top of page
mmu_circThoc1_302
Basic information of circular RNA
PanCircBase ID:
mmu_circThoc1_302
mm39_Chr. Position ID:
chr18|9963262|9970328|+
Gene name:
Thoc1
Transcript:
ENSMUST00000025137.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,7,8,9
Exon/intron offsets:
0,560,5488,6992
Genomic length:
7066
Exon/intron sizes in nt:
49,96,83,74
Flanking exon/introns:
chr18:9962491-9963262|chr18:9970328-9975598
Splice length:
302
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AATACATTCTATTCTGCTGGCAAAAATTATTTACTGCGTATGTGCAATGATCTCCTCAGAAGATTGTCTAAATCTCAGAATACAGTTTTCTGTGGAAGAATTCAACTCTTTTTGGCCAGGCTTTTTCCTCTATCTGAGAAATCAGGTCTTAATTTGCAGAGTCAGTTTAACCTGGAAAACGTCACTGTTTTCAATACAAACGAGCAGGAGAGCACCCTGGGTCAGAAGCATACTGAGGATAGAGAGGAAGGGATGGATGTAGAAGAAGGTGAAATGGGAGATGATGAAGCCCCGACAACTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CACCCTGGGTCAGAAGCATA
59.09
AGGAGATCATTGCACATACGCA
60.16
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCCTGGGTCAGAAGCATAC
59.09
AGGAGATCATTGCACATACGCA
60.16
145
PCR template sequence:
AGCAGGAGAGCACCCTGGGTCAGAAGCATACTGAGGATAGAGAGGAAGGGATGGATGTAGAAGAAGGTGAAATGGGAGATGATGAAGCCCCGACAACTTGAATACATTCTATTCTGCTGGCAAAAATTATTTACTGCGTATGTGCAATGATCTCCTCAGAAGATTGTCTAAATCTCAGAATACAGTTTTCTGTGGAAGAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-32-5p(1), mmu-miR-25-3p(1), mmu-miR-363-3p(1), mmu-miR-382-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CCCCGACAACTTGAATACATTCTATT
siRNA sets
AATGTATTCAAGTTGTCGG, GAATGTATTCAAGTTGTCG, ATAGAATGTATTCAAGTTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTHOC1_302_ORF_1
1.029
0.041684828
0.219580404
264
ORF sequence:
ATGTGCAATGATCTCCTCAGAAGATTGTCTAAATCTCAGAATACAGTTTTCTGTGGAAGAATTCAACTCTTTTTGGCCAGGCTTTTTCCTCTATCTGAGAAATCAGGTCTTAATTTGCAGAGTCAGTTTAACCTGGAAAACGTCACTGTTTTCAATACAAACGAGCAGGAGAGCACCCTGGGTCAGAAGCATACTGAGGATAGAGAGGAAGGGATGGATGTAGAAGAAGGTGAAATGGGAGATGATGAAGCCCCGACAACTTGA
Peptide sequence:
MCNDLLRRLSKSQNTVFCGRIQLFLARLFPLSEKSGLNLQSQFNLENVTVFNTNEQESTLGQKHTEDREEGMDVEEGEMGDDEAPTT
IRESfinder result
IRESfinder score
0.748095776
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page