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mmu_circVldlr_366
Basic information of circular RNA
PanCircBase ID:
mmu_circVldlr_366
mm39_Chr. Position ID:
chr19|27215909|27217141|+
Gene name:
Vldlr
Transcript:
ENSMUST00000164509.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
6,7,8
Exon/intron offsets:
0,214,1112
Genomic length:
1232
Exon/intron sizes in nt:
12,31,23,120
Flanking exon/introns:
chr19:27215824-27215909|chr19:27217141-27217244
Splice length:
366
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CTTCTCGAACCTGCCGACCTGACCAGTTTGAATGTGAAGATGGTAGCTGTATCCACGGCAGCAGGCAATGCAATGGCATCCGAGACTGTGTTGATGGCTCTGATGAAGTCAACTGCAAAAACGTCAATCAGTGCCTGGGCCCTGGAAAGTTCAAGTGCAGAAGCGGGGAATGCATAGACATGAGCAAAGTATGTGACCAGGAACAAGACTGCAGAGACTGGAGTGACGAGCCCCTGAAGGAATGCCATATCAACGAATGCCTGGTCAATAATGGTGGCTGTTCCCATATCTGCAAAGACCTAGTTATAGGTTATGAGTGTGATTGTGCAGCTGGGTTTGAACTGATAGATAGGAAAACCTGTGGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGCAGCTGGGTTTGAACTG
59.97
AGCCATCAACACAGTCTCGG
60.04
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTGCAGCTGGGTTTGAACTG
59.97
GCCATCAACACAGTCTCGGA
60.04
140
PCR template sequence:
AATAATGGTGGCTGTTCCCATATCTGCAAAGACCTAGTTATAGGTTATGAGTGTGATTGTGCAGCTGGGTTTGAACTGATAGATAGGAAAACCTGTGGAGCTTCTCGAACCTGCCGACCTGACCAGTTTGAATGTGAAGATGGTAGCTGTATCCACGGCAGCAGGCAATGCAATGGCATCCGAGACTGTGTTGATGGCTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-181a-5p(1), mmu-miR-33-5p(1), mmu-miR-181b-5p(1), mmu-miR-370-3p(1), mmu-miR-129-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAAACCTGTGGAGCTTCTCGAACCTG
siRNA sets
TTCGAGAAGCTCCACAGGT, GTTCGAGAAGCTCCACAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVLDLR_366_ORF_1
1.0856
0.204362881
0.82886024
552
ORF sequence:
ATGAGCAAAGTATGTGACCAGGAACAAGACTGCAGAGACTGGAGTGACGAGCCCCTGAAGGAATGCCATATCAACGAATGCCTGGTCAATAATGGTGGCTGTTCCCATATCTGCAAAGACCTAGTTATAGGTTATGAGTGTGATTGTGCAGCTGGGTTTGAACTGATAGATAGGAAAACCTGTGGAGCTTCTCGAACCTGCCGACCTGACCAGTTTGAATGTGAAGATGGTAGCTGTATCCACGGCAGCAGGCAATGCAATGGCATCCGAGACTGTGTTGATGGCTCTGATGAAGTCAACTGCAAAAACGTCAATCAGTGCCTGGGCCCTGGAAAGTTCAAGTGCAGAAGCGGGGAATGCATAGACATGAGCAAAGTATGTGACCAGGAACAAGACTGCAGAGACTGGAGTGACGAGCCCCTGAAGGAATGCCATATCAACGAATGCCTGGTCAATAATGGTGGCTGTTCCCATATCTGCAAAGACCTAGTTATAGGTTATGAGTGTGATTGTGCAGCTGGGTTTGAACTGATAGATAGGAAAACCTGTGGA
Peptide sequence:
MSKVCDQEQDCRDWSDEPLKECHINECLVNNGGCSHICKDLVIGYECDCAAGFELIDRKTCGASRTCRPDQFECEDGSCIHGSRQCNGIRDCVDGSDEVNCKNVNQCLGPGKFKCRSGECIDMSKVCDQEQDCRDWSDEPLKECHINECLVNNGGCSHICKDLVIGYECDCAAGFELIDRKTCG
IRESfinder result
IRESfinder score
0.328117035
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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