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mmu_circVars2_379
Basic information of circular RNA
PanCircBase ID:
mmu_circVars2_379
mm39_Chr. Position ID:
chr17|35970366|35971019|-
Gene name:
Vars2
Transcript:
ENSMUST00000043674.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
22,21,20,19
Exon/intron offsets:
0,177,325,527
Genomic length:
653
Exon/intron sizes in nt:
7,96,91,05,126
Flanking exon/introns:
chr17:35970281-35970366|chr17:35971019-35971105
Splice length:
379
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ACGCCAGACCTTGCTCACTTCTACCCCCTCACCCTCTTGGAAACGGGTAGTGACCTGCTGATGTTCTGGGTGGGCCGCATGGTCATGCTGGGGACCCAGCTCACTGGGCAGCTCCCCTTCAGCAAGGTGCTTCTTCACTCCATGGTTCGGGACAGGCAGGGCCGGAAGATGAGCAAGTCCCTGGGGAACGTGCTAGACCCACGGGACATCATTAGCGGGCAGGAGCTGCAGGTGCTGCAGGCCAAGCTGAGAGACGGTAACTTGGACCCTGGAGAGCTCGCCGTTGCAGCCGCAGCACAGAAAAAGGACTTTCCTTACGGGATCCCTGAGTGTGGGACGGATGCCCTGAGATTTGCACTGTGCTCCCATGGAATCCTGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCGCAGCACAGAAAAAGGAC
60.04
CACCCAGAACATCAGCAGGT
59.96
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCGCAGCACAGAAAAAGGAC
60.04
CCCAGAACATCAGCAGGTCA
59.67
160
PCR template sequence:
GCCGTTGCAGCCGCAGCACAGAAAAAGGACTTTCCTTACGGGATCCCTGAGTGTGGGACGGATGCCCTGAGATTTGCACTGTGCTCCCATGGAATCCTGGACGCCAGACCTTGCTCACTTCTACCCCCTCACCCTCTTGGAAACGGGTAGTGACCTGCTGATGTTCTGGGTGGGCCGCATGGTCATGCTGGGGACCCAGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-19b-3p(1), mmu-miR-19a-3p(1), mmu-miR-148b-3p(1), mmu-miR-216a-5p(1), mmu-miR-128-3p(1), mmu-miR-22-3p(1), mmu-miR-130b-3p(1), mmu-miR-721(1), mmu-miR-188-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CATGGAATCCTGGACGCCAGACCTTG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVARS2_379_ORF_1
1.309
0.404103957
0.837538437
390
ORF sequence:
ATGGAATCCTGGACGCCAGACCTTGCTCACTTCTACCCCCTCACCCTCTTGGAAACGGGTAGTGACCTGCTGATGTTCTGGGTGGGCCGCATGGTCATGCTGGGGACCCAGCTCACTGGGCAGCTCCCCTTCAGCAAGGTGCTTCTTCACTCCATGGTTCGGGACAGGCAGGGCCGGAAGATGAGCAAGTCCCTGGGGAACGTGCTAGACCCACGGGACATCATTAGCGGGCAGGAGCTGCAGGTGCTGCAGGCCAAGCTGAGAGACGGTAACTTGGACCCTGGAGAGCTCGCCGTTGCAGCCGCAGCACAGAAAAAGGACTTTCCTTACGGGATCCCTGAGTGTGGGACGGATGCCCTGAGATTTGCACTGTGCTCCCATGGAATCCTG
Peptide sequence:
MESWTPDLAHFYPLTLLETGSDLLMFWVGRMVMLGTQLTGQLPFSKVLLHSMVRDRQGRKMSKSLGNVLDPRDIISGQELQVLQAKLRDGNLDPGELAVAAAAQKKDFPYGIPECGTDALRFALCSHGIL
IRESfinder result
IRESfinder score
0.3915312
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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