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mmu_circLpin2_1268
Basic information of circular RNA
PanCircBase ID:
mmu_circLpin2_1268
mm39_Chr. Position ID:
chr17|71521958|71540922|+
Gene name:
Lpin2
Transcript:
ENSMUST00000129635.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
2,3,4,5,6,7,8
Exon/intron offsets:
0,7091,9976,14344,15308,16219,18864
Genomic length:
18964
Exon/intron sizes in nt:
2,01,96,30,21,08,12,43,00,000
Flanking exon/introns:
chr17:71491075-71521958|chr17:71540922-71544380
Splice length:
1268
Other database IDs:
circAtlas: mmu-Lpin2_0001
circBase: hsa_circ_0108198, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_156885
Human Ortholog IDs:
Mature spliced Sequence:
TCTCAAACCATGAATTATGTGGGCCAGCTGGCTGGGCAGGTGCTCGTCACTGTGAAGGAACTCTACAAGGGCATTAACCAAGCCACGTTGTCTGGATGCATCGATGTGGTCGTGGTGAGGCAGCAGGATGGCTCCTACCAGTGCTCGCCTTTTCACGTACGCTTCGGGAAGCTGGGTGTCCTGAGGTCCAAGGAGAAAGTGATTGACATAGAAATCAATGGCAGTGCTGTGGATCTTCACATGAAATTGGGTGATAATGGGGAAGCCTTCTTTGTAGAGGAGACTGAAGAAGAATATGAAAAATTACCTGCTTATCTTGCCACCTCACCAATTCCCACTGAAGACCAGTTCTTTAAACATATTGAAACCCCTTTGGTGAAATCAAGTGGAAATGAAAGGCCAGCTCAGAGTTCAGACGTTTCTCACACCTTGGAATCAGAGGCAGTTTTCACTCAGAGTTCTGTGAAAAAGAAGAAACGAAGGAGAAAGAAGTGCAAACAGGACAATAGGAAGGAGGAGCAGGCAGCTTCCCCTGTTGCAGAAGATGTAGGTGATGTGGGTGTGAGCTCAGATGATGAGAAGAGAGCCCAGGCAGCAAGAGGATCTTCAAATGCTTCCTTAAAGGAAGAGGACTACAAGGAGCCTTCACTCTTCCATTCTGGGGATAACTACCCCTTATCTGATGGAGATTGGTCCCCATTAGAAACCACCTACCCTCAGGCTGTGTGCCCCAAGAGTGACTCTGAGCTGGAGGTGAAGCCATCTGAGAGCCTCCTCAGATCTGAGCCGCACATGGAGTGGACGTGGGGCGGGTTCCCAGAGTCCACCAAGGTCACCAAAAGAGAACGGTATGACTATCATCCAAGGACAGCTACGATTACACCATCAGAGAACACACATTTCAGGGTAATTCCCAGTGAAGACAGCCTCATAAGAGAAGTTGAAAAGGATGCTACTGTTGAAGATACTACCTGTACCATAGTGAAACCCAAACCTAGAGCCCTGTGTAAGCAACTGAGTGATGCAGCGTCTACTGAGCTTCCCGAATCACCTCTTGAAGCACCTCAGATTTCATCGTTATTAGATGCAGACCCTGTTCCCAGCCCATCAGCAGAGGCTCCCTCAGAACCCAAACCAGCTGCTAAAGACTCACCAACAAAAAAGAAAGGTGTTCACAAAAGAAGCCAGCACCAGGGACCTGATGACATTTACCTTGATGACTTAAAGGCTCTTGAGCCTGAAGTGGCGGCTCTCTATTTCCCTAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAAAAGAAGCCAGCACCAGG
59.68
TTCCTTCACAGTGACGAGCA
59.25
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAAAAGAAGCCAGCACCAGG
59.68
CGTGGCTTGGTTAATGCCCT
60.97
180
PCR template sequence:
GTGTTCACAAAAGAAGCCAGCACCAGGGACCTGATGACATTTACCTTGATGACTTAAAGGCTCTTGAGCCTGAAGTGGCGGCTCTCTATTTCCCTAAAAGTCTCAAACCATGAATTATGTGGGCCAGCTGGCTGGGCAGGTGCTCGTCACTGTGAAGGAACTCTACAAGGGCATTAACCAAGCCACGTTGTCTGGATGCA
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-29b-2-5p(3), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-31-5p(1), mmu-miR-196a-5p(1), mmu-miR-326-3p(1), mmu-miR-128-3p(1), mmu-miR-24-3p(1), mmu-miR-127-5p(1), mmu-miR-342-3p(1), mmu-miR-1187(1), mmu-miR-335-3p(1), mmu-miR-484(1), mmu-miR-452-3p(1), mmu-miR-193b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTTCCCTAAAAGTCTCAAACCATGA
siRNA sets
ATGGTTTGAGACTTTTAGG, TGGTTTGAGACTTTTAGGG, CATGGTTTGAGACTTTTAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCLPIN2_1268_ORF_1
1.0689
0.218808114
0.998841166
1272
ORF sequence:
ATGAATTATGTGGGCCAGCTGGCTGGGCAGGTGCTCGTCACTGTGAAGGAACTCTACAAGGGCATTAACCAAGCCACGTTGTCTGGATGCATCGATGTGGTCGTGGTGAGGCAGCAGGATGGCTCCTACCAGTGCTCGCCTTTTCACGTACGCTTCGGGAAGCTGGGTGTCCTGAGGTCCAAGGAGAAAGTGATTGACATAGAAATCAATGGCAGTGCTGTGGATCTTCACATGAAATTGGGTGATAATGGGGAAGCCTTCTTTGTAGAGGAGACTGAAGAAGAATATGAAAAATTACCTGCTTATCTTGCCACCTCACCAATTCCCACTGAAGACCAGTTCTTTAAACATATTGAAACCCCTTTGGTGAAATCAAGTGGAAATGAAAGGCCAGCTCAGAGTTCAGACGTTTCTCACACCTTGGAATCAGAGGCAGTTTTCACTCAGAGTTCTGTGAAAAAGAAGAAACGAAGGAGAAAGAAGTGCAAACAGGACAATAGGAAGGAGGAGCAGGCAGCTTCCCCTGTTGCAGAAGATGTAGGTGATGTGGGTGTGAGCTCAGATGATGAGAAGAGAGCCCAGGCAGCAAGAGGATCTTCAAATGCTTCCTTAAAGGAAGAGGACTACAAGGAGCCTTCACTCTTCCATTCTGGGGATAACTACCCCTTATCTGATGGAGATTGGTCCCCATTAGAAACCACCTACCCTCAGGCTGTGTGCCCCAAGAGTGACTCTGAGCTGGAGGTGAAGCCATCTGAGAGCCTCCTCAGATCTGAGCCGCACATGGAGTGGACGTGGGGCGGGTTCCCAGAGTCCACCAAGGTCACCAAAAGAGAACGGTATGACTATCATCCAAGGACAGCTACGATTACACCATCAGAGAACACACATTTCAGGGTAATTCCCAGTGAAGACAGCCTCATAAGAGAAGTTGAAAAGGATGCTACTGTTGAAGATACTACCTGTACCATAGTGAAACCCAAACCTAGAGCCCTGTGTAAGCAACTGAGTGATGCAGCGTCTACTGAGCTTCCCGAATCACCTCTTGAAGCACCTCAGATTTCATCGTTATTAGATGCAGACCCTGTTCCCAGCCCATCAGCAGAGGCTCCCTCAGAACCCAAACCAGCTGCTAAAGACTCACCAACAAAAAAGAAAGGTGTTCACAAAAGAAGCCAGCACCAGGGACCTGATGACATTTACCTTGATGACTTAAAGGCTCTTGAGCCTGAAGTGGCGGCTCTCTATTTCCCTAAAAGTCTCAAACCATGA
Peptide sequence:
MNYVGQLAGQVLVTVKELYKGINQATLSGCIDVVVVRQQDGSYQCSPFHVRFGKLGVLRSKEKVIDIEINGSAVDLHMKLGDNGEAFFVEETEEEYEKLPAYLATSPIPTEDQFFKHIETPLVKSSGNERPAQSSDVSHTLESEAVFTQSSVKKKKRRRKKCKQDNRKEEQAASPVAEDVGDVGVSSDDEKRAQAARGSSNASLKEEDYKEPSLFHSGDNYPLSDGDWSPLETTYPQAVCPKSDSELEVKPSESLLRSEPHMEWTWGGFPESTKVTKRERYDYHPRTATITPSENTHFRVIPSEDSLIREVEKDATVEDTTCTIVKPKPRALCKQLSDAASTELPESPLEAPQISSLLDADPVPSPSAEAPSEPKPAAKDSPTKKKGVHKRSQHQGPDDIYLDDLKALEPEVAALYFPKSLKP
IRESfinder result
IRESfinder score
0.560036864
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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