top of page
mmu_circSmad2_761
Basic information of circular RNA
PanCircBase ID:
mmu_circSmad2_761
mm39_Chr. Position ID:
chr18|76419930|76433066|+
Gene name:
Smad2
Transcript:
ENSMUST00000168423.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
3,4,5,6,7,8
Exon/intron offsets:
0,1068,2179,6050,11588,12923
Genomic length:
13136
Exon/intron sizes in nt:
90,19,41,35,75,54,213
Flanking exon/introns:
chr18:76395798-76419930|chr18:76433066-76435149
Splice length:
761
Other database IDs:
circBase: hsa_circ_0047607
Human Ortholog IDs:
Mature spliced Sequence:
CACTTGCTCTGAAATTTGGGGACTGAGTACAGCAAATACGGTAGATCAGTGGGACACAACAGGCCTTTACAGCTTCTCTGAACAAACCAGGTCTCTTGATGGCCGTCTTCAGGTTTCACACCGGAAAGGGTTGCCACATGTTATATATTGCCGGCTCTGGCGCTGGCCGGACCTTCACAGTCATCATGAGCTCAAGGCAATCGAAAACTGCGAATATGCTTTTAATCTGAAAAAAGATGAAGTGTGTGTAAATCCGTACCACTACCAGAGAGTTGAGACCCCAGTCTTGCCTCCAGTCTTAGTGCCTCGGCACACGGAGATTCTAACAGAACTGCCGCCCCTGGATGACTACACCCACTCCATTCCAGAAAACACAAATTTCCCAGCAGGAATTGAGCCACAGAGTAATTACATCCCAGAAACACCACCACCTGGATATATCAGTGAAGATGGAGAAACAAGTGACCAACAGTTGAACCAAAGTATGGACACAGGCTCTCCGGCTGAACTGTCTCCTACTACTCTCTCTCCTGTTAATCACAGCTTGGATTTGCAGCCAGTTACTTACTCGGAACCTGCATTCTGGTGTTCAATCGCATACTATGAACTAAACCAGAGGGTTGGAGAGACCTTCCATGCGTCACAGCCCTCGCTCACTGTAGACGGCTTCACAGACCCATCAAACTCGGAGAGGTTCTGCTTAGGCTTGCTCTCCAACGTTAACCGAAATGCCACTGTAGAAATGACAAGAAGACATATAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGGCTTCACAGACCCATCAA
60.32
GCCTGTTGTGTCCCACTGAT
60.25
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGGAGAGGTTCTGCTTAGGC
60.18
AAAGGCCTGTTGTGTCCCAC
60.76
143
PCR template sequence:
GACGGCTTCACAGACCCATCAAACTCGGAGAGGTTCTGCTTAGGCTTGCTCTCCAACGTTAACCGAAATGCCACTGTAGAAATGACAAGAAGACATATAGCACTTGCTCTGAAATTTGGGGACTGAGTACAGCAAATACGGTAGATCAGTGGGACACAACAGGCCTTTACAGCTTCTCTGAACAAACCAGGTCTCTTGAT
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-139-5p(2), mmu-miR-9-5p(1), mmu-miR-31-5p(1), mmu-miR-185-5p(1), mmu-miR-370-3p(1), mmu-miR-344d-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAAGACATATAGCACTTGCTCTGAA
siRNA sets
CAAGTGCTATATGTCTTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMAD2_761_ORF_1
0.762
0.062625477
0.194809317
303
ORF sequence:
ATGGACACAGGCTCTCCGGCTGAACTGTCTCCTACTACTCTCTCTCCTGTTAATCACAGCTTGGATTTGCAGCCAGTTACTTACTCGGAACCTGCATTCTGGTGTTCAATCGCATACTATGAACTAAACCAGAGGGTTGGAGAGACCTTCCATGCGTCACAGCCCTCGCTCACTGTAGACGGCTTCACAGACCCATCAAACTCGGAGAGGTTCTGCTTAGGCTTGCTCTCCAACGTTAACCGAAATGCCACTGTAGAAATGACAAGAAGACATATAGCACTTGCTCTGAAATTTGGGGACTGA
Peptide sequence:
MDTGSPAELSPTTLSPVNHSLDLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNSERFCLGLLSNVNRNATVEMTRRHIALALKFGD
IRESfinder result
IRESfinder score
0.577052218
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page