top of page
mmu_circVps13b_1188
Basic information of circular RNA
PanCircBase ID:
mmu_circVps13b_1188
mm39_Chr. Position ID:
chr15|35617743|35646527|+
Gene name:
Vps13b
Transcript:
ENSMUST00000048646.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
24,25,26,27,28,29
Exon/intron offsets:
0,6004,22255,22932,24800,28375
Genomic length:
28784
Exon/intron sizes in nt:
22,12,04,17,21,15,67,400
Flanking exon/introns:
chr15:35607510-35617743|chr15:35646527-35652400
Splice length:
1188
Other database IDs:
circAtlas: mmu-Vps13b_0188
circBase: hsa_circ_0135262, circAtlas: hsa-VPS13B_0080, CIRCpedia: HSA_CIRCpedia_59594
Human Ortholog IDs:
Mature spliced Sequence:
GTGATGCATTTCCTTGGACCATAAGCTTGCATCATTTCAGCATATATACCCTTCTTGGAAAGCAAGTGACTCTTTCCCTTGTGGAGCCTATGGGATGTACCTCTACTCTAGCAGTCACATCTCAAAAGCTGCTTCCTGTGGGACCCGATGGAAGGCATTCATTTGTTGTCTGTCTTCATGTTGACTTAGAGTCATTAGAGATAAAATGCTCTAATCCCCAGGTCCAGCTCATTTATGAATTGGCTGATACGATGAGTAAAGTCTGGAGTAAAATTCAGAAGAGAGGCAATCTTAGTCCATCTTCAGTCTACCCAGAGACAGTGGCAGGGCCTATCCCTGGTTCTCCAGTTTGGAGCAGCGTAGGTACAGCTCCACCAGACACCAGCACATGCAGCCCATCTGCTGACATAGGAACTACTACTGAGGGAGATTCGGTTCAAGCTGGTGATGATTCGCCATTCTCAGACTCTGTTACCTTGGAACAAACTACCAGTAACATTGGTGGGTCCAGCGGCCGTGTTAGTCTGTGGATGCAGTGGGTGCTCCCCAAAGCTACTGTGAAGCTCTTTGCTCCAGACCTTGAAAAAAAAGGCACAGAGGTCTGCATGGTCAGTGAACTGGAAGACCTCAGTGCATCCATAGACGTGCAGGATGTGTACACCAAAGTCAAGTGTAAGGTAGAGAGTTTCAGTATCGACCACTATCAAAGCAGGCCTGGGGAAGGTTGGCAGTCAGGACATTTTGAAGGAGTGTTTCTGCAGTGCAAAGAAAAACCTGTGACAACTACAAAACTTCTAGATGGTGCTCATCAGCAGCATGGATTTCTTTCTCTGACATACACCAAAGCTGTAACAAAAAATGTCCGCCACAAGTTAACCTCAAGAAATGAGCGAAGAAGCTTTTATAAGTTATCTGAAGGTTTAATGGATGGCTCGCCTCATTTTCTTCATGAAATTCTTCTTTCTGCACAAGCGTTTGATATTGTTGTGTGCTTTCCTTTACTTAATGCAATTGCAAGTGTATTTCACACTAAACTCCCAAAGACCCAAAGAGAGAAAAGAAAATCTTCAGGTCAGCCCATGAGGACCCATACGCTGACTTCACGCAATTTACCTTTGATTTATATCAATACAAGTGTCATCAGAATTTTTGTTCCCCAAACAGAAGAAACACAGTCAACTGTTGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACGCTGACTTCACGCAATTT
59.06
AGGGAAAGAGTCACTTGCTT
56.67
176
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CATACGCTGACTTCACGCAA
58.93
AGGGAAAGAGTCACTTGCTT
56.67
179
PCR template sequence:
CATACGCTGACTTCACGCAATTTACCTTTGATTTATATCAATACAAGTGTCATCAGAATTTTTGTTCCCCAAACAGAAGAAACACAGTCAACTGTTGCAGGTGATGCATTTCCTTGGACCATAAGCTTGCATCATTTCAGCATATATACCCTTCTTGGAAAGCAAGTGACTCTTTCCCTTGTGGAGCCTATGGGATGTAC
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-9-5p(1), mmu-miR-134-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-217-5p(1), mmu-miR-138-5p(1), mmu-miR-434-3p(1), mmu-miR-382-3p(1), mmu-miR-188-3p(1), mmu-miR-697(1), mmu-miR-202-3p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCAACTGTTGCAGGTGATGCATTTCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVPS13B_1188_ORF_1
0.8788
-0.001838552
0.999997306
2286
ORF sequence:
ATGGGATGTACCTCTACTCTAGCAGTCACATCTCAAAAGCTGCTTCCTGTGGGACCCGATGGAAGGCATTCATTTGTTGTCTGTCTTCATGTTGACTTAGAGTCATTAGAGATAAAATGCTCTAATCCCCAGGTCCAGCTCATTTATGAATTGGCTGATACGATGAGTAAAGTCTGGAGTAAAATTCAGAAGAGAGGCAATCTTAGTCCATCTTCAGTCTACCCAGAGACAGTGGCAGGGCCTATCCCTGGTTCTCCAGTTTGGAGCAGCGTAGGTACAGCTCCACCAGACACCAGCACATGCAGCCCATCTGCTGACATAGGAACTACTACTGAGGGAGATTCGGTTCAAGCTGGTGATGATTCGCCATTCTCAGACTCTGTTACCTTGGAACAAACTACCAGTAACATTGGTGGGTCCAGCGGCCGTGTTAGTCTGTGGATGCAGTGGGTGCTCCCCAAAGCTACTGTGAAGCTCTTTGCTCCAGACCTTGAAAAAAAAGGCACAGAGGTCTGCATGGTCAGTGAACTGGAAGACCTCAGTGCATCCATAGACGTGCAGGATGTGTACACCAAAGTCAAGTGTAAGGTAGAGAGTTTCAGTATCGACCACTATCAAAGCAGGCCTGGGGAAGGTTGGCAGTCAGGACATTTTGAAGGAGTGTTTCTGCAGTGCAAAGAAAAACCTGTGACAACTACAAAACTTCTAGATGGTGCTCATCAGCAGCATGGATTTCTTTCTCTGACATACACCAAAGCTGTAACAAAAAATGTCCGCCACAAGTTAACCTCAAGAAATGAGCGAAGAAGCTTTTATAAGTTATCTGAAGGTTTAATGGATGGCTCGCCTCATTTTCTTCATGAAATTCTTCTTTCTGCACAAGCGTTTGATATTGTTGTGTGCTTTCCTTTACTTAATGCAATTGCAAGTGTATTTCACACTAAACTCCCAAAGACCCAAAGAGAGAAAAGAAAATCTTCAGGTCAGCCCATGAGGACCCATACGCTGACTTCACGCAATTTACCTTTGATTTATATCAATACAAGTGTCATCAGAATTTTTGTTCCCCAAACAGAAGAAACACAGTCAACTGTTGCAGGTGATGCATTTCCTTGGACCATAAGCTTGCATCATTTCAGCATATATACCCTTCTTGGAAAGCAAGTGACTCTTTCCCTTGTGGAGCCTATGGGATGTACCTCTACTCTAGCAGTCACATCTCAAAAGCTGCTTCCTGTGGGACCCGATGGAAGGCATTCATTTGTTGTCTGTCTTCATGTTGACTTAGAGTCATTAGAGATAAAATGCTCTAATCCCCAGGTCCAGCTCATTTATGAATTGGCTGATACGATGAGTAAAGTCTGGAGTAAAATTCAGAAGAGAGGCAATCTTAGTCCATCTTCAGTCTACCCAGAGACAGTGGCAGGGCCTATCCCTGGTTCTCCAGTTTGGAGCAGCGTAGGTACAGCTCCACCAGACACCAGCACATGCAGCCCATCTGCTGACATAGGAACTACTACTGAGGGAGATTCGGTTCAAGCTGGTGATGATTCGCCATTCTCAGACTCTGTTACCTTGGAACAAACTACCAGTAACATTGGTGGGTCCAGCGGCCGTGTTAGTCTGTGGATGCAGTGGGTGCTCCCCAAAGCTACTGTGAAGCTCTTTGCTCCAGACCTTGAAAAAAAAGGCACAGAGGTCTGCATGGTCAGTGAACTGGAAGACCTCAGTGCATCCATAGACGTGCAGGATGTGTACACCAAAGTCAAGTGTAAGGTAGAGAGTTTCAGTATCGACCACTATCAAAGCAGGCCTGGGGAAGGTTGGCAGTCAGGACATTTTGAAGGAGTGTTTCTGCAGTGCAAAGAAAAACCTGTGACAACTACAAAACTTCTAGATGGTGCTCATCAGCAGCATGGATTTCTTTCTCTGACATACACCAAAGCTGTAACAAAAAATGTCCGCCACAAGTTAACCTCAAGAAATGAGCGAAGAAGCTTTTATAAGTTATCTGAAGGTTTAATGGATGGCTCGCCTCATTTTCTTCATGAAATTCTTCTTTCTGCACAAGCGTTTGATATTGTTGTGTGCTTTCCTTTACTTAATGCAATTGCAAGTGTATTTCACACTAAACTCCCAAAGACCCAAAGAGAGAAAAGAAAATCTTCAGGTCAGCCCATGAGGACCCATACGCTGACTTCACGCAATTTACCTTTGATTTATATCAATACAAGTGTCATCAGAATTTTTGTTCCCCAAACAGAAGAAACACAGTCAACTGTTGCA
Peptide sequence:
MGCTSTLAVTSQKLLPVGPDGRHSFVVCLHVDLESLEIKCSNPQVQLIYELADTMSKVWSKIQKRGNLSPSSVYPETVAGPIPGSPVWSSVGTAPPDTSTCSPSADIGTTTEGDSVQAGDDSPFSDSVTLEQTTSNIGGSSGRVSLWMQWVLPKATVKLFAPDLEKKGTEVCMVSELEDLSASIDVQDVYTKVKCKVESFSIDHYQSRPGEGWQSGHFEGVFLQCKEKPVTTTKLLDGAHQQHGFLSLTYTKAVTKNVRHKLTSRNERRSFYKLSEGLMDGSPHFLHEILLSAQAFDIVVCFPLLNAIASVFHTKLPKTQREKRKSSGQPMRTHTLTSRNLPLIYINTSVIRIFVPQTEETQSTVAGDAFPWTISLHHFSIYTLLGKQVTLSLVEPMGCTSTLAVTSQKLLPVGPDGRHSFVVCLHVDLESLEIKCSNPQVQLIYELADTMSKVWSKIQKRGNLSPSSVYPETVAGPIPGSPVWSSVGTAPPDTSTCSPSADIGTTTEGDSVQAGDDSPFSDSVTLEQTTSNIGGSSGRVSLWMQWVLPKATVKLFAPDLEKKGTEVCMVSELEDLSASIDVQDVYTKVKCKVESFSIDHYQSRPGEGWQSGHFEGVFLQCKEKPVTTTKLLDGAHQQHGFLSLTYTKAVTKNVRHKLTSRNERRSFYKLSEGLMDGSPHFLHEILLSAQAFDIVVCFPLLNAIASVFHTKLPKTQREKRKSSGQPMRTHTLTSRNLPLIYINTSVIRIFVPQTEETQSTVA
IRESfinder result
IRESfinder score
0.754816923
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page