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mmu_circLsg1_624
Basic information of circular RNA
PanCircBase ID:
mmu_circLsg1_624
mm39_Chr. Position ID:
chr16|30383463|30388248|-
Gene name:
Lsg1
Transcript:
ENSMUST00000117363.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
13,12,11,10,9
Exon/intron offsets:
0,784,3065,4459,4683
Genomic length:
4785
Exon/intron sizes in nt:
1,74,80,12,41,44,102
Flanking exon/introns:
chr16:30380680-30383463|chr16:30388248-30389982
Splice length:
624
Other database IDs:
circAtlas: mmu-Lsg1_0019
Human Ortholog IDs:
Mature spliced Sequence:
GTGGGCTACCCTAATGTTGGTAAGAGCTCAACCATCAACACCATCATGGGCAACAAGAAAGTATCGGTGTCTGCCACGCCAGGCCACACCAAGCATTTCCAGACCCTGTACGTGGAGCCTGGCCTCTGCCTGTGTGACTGCCCGGGCCTGGTGATGCCATCTTTCGTGTCCACCAAAGCAGAGATGATTTGCAATGGGATCCTCCCTATCGACCAGATGAGAGACCACGTTCCACCCGTATCACTAGTTTGCCAGAATATCCCACGGCGAGTTTTGGAAGTGACATATGGTATTAACATTATAAAGCCTAGAGAAGATGAAGACCCCTACCGACCTCCAACCTCAGAAGAACTGTTGACGGCTTATGGATGCATGAGAGGATTCATGACAGCACATGGGCAGCCAGACCAGCCTCGATCTGCACGGTACATCCTAAAGGACTATGTTGGAGGTAAACTACTGTATTGCCACCCTCCTCCTGGAAAAGACCCTGTGGCGTTCCAGCACCAACACCAGCAGCTCCTAGAGAGCAAAGTAAAAGGTGGAGAACTGAGACTTCAGCCGGGCAAAGGCCGAAAAGCCAAACAGATCGAAAATGTAGTCGACAAAACTTTTTTCCATCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGACTTCAGCCGGGCAAAG
61.3
GAAATGCTTGGTGTGGCCTG
60.04
172
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGACTTCAGCCGGGCAAA
60.3
GAAATGCTTGGTGTGGCCTG
60.04
172
PCR template sequence:
AGAGAGCAAAGTAAAAGGTGGAGAACTGAGACTTCAGCCGGGCAAAGGCCGAAAAGCCAAACAGATCGAAAATGTAGTCGACAAAACTTTTTTCCATCAGGTGGGCTACCCTAATGTTGGTAAGAGCTCAACCATCAACACCATCATGGGCAACAAGAAAGTATCGGTGTCTGCCACGCCAGGCCACACCAAGCATTTCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-298-5p(1), mmu-miR-138-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTTTTCCATCAGGTGGGCTACCCTA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCLSG1_624_ORF_1
1.0163
0.261965637
0.998290726
1203
ORF sequence:
ATGGGCAACAAGAAAGTATCGGTGTCTGCCACGCCAGGCCACACCAAGCATTTCCAGACCCTGTACGTGGAGCCTGGCCTCTGCCTGTGTGACTGCCCGGGCCTGGTGATGCCATCTTTCGTGTCCACCAAAGCAGAGATGATTTGCAATGGGATCCTCCCTATCGACCAGATGAGAGACCACGTTCCACCCGTATCACTAGTTTGCCAGAATATCCCACGGCGAGTTTTGGAAGTGACATATGGTATTAACATTATAAAGCCTAGAGAAGATGAAGACCCCTACCGACCTCCAACCTCAGAAGAACTGTTGACGGCTTATGGATGCATGAGAGGATTCATGACAGCACATGGGCAGCCAGACCAGCCTCGATCTGCACGGTACATCCTAAAGGACTATGTTGGAGGTAAACTACTGTATTGCCACCCTCCTCCTGGAAAAGACCCTGTGGCGTTCCAGCACCAACACCAGCAGCTCCTAGAGAGCAAAGTAAAAGGTGGAGAACTGAGACTTCAGCCGGGCAAAGGCCGAAAAGCCAAACAGATCGAAAATGTAGTCGACAAAACTTTTTTCCATCAGGTGGGCTACCCTAATGTTGGTAAGAGCTCAACCATCAACACCATCATGGGCAACAAGAAAGTATCGGTGTCTGCCACGCCAGGCCACACCAAGCATTTCCAGACCCTGTACGTGGAGCCTGGCCTCTGCCTGTGTGACTGCCCGGGCCTGGTGATGCCATCTTTCGTGTCCACCAAAGCAGAGATGATTTGCAATGGGATCCTCCCTATCGACCAGATGAGAGACCACGTTCCACCCGTATCACTAGTTTGCCAGAATATCCCACGGCGAGTTTTGGAAGTGACATATGGTATTAACATTATAAAGCCTAGAGAAGATGAAGACCCCTACCGACCTCCAACCTCAGAAGAACTGTTGACGGCTTATGGATGCATGAGAGGATTCATGACAGCACATGGGCAGCCAGACCAGCCTCGATCTGCACGGTACATCCTAAAGGACTATGTTGGAGGTAAACTACTGTATTGCCACCCTCCTCCTGGAAAAGACCCTGTGGCGTTCCAGCACCAACACCAGCAGCTCCTAGAGAGCAAAGTAAAAGGTGGAGAACTGAGACTTCAGCCGGGCAAAGGCCGAAAAGCCAAACAGATCGAAAATGTAGTCGACAAAACTTTTTTCCATCAG
Peptide sequence:
MGNKKVSVSATPGHTKHFQTLYVEPGLCLCDCPGLVMPSFVSTKAEMICNGILPIDQMRDHVPPVSLVCQNIPRRVLEVTYGINIIKPREDEDPYRPPTSEELLTAYGCMRGFMTAHGQPDQPRSARYILKDYVGGKLLYCHPPPGKDPVAFQHQHQQLLESKVKGGELRLQPGKGRKAKQIENVVDKTFFHQVGYPNVGKSSTINTIMGNKKVSVSATPGHTKHFQTLYVEPGLCLCDCPGLVMPSFVSTKAEMICNGILPIDQMRDHVPPVSLVCQNIPRRVLEVTYGINIIKPREDEDPYRPPTSEELLTAYGCMRGFMTAHGQPDQPRSARYILKDYVGGKLLYCHPPPGKDPVAFQHQHQQLLESKVKGGELRLQPGKGRKAKQIENVVDKTFFHQ
IRESfinder result
IRESfinder score
0.44458706
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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