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mmu_ciVirma_1688
Basic information of circular RNA
PanCircBase ID:
mmu_ciVirma_1688
mm39_Chr. Position ID:
chr4|11519414|11521102|+
Gene name:
Virma
Transcript:
ENSMUST00000055372.14
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
9
Exon/intron offsets:
0
Genomic length:
1688
Exon/intron sizes in nt:
1688
Flanking exon/introns:
chr4:11519414-11521104
Splice length:
1688
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAATTTTCTATTTACTTTTAAAAATCTCAATTACATTAGGAATCTAGGTCACTCATAGGCTAGTTTCTTTACCAAAGAAGTGTCTTTGGCACAGGCGCATGTAATGTATGAATGTATGTATGAATGTGTATCTTAAGATCTACCTACCTATCTATATACTCACATATATCCATATATGTTTTGTCATAACTTGCTAGGTAAGAGCTAGAATAACAGGAGTCTCTGTGCTGTGTCTGGTGAGCAGTGCAGTGAACTTTCTCCAGCTTCTTTTAGTCCCTCCTGGTATTGAGAAAGGTTACAAGTACAGTATCCCTCTGTCTTGTGGAGAAGGGAATGTTAAAGCCCAGAAGTATACACTCTAAGGGTACTGCTCACACTGTCTTACTGTCTGTTCTCCCAGCTTCACGGTGCTCTGATTTTTGGATTGCTTTGGCTGAGTGGGGGGAGTTGGGGGAGATAATGATATTGAAGAGCTGCCCAGTAGGGCAGAGGATTTTAGCATGAGAGAAGAGAGACCTGCTCGCTTCCTTGCTTATGTCATGGGAAACCAGACAAGATGGGCACGTTCAGGGTCGCATGGCCGTATTATCAAGCAGAGTAGAAACATACAGGTAACCAGTTGCCTTCAGAATGGGGTGACCCCGTCATGAAAGGCGAACTACAGTGGCTTCTGCCTAGCTGTAGTGTCTTAGTGATTCTGTGGTGAAAGACAAGTGAGGGTGGCAGATGATCTCATTCGCTCGTAGATGAAGCTTTAAAGGAGGTTTTAAAGAGAGACATATGTCCTAATGTCATGGTTAATGAGATATGGTTGTGAACATTTCCTTGTTCATTTGTTCTTGTTCATTTTACTTCCCACTGTAATGTATATGAATTTGTTTTCATATCAGTTGTCTCTCCTTACTTATCAAAAATACTTTATCAAAAAGACCTTATTTCAAGGGAAAAAACTAGGCATGGGAGAAATACATCTGAGCCTGGCATGGTAGTGCATGCCTGTAATCCCAGTCCTTGGAAGGCTGAGGCAGGAGGATTGTGAATTTGAAGTCATCCTTAAATCTTTTGATACATAGTAAGACTGTGTGCACTGAGCACTTAGCTTTTTTTCTTGTCTTTGTTGTGTAAACAATGCAACATGTACTCACACAGTATTTAGATCATATTAAGTATCCCAAGTCGTGTGGAGTTGACTGAAAGTAGATGGGAGGATGTGCACATGCCATTTAAGGTACTGATGACCCCATGGACTTAGGTATCTGTACGGGTCCTGGAACCAGTATTGCACGGCTACTGAGGGATGGCTGTTACTGATACTCTCTTCAGGTGAATCCAAAGTGAAGTGTAAGCCGGGCAGTGGTGGCGCACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCGGGCGGATTTCTGAGTTCAAGGACAGCCTGGCCTACACAGAGAAAAAAAAAAAAAGAAAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAAGAAGAAAGAAAAAAGAAAGTGAAGTGTAAAATCTCATTCTTTATTTTCAAGAAGTTAGGTGATGTGCTAATGTTGGATTGTAAATTTCCTCGATCTCTTTAAAAGAACATACGAAAACTGTTTAAAATTATCCCTGAAGAGTTACTTTCGTACCGCACACTAACCCTGATTTTATTCC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGAAGAGTTACTTTCGTACCGCA
60
GCCTGTGCCAAAGACACTTC
59.69
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAAGAGTTACTTTCGTACCGCAC
59.64
GCCTGTGCCAAAGACACTTC
59.69
140
PCR template sequence:
TGTAAATTTCCTCGATCTCTTTAAAAGAACATACGAAAACTGTTTAAAATTATCCCTGAAGAGTTACTTTCGTACCGCACACTAACCCTGATTTTATTCCGTAATTTTCTATTTACTTTTAAAAATCTCAATTACATTAGGAATCTAGGTCACTCATAGGCTAGTTTCTTTACCAAAGAAGTGTCTTTGGCACAGGCGCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
34
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-181a-5p(1), mmu-miR-200c-3p(1), mmu-miR-335-5p(1), mmu-miR-33-5p(1), mmu-miR-152-3p(1), mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-298-5p(1), mmu-miR-203-3p(1), mmu-miR-433-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-127-5p(1), mmu-miR-199b-3p(1), mmu-miR-194-5p(1), mmu-miR-199a-3p(1), mmu-miR-467b-5p(1), mmu-miR-215-5p(1), mmu-miR-297a-5p(1), mmu-miR-466d-3p(1), mmu-miR-224-5p(1), mmu-miR-705(1), mmu-miR-29b-2-5p(1), mmu-miR-802-5p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1), mmu-miR-190b-5p(1), mmu-miR-484(1), mmu-miR-466b-3p(1), mmu-miR-323-3p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGATTTTATTCCGTAATTTTCTATT
siRNA sets
AAATTACGGAATAAAATCA, AAAATTACGGAATAAAATC, AATAGAAAATTACGGAATA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.784924562
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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