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mmu_circUbr1_549
Basic information of circular RNA
PanCircBase ID:
mmu_circUbr1_549
mm39_Chr. Position ID:
chr2|120696870|120705980|-
Gene name:
Ubr1
Transcript:
ENSMUST00000028728.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
45,44,43,42,41
Exon/intron offsets:
0,1836,4599,6734,8976
Genomic length:
9110
Exon/intron sizes in nt:
17,17,85,71,09,134
Flanking exon/introns:
chr2:120694900-120696870|chr2:120705980-120707439
Splice length:
549
Other database IDs:
circBase: hsa_circ_0034883
Human Ortholog IDs:
Mature spliced Sequence:
CCTCGCTGGGTGCGGTGCTCCCGGCTGGTACCTGTGGCTCTCCCTGAGGAACGGCATCACCCCTTACCTCCGCTGTGCTGCACTGCTTTTCCACTATTTACTTGGAGTAGCTCCGCCTGAAGAACTGTTTGCCAATTCTGCTGAAGGAGAATTCAGTGCACTCTGTAGCTATCTATCTTTACCCACAAATTTGTTCCTGCTTTTCCAGGAATATTGGGATACCATAAGGCCCTTACTACAGAGGTGGTGTGGAGATCCTGCCTTACTCAAGTCTTTGAAGCAGAAAAGTGCTGTGGTCAGGTACCCTAGAAAAAGAAATAGTTTGATAGAGCTTCCTGAGGACTACAGCTGTCTTCTAAATCAGGCTTCTCACTTTAGGTGTCCACGGTCTGCAGATGATGAGCGAAAGCATCCTGTCCTCTGTCTTTTCTGTGGGGCCATCCTGTGTTCTCAGAACATCTGTTGCCAAGAAATAGTGAATGGGGAAGAGGTTGGAGCGTGCGTTTTTCATGCGCTTCATTGTGGTGCTGGAGTCTGCATTTTCTTAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAGCGTGCGTTTTTCATG
60.04
GGAAAAGCAGTGCAGCACAG
60.32
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTTGGAGCGTGCGTTTTTCA
60.25
GGAAAAGCAGTGCAGCACAG
60.32
151
PCR template sequence:
CTCAGAACATCTGTTGCCAAGAAATAGTGAATGGGGAAGAGGTTGGAGCGTGCGTTTTTCATGCGCTTCATTGTGGTGCTGGAGTCTGCATTTTCTTAAACCTCGCTGGGTGCGGTGCTCCCGGCTGGTACCTGTGGCTCTCCCTGAGGAACGGCATCACCCCTTACCTCCGCTGTGCTGCACTGCTTTTCCACTATTTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-34c-5p(1), mmu-miR-29b-3p(1), mmu-miR-152-3p(1), mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-298-5p(1), mmu-miR-182-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCATTTTCTTAAACCTCGCTGGGTGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.768786611
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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