence:
TCATGTCCCATCCCCAGCCGTGCCTAAATTAACGATGGCAAAGTGCAGGCGGAATGTGGAGAACTTCCTGGATGCTTGCAGAAAAATCGGTGTACCCCAGTCACTGTCAGGGTTGGATGGAGTGAGCTGCGTGGCTACCCGGCCTCATTCTTCTGCCTTCACACCTCTCAAGAGCGAAAACAGAGTTGATGTCACCTCAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-141-3p(1), mmu-miR-214-3p(1), mmu-miR-503-5p(1), mmu-miR-1198-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CGGTGTACCCCAGTCACTGTCAGGGT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCLRCH3_552_ORF_1
1.048
0.122215495
0.987471528
996
ORF sequence:
ATGACAGAGACAGTCCATCATTCCCCTGCGTATTCCTTTCCTGCTGCTACCCAGAGAAATCAGCCCCAGCGCCCTGAAAGCTTCCTTTTCCGAGCTGCTGTCAGGGCAGAAGCTAATAAAGGTCGTGCATCCCCGCTTCTCCTGTCATCTGCACCTGCAACTGATCCTACAGATGCTATAACAAGACAGAGAGAAGAAGAGCTGAAATTAATAGATCAGCTACGAAAACACATTGAGTACCGGTTGAAAGTCTCTTTGCCCTGTGACCTTGGAGCAGCTCTAACTGACGGTGTTGTACTTTGCCACTTGGCCAATCATGTTCGGCCTCGATCTGTCCCAAGCATTCATGTCCCATCCCCAGCCGTGCCTAAATTAACGATGGCAAAGTGCAGGCGGAATGTGGAGAACTTCCTGGATGCTTGCAGAAAAATCGGTGTACCCCAGTCACTGTCAGGGTTGGATGGAGTGAGCTGCGTGGCTACCCGGCCTCATTCTTCTGCCTTCACACCTCTCAAGAGCGAAAACAGAGTTGATGTCACCTCAAGCTTTCCTATGACAGAGACAGTCCATCATTCCCCTGCGTATTCCTTTCCTGCTGCTACCCAGAGAAATCAGCCCCAGCGCCCTGAAAGCTTCCTTTTCCGAGCTGCTGTCAGGGCAGAAGCTAATAAAGGTCGTGCATCCCCGCTTCTCCTGTCATCTGCACCTGCAACTGATCCTACAGATGCTATAACAAGACAGAGAGAAGAAGAGCTGAAATTAATAGATCAGCTACGAAAACACATTGAGTACCGGTTGAAAGTCTCTTTGCCCTGTGACCTTGGAGCAGCTCTAACTGACGGTGTTGTACTTTGCCACTTGGCCAATCATGTTCGGCCTCGATCTGTCCCAAGCATTCATGTCCCATCCCCAGCCGTGCCTAAATTAACGATGGCAAAGTGCAGGCGGAATGTGGAGAACTTCCTGGATGCTTGCAGAAAAATCGGTGTACCCCAG
Peptide sequence:
MTETVHHSPAYSFPAATQRNQPQRPESFLFRAAVRAEANKGRASPLLLSSAPATDPTDAITRQREEELKLIDQLRKHIEYRLKVSLPCDLGAALTDGVVLCHLANHVRPRSVPSIHVPSPAVPKLTMAKCRRNVENFLDACRKIGVPQSLSGLDGVSCVATRPHSSAFTPLKSENRVDVTSSFPMTETVHHSPAYSFPAATQRNQPQRPESFLFRAAVRAEANKGRASPLLLSSAPATDPTDAITRQREEELKLIDQLRKHIEYRLKVSLPCDLGAALTDGVVLCHLANHVRPRSVPSIHVPSPAVPKLTMAKCRRNVENFLDACRKIGVPQ
IRESfinder result
IRESfinder score
0.498853164
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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