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mmu_circLimch1_1650
Basic information of circular RNA
PanCircBase ID:
mmu_circLimch1_1650
mm39_Chr. Position ID:
chr5|67111011|67159992|+
Gene name:
Limch1
Transcript:
ENSMUST00000101164.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
4,5,6,7,8,9,10,11,12,13
Exon/intron offsets:
0,5919,7488,15407,20741,39474,43451,44978,45311,48759
Genomic length:
48981
Exon/intron sizes in nt:
1,07,31,11,11,96,25,33,00,00,00,00,00,000
Flanking exon/introns:
chr5:67039311-67111011|chr5:67159992-67173807
Splice length:
1650
Other database IDs:
circBase: hsa_circ_0126373, circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GACAATACCATCTTATTCTTGAGAGGCTGTAAGGAGCTTGGCCTTAAAGAATCTCAACTCTTTGACCCGAGTGACCTCCAGGATACCTCCAACAGGGTCACTGTCAAGAACCTCGATTATAGCAGGAAGCTGAAAAACGTGCTAGTGACCATTTACTGGCTGGGGAAAGCTGCAAACAGCTGTGCATCCTACGGTGGAACCACACTGAACCTGAAGGAGTTTGAAGGGCTGTTGGCTCAGATGCGAAAGGAGACTGACGACATTGATAGCCCGAAGCGCAGCATCCGAGACAGTGGCTACATCGACTGCTGGGACTCTGAACGCAGCGACTCCCTCTCTCCTCCTCGCCACGGACGGGATGACTCCTTTGACAGCCTGGATTCTTTTGGCTCCCGCTCCAGGCAGACACCTTCGCCAGATGTAGTTCTCAGGGGAAGCAGTGATGGAAGAGGAAGCGATTCTGAATCAGACTTGCCGCACCGGAAGTTGCCAGATGTGAAGAAAGATGATATGTCCGCACGAAGGACTTCTCATGGTGAGCCGAAATCAGCAGTGCCTTTTAACCAGTACCTCCCGAACAAAAGCAACCAGACGGCCTACGTCCCGGCGCCTCTGAGAAAGAAGAAGGCGGAGCGGGAGGAATTCAGGAAGAGTTGGAGCACCGCCACCTCCCCCCTGGGTGGGGAAAGGCCCTTCAGATACGGTCCCAGAACTCCTGTGTCAGATGACGCAGAGAGCACGAGTATGTTTGACATGCGGTGTGAGGAGGAGGCAGCGGTGCTGCCGCACAGCAGGGCCCGCCAGGAGCAGCTGCAGCTGATAAATAACCAGCTGAGGGAAGAGGACGACAAATGGCAAGATGACCTGGCTCGCTGGAAGAGCCGGAGAAGAAGCGCTTCTCAGGACTTGATCAAGAAAGAGGAAGAAAGGAAAAAAATGGAGAAGCTGATGTCTGGGGAAGATGGGACAAGTGAGCGGAGGAAAAGCATCAAAACTTACAGAGAAATCGTCCAAGAAAAAGAGCGGAGAGAGAGGGAACTTCATGAGGCGTACAAGAACGCAAGGTCGCAGGAGGAGGCCGAGGGGATCCTCCAGCAGTACATCGAGAGGTTCACCATCAGTGAGGCTGTCCTCGAACGCTTGGAGATGCCAAAAATCCTGGAAAGAAGCCATTCAACAGAGCCAAACGTGTCCTCCTTCCCAAACGACCCCAGCCCCATGAAGTACCTGCGGCAGCAGTCACTGCCCCCACCCAAGTTCACTGCCACGGTTGAGACCACCATAGCTCGCACCAGTGTCCCAGAGAGCATTGCGTCAGCAGGCACTGGGTCTCCAAGCAAAATCATCACTCCAAACACAGTGCCTATGCTGACACCCAGGCCTTACTCCCAGCCCAAAAACTCTCAAGAGGTTCTGAAGACTTTTAAGGTAGATGGGAAGGTCAGCATGAATGGGGAAATGGCCCCTGGAGATGAGGAAGGAAAGGAAAAAGAAGGCCCTGCAGCTGCAGCCCCTGGCCCTTCCTTAACCAAGTCCCAGATGTTTGAAGGTGTGGCCACGGTGCACGACTCTCCTGTGCAGGTGAAACAAGGCAGCAACAGCATCGAGATCAACATCAAGAAGCCAAATTCTGCTCCCCAGGAACTGACA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGCAGGTGAAACAAGGCAG
59.97
GGAGGTCACTCGGGTCAAAG
60.04
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGTGCAGGTGAAACAAGGC
59.97
GGAGGTCACTCGGGTCAAAG
60.04
156
PCR template sequence:
TGTGGCCACGGTGCACGACTCTCCTGTGCAGGTGAAACAAGGCAGCAACAGCATCGAGATCAACATCAAGAAGCCAAATTCTGCTCCCCAGGAACTGACAGACAATACCATCTTATTCTTGAGAGGCTGTAAGGAGCTTGGCCTTAAAGAATCTCAACTCTTTGACCCGAGTGACCTCCAGGATACCTCCAACAGGGTCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
17
Interacting miRNAs (#binding sites)
mmu-miR-34a-5p(2), mmu-miR-140-5p(1), mmu-miR-134-5p(1), mmu-miR-135a-5p(1), mmu-miR-34c-5p(1), mmu-miR-222-3p(1), mmu-miR-125b-5p(1), mmu-miR-185-5p(1), mmu-miR-136-5p(1), mmu-miR-351-5p(1), mmu-miR-125a-5p(1), mmu-miR-370-3p(1), mmu-miR-34b-5p(1), mmu-miR-690(1), mmu-miR-342-3p(1), mmu-miR-207(1), mmu-miR-452-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCAGGAACTGACAGACAATACCATCT
siRNA sets
TATTGTCTGTCAGTTCCTG, GTATTGTCTGTCAGTTCCT, ATGGTATTGTCTGTCAGTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCLIMCH1_1650_ORF_1
0.8647
0.396202988
0.999999998
3060
ORF sequence:
ATGCGAAAGGAGACTGACGACATTGATAGCCCGAAGCGCAGCATCCGAGACAGTGGCTACATCGACTGCTGGGACTCTGAACGCAGCGACTCCCTCTCTCCTCCTCGCCACGGACGGGATGACTCCTTTGACAGCCTGGATTCTTTTGGCTCCCGCTCCAGGCAGACACCTTCGCCAGATGTAGTTCTCAGGGGAAGCAGTGATGGAAGAGGAAGCGATTCTGAATCAGACTTGCCGCACCGGAAGTTGCCAGATGTGAAGAAAGATGATATGTCCGCACGAAGGACTTCTCATGGTGAGCCGAAATCAGCAGTGCCTTTTAACCAGTACCTCCCGAACAAAAGCAACCAGACGGCCTACGTCCCGGCGCCTCTGAGAAAGAAGAAGGCGGAGCGGGAGGAATTCAGGAAGAGTTGGAGCACCGCCACCTCCCCCCTGGGTGGGGAAAGGCCCTTCAGATACGGTCCCAGAACTCCTGTGTCAGATGACGCAGAGAGCACGAGTATGTTTGACATGCGGTGTGAGGAGGAGGCAGCGGTGCTGCCGCACAGCAGGGCCCGCCAGGAGCAGCTGCAGCTGATAAATAACCAGCTGAGGGAAGAGGACGACAAATGGCAAGATGACCTGGCTCGCTGGAAGAGCCGGAGAAGAAGCGCTTCTCAGGACTTGATCAAGAAAGAGGAAGAAAGGAAAAAAATGGAGAAGCTGATGTCTGGGGAAGATGGGACAAGTGAGCGGAGGAAAAGCATCAAAACTTACAGAGAAATCGTCCAAGAAAAAGAGCGGAGAGAGAGGGAACTTCATGAGGCGTACAAGAACGCAAGGTCGCAGGAGGAGGCCGAGGGGATCCTCCAGCAGTACATCGAGAGGTTCACCATCAGTGAGGCTGTCCTCGAACGCTTGGAGATGCCAAAAATCCTGGAAAGAAGCCATTCAACAGAGCCAAACGTGTCCTCCTTCCCAAACGACCCCAGCCCCATGAAGTACCTGCGGCAGCAGTCACTGCCCCCACCCAAGTTCACTGCCACGGTTGAGACCACCATAGCTCGCACCAGTGTCCCAGAGAGCATTGCGTCAGCAGGCACTGGGTCTCCAAGCAAAATCATCACTCCAAACACAGTGCCTATGCTGACACCCAGGCCTTACTCCCAGCCCAAAAACTCTCAAGAGGTTCTGAAGACTTTTAAGGTAGATGGGAAGGTCAGCATGAATGGGGAAATGGCCCCTGGAGATGAGGAAGGAAAGGAAAAAGAAGGCCCTGCAGCTGCAGCCCCTGGCCCTTCCTTAACCAAGTCCCAGATGTTTGAAGGTGTGGCCACGGTGCACGACTCTCCTGTGCAGGTGAAACAAGGCAGCAACAGCATCGAGATCAACATCAAGAAGCCAAATTCTGCTCCCCAGGAACTGACAGACAATACCATCTTATTCTTGAGAGGCTGTAAGGAGCTTGGCCTTAAAGAATCTCAACTCTTTGACCCGAGTGACCTCCAGGATACCTCCAACAGGGTCACTGTCAAGAACCTCGATTATAGCAGGAAGCTGAAAAACGTGCTAGTGACCATTTACTGGCTGGGGAAAGCTGCAAACAGCTGTGCATCCTACGGTGGAACCACACTGAACCTGAAGGAGTTTGAAGGGCTGTTGGCTCAGATGCGAAAGGAGACTGACGACATTGATAGCCCGAAGCGCAGCATCCGAGACAGTGGCTACATCGACTGCTGGGACTCTGAACGCAGCGACTCCCTCTCTCCTCCTCGCCACGGACGGGATGACTCCTTTGACAGCCTGGATTCTTTTGGCTCCCGCTCCAGGCAGACACCTTCGCCAGATGTAGTTCTCAGGGGAAGCAGTGATGGAAGAGGAAGCGATTCTGAATCAGACTTGCCGCACCGGAAGTTGCCAGATGTGAAGAAAGATGATATGTCCGCACGAAGGACTTCTCATGGTGAGCCGAAATCAGCAGTGCCTTTTAACCAGTACCTCCCGAACAAAAGCAACCAGACGGCCTACGTCCCGGCGCCTCTGAGAAAGAAGAAGGCGGAGCGGGAGGAATTCAGGAAGAGTTGGAGCACCGCCACCTCCCCCCTGGGTGGGGAAAGGCCCTTCAGATACGGTCCCAGAACTCCTGTGTCAGATGACGCAGAGAGCACGAGTATGTTTGACATGCGGTGTGAGGAGGAGGCAGCGGTGCTGCCGCACAGCAGGGCCCGCCAGGAGCAGCTGCAGCTGATAAATAACCAGCTGAGGGAAGAGGACGACAAATGGCAAGATGACCTGGCTCGCTGGAAGAGCCGGAGAAGAAGCGCTTCTCAGGACTTGATCAAGAAAGAGGAAGAAAGGAAAAAAATGGAGAAGCTGATGTCTGGGGAAGATGGGACAAGTGAGCGGAGGAAAAGCATCAAAACTTACAGAGAAATCGTCCAAGAAAAAGAGCGGAGAGAGAGGGAACTTCATGAGGCGTACAAGAACGCAAGGTCGCAGGAGGAGGCCGAGGGGATCCTCCAGCAGTACATCGAGAGGTTCACCATCAGTGAGGCTGTCCTCGAACGCTTGGAGATGCCAAAAATCCTGGAAAGAAGCCATTCAACAGAGCCAAACGTGTCCTCCTTCCCAAACGACCCCAGCCCCATGAAGTACCTGCGGCAGCAGTCACTGCCCCCACCCAAGTTCACTGCCACGGTTGAGACCACCATAGCTCGCACCAGTGTCCCAGAGAGCATTGCGTCAGCAGGCACTGGGTCTCCAAGCAAAATCATCACTCCAAACACAGTGCCTATGCTGACACCCAGGCCTTACTCCCAGCCCAAAAACTCTCAAGAGGTTCTGAAGACTTTTAAGGTAGATGGGAAGGTCAGCATGAATGGGGAAATGGCCCCTGGAGATGAGGAAGGAAAGGAAAAAGAAGGCCCTGCAGCTGCAGCCCCTGGCCCTTCCTTAACCAAGTCCCAGATGTTTGAAGGTGTGGCCACGGTGCACGACTCTCCTGTGCAGGTGAAACAAGGCAGCAACAGCATCGAGATCAACATCAAGAAGCCAAATTCTGCTCCCCAGGAACTGACA
Peptide sequence:
MRKETDDIDSPKRSIRDSGYIDCWDSERSDSLSPPRHGRDDSFDSLDSFGSRSRQTPSPDVVLRGSSDGRGSDSESDLPHRKLPDVKKDDMSARRTSHGEPKSAVPFNQYLPNKSNQTAYVPAPLRKKKAEREEFRKSWSTATSPLGGERPFRYGPRTPVSDDAESTSMFDMRCEEEAAVLPHSRARQEQLQLINNQLREEDDKWQDDLARWKSRRRSASQDLIKKEEERKKMEKLMSGEDGTSERRKSIKTYREIVQEKERRERELHEAYKNARSQEEAEGILQQYIERFTISEAVLERLEMPKILERSHSTEPNVSSFPNDPSPMKYLRQQSLPPPKFTATVETTIARTSVPESIASAGTGSPSKIITPNTVPMLTPRPYSQPKNSQEVLKTFKVDGKVSMNGEMAPGDEEGKEKEGPAAAAPGPSLTKSQMFEGVATVHDSPVQVKQGSNSIEINIKKPNSAPQELTDNTILFLRGCKELGLKESQLFDPSDLQDTSNRVTVKNLDYSRKLKNVLVTIYWLGKAANSCASYGGTTLNLKEFEGLLAQMRKETDDIDSPKRSIRDSGYIDCWDSERSDSLSPPRHGRDDSFDSLDSFGSRSRQTPSPDVVLRGSSDGRGSDSESDLPHRKLPDVKKDDMSARRTSHGEPKSAVPFNQYLPNKSNQTAYVPAPLRKKKAEREEFRKSWSTATSPLGGERPFRYGPRTPVSDDAESTSMFDMRCEEEAAVLPHSRARQEQLQLINNQLREEDDKWQDDLARWKSRRRSASQDLIKKEEERKKMEKLMSGEDGTSERRKSIKTYREIVQEKERRERELHEAYKNARSQEEAEGILQQYIERFTISEAVLERLEMPKILERSHSTEPNVSSFPNDPSPMKYLRQQSLPPPKFTATVETTIARTSVPESIASAGTGSPSKIITPNTVPMLTPRPYSQPKNSQEVLKTFKVDGKVSMNGEMAPGDEEGKEKEGPAAAAPGPSLTKSQMFEGVATVHDSPVQVKQGSNSIEINIKKPNSAPQELT
IRESfinder result
IRESfinder score
0.307102768
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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