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mmu_circLpgat1_723
Basic information of circular RNA
PanCircBase ID:
mmu_circLpgat1_723
mm39_Chr. Position ID:
chr1|191481651|191508541|+
Gene name:
Lpgat1
Transcript:
ENSMUST00000110855.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
3,4,5,6,7
Exon/intron offsets:
0,6392,10434,14005,26783
Genomic length:
26890
Exon/intron sizes in nt:
1,19,96,27,41,27,107
Flanking exon/introns:
chr1:191451730-191481651|chr1:191508541-191510494
Splice length:
723
Other database IDs:
CIRCpedia: MMU_CIRCpedia_215271, circAtlas: mmu-Lpgat1_0006
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_160074
Human Ortholog IDs:
Mature spliced Sequence:
TGATGGAATGGGGGGAAGATATTAAAGCAATCGCTAAAGATGAAGCAGTGATGTTGGTGAACCACCAGGCAACTGGAGATGTGTGTACATTGATGATGTGCCTACAGGATAAAGGACCGGTTGTCGCTCAGATGATGTGGCTGATGGATCATATTTTCAAGTATACAAACTTTGGAATTGTTTCTCTTATTCATGGAGACTTCTTTATAAGACAGGGAAGAGCCTACCGCGACCAACAGCTGCTGGTTCTCAAGAAGCACCTTGAACATAATTACAGGAGCAGAGATCGAAAATGGATCGTTTTGTTTCCGGAAGGGGGCTTCCTCAGGAAGAGGCGAGAAACAAGCCAGGCATTTGCCAAGAAAAATAACTTGCCATTTCTTACACATGTCACTTTGCCAAGGTTTGGGGCAACAAACATTATTTTGAAGGCACTTGTAGCACGGCAGGAAAATGGAAGCCCAGCAGGAGGAGACGCTAGAGGCTTAGAATGCAAATCAAGAGGCCTCCAGTGGATAATAGATACAACCATAGCTTATCCCAAAGCTGAACCAATAGACATTCAGACCTGGATCCTGGGGTACAGGAAACCAACAGTCACTCATGTCCATTACAGGATTTTCCCAATTGGAGATGTGCCCTTGGAGACCGAGGACCTCACCAGCTGGCTCTATCAGCGCTTTATTGAGAAGGAGGACCTCCTGTCCCATTTTTATAAGACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGATGTGCCCTTGGAGACC
60.11
ACACACATCTCCAGTTGCCT
59.23
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGAGATGTGCCCTTGGAGAC
60.11
ACACACATCTCCAGTTGCCT
59.23
180
PCR template sequence:
CCAATTGGAGATGTGCCCTTGGAGACCGAGGACCTCACCAGCTGGCTCTATCAGCGCTTTATTGAGAAGGAGGACCTCCTGTCCCATTTTTATAAGACAGTGATGGAATGGGGGGAAGATATTAAAGCAATCGCTAAAGATGAAGCAGTGATGTTGGTGAACCACCAGGCAACTGGAGATGTGTGTACATTGATGATGTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-20a-5p(1), mmu-miR-106b-5p(1), mmu-miR-18a-5p(1), mmu-miR-339-5p(1), mmu-miR-511-3p(1), mmu-miR-370-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTTATAAGACAGTGATGGAATGGGG
siRNA sets
ATTCCATCACTGTCTTATA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCLPGAT1_723_ORF_1
0.898
0.101756025
0.999270371
1443
ORF sequence:
ATGGAATGGGGGGAAGATATTAAAGCAATCGCTAAAGATGAAGCAGTGATGTTGGTGAACCACCAGGCAACTGGAGATGTGTGTACATTGATGATGTGCCTACAGGATAAAGGACCGGTTGTCGCTCAGATGATGTGGCTGATGGATCATATTTTCAAGTATACAAACTTTGGAATTGTTTCTCTTATTCATGGAGACTTCTTTATAAGACAGGGAAGAGCCTACCGCGACCAACAGCTGCTGGTTCTCAAGAAGCACCTTGAACATAATTACAGGAGCAGAGATCGAAAATGGATCGTTTTGTTTCCGGAAGGGGGCTTCCTCAGGAAGAGGCGAGAAACAAGCCAGGCATTTGCCAAGAAAAATAACTTGCCATTTCTTACACATGTCACTTTGCCAAGGTTTGGGGCAACAAACATTATTTTGAAGGCACTTGTAGCACGGCAGGAAAATGGAAGCCCAGCAGGAGGAGACGCTAGAGGCTTAGAATGCAAATCAAGAGGCCTCCAGTGGATAATAGATACAACCATAGCTTATCCCAAAGCTGAACCAATAGACATTCAGACCTGGATCCTGGGGTACAGGAAACCAACAGTCACTCATGTCCATTACAGGATTTTCCCAATTGGAGATGTGCCCTTGGAGACCGAGGACCTCACCAGCTGGCTCTATCAGCGCTTTATTGAGAAGGAGGACCTCCTGTCCCATTTTTATAAGACAGTGATGGAATGGGGGGAAGATATTAAAGCAATCGCTAAAGATGAAGCAGTGATGTTGGTGAACCACCAGGCAACTGGAGATGTGTGTACATTGATGATGTGCCTACAGGATAAAGGACCGGTTGTCGCTCAGATGATGTGGCTGATGGATCATATTTTCAAGTATACAAACTTTGGAATTGTTTCTCTTATTCATGGAGACTTCTTTATAAGACAGGGAAGAGCCTACCGCGACCAACAGCTGCTGGTTCTCAAGAAGCACCTTGAACATAATTACAGGAGCAGAGATCGAAAATGGATCGTTTTGTTTCCGGAAGGGGGCTTCCTCAGGAAGAGGCGAGAAACAAGCCAGGCATTTGCCAAGAAAAATAACTTGCCATTTCTTACACATGTCACTTTGCCAAGGTTTGGGGCAACAAACATTATTTTGAAGGCACTTGTAGCACGGCAGGAAAATGGAAGCCCAGCAGGAGGAGACGCTAGAGGCTTAGAATGCAAATCAAGAGGCCTCCAGTGGATAATAGATACAACCATAGCTTATCCCAAAGCTGAACCAATAGACATTCAGACCTGGATCCTGGGGTACAGGAAACCAACAGTCACTCATGTCCATTACAGGATTTTCCCAATTGGAGATGTGCCCTTGGAGACCGAGGACCTCACCAGCTGGCTCTATCAGCGCTTTATTGAGAAGGAGGACCTCCTGTCCCATTTTTATAAGACA
Peptide sequence:
MEWGEDIKAIAKDEAVMLVNHQATGDVCTLMMCLQDKGPVVAQMMWLMDHIFKYTNFGIVSLIHGDFFIRQGRAYRDQQLLVLKKHLEHNYRSRDRKWIVLFPEGGFLRKRRETSQAFAKKNNLPFLTHVTLPRFGATNIILKALVARQENGSPAGGDARGLECKSRGLQWIIDTTIAYPKAEPIDIQTWILGYRKPTVTHVHYRIFPIGDVPLETEDLTSWLYQRFIEKEDLLSHFYKTVMEWGEDIKAIAKDEAVMLVNHQATGDVCTLMMCLQDKGPVVAQMMWLMDHIFKYTNFGIVSLIHGDFFIRQGRAYRDQQLLVLKKHLEHNYRSRDRKWIVLFPEGGFLRKRRETSQAFAKKNNLPFLTHVTLPRFGATNIILKALVARQENGSPAGGDARGLECKSRGLQWIIDTTIAYPKAEPIDIQTWILGYRKPTVTHVHYRIFPIGDVPLETEDLTSWLYQRFIEKEDLLSHFYKT
IRESfinder result
IRESfinder score
0.505343991
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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