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mmu_circRalgapa2_928
Basic information of circular RNA
PanCircBase ID:
mmu_circRalgapa2_928
mm39_Chr. Position ID:
chr2|146187305|146203439|-
Gene name:
Ralgapa2
Transcript:
ENSMUST00000109986.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
32,31,30,29,28,27,26,25
Exon/intron offsets:
0,1323,1730,3062,7785,11702,12571,16005
Genomic length:
16134
Exon/intron sizes in nt:
1,84,13,86,91,11,10,95,00,00,000
Flanking exon/introns:
chr2:146184669-146187305|chr2:146203439-146229147
Splice length:
928
Other database IDs:
circAtlas: mmu-Ralgapa2_0019
circBase: hsa_circ_0059564, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_345702
Human Ortholog IDs:
Mature spliced Sequence:
GATGTCTTAAACACCATCATAAAAAACTGCTCACCCCGCTTTTTCTCCCTGGGTTTGCCTGGCTTCTCTATGCTGGTGGGGGACTTTATCACTGCTGCTGCCAGGGTCCTCAGTACAGACATGTTGGCGGCACCCCGTTCAGAAGCTCTCACTCTCCTTGGTTCCCTTGTCTGCTTCCCAAATACCTACCAGGAGATCCCTCTGCTGCAGTCAGTGCCAGAAGTGAGTGATGTTGTCACGGGAGCGGAAGACGTCAAGCATTACCTCATAAATATTTTACTGAAGAATGCTACCGAGGAACCAAATGAATGTGCAAGATGCATCGCCATTTGCTCCCTCGGGGTCTGGATCTGTGAAGAGCTTGCACAGAGTGCCAGCCATCCTCAGGTGAAGGATGCCATCAATGTGATAGGTGTAACTTTGAAGTTTCCTAACAAGATCGTGGCTCAGGTAGCCTGTGATGTTCTTCAGTTGTTGGTTTCCTACTGGGAAAAGCTGCAGATGTTTGAAACTGCTCTACCCCGCAAAATGGCAGAAATTCTTGTGGCCACAATTGCGTTCCTTTTACCAAGTGCAGAGTACTCGTCAGTGGAAACAGATAAAAAGTTTATTGTGTCCTTGCTCCTTTGTCTCTTGGACTGGTGCATGGCGCTGCCCGTGAGTGCCCTCCTCCACCCTGTGTCCACAGCAGTTCTAGAGGAGCTGCACCCATCCCGGGCCCCCTTGCTGGATTATATCTACAGGGTTCTGCACTGCTGTGTCTGTGGCTCCAGCACATACACACAGCAAAGTCACTATACTCTGACCTTGGCTGACCTGTCATCCACGGATTATGACCCCTTCCTACCTCTGGCAAACGTGAGGAACTCCGAGCCAATCCAGTATCATTCATCAGCAGACCTGGGGAACCTGCTGACCGTGGAAGAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGACCCCTTCCTACCTCTGG
59.96
TCCCCCACCAGCATAGAGAA
59.96
178
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGACCCCTTCCTACCTCTGG
59.96
CAGGCAAACCCAGGGAGAAA
60.18
156
PCR template sequence:
GATTATGACCCCTTCCTACCTCTGGCAAACGTGAGGAACTCCGAGCCAATCCAGTATCATTCATCAGCAGACCTGGGGAACCTGCTGACCGTGGAAGAGGGATGTCTTAAACACCATCATAAAAAACTGCTCACCCCGCTTTTTCTCCCTGGGTTTGCCTGGCTTCTCTATGCTGGTGGGGGACTTTATCACTGCTGCTG
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-let-7a-5p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-let-7c-5p(1), mmu-miR-10b-5p(1), mmu-miR-10a-5p(1), mmu-miR-181b-5p(1), mmu-let-7d-5p(1), mmu-miR-501-3p(1), mmu-miR-297a-5p(1), mmu-miR-342-5p(1), mmu-miR-98-5p(1), mmu-miR-3470b(1), mmu-miR-544-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACCGTGGAAGAGGGATGTCTTAAACA
siRNA sets
TTTAAGACATCCCTCTTCC, TTAAGACATCCCTCTTCCA, TAAGACATCCCTCTTCCAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRALGAPA2_928_ORF_1
0.9732
0.138616084
0.992956896
1089
ORF sequence:
ATGCTGGTGGGGGACTTTATCACTGCTGCTGCCAGGGTCCTCAGTACAGACATGTTGGCGGCACCCCGTTCAGAAGCTCTCACTCTCCTTGGTTCCCTTGTCTGCTTCCCAAATACCTACCAGGAGATCCCTCTGCTGCAGTCAGTGCCAGAAGTGAGTGATGTTGTCACGGGAGCGGAAGACGTCAAGCATTACCTCATAAATATTTTACTGAAGAATGCTACCGAGGAACCAAATGAATGTGCAAGATGCATCGCCATTTGCTCCCTCGGGGTCTGGATCTGTGAAGAGCTTGCACAGAGTGCCAGCCATCCTCAGGTGAAGGATGCCATCAATGTGATAGGTGTAACTTTGAAGTTTCCTAACAAGATCGTGGCTCAGGTAGCCTGTGATGTTCTTCAGTTGTTGGTTTCCTACTGGGAAAAGCTGCAGATGTTTGAAACTGCTCTACCCCGCAAAATGGCAGAAATTCTTGTGGCCACAATTGCGTTCCTTTTACCAAGTGCAGAGTACTCGTCAGTGGAAACAGATAAAAAGTTTATTGTGTCCTTGCTCCTTTGTCTCTTGGACTGGTGCATGGCGCTGCCCGTGAGTGCCCTCCTCCACCCTGTGTCCACAGCAGTTCTAGAGGAGCTGCACCCATCCCGGGCCCCCTTGCTGGATTATATCTACAGGGTTCTGCACTGCTGTGTCTGTGGCTCCAGCACATACACACAGCAAAGTCACTATACTCTGACCTTGGCTGACCTGTCATCCACGGATTATGACCCCTTCCTACCTCTGGCAAACGTGAGGAACTCCGAGCCAATCCAGTATCATTCATCAGCAGACCTGGGGAACCTGCTGACCGTGGAAGAGGGATGTCTTAAACACCATCATAAAAAACTGCTCACCCCGCTTTTTCTCCCTGGGTTTGCCTGGCTTCTCTATGCTGGTGGGGGACTTTATCACTGCTGCTGCCAGGGTCCTCAGTACAGACATGTTGGCGGCACCCCGTTCAGAAGCTCTCACTCTCCTTGGTTCCCTTGTCTGCTTCCCAAATACCTACCAGGAGATCCCTCTGCTGCAGTCAGTGCCAGAAGTGAGTGA
Peptide sequence:
MLVGDFITAAARVLSTDMLAAPRSEALTLLGSLVCFPNTYQEIPLLQSVPEVSDVVTGAEDVKHYLINILLKNATEEPNECARCIAICSLGVWICEELAQSASHPQVKDAINVIGVTLKFPNKIVAQVACDVLQLLVSYWEKLQMFETALPRKMAEILVATIAFLLPSAEYSSVETDKKFIVSLLLCLLDWCMALPVSALLHPVSTAVLEELHPSRAPLLDYIYRVLHCCVCGSSTYTQQSHYTLTLADLSSTDYDPFLPLANVRNSEPIQYHSSADLGNLLTVEEGCLKHHHKKLLTPLFLPGFAWLLYAGGGLYHCCCQGPQYRHVGGTPFRSSHSPWFPCLLPKYLPGDPSAAVSARSE
IRESfinder result
IRESfinder score
0.637772894
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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