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mmu_ciSmad2_1279
Basic information of circular RNA
PanCircBase ID:
mmu_ciSmad2_1279
mm39_Chr. Position ID:
chr18|76431572|76432851|+
Gene name:
Smad2
Transcript:
ENSMUST00000168423.9
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
7
Exon/intron offsets:
0
Genomic length:
1279
Exon/intron sizes in nt:
1279
Flanking exon/introns:
chr18:76431572-76432853
Splice length:
1279
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTAGCTGGGACTCCTCCATTCTCACTGTCTGAAGGAAAGTTCTCTCTGGAAATTGCTTTTGTCTGTCTGAGGAAGACTACTCAGAGGGTGCACACTAGTGTCTTTAAGAACAGTTGGGATTATAGTTGATCCTAAAGGCTTTTTCTTGGTGGTAAGGAGTTTATGAAACAGTCTGAGTCACTAGAACTGTTCTTTATGAAGTTGTATAATTTAAGGTCTTATGGGTGTCTAGGGTGTATTTTACAGTAGCAGTCAGTGGGAAAGATGTATATATACACAAGTCACATATGCGTGCACACACATTTGTGTTGCTTGTTTTGAGCCCACATTTCCCCTGCTGTTTCATATTCTTCAGCTTCTATATATTGAAATTTATTTTATAAAATTGTCATATTTTTTTCTCTTGTGATCTTCCTTTCGATACATCTCGGTAAAAATTGACAAAGATAATTGCACATGGTCCTTGTCTTAGTTAGGGTTTTACTGCTGTGAACAGACACCATGACCAAGGCTACTCTTAAAAGGACAACTTTAAATTGAGGCTGGCTTACAGATTTAGAGGTTCAGTCCATCAAGGCAGGAACATGGCAGCATCCAGGCTGGCATGGTGCAGGAGGAGCTGAGAGTTCTACATCTTCATCTGAAGGCTGCTAGCAGAATACTGACTTCCAGGCAGCTAGGATGAGGGTTTTGAAGCCCGTACCCACAGTTGACACACCCACCCCAACAGGACCACACCCTCTAGTAGTGCCACTCCCTGGGCCGAGCGCATATGTAATATGAACTGTCACAGTCCTCGTTTTCTGTTAGTACGTCATCAGTTTTCGCTTGTGCACACTGCTTCTTACATGGATGCAGATGGGCAGGGAAGTGTGCTGAGTCTTCTCCCAATGGAGTATCTCTTCGTTCTAGGGCTTTTGACTTTGCTGTTTATTCAACTCTATATTTCGTCCTGTCCAAAATTACCTTCACAATGCATTTTAGATACCCACCCACCCAAGTATAGTAGGGTGACCAATTTTCCCTGTTGTGATTATTTAAAACGGATGAATAATCCAGCATAAATTAACTTTATTTGATGGGGAAGTTTAAAAAAACTGTATCTGTTATGATCTATGGGAATAAGTTTTATATGAAAAACACTGACCCTCTGGTCTGTCCTATGGAGACTAGTACAGATGTCCCAGTGACTTCCTCAGCCTCGCCTGTCTGCGGTCTGCAGTGCCTTGTGCTCAGCATCTCGCGTTGTTCAACCAGCATCTCTTCTTGTACTTC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCCTTGTGCTCAGCATCTC
60.68
GTGTGCACCCTCTGAGTAGT
59.03
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCATCTCGCGTTGTTCAACC
60.45
AGTGTGCACCCTCTGAGTAG
58.74
140
PCR template sequence:
CAGATGTCCCAGTGACTTCCTCAGCCTCGCCTGTCTGCGGTCTGCAGTGCCTTGTGCTCAGCATCTCGCGTTGTTCAACCAGCATCTCTTCTTGTACTTCGTAAGTAGCTGGGACTCCTCCATTCTCACTGTCTGAAGGAAAGTTCTCTCTGGAAATTGCTTTTGTCTGTCTGAGGAAGACTACTCAGAGGGTGCACACT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-miR-669d-5p(2), mmu-miR-20b-5p(1), mmu-miR-15a-5p(1), mmu-miR-20a-5p(1), mmu-miR-33-5p(1), mmu-miR-301b-3p(1), mmu-miR-382-5p(1), mmu-miR-301a-3p(1), mmu-miR-383-5p(1), mmu-miR-224-5p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTTCTTGTACTTCGTAAGTAGCTGGG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CISMAD2_1279_ORF_3
0.7579
-0.062566459
0.063044036
201
ORF sequence:
ATGGGGAAGTTTAAAAAAACTGTATCTGTTATGATCTATGGGAATAAGTTTTATATGAAAAACACTGACCCTCTGGTCTGTCCTATGGAGACTAGTACAGATGTCCCAGTGACTTCCTCAGCCTCGCCTGTCTGCGGTCTGCAGTGCCTTGTGCTCAGCATCTCGCGTTGTTCAACCAGCATCTCTTCTTGTACTTCGTAA
Peptide sequence:
MGKFKKTVSVMIYGNKFYMKNTDPLVCPMETSTDVPVTSSASPVCGLQCLVLSISRCSTSISSCTS
IRESfinder result
IRESfinder score
0.834226582
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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