top of page
mmu_circLetm1_543
Basic information of circular RNA
PanCircBase ID:
mmu_circLetm1_543
mm39_Chr. Position ID:
chr5|33903583|33906217|-
Gene name:
Letm1
Transcript:
ENSMUST00000005431.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
11,10,9,8
Exon/intron offsets:
0,1136,1921,2502
Genomic length:
2634
Exon/intron sizes in nt:
1,35,13,51,41,132
Flanking exon/introns:
chr5:33902547-33903583|chr5:33906217-33909835
Splice length:
543
Other database IDs:
CIRCpedia: MMU_CIRCpedia_16969, circAtlas: mmu-Letm1_0003
circBase: hsa_circ_0068884, CIRCpedia: HSA_CIRCpedia_48005
Human Ortholog IDs:
Mature spliced Sequence:
TGGCTGGACTTGCACCTGCATCACGAGATCCCCACATCATTGCTCATACTGTCCCGGGCCATGTACCTCCCAGACACCCTCTCACCTGCTGACCAGCTGAAGTCCACCTTGCAGACCCTTCCAGAAATTGTGGCAAAGGAGGCCCAGGTGAAAGTGGCCGAGGTGGAGGGCGAAAAGGTAGACAACAAGGCGAAGCTGGAGGCCACACTGCAGGAAGAGGCCGCCATCCAGCAAGAACACCTGGAAGAACTAAAGAGAGCCTCTGAGGCTGTGAAGGACATCCAGCCAGAAGTAGCGGAAGCCACTCTCCCTGGGAGGCCAGGGCCTGAGCCTCAGCCTCCAGTGGATGATGTGATCCTGCCCTCAGAGGTCCTGACGGATACGGCACCTGTACTGGAAGGTCTGAAGGGTGAAGAGATTACCAAGGAGGAGATTGACATCCTCAGTGACGCCTGCTCCAAGCTGCAGGAGCAGAAGAAGTCCCTGACCAAGGAGAAGGAGGAGCTGGAGCTGCTCAAAGAGGACGTCCAGGACTACAGTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGGAGCAGAAGAAGTCCC
60.39
AGAGGGTGTCTGGGAGGTAC
59.96
161
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCAAGGAGAAGGAGGAGCT
59.88
GAGAGGGTGTCTGGGAGGTA
59.66
140
PCR template sequence:
CAGTGACGCCTGCTCCAAGCTGCAGGAGCAGAAGAAGTCCCTGACCAAGGAGAAGGAGGAGCTGGAGCTGCTCAAAGAGGACGTCCAGGACTACAGTGAGTGGCTGGACTTGCACCTGCATCACGAGATCCCCACATCATTGCTCATACTGTCCCGGGCCATGTACCTCCCAGACACCCTCTCACCTGCTGACCAGCTGA
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-1904(2), mmu-miR-9-5p(1), mmu-miR-207(1), mmu-miR-202-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGACTACAGTGAGTGGCTGGACTTGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCLETM1_543_ORF_1
1.1581
0.615458124
0.998893491
1026
ORF sequence:
ATGTACCTCCCAGACACCCTCTCACCTGCTGACCAGCTGAAGTCCACCTTGCAGACCCTTCCAGAAATTGTGGCAAAGGAGGCCCAGGTGAAAGTGGCCGAGGTGGAGGGCGAAAAGGTAGACAACAAGGCGAAGCTGGAGGCCACACTGCAGGAAGAGGCCGCCATCCAGCAAGAACACCTGGAAGAACTAAAGAGAGCCTCTGAGGCTGTGAAGGACATCCAGCCAGAAGTAGCGGAAGCCACTCTCCCTGGGAGGCCAGGGCCTGAGCCTCAGCCTCCAGTGGATGATGTGATCCTGCCCTCAGAGGTCCTGACGGATACGGCACCTGTACTGGAAGGTCTGAAGGGTGAAGAGATTACCAAGGAGGAGATTGACATCCTCAGTGACGCCTGCTCCAAGCTGCAGGAGCAGAAGAAGTCCCTGACCAAGGAGAAGGAGGAGCTGGAGCTGCTCAAAGAGGACGTCCAGGACTACAGTGAGTGGCTGGACTTGCACCTGCATCACGAGATCCCCACATCATTGCTCATACTGTCCCGGGCCATGTACCTCCCAGACACCCTCTCACCTGCTGACCAGCTGAAGTCCACCTTGCAGACCCTTCCAGAAATTGTGGCAAAGGAGGCCCAGGTGAAAGTGGCCGAGGTGGAGGGCGAAAAGGTAGACAACAAGGCGAAGCTGGAGGCCACACTGCAGGAAGAGGCCGCCATCCAGCAAGAACACCTGGAAGAACTAAAGAGAGCCTCTGAGGCTGTGAAGGACATCCAGCCAGAAGTAGCGGAAGCCACTCTCCCTGGGAGGCCAGGGCCTGAGCCTCAGCCTCCAGTGGATGATGTGATCCTGCCCTCAGAGGTCCTGACGGATACGGCACCTGTACTGGAAGGTCTGAAGGGTGAAGAGATTACCAAGGAGGAGATTGACATCCTCAGTGACGCCTGCTCCAAGCTGCAGGAGCAGAAGAAGTCCCTGACCAAGGAGAAGGAGGAGCTGGAGCTGCTCAAAGAGGACGTCCAGGACTACAGTGAG
Peptide sequence:
MYLPDTLSPADQLKSTLQTLPEIVAKEAQVKVAEVEGEKVDNKAKLEATLQEEAAIQQEHLEELKRASEAVKDIQPEVAEATLPGRPGPEPQPPVDDVILPSEVLTDTAPVLEGLKGEEITKEEIDILSDACSKLQEQKKSLTKEKEELELLKEDVQDYSEWLDLHLHHEIPTSLLILSRAMYLPDTLSPADQLKSTLQTLPEIVAKEAQVKVAEVEGEKVDNKAKLEATLQEEAAIQQEHLEELKRASEAVKDIQPEVAEATLPGRPGPEPQPPVDDVILPSEVLTDTAPVLEGLKGEEITKEEIDILSDACSKLQEQKKSLTKEKEELELLKEDVQDYSE
IRESfinder result
IRESfinder score
0.356300017
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page