top of page
mmu_circSmad1_596
Basic information of circular RNA
PanCircBase ID:
mmu_circSmad1_596
mm39_Chr. Position ID:
chr8|80070282|80080075|-
Gene name:
Smad1
Transcript:
ENSMUST00000066091.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
6,5,4
Exon/intron offsets:
0,5937,9676
Genomic length:
9793
Exon/intron sizes in nt:
25,72,22,117
Flanking exon/introns:
chr8:80066421-80070282|chr8:80080075-80082840
Splice length:
596
Other database IDs:
circBase: mmu_circ_0015009, CIRCpedia: MMU_CIRCpedia_30108, circAtlas: mmu-Smad1_0004
Human Ortholog IDs:
Mature spliced Sequence:
CTGACACACCCCCACCTGCTTACCTGCCTCCTGAAGACCCCATGGCCCAGGATGGCTCTCAGCCCATGGACACGAACATGATGGCGCCTCCACTGCCCGCTGAAATCAGCAGAGGAGATGTTCAGGCAGTTGCTTACGAGGAACCAAAACACTGGTGCTCTATTGTGTACTATGAGCTCAACAACCGTGTGGGTGAAGCGTTCCACGCCTCGTCCACCAGCGTGCTGGTGGATGGTTTCACAGATCCGTCCAACAATAAGAACCGCTTCTGCCTTGGCTTGCTCTCCAACGTTAACCGGAATTCCACTATTGAAAACACCAGGCGACATATTGGGAAAGGAGTCCACCTTTATTACGTTGGAGGAGAGGTGTATGCGGAATGCCTCAGTGACAGCAGCATCTTCGTGCAGAGCCGGAACTGCAACTACCACCACGGCTTTCACCCCACCACCGTCTGCAAGATCCCCAGCGGGTGCAGCTTGAAAATCTTCAACAACCAAGAGTTTGCTCAGCTACTGGCGCAGTCTGTGAACCACGGGTTCGAGACCGTGTATGAACTCACCAAAATGTGCACTATTCGGATGAGCTTCGTGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTACTGGCGCAGTCTGTGAA
60.04
TCATGTTCGTGTCCATGGGC
60.68
165
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTACTGGCGCAGTCTGTGAA
60.04
ATGTTCGTGTCCATGGGCTG
60.68
163
PCR template sequence:
CCAAGAGTTTGCTCAGCTACTGGCGCAGTCTGTGAACCACGGGTTCGAGACCGTGTATGAACTCACCAAAATGTGCACTATTCGGATGAGCTTCGTGAAGCTGACACACCCCCACCTGCTTACCTGCCTCCTGAAGACCCCATGGCCCAGGATGGCTCTCAGCCCATGGACACGAACATGATGGCGCCTCCACTGCCCGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-199a-5p(1), mmu-miR-709(1), mmu-miR-431-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GAGCTTCGTGAAGCTGACACACCCCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMAD1_596_ORF_1
0.8825
0.328872777
0.909236096
636
ORF sequence:
ATGGCCCAGGATGGCTCTCAGCCCATGGACACGAACATGATGGCGCCTCCACTGCCCGCTGAAATCAGCAGAGGAGATGTTCAGGCAGTTGCTTACGAGGAACCAAAACACTGGTGCTCTATTGTGTACTATGAGCTCAACAACCGTGTGGGTGAAGCGTTCCACGCCTCGTCCACCAGCGTGCTGGTGGATGGTTTCACAGATCCGTCCAACAATAAGAACCGCTTCTGCCTTGGCTTGCTCTCCAACGTTAACCGGAATTCCACTATTGAAAACACCAGGCGACATATTGGGAAAGGAGTCCACCTTTATTACGTTGGAGGAGAGGTGTATGCGGAATGCCTCAGTGACAGCAGCATCTTCGTGCAGAGCCGGAACTGCAACTACCACCACGGCTTTCACCCCACCACCGTCTGCAAGATCCCCAGCGGGTGCAGCTTGAAAATCTTCAACAACCAAGAGTTTGCTCAGCTACTGGCGCAGTCTGTGAACCACGGGTTCGAGACCGTGTATGAACTCACCAAAATGTGCACTATTCGGATGAGCTTCGTGAAGCTGACACACCCCCACCTGCTTACCTGCCTCCTGAAGACCCCATGGCCCAGGATGGCTCTCAGCCCATGGACACGAACATGA
Peptide sequence:
MAQDGSQPMDTNMMAPPLPAEISRGDVQAVAYEEPKHWCSIVYYELNNRVGEAFHASSTSVLVDGFTDPSNNKNRFCLGLLSNVNRNSTIENTRRHIGKGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPTTVCKIPSGCSLKIFNNQEFAQLLAQSVNHGFETVYELTKMCTIRMSFVKLTHPHLLTCLLKTPWPRMALSPWTRT
IRESfinder result
IRESfinder score
0.412549292
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page