top of page
mmu_circTbc1d8_700
Basic information of circular RNA
PanCircBase ID:
mmu_circTbc1d8_700
mm39_Chr. Position ID:
chr1|39441763|39465259|-
Gene name:
Tbc1d8
Transcript:
ENSMUST00000054462.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,4,3,2
Exon/intron offsets:
0,2608,4069,23385
Genomic length:
23496
Exon/intron sizes in nt:
2,41,22,91,19,111
Flanking exon/introns:
chr1:39433353-39441763|chr1:39465259-39517520
Splice length:
700
Other database IDs:
circAtlas: mmu-Tbc1d8_0008
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_37266
Human Ortholog IDs:
Mature spliced Sequence:
GTCGCCTTGTCGGTGCCCTGGACGCGGTGCTGGATTCCAGCGCACGGGTTGCTCCATTTCGGATTCTGCTTCAAGTTCCTGGGTCGCAGGTGTATTCTCCCATAGCATGTGGTGCAACATTGGAGGAAATCAACCGGCACTGGGACTGGCTGGAGCAGAACCTGCTGCACACCCTGTCAGTCTTTGACAACAAAGATGACATCGCCAGCTTTGTCAAAGGGAAGGTGAAGGCTCTGATCGCAGAGGAGACCAGCAGCAGACTGGCAGAGCAGGAGGAGGAGCCCGAGAAGTTCCGAGAAGCTCTGGTGAAGTTCGAGGCCAGGTTCAACTTCCCCGAGGCGGAGAAGCTGGTCACGTACTACTCGTGCTGCTGCTGGAAGGGCAGGGTGCCCCGCCAGGGCTGGCTGTACCTCAGCATCAACCACCTCTGCTTCTATTCCTTCTTCCTGGGCAAGGAGCTTAAACTTGTGATCCCCTGGGTCGATATCCAGAAGCTGGAGCGAACCTCCAATGTCTTTCTCACGGACACCATCCGGATCACTACACAGAATAAGGAGCGAGACTTCTCCACGTTTCTGAACCTGGACGAGGTGTTCAAGATCATGGAGCAGCTGGCAGATGTCACGCTCCGGAGGCTGCTGGACAACGAGGTTTTTGATCTTGACCCCGACCTGCAGGAGCCTAGCCAGATCACAAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGATCTTGACCCCGACCTG
59.39
GGAGAATACACCTGCGACCC
60.18
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTGATCTTGACCCCGACCTG
59.39
GAGAATACACCTGCGACCCA
59.46
145
PCR template sequence:
TCATGGAGCAGCTGGCAGATGTCACGCTCCGGAGGCTGCTGGACAACGAGGTTTTTGATCTTGACCCCGACCTGCAGGAGCCTAGCCAGATCACAAAGAGGTCGCCTTGTCGGTGCCCTGGACGCGGTGCTGGATTCCAGCGCACGGGTTGCTCCATTTCGGATTCTGCTTCAAGTTCCTGGGTCGCAGGTGTATTCTCC
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-15a-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-15b-5p(1), mmu-miR-298-5p(1), mmu-miR-339-5p(1), mmu-miR-503-5p(1), mmu-miR-434-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
AGATCACAAAGAGGTCGCCTTGTCGG
siRNA sets
AAGGCGACCTCTTTGTGAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTBC1D8_700_ORF_1
1.2944
0.456208548
0.990294144
780
ORF sequence:
ATGTCACGCTCCGGAGGCTGCTGGACAACGAGGTTTTTGATCTTGACCCCGACCTGCAGGAGCCTAGCCAGATCACAAAGAGGTCGCCTTGTCGGTGCCCTGGACGCGGTGCTGGATTCCAGCGCACGGGTTGCTCCATTTCGGATTCTGCTTCAAGTTCCTGGGTCGCAGGTGTATTCTCCCATAGCATGTGGTGCAACATTGGAGGAAATCAACCGGCACTGGGACTGGCTGGAGCAGAACCTGCTGCACACCCTGTCAGTCTTTGACAACAAAGATGACATCGCCAGCTTTGTCAAAGGGAAGGTGAAGGCTCTGATCGCAGAGGAGACCAGCAGCAGACTGGCAGAGCAGGAGGAGGAGCCCGAGAAGTTCCGAGAAGCTCTGGTGAAGTTCGAGGCCAGGTTCAACTTCCCCGAGGCGGAGAAGCTGGTCACGTACTACTCGTGCTGCTGCTGGAAGGGCAGGGTGCCCCGCCAGGGCTGGCTGTACCTCAGCATCAACCACCTCTGCTTCTATTCCTTCTTCCTGGGCAAGGAGCTTAAACTTGTGATCCCCTGGGTCGATATCCAGAAGCTGGAGCGAACCTCCAATGTCTTTCTCACGGACACCATCCGGATCACTACACAGAATAAGGAGCGAGACTTCTCCACGTTTCTGAACCTGGACGAGGTGTTCAAGATCATGGAGCAGCTGGCAGATGTCACGCTCCGGAGGCTGCTGGACAACGAGGTTTTTGATCTTGACCCCGACCTGCAGGAGCCTAGCCAGATCACAAAG
Peptide sequence:
MSRSGGCWTTRFLILTPTCRSLARSQRGRLVGALDAVLDSSARVAPFRILLQVPGSQVYSPIACGATLEEINRHWDWLEQNLLHTLSVFDNKDDIASFVKGKVKALIAEETSSRLAEQEEEPEKFREALVKFEARFNFPEAEKLVTYYSCCCWKGRVPRQGWLYLSINHLCFYSFFLGKELKLVIPWVDIQKLERTSNVFLTDTIRITTQNKERDFSTFLNLDEVFKIMEQLADVTLRRLLDNEVFDLDPDLQEPSQITK
IRESfinder result
IRESfinder score
0.32569746
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page