top of page
mmu_circRock1_425
Basic information of circular RNA
PanCircBase ID:
mmu_circRock1_425
mm39_Chr. Position ID:
chr18|10084317|10093977|-
Gene name:
Rock1
Transcript:
ENSMUST00000067947.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
24,23,22,21
Exon/intron offsets:
0,6495,7811,9590
Genomic length:
9660
Exon/intron sizes in nt:
94,166,95,70
Flanking exon/introns:
chr18:10083210-10084317|chr18:10093977-10095412
Splice length:
425
Other database IDs:
circAtlas: mmu-Rock1_0071
Human Ortholog IDs:
Mature spliced Sequence:
GCAATATAGGGGAAATGAAGGGCAAATGCGGGAGTTACAAGATCAACTTGAAGCTGAGCAGTATTTCTCTACACTTTATAAAACCCAAGTAAAGGAGCTTAAAGAAGAAATTGAAGAAAAAAACCGAGAAAATTTAAGGAAAATACAGGAACTGCAAAGTGAAAAAGAAACTCTCTCTACTCAGTTGGATTTAGCAGAAACAAAAGCTGAGTCTGAGCAGCTGGCGCGAGGGATTCTGGAAGAACAGTATTTTGAGTTGACTCAGGAAAGCAAGAAAGCTGCTTCAAGAAATAGACAAGAGATTACAGATAAAGATCATACTGTTAGTCGGCTTGAAGAAACAAACAGTGTGCTAACCAAAGATATTGAAATGCTAAGAAAAGAAAATGAAGAGCTAAATGAAAGAATGAGGACAGCAGAAGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTCGGCTTGAAGAAACAAACA
58.99
TTGTAACTCCCGCATTTGCC
59.11
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTCGGCTTGAAGAAACAAACAG
59.93
TTGTAACTCCCGCATTTGCC
59.11
140
PCR template sequence:
AGTCGGCTTGAAGAAACAAACAGTGTGCTAACCAAAGATATTGAAATGCTAAGAAAAGAAAATGAAGAGCTAAATGAAAGAATGAGGACAGCAGAAGAAGGCAATATAGGGGAAATGAAGGGCAAATGCGGGAGTTACAAGATCAACTTGAAGCTGAGCAGTATTTCTCTACACTTTATAAAACCCAAGTAAAGGAGCTT
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-9-5p(1), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-200c-3p(1), mmu-miR-205-5p(1), mmu-miR-539-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACAGCAGAAGAAGGCAATATAGGGGA
siRNA sets
TATATTGCCTTCTTCTGCT,CTATATTGCCTTCTTCTGC,TATTGCCTTCTTCTGCTGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCROCK1_425_ORF_1
1.0492
0.120602099
0.675174504
492
ORF sequence:
ATGCGGGAGTTACAAGATCAACTTGAAGCTGAGCAGTATTTCTCTACACTTTATAAAACCCAAGTAAAGGAGCTTAAAGAAGAAATTGAAGAAAAAAACCGAGAAAATTTAAGGAAAATACAGGAACTGCAAAGTGAAAAAGAAACTCTCTCTACTCAGTTGGATTTAGCAGAAACAAAAGCTGAGTCTGAGCAGCTGGCGCGAGGGATTCTGGAAGAACAGTATTTTGAGTTGACTCAGGAAAGCAAGAAAGCTGCTTCAAGAAATAGACAAGAGATTACAGATAAAGATCATACTGTTAGTCGGCTTGAAGAAACAAACAGTGTGCTAACCAAAGATATTGAAATGCTAAGAAAAGAAAATGAAGAGCTAAATGAAAGAATGAGGACAGCAGAAGAAGGCAATATAGGGGAAATGAAGGGCAAATGCGGGAGTTACAAGATCAACTTGAAGCTGAGCAGTATTTCTCTACACTTTATAAAACCCAAGTAA
Peptide sequence:
MRELQDQLEAEQYFSTLYKTQVKELKEEIEEKNRENLRKIQELQSEKETLSTQLDLAETKAESEQLARGILEEQYFELTQESKKAASRNRQEITDKDHTVSRLEETNSVLTKDIEMLRKENEELNERMRTAEEGNIGEMKGKCGSYKINLKLSSISLHFIKPK
IRESfinder result
IRESfinder score
0.59154247
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page