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mmu_circRsu1_450
Basic information of circular RNA
PanCircBase ID:
mmu_circRsu1_450
mm39_Chr. Position ID:
chr2|13174808|13223938|-
Gene name:
Rsu1
Transcript:
ENSMUST00000114791.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
7,6,5,4
Exon/intron offsets:
0,46772,47191,49011
Genomic length:
49130
Exon/intron sizes in nt:
13,31,15,83,119
Flanking exon/introns:
chr2:13082418-13174808|chr2:13223938-13229115
Splice length:
450
Other database IDs:
CIRCpedia: MMU_CIRCpedia_215913, circAtlas: mmu-Rsu1_0007
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_75837
Human Ortholog IDs:
Mature spliced Sequence:
CATGAATAGGTTGAACACGCTGCCTCGAGGATTCGGCTCCCTCCCGGCTCTGGAGGTCCTGGACTTAACTTACAACAACCTGAATGAACATTCTCTTCCGGGAAACTTCTTCTACCTCACCACCCTGCGTGCACTCTATCTAAGCGACAACGATTTTGAAATCCTGCCTCCAGATATTGGGAAGCTCACAAAGTTGCAGATACTCAGCCTCAGGGATAATGACCTGATCTCACTGCCTAAGGAAATCGGGGAGCTGACCCAGCTGAAGGAGCTCCACATTCAGGGGAACCGCCTGACCGTTCTGCCTCCAGAGCTTGGCAACTTGGATCTAACTGGTCAGAAGCAGGTCTTCAAAGCAGAGAACAACCCCTGGGTTACCCCGATTGCTGACCAGTTCCAGCTTGGCGTCTCCCACGTTTTCGAATATATTCGTTCAGAAACTTACAAGTA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTTACCCCGATTGCTGACCA
60.04
AAGTCCAGGACCTCCAGAGC
60.91
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCAGAGAACAACCCCTGG
59.89
AAGTCCAGGACCTCCAGAGC
60.91
163
PCR template sequence:
TCAAAGCAGAGAACAACCCCTGGGTTACCCCGATTGCTGACCAGTTCCAGCTTGGCGTCTCCCACGTTTTCGAATATATTCGTTCAGAAACTTACAAGTACATGAATAGGTTGAACACGCTGCCTCGAGGATTCGGCTCCCTCCCGGCTCTGGAGGTCCTGGACTTAACTTACAACAACCTGAATGAACATTCTCTTCCG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-34c-5p(2), mmu-miR-34b-5p(2), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-34a-5p(1), mmu-let-7c-5p(1), mmu-miR-709(1), mmu-let-7d-5p(1), mmu-miR-98-5p(1), mmu-miR-670-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAACTTACAAGTACATGAATAGGTTG
siRNA sets
TATTCATGTACTTGTAAGT, ATTCATGTACTTGTAAGTT, CAACCTATTCATGTACTTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRSU1_450_ORF_1
1.281
0.335042296
0.993042518
897
ORF sequence:
ATGAATAGGTTGAACACGCTGCCTCGAGGATTCGGCTCCCTCCCGGCTCTGGAGGTCCTGGACTTAACTTACAACAACCTGAATGAACATTCTCTTCCGGGAAACTTCTTCTACCTCACCACCCTGCGTGCACTCTATCTAAGCGACAACGATTTTGAAATCCTGCCTCCAGATATTGGGAAGCTCACAAAGTTGCAGATACTCAGCCTCAGGGATAATGACCTGATCTCACTGCCTAAGGAAATCGGGGAGCTGACCCAGCTGAAGGAGCTCCACATTCAGGGGAACCGCCTGACCGTTCTGCCTCCAGAGCTTGGCAACTTGGATCTAACTGGTCAGAAGCAGGTCTTCAAAGCAGAGAACAACCCCTGGGTTACCCCGATTGCTGACCAGTTCCAGCTTGGCGTCTCCCACGTTTTCGAATATATTCGTTCAGAAACTTACAAGTACATGAATAGGTTGAACACGCTGCCTCGAGGATTCGGCTCCCTCCCGGCTCTGGAGGTCCTGGACTTAACTTACAACAACCTGAATGAACATTCTCTTCCGGGAAACTTCTTCTACCTCACCACCCTGCGTGCACTCTATCTAAGCGACAACGATTTTGAAATCCTGCCTCCAGATATTGGGAAGCTCACAAAGTTGCAGATACTCAGCCTCAGGGATAATGACCTGATCTCACTGCCTAAGGAAATCGGGGAGCTGACCCAGCTGAAGGAGCTCCACATTCAGGGGAACCGCCTGACCGTTCTGCCTCCAGAGCTTGGCAACTTGGATCTAACTGGTCAGAAGCAGGTCTTCAAAGCAGAGAACAACCCCTGGGTTACCCCGATTGCTGACCAGTTCCAGCTTGGCGTCTCCCACGTTTTCGAATATATTCGTTCAGAAACTTACAAG
Peptide sequence:
MNRLNTLPRGFGSLPALEVLDLTYNNLNEHSLPGNFFYLTTLRALYLSDNDFEILPPDIGKLTKLQILSLRDNDLISLPKEIGELTQLKELHIQGNRLTVLPPELGNLDLTGQKQVFKAENNPWVTPIADQFQLGVSHVFEYIRSETYKYMNRLNTLPRGFGSLPALEVLDLTYNNLNEHSLPGNFFYLTTLRALYLSDNDFEILPPDIGKLTKLQILSLRDNDLISLPKEIGELTQLKELHIQGNRLTVLPPELGNLDLTGQKQVFKAENNPWVTPIADQFQLGVSHVFEYIRSETYK
IRESfinder result
IRESfinder score
0.649646103
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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