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mmu_circLimch1_952
Basic information of circular RNA
PanCircBase ID:
mmu_circLimch1_952
mm39_Chr. Position ID:
chr5|67150485|67159992|+
Gene name:
Limch1
Transcript:
ENSMUST00000101164.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
9,10,11,12,13
Exon/intron offsets:
0,3977,5504,5837,9285
Genomic length:
9507
Exon/intron sizes in nt:
3,61,27,15,84,09,222
Flanking exon/introns:
chr5:67132005-67150485|chr5:67159992-67173807
Splice length:
952
Other database IDs:
circAtlas: mmu-Limch1_0007
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_48650
Human Ortholog IDs:
Mature spliced Sequence:
ATACGGTCCCAGAACTCCTGTGTCAGATGACGCAGAGAGCACGAGTATGTTTGACATGCGGTGTGAGGAGGAGGCAGCGGTGCTGCCGCACAGCAGGGCCCGCCAGGAGCAGCTGCAGCTGATAAATAACCAGCTGAGGGAAGAGGACGACAAATGGCAAGATGACCTGGCTCGCTGGAAGAGCCGGAGAAGAAGCGCTTCTCAGGACTTGATCAAGAAAGAGGAAGAAAGGAAAAAAATGGAGAAGCTGATGTCTGGGGAAGATGGGACAAGTGAGCGGAGGAAAAGCATCAAAACTTACAGAGAAATCGTCCAAGAAAAAGAGCGGAGAGAGAGGGAACTTCATGAGGCGTACAAGAACGCAAGGTCGCAGGAGGAGGCCGAGGGGATCCTCCAGCAGTACATCGAGAGGTTCACCATCAGTGAGGCTGTCCTCGAACGCTTGGAGATGCCAAAAATCCTGGAAAGAAGCCATTCAACAGAGCCAAACGTGTCCTCCTTCCCAAACGACCCCAGCCCCATGAAGTACCTGCGGCAGCAGTCACTGCCCCCACCCAAGTTCACTGCCACGGTTGAGACCACCATAGCTCGCACCAGTGTCCCAGAGAGCATTGCGTCAGCAGGCACTGGGTCTCCAAGCAAAATCATCACTCCAAACACAGTGCCTATGCTGACACCCAGGCCTTACTCCCAGCCCAAAAACTCTCAAGAGGTTCTGAAGACTTTTAAGGTAGATGGGAAGGTCAGCATGAATGGGGAAATGGCCCCTGGAGATGAGGAAGGAAAGGAAAAAGAAGGCCCTGCAGCTGCAGCCCCTGGCCCTTCCTTAACCAAGTCCCAGATGTTTGAAGGTGTGGCCACGGTGCACGACTCTCCTGTGCAGGTGAAACAAGGCAGCAACAGCATCGAGATCAACATCAAGAAGCCAAATTCTGCTCCCCAGGAACTGACA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGCAGGTGAAACAAGGCAG
59.97
TCCTCACACCGCATGTCAAA
59.89
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGTGCAGGTGAAACAAGGC
59.97
TCCTCACACCGCATGTCAAA
59.89
146
PCR template sequence:
TGTGGCCACGGTGCACGACTCTCCTGTGCAGGTGAAACAAGGCAGCAACAGCATCGAGATCAACATCAAGAAGCCAAATTCTGCTCCCCAGGAACTGACAATACGGTCCCAGAACTCCTGTGTCAGATGACGCAGAGAGCACGAGTATGTTTGACATGCGGTGTGAGGAGGAGGCAGCGGTGCTGCCGCACAGCAGGGCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-34a-5p(2), mmu-miR-134-5p(1), mmu-miR-135a-5p(1), mmu-miR-34c-5p(1), mmu-miR-136-5p(1), mmu-miR-370-3p(1), mmu-miR-34b-5p(1), mmu-miR-342-3p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
CCAGGAACTGACAATACGGTCCCAGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCLIMCH1_952_ORF_1
1.1437
0.404920431
0.994776189
936
ORF sequence:
ATGTTTGACATGCGGTGTGAGGAGGAGGCAGCGGTGCTGCCGCACAGCAGGGCCCGCCAGGAGCAGCTGCAGCTGATAAATAACCAGCTGAGGGAAGAGGACGACAAATGGCAAGATGACCTGGCTCGCTGGAAGAGCCGGAGAAGAAGCGCTTCTCAGGACTTGATCAAGAAAGAGGAAGAAAGGAAAAAAATGGAGAAGCTGATGTCTGGGGAAGATGGGACAAGTGAGCGGAGGAAAAGCATCAAAACTTACAGAGAAATCGTCCAAGAAAAAGAGCGGAGAGAGAGGGAACTTCATGAGGCGTACAAGAACGCAAGGTCGCAGGAGGAGGCCGAGGGGATCCTCCAGCAGTACATCGAGAGGTTCACCATCAGTGAGGCTGTCCTCGAACGCTTGGAGATGCCAAAAATCCTGGAAAGAAGCCATTCAACAGAGCCAAACGTGTCCTCCTTCCCAAACGACCCCAGCCCCATGAAGTACCTGCGGCAGCAGTCACTGCCCCCACCCAAGTTCACTGCCACGGTTGAGACCACCATAGCTCGCACCAGTGTCCCAGAGAGCATTGCGTCAGCAGGCACTGGGTCTCCAAGCAAAATCATCACTCCAAACACAGTGCCTATGCTGACACCCAGGCCTTACTCCCAGCCCAAAAACTCTCAAGAGGTTCTGAAGACTTTTAAGGTAGATGGGAAGGTCAGCATGAATGGGGAAATGGCCCCTGGAGATGAGGAAGGAAAGGAAAAAGAAGGCCCTGCAGCTGCAGCCCCTGGCCCTTCCTTAACCAAGTCCCAGATGTTTGAAGGTGTGGCCACGGTGCACGACTCTCCTGTGCAGGTGAAACAAGGCAGCAACAGCATCGAGATCAACATCAAGAAGCCAAATTCTGCTCCCCAGGAACTGACAATACGGTCCCAGAACTCCTGTGTCAGATGA
Peptide sequence:
MFDMRCEEEAAVLPHSRARQEQLQLINNQLREEDDKWQDDLARWKSRRRSASQDLIKKEEERKKMEKLMSGEDGTSERRKSIKTYREIVQEKERRERELHEAYKNARSQEEAEGILQQYIERFTISEAVLERLEMPKILERSHSTEPNVSSFPNDPSPMKYLRQQSLPPPKFTATVETTIARTSVPESIASAGTGSPSKIITPNTVPMLTPRPYSQPKNSQEVLKTFKVDGKVSMNGEMAPGDEEGKEKEGPAAAAPGPSLTKSQMFEGVATVHDSPVQVKQGSNSIEINIKKPNSAPQELTIRSQNSCVR
IRESfinder result
IRESfinder score
0.254491855
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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