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mmu_circRaph1_474
Basic information of circular RNA
PanCircBase ID:
mmu_circRaph1_474
mm39_Chr. Position ID:
chr1|60532696|60537693|-
Gene name:
Raph1
Transcript:
ENSMUST00000140485.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
13,12,11,10
Exon/intron offsets:
0,1877,2687,4886
Genomic length:
4997
Exon/intron sizes in nt:
14,31,21,99,111
Flanking exon/introns:
chr1:60529480-60532696|chr1:60537693-60538638
Splice length:
474
Other database IDs:
circBase: mmu_circ_0008859, CIRCpedia: MMU_CIRCpedia_24904, circAtlas: mmu-Raph1_0019
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_153286
Human Ortholog IDs:
Mature spliced Sequence:
GTATCTCGGGATCTAGTGTGCTTTCTCCAGCTGGATCATGTAAATGTATACTATGGACAGGACTATCGGAACAAATACAAAGCACCCACAGACTGCTGCCTGGCATTAAAGCACCCACAGATCCAGAAGAAGTCTCAGTATATCAAGTACCTTTGCTGTGATGATGCAAGGACCCTGCATCAGTGGGTCAATGGAATCCGCATTGCCAAGTATGGGAAGCAGCTCTACACGAATTACCAAGAAGCCTTGAAGAGGACAGAGTCCGCTTATGATTGGACTTCGTTATCCAGCTCCAGCATTAAATCCGGATCCAGTTCTTCCAGTATCCCGGAGTCTCAGTCAAACCACTCTAATCAGTCTGACAGCGGAGTGTCTGACACCCTGCCAACTGGACATATCCGTTCCCAAAGTACCGTGAGCTCCATCTTCTCGGAAGCCTGGAAGCGAGGCACTCAGCTGGAAGAGTCCAGCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCGTTCCCAAAGTACCGTGA
59.97
AGCAGTCTGTGGGTGCTTTG
60.82
173
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCGTTCCCAAAGTACCGTGA
59.97
CAGCAGTCTGTGGGTGCTTT
60.82
174
PCR template sequence:
TGACACCCTGCCAACTGGACATATCCGTTCCCAAAGTACCGTGAGCTCCATCTTCTCGGAAGCCTGGAAGCGAGGCACTCAGCTGGAAGAGTCCAGCAAGGTATCTCGGGATCTAGTGTGCTTTCTCCAGCTGGATCATGTAAATGTATACTATGGACAGGACTATCGGAACAAATACAAAGCACCCACAGACTGCTGCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-140-5p(1), mmu-miR-155-5p(1), mmu-miR-182-5p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAGTCCAGCAAGGTATCTCGGGATC
siRNA sets
GATCCCGAGATACCTTGCT
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
0.590875793
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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