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mmu_circVmp1_608
Basic information of circular RNA
PanCircBase ID:
mmu_circVmp1_608
mm39_Chr. Position ID:
chr11|86534323|86556704|-
Gene name:
Vmp1
Transcript:
ENSMUST00000018315.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,17625,19985,21156,22279
Genomic length:
22381
Exon/intron sizes in nt:
1,68,11,19,11,36,102
Flanking exon/introns:
chr11:86526132-86534323|chr11:86556704-86574565
Splice length:
608
Other database IDs:
CIRCpedia: MMU_CIRCpedia_32529, circAtlas: mmu-Vmp1_0012
circBase: hsa_circ_0107277, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_21661
Human Ortholog IDs:
Mature spliced Sequence:
CTCCTCCAGAGTTCCTGATCTATGAAATGGCAGAGAATGGAAAAAATTGTGACCAGAGACGCATAGCAATGAGTAAGGATCAGCACAATGGAAGTCTCACAGACCCCTCTTCAGTTCATGAGAAGAAGAGAAGGGATCGGGAAGAAAGACAGAATATTGTCCTGTGGAGACAGCCACTCATTACCTTGCAGTATTTCTCTCTGGAAACTCTTGTAGTTTTGAAGGAATGGACCTCAAAATTGTGGCATCGTCAAAGCATTGTGGTGTCCTTTTTACTGCTGCTTGCTGCGCTTGTAGCTACGTATTATGTGGAAGGAGCGCACCAACAGTATGTGCAGCGGATAGAGAAGCAGTTTCTTTTGTATGCATACTGGATAGGCCTGGGGATTTTGTCCTCTGTTGGTCTTGGAACAGGACTGCACACCTTTCTGCTTTATCTGGGCCCACATATAGCTTCAGTTACATTAGCTGCTTATGAATGCAATTCGGTGAATTTCCCTGAGCCACCCTATCCTGACCAGATTATCTGCCCAGAGGAAGAAGGCGCTGAGGGAGCCATTTCTTTGTGGAGTATCATCTCAAAAGTTAGAATTGAAGCCTGCATGTGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGAGGAAGAAGGCGCTGAG
60.46
GCTATGCGTCTCTGGTCACA
59.83
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGAGGAAGAAGGCGCTGAG
60.46
TGCTATGCGTCTCTGGTCAC
59.83
145
PCR template sequence:
CTATCCTGACCAGATTATCTGCCCAGAGGAAGAAGGCGCTGAGGGAGCCATTTCTTTGTGGAGTATCATCTCAAAAGTTAGAATTGAAGCCTGCATGTGGCTCCTCCAGAGTTCCTGATCTATGAAATGGCAGAGAATGGAAAAAATTGTGACCAGAGACGCATAGCAATGAGTAAGGATCAGCACAATGGAAGTCTCAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-200c-3p(1), mmu-miR-143-3p(1), mmu-miR-381-3p(1), mmu-miR-24-3p(1), mmu-miR-127-5p(1), mmu-miR-369-3p(1), mmu-miR-539-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGCCTGCATGTGGCTCCTCCAGAGTT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVMP1_608_ORF_1
0.7957
0.023885584
0.653764159
600
ORF sequence:
ATGGCAGAGAATGGAAAAAATTGTGACCAGAGACGCATAGCAATGAGTAAGGATCAGCACAATGGAAGTCTCACAGACCCCTCTTCAGTTCATGAGAAGAAGAGAAGGGATCGGGAAGAAAGACAGAATATTGTCCTGTGGAGACAGCCACTCATTACCTTGCAGTATTTCTCTCTGGAAACTCTTGTAGTTTTGAAGGAATGGACCTCAAAATTGTGGCATCGTCAAAGCATTGTGGTGTCCTTTTTACTGCTGCTTGCTGCGCTTGTAGCTACGTATTATGTGGAAGGAGCGCACCAACAGTATGTGCAGCGGATAGAGAAGCAGTTTCTTTTGTATGCATACTGGATAGGCCTGGGGATTTTGTCCTCTGTTGGTCTTGGAACAGGACTGCACACCTTTCTGCTTTATCTGGGCCCACATATAGCTTCAGTTACATTAGCTGCTTATGAATGCAATTCGGTGAATTTCCCTGAGCCACCCTATCCTGACCAGATTATCTGCCCAGAGGAAGAAGGCGCTGAGGGAGCCATTTCTTTGTGGAGTATCATCTCAAAAGTTAGAATTGAAGCCTGCATGTGGCTCCTCCAGAGTTCCTGA
Peptide sequence:
MAENGKNCDQRRIAMSKDQHNGSLTDPSSVHEKKRRDREERQNIVLWRQPLITLQYFSLETLVVLKEWTSKLWHRQSIVVSFLLLLAALVATYYVEGAHQQYVQRIEKQFLLYAYWIGLGILSSVGLGTGLHTFLLYLGPHIASVTLAAYECNSVNFPEPPYPDQIICPEEEGAEGAISLWSIISKVRIEACMWLLQSS
IRESfinder result
IRESfinder score
0.714573719
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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