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mmu_circStradb_519
Basic information of circular RNA
PanCircBase ID:
mmu_circStradb_519
mm39_Chr. Position ID:
chr1|59016117|59028957|+
Gene name:
Stradb
Transcript:
ENSMUST00000114296.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
2,3,4,5,6
Exon/intron offsets:
0,2975,8330,11547,12731
Genomic length:
12840
Exon/intron sizes in nt:
1,07,81,10,01,22,109
Flanking exon/introns:
chr1:59013009-59016117|chr1:59028957-59030171
Splice length:
519
Other database IDs:
circBase: mmu_circ_0008827, CIRCpedia: MMU_CIRCpedia_37769, circAtlas: mmu-Stradb_0002
Human Ortholog IDs:
Mature spliced Sequence:
TGGGCTATATCTGCAACTTGAAGGGAAGATAAAAGAAACATCTTCTTTGGAATAGATGGGAATTTTTTTCACTTTCTGTGAACTAAAGCGATTCAATGTCTCTTTTGGATTGTTTCTGTGCTTCACGAACACGAGTCGAATCACTCAGACCCGAAAAACAGTCTGAAACCAGTATCCATCAGTACTTGGTTGATGAGTCAGCCATTTCCCGGCCCCCTCCGTCTGCTAGAGCCAGTGAGGTGATCTGCTCCACTGACGTGTCTCACTATGAACTGCAAGTGGAGATAGGAAGAGGGTTTGACAACTTGACCTCTGTTCATCTTGCACGGCACACTCCTACAGGAACACTGGTAACTGTAAAGATTACAAACCTGGAAAGCTGCACTGAAGAACGTCTGAAAGCTTTACAGAGAGCAGTGATTCTATCTCACTTTTTCCAACATCCCAATATTACAACTTATTGGACAGTGTTCACTGTTGGCAGCTGGCTTTGGGTTATTTCTCCATTTATGGCCTACG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGTTCACTGTTGGCAGCTG
59.97
TCGCTTTAGTTCACAGAAAGT
55.49
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGTGTTCACTGTTGGCAGC
59.97
TCGCTTTAGTTCACAGAAAGT
55.49
145
PCR template sequence:
ATTCTATCTCACTTTTTCCAACATCCCAATATTACAACTTATTGGACAGTGTTCACTGTTGGCAGCTGGCTTTGGGTTATTTCTCCATTTATGGCCTACGTGGGCTATATCTGCAACTTGAAGGGAAGATAAAAGAAACATCTTCTTTGGAATAGATGGGAATTTTTTTCACTTTCTGTGAACTAAAGCGATTCAATGTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-199a-5p(1), mmu-miR-429-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-22-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-539-5p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTATGGCCTACGTGGGCTATATCTG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSTRADB_519_ORF_1
0.5879
0.020008546
0.309668382
456
ORF sequence:
ATGTCTCTTTTGGATTGTTTCTGTGCTTCACGAACACGAGTCGAATCACTCAGACCCGAAAAACAGTCTGAAACCAGTATCCATCAGTACTTGGTTGATGAGTCAGCCATTTCCCGGCCCCCTCCGTCTGCTAGAGCCAGTGAGGTGATCTGCTCCACTGACGTGTCTCACTATGAACTGCAAGTGGAGATAGGAAGAGGGTTTGACAACTTGACCTCTGTTCATCTTGCACGGCACACTCCTACAGGAACACTGGTAACTGTAAAGATTACAAACCTGGAAAGCTGCACTGAAGAACGTCTGAAAGCTTTACAGAGAGCAGTGATTCTATCTCACTTTTTCCAACATCCCAATATTACAACTTATTGGACAGTGTTCACTGTTGGCAGCTGGCTTTGGGTTATTTCTCCATTTATGGCCTACGTGGGCTATATCTGCAACTTGAAGGGAAGATAA
Peptide sequence:
MSLLDCFCASRTRVESLRPEKQSETSIHQYLVDESAISRPPPSARASEVICSTDVSHYELQVEIGRGFDNLTSVHLARHTPTGTLVTVKITNLESCTEERLKALQRAVILSHFFQHPNITTYWTVFTVGSWLWVISPFMAYVGYICNLKGR
IRESfinder result
IRESfinder score
0.80970749
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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