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mmu_circTubd1_232
Basic information of circular RNA
PanCircBase ID:
mmu_circTubd1_232
mm39_Chr. Position ID:
chr11|86445898|86446130|+
Gene name:
Tubd1
Transcript:
ENSMUST00000167178.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
1
Exon/intron indexes:
5
Exon/intron offsets:
0
Genomic length:
232
Exon/intron sizes in nt:
232
Flanking exon/introns:
chr11:86443830-86445898|chr11:86446130-86448550
Splice length:
232
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_120259
Human Ortholog IDs:
Mature spliced Sequence:
GTCATTGTGCAGAACTACAACTCCATCTTGACTCTCTCTCACCTGTACCGGTCTTCAGATGCCCTTCTCATTCACGAGAATGACGCTGTCCATAAGATCTGTGCCAAACGGATGAACATCAAGCAGATCTCCTTCAGAGACTTAAATCAAGTTCTTGCCCACCAGCTGGGGAGTGTGTTCCAGCCTACATACTCTGAGGACAGCTCATTTCACTACCGCAGAAATCCACTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGGAGTGTGTTCCAGCCTAC
60.04
GGACAGCGTCATTCTCGTGA
60.11
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGAGTGTGTTCCAGCCTAC
60.04
TGGACAGCGTCATTCTCGTG
60.39
156
PCR template sequence:
TTCAGAGACTTAAATCAAGTTCTTGCCCACCAGCTGGGGAGTGTGTTCCAGCCTACATACTCTGAGGACAGCTCATTTCACTACCGCAGAAATCCACTAGGTCATTGTGCAGAACTACAACTCCATCTTGACTCTCTCTCACCTGTACCGGTCTTCAGATGCCCTTCTCATTCACGAGAATGACGCTGTCCATAAGATCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-680(1)
siRNAs for circular RNA silencing
Junction sequence
AGAAATCCACTAGGTCATTGTGCAGA
siRNA sets
TCTGCACAATGACCTAGTG, TGCACAATGACCTAGTGGA, AATGACCTAGTGGATTTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTUBD1_232_ORF_1
0.6168
-0.011885701
0.063958358
204
ORF sequence:
ATGAACATCAAGCAGATCTCCTTCAGAGACTTAAATCAAGTTCTTGCCCACCAGCTGGGGAGTGTGTTCCAGCCTACATACTCTGAGGACAGCTCATTTCACTACCGCAGAAATCCACTAGGTCATTGTGCAGAACTACAACTCCATCTTGACTCTCTCTCACCTGTACCGGTCTTCAGATGCCCTTCTCATTCACGAGAATGA
Peptide sequence:
MNIKQISFRDLNQVLAHQLGSVFQPTYSEDSSFHYRRNPLGHCAELQLHLDSLSPVPVFRCPSHSRE
IRESfinder result
IRESfinder score
0.729389769
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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