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mmu_circLama3_1700
Basic information of circular RNA
PanCircBase ID:
mmu_circLama3_1700
mm39_Chr. Position ID:
chr18|12535091|12583551|+
Gene name:
Lama3
Transcript:
ENSMUST00000092070.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
16
Exon/intron indexes:
3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18
Exon/intron offsets:
0,760,1940,5452,9505,11704,17131,17762,19102,27846,37299,39060,46230,47497,47776,48360
Genomic length:
48460
Exon/intron sizes in nt:
11,81,19,17,19,21,16,10,00,00,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr18:12502661-12535091|chr18:12583551-12586776
Splice length:
1700
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CTCTTCCATGTGGCTTATATCTTAATCAAATTTGCAAACTCTCCCCGCCCTGATCTTTGGATCCTGGAAAGATCTGTAGACTTTGGAAGCACCTACTCACCATGGCAGTATTTTGCTCATTCTAGAAGAGATTGTGTAGAACAGTTTGGGCAAGAAGCAAACATGGCAATTACCCAGGACGACCAGATGCTCTGTGTCACGGAGTATTCCCGTATCGTGCCTCTGGAAAATGGCGAGATTGTTGTATCCTTGATAAATGGTCGTCCAGGTGCAAAAAAGTTTGCTTTCTCTGACACTCTGAGGGAGTTTACTAAGGCAACAAACATCCGCTTGCGGTTTCTGCGAACCAACACCCTCCTCGGGCATCTTATTTCCAAGGCAGAGCGAGACCCCACTGTCACGCGCCGGTATTATTACAGCATAAAGGATATCAGTGTTGGTGGGCGGTGTGTTTGCAACGGCCATGCGGAGGCGTGCAGTGCTGACAACCCTGAAAAGCAGTTCCGATGCGAATGCCAGCACCATACCTGTGGAGACACGTGTAACCGCTGCTGTGCAGGTTACAATCAGAGGCGCTGGCAGCCTGCTGGTCAGGAGCAGCACAATGAGTGTGAAGCCTGCAACTGCCATGGGCATGCTGTGGACTGCTACTATGACCCAGACGTGGAGCACCAGCAGGCGAGCTTGAACAGCAAAGGCGTCTACGCAGGTGGAGGGGTCTGCATCAACTGTCAGCACAACACTGCAGGCGTGAACTGTGAAAAGTGTGCGAAGGGTTACTTCCGGCCCCATGGAGTTCCGGTGGATGCACTGCATGGATGCATCCCTTGCAGCTGTGACCCAGAACGCGCAGATGACTGTGACCAGGGCTCAGGCCACTGCCATTGTAAGCCAAATTTCTCCGGAGACTACTGTGAGACGTGTGCAGATGGGTACTATAATTTTCCATTTTGCTTGAGAATTCCAGTCTTTCCCAACTACACTCCAAGTCCAGAAGATCCAGTGGCTGGCAATATAAAAGGGTGTGACTGTAACTTGGAAGGTGTTCTCCCAGAGATATGTGACGATCGTGGCAGGTGCCTGTGCCGCCCTGGGGTTGAGGGTCCCCAGTGTGACTCCTGCCGCTCGGGCTCCTATTCATTTCCCATATGCCAAGCTTGCCAGTGTTCGACGATTGGATCCTATCCAGTGCCCTGTGACCCGGGGAATGGCCAGTGTGACTGCCTGCCTGGAATTACCGGGAGGCAGTGTGACAGGTGTCTCTCGGGAGCCTATGACTTTCCATACTGCCAAGGGTCCGGCAGTGTTTGCCATCCAGCTGGGACCCTTGACTCCAGCCTGGGTTATTGTCAGTGCAAGCAGCATGTTGCAAGTCCTACATGTAGTGTCTGCAAACCATTATATTGGAATCTGGCCAAAGAAAACCCCCGTGGATGCTCAGAGTGCCAGTGCCATGAAGCAGGGACATTGAGTGGAATTGGAGAGTGTGGGCAGGAGGACGGTGACTGTAGCTGCAAAGCCCATGTAACTGGTGATGCCTGCGACACCTGTGAAGATGGGTTTTTCTCTTTGGAGAAGAGCAATTACTTTGGCTGTCAAGGGTGTCAGTGTGACATTGGTGGAGCACTCACCACCATGTGTAGTGGGCCCTCGGGAGTATGCCAGTGCAGAGAGCACGTGGAGGGGAAACAGTGCCAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGACATTGGTGGAGCACT
59.53
GCGGGGAGAGTTTGCAAATT
59.4
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTGTGACATTGGTGGAGCA
59.53
GCGGGGAGAGTTTGCAAATT
59.4
142
PCR template sequence:
GGTGTCAGTGTGACATTGGTGGAGCACTCACCACCATGTGTAGTGGGCCCTCGGGAGTATGCCAGTGCAGAGAGCACGTGGAGGGGAAACAGTGCCAGAGCTCTTCCATGTGGCTTATATCTTAATCAAATTTGCAAACTCTCCCCGCCCTGATCTTTGGATCCTGGAAAGATCTGTAGACTTTGGAAGCACCTACTCAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
22
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-34a-5p(1), mmu-miR-200c-3p(1), mmu-miR-152-3p(1), mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-138-5p(1), mmu-miR-139-5p(1), mmu-miR-503-5p(1), mmu-miR-676-3p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-370-3p(1), mmu-miR-183-5p(1), mmu-miR-324-3p(1), mmu-miR-129-5p(1), mmu-miR-539-5p(1), mmu-miR-452-3p(1), mmu-miR-1199-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AACAGTGCCAGAGCTCTTCCATGTGG
siRNA sets
CATGGAAGAGCTCTGGCAC, CACATGGAAGAGCTCTGGC, ATGGAAGAGCTCTGGCACT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCLAMA3_1700_ORF_1
1.0394
0.135125549
0.999939888
1740
ORF sequence:
ATGCCAGTGCAGAGAGCACGTGGAGGGGAAACAGTGCCAGAGCTCTTCCATGTGGCTTATATCTTAATCAAATTTGCAAACTCTCCCCGCCCTGATCTTTGGATCCTGGAAAGATCTGTAGACTTTGGAAGCACCTACTCACCATGGCAGTATTTTGCTCATTCTAGAAGAGATTGTGTAGAACAGTTTGGGCAAGAAGCAAACATGGCAATTACCCAGGACGACCAGATGCTCTGTGTCACGGAGTATTCCCGTATCGTGCCTCTGGAAAATGGCGAGATTGTTGTATCCTTGATAAATGGTCGTCCAGGTGCAAAAAAGTTTGCTTTCTCTGACACTCTGAGGGAGTTTACTAAGGCAACAAACATCCGCTTGCGGTTTCTGCGAACCAACACCCTCCTCGGGCATCTTATTTCCAAGGCAGAGCGAGACCCCACTGTCACGCGCCGGTATTATTACAGCATAAAGGATATCAGTGTTGGTGGGCGGTGTGTTTGCAACGGCCATGCGGAGGCGTGCAGTGCTGACAACCCTGAAAAGCAGTTCCGATGCGAATGCCAGCACCATACCTGTGGAGACACGTGTAACCGCTGCTGTGCAGGTTACAATCAGAGGCGCTGGCAGCCTGCTGGTCAGGAGCAGCACAATGAGTGTGAAGCCTGCAACTGCCATGGGCATGCTGTGGACTGCTACTATGACCCAGACGTGGAGCACCAGCAGGCGAGCTTGAACAGCAAAGGCGTCTACGCAGGTGGAGGGGTCTGCATCAACTGTCAGCACAACACTGCAGGCGTGAACTGTGAAAAGTGTGCGAAGGGTTACTTCCGGCCCCATGGAGTTCCGGTGGATGCACTGCATGGATGCATCCCTTGCAGCTGTGACCCAGAACGCGCAGATGACTGTGACCAGGGCTCAGGCCACTGCCATTGTAAGCCAAATTTCTCCGGAGACTACTGTGAGACGTGTGCAGATGGGTACTATAATTTTCCATTTTGCTTGAGAATTCCAGTCTTTCCCAACTACACTCCAAGTCCAGAAGATCCAGTGGCTGGCAATATAAAAGGGTGTGACTGTAACTTGGAAGGTGTTCTCCCAGAGATATGTGACGATCGTGGCAGGTGCCTGTGCCGCCCTGGGGTTGAGGGTCCCCAGTGTGACTCCTGCCGCTCGGGCTCCTATTCATTTCCCATATGCCAAGCTTGCCAGTGTTCGACGATTGGATCCTATCCAGTGCCCTGTGACCCGGGGAATGGCCAGTGTGACTGCCTGCCTGGAATTACCGGGAGGCAGTGTGACAGGTGTCTCTCGGGAGCCTATGACTTTCCATACTGCCAAGGGTCCGGCAGTGTTTGCCATCCAGCTGGGACCCTTGACTCCAGCCTGGGTTATTGTCAGTGCAAGCAGCATGTTGCAAGTCCTACATGTAGTGTCTGCAAACCATTATATTGGAATCTGGCCAAAGAAAACCCCCGTGGATGCTCAGAGTGCCAGTGCCATGAAGCAGGGACATTGAGTGGAATTGGAGAGTGTGGGCAGGAGGACGGTGACTGTAGCTGCAAAGCCCATGTAACTGGTGATGCCTGCGACACCTGTGAAGATGGGTTTTTCTCTTTGGAGAAGAGCAATTACTTTGGCTGTCAAGGGTGTCAGTGTGACATTGGTGGAGCACTCACCACCATGTGTAGTGGGCCCTCGGGAGTATGCCAGTGCAGAGAGCACGTGGAGGGGAAACAGTGCCAG
Peptide sequence:
MPVQRARGGETVPELFHVAYILIKFANSPRPDLWILERSVDFGSTYSPWQYFAHSRRDCVEQFGQEANMAITQDDQMLCVTEYSRIVPLENGEIVVSLINGRPGAKKFAFSDTLREFTKATNIRLRFLRTNTLLGHLISKAERDPTVTRRYYYSIKDISVGGRCVCNGHAEACSADNPEKQFRCECQHHTCGDTCNRCCAGYNQRRWQPAGQEQHNECEACNCHGHAVDCYYDPDVEHQQASLNSKGVYAGGGVCINCQHNTAGVNCEKCAKGYFRPHGVPVDALHGCIPCSCDPERADDCDQGSGHCHCKPNFSGDYCETCADGYYNFPFCLRIPVFPNYTPSPEDPVAGNIKGCDCNLEGVLPEICDDRGRCLCRPGVEGPQCDSCRSGSYSFPICQACQCSTIGSYPVPCDPGNGQCDCLPGITGRQCDRCLSGAYDFPYCQGSGSVCHPAGTLDSSLGYCQCKQHVASPTCSVCKPLYWNLAKENPRGCSECQCHEAGTLSGIGECGQEDGDCSCKAHVTGDACDTCEDGFFSLEKSNYFGCQGCQCDIGGALTTMCSGPSGVCQCREHVEGKQCQ
IRESfinder result
IRESfinder score
0.420922307
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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