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mmu_circLmbrd1_783
Basic information of circular RNA
PanCircBase ID:
mmu_circLmbrd1_783
mm39_Chr. Position ID:
chr1|24745057|24784051|+
Gene name:
Lmbrd1
Transcript:
ENSMUST00000191471.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
5,6,7,8,9,10,11,12
Exon/intron offsets:
0,5535,8932,22569,25770,37906,38279,38889
Genomic length:
38994
Exon/intron sizes in nt:
6,88,97,41,26,15,36,51,00,000
Flanking exon/introns:
chr1:24743999-24745057|chr1:24784051-24785885
Splice length:
783
Other database IDs:
circAtlas: mmu-Lmbrd1_0026
Human Ortholog IDs:
Mature spliced Sequence:
CAAATTAAAACGGCGCTCAAGTACACTTTGGGATTTGTTGTGATCTGCGCTCTGCTGCTTCTCGTTGGTGCCTTTGTGCCTCTGCATCTGCCCAACAACAACAACTCAACAGAGTGGGAAAAGGTGAAGCTCCTGTTTGAAGACCTTGGAACTGGTCAAGGCCTGGCAGCTCTGTCCTTTTCCATCAGCTCTCTGACCTTGATTGGGATGCTGGCGGCCATAACCTACACAGCGTACGGCATGTCGGCATTACCTTTAAACCTAATCAAAGGCACTAGAAGCACTGCCTACGAGCGCCTGGAGAACACGGAGGACATCGAGGAAGTGGAGCAGCACATTCAGACGATTCGATCCAAGAGCAAAGATGGTCGACCTTTGCCAGCGAGGGATAGACGTGCCTTAAAGCAATGTGAAGAAAGACTAAGAACGCTTAGGAAAAGAGAGCGGCACTTGGAATTCATTGAAAACAGCTGGTGGACGAAATTTTGTGGTGCCCTGCGCCCCCTGAAGATCATTTGGGGAATATTTTTCATCCTCGTTGCGTTGCTGTTTGTAATTTCTCTCTTCCTGTCAAATTTGGATAAAGCTCTTCATTCAGCAGGAATAGATTCGGGTTTCATCATCTTCGGAACTAACCTGAGCAATCCACTGAACATGCTTTTGCCGTTGTTACAAACAGTGTTCCCTCTTGATTACATTCTTATAACAATTATTATTATGTACTTTATTTTTACTTCGATGGCAGGAATTCGAAACATTGGCATTTGGTTCTTTTGGATTAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTTCGATGGCAGGAATTCGA
59.79
TGTTGTTGGGCAGATGCAGA
60.18
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTTCGATGGCAGGAATTCGA
59.79
GTTGTTGGGCAGATGCAGAG
59.48
150
PCR template sequence:
CCCTCTTGATTACATTCTTATAACAATTATTATTATGTACTTTATTTTTACTTCGATGGCAGGAATTCGAAACATTGGCATTTGGTTCTTTTGGATTAGGCAAATTAAAACGGCGCTCAAGTACACTTTGGGATTTGTTGTGATCTGCGCTCTGCTGCTTCTCGTTGGTGCCTTTGTGCCTCTGCATCTGCCCAACAACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(1), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-199a-5p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-15b-5p(1), mmu-miR-23a-3p(1), mmu-miR-22-3p(1), mmu-miR-370-3p(1), mmu-miR-34b-5p(1), mmu-miR-539-5p(1), mmu-miR-3470b(1), mmu-miR-540-3p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTTTTGGATTAGGCAAATTAAAACGG
siRNA sets
TTTTAATTTGCCTAATCCA, GTTTTAATTTGCCTAATCC, TAATTTGCCTAATCCAAAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCLMBRD1_783_ORF_1
0.9547
0.127667463
0.998914528
1359
ORF sequence:
ATGCTGGCGGCCATAACCTACACAGCGTACGGCATGTCGGCATTACCTTTAAACCTAATCAAAGGCACTAGAAGCACTGCCTACGAGCGCCTGGAGAACACGGAGGACATCGAGGAAGTGGAGCAGCACATTCAGACGATTCGATCCAAGAGCAAAGATGGTCGACCTTTGCCAGCGAGGGATAGACGTGCCTTAAAGCAATGTGAAGAAAGACTAAGAACGCTTAGGAAAAGAGAGCGGCACTTGGAATTCATTGAAAACAGCTGGTGGACGAAATTTTGTGGTGCCCTGCGCCCCCTGAAGATCATTTGGGGAATATTTTTCATCCTCGTTGCGTTGCTGTTTGTAATTTCTCTCTTCCTGTCAAATTTGGATAAAGCTCTTCATTCAGCAGGAATAGATTCGGGTTTCATCATCTTCGGAACTAACCTGAGCAATCCACTGAACATGCTTTTGCCGTTGTTACAAACAGTGTTCCCTCTTGATTACATTCTTATAACAATTATTATTATGTACTTTATTTTTACTTCGATGGCAGGAATTCGAAACATTGGCATTTGGTTCTTTTGGATTAGGCAAATTAAAACGGCGCTCAAGTACACTTTGGGATTTGTTGTGATCTGCGCTCTGCTGCTTCTCGTTGGTGCCTTTGTGCCTCTGCATCTGCCCAACAACAACAACTCAACAGAGTGGGAAAAGGTGAAGCTCCTGTTTGAAGACCTTGGAACTGGTCAAGGCCTGGCAGCTCTGTCCTTTTCCATCAGCTCTCTGACCTTGATTGGGATGCTGGCGGCCATAACCTACACAGCGTACGGCATGTCGGCATTACCTTTAAACCTAATCAAAGGCACTAGAAGCACTGCCTACGAGCGCCTGGAGAACACGGAGGACATCGAGGAAGTGGAGCAGCACATTCAGACGATTCGATCCAAGAGCAAAGATGGTCGACCTTTGCCAGCGAGGGATAGACGTGCCTTAAAGCAATGTGAAGAAAGACTAAGAACGCTTAGGAAAAGAGAGCGGCACTTGGAATTCATTGAAAACAGCTGGTGGACGAAATTTTGTGGTGCCCTGCGCCCCCTGAAGATCATTTGGGGAATATTTTTCATCCTCGTTGCGTTGCTGTTTGTAATTTCTCTCTTCCTGTCAAATTTGGATAAAGCTCTTCATTCAGCAGGAATAGATTCGGGTTTCATCATCTTCGGAACTAACCTGAGCAATCCACTGAACATGCTTTTGCCGTTGTTACAAACAGTGTTCCCTCTTGATTACATTCTTATAACAATTATTATTATGTACTTTATTTTTACTTCGATGGCAGGAATTCGAAACATTGGCATTTGGTTCTTTTGGATTAGG
Peptide sequence:
MLAAITYTAYGMSALPLNLIKGTRSTAYERLENTEDIEEVEQHIQTIRSKSKDGRPLPARDRRALKQCEERLRTLRKRERHLEFIENSWWTKFCGALRPLKIIWGIFFILVALLFVISLFLSNLDKALHSAGIDSGFIIFGTNLSNPLNMLLPLLQTVFPLDYILITIIIMYFIFTSMAGIRNIGIWFFWIRQIKTALKYTLGFVVICALLLLVGAFVPLHLPNNNNSTEWEKVKLLFEDLGTGQGLAALSFSISSLTLIGMLAAITYTAYGMSALPLNLIKGTRSTAYERLENTEDIEEVEQHIQTIRSKSKDGRPLPARDRRALKQCEERLRTLRKRERHLEFIENSWWTKFCGALRPLKIIWGIFFILVALLFVISLFLSNLDKALHSAGIDSGFIIFGTNLSNPLNMLLPLLQTVFPLDYILITIIIMYFIFTSMAGIRNIGIWFFWIR
IRESfinder result
IRESfinder score
0.671143447
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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